Professor of Bacteriology, Professor of Civil and Environmental Engineering, McMahon Lab, University of Wisconsin-Madison Collaborated with JGI since 2005 We have worked together on projects related to sewage treatment and freshwater lakes. Activated sludge wastewater treatment processes are used throughout the world to purify trillions of gallons of sewage annually. Many treatment plants employ specialized…
Project Management Office: Miranda Harmon-Smith
Miranda Harmon-Smith is in her ninth year at JGI, having started as a technician on the Sanger sequencing line before moving up, first to supervisor, then ultimately joining the PMO in 2012. It was her second “real” job after three years doing brain tumor research at the University of California, San Francisco and following her…
How Scavenging Fungi Became a Plant’s Best Friend
Glomeromycota is an ancient lineage of fungi that has a symbiotic relationship with roots that goes back nearly 420 million years to the earliest plants. More than two thirds of the world’s plants depend on this soil-dwelling symbiotic fungus to survive, including critical agricultural crops such as wheat, cassava, and rice. The analysis of the…
Monkeying around with gene shuffling
The iconic monkey flower’s genome harbors “hot spots” of genetic exchange The Science By analyzing the genomes of a wild population of Mimulus guttatus, also known as the monkey flower, researchers were able to pinpoint “hot spots” in the plant’s DNA code (http://www.jgi.doe.gov/News/news_13_11_18.html with high rates of gene-shuffling recombination. They also provided a reference genome…
The Inner Workings of a Bacterial Black Box Caught on Time-lapse Video
Cyanobacteria, found in just about every ecosystem on Earth, are one of the few bacteria that can create their own energy through photosynthesis and “fix” carbon – from carbon dioxide molecules – and convert it into fuel inside of miniscule compartments called carboxysomes. Using a pioneering visualization method, researchers from the University of California, Berkeley,…
Monkey Flower See, Monkey Flower Do — Model Plant’s Legacy Highlights Gene-Shuffling Hotspots
Genomic variation is a feature of all natural populations and is vitally important in order to survive changes in their environments. Genetic variation among individuals, to which DNA recombination is an important contributor, is passed from parents to offspring and helps explain that different individuals in the population may harbor a diverse set of traits….
On the hunt for industrial enzymes
Researchers mined DOE JGI’s database of fungal genomes for candidate enzymes for use in a variety of industrial processes. The Science By screening genomes of fungi made publicly available by the DOE Joint Genome Institute researchers identified new versions of enzymes called lipases and sterol esterases. To further study the most promising enzymes, they created…
Salt-tolerant trees and their symbionts
Over 800 million hectares of land throughout the world are salt-affected and a common method for dealing with salt stress problems is to reclaim affected soils with fast-growing salt- tolerant tree species such as Casuarina trees. Fast growing trees from the Casuarinaceae family have been successfully introduced in several tropical and subtropical countries to prevent…
Pilot phase of the Thousand Microbial Genomes project
The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the DOE JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. At the time the major project goals were to provide evidence to support the use of the phylogenetic diversity of organisms in the tree…
Carboxysomes and the carbon cycle
Cyanobacteria thrive in a diverse range of habitats. In the oceans they are estimated to fix 40 percent of total carbon globally. Long used as a simple model organism to study plant photosynthesis, they are becoming a platform for production of biofuels and industrially important compounds. All cyanobacteria carry out the key step of carbon…