Tag Archives: jbei

Less Toxic Metabolites, More Chemical Product

The first dynamic regulatory system that prevents the build-up of toxic metabolites in engineered microbes has been reported by a team of researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI). The JBEI researchers used their system to double the production in Escherichia coli (E. coli) of amorphadiene, a precursor to the premier antimalarial drug artemisinin.

Using genome-wide transcriptional analysis, the JBEI researchers identified native regions of DNA – called “promoters” – in E. coli that respond to toxic metabolites by promoting the expression of protective genes. They then developed a system based on these promoters for regulating artificial metabolic pathways engineered into the E.coli to enable the bacterium to produce amorphadiene. (more…)

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Microbial Who-Done-It for Biofuels

New Technique Identifies Populations Within a Microbial Community Responsible for Biomass Deconstruction

One of the keys to commercialization of advanced biofuels is the development of cost-competitive ways to extract fermentable sugars from lignocellulosic biomass. The use of enzymes from thermophiles – microbes that thrive at extremely high temperatures and alkaline conditions – holds promise for achieving this. Finding the most effective of these microbial enzymes, however, has been a challenge. That challenge has now been met by a collaboration led by researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI).

Working with a compost-derived consortium of thermophillic bacterium adapted to grow on switchgrass, a leading potential fuel crop, and using a combination of metagenomic and metaproteomic technologies, the collaboration has identified individual microbial species whose enzymes were the most active in deconstructing the switchgrass biomass. Major institutes in addition to JBEI participating in this collaboration included DOE’s Joint Genome Institute (JGI), and EMSL, the Environmental Molecular Sciences Laboratory, a national scientific user facility at Pacific Northwest National Laboratory (PNNL). (more…)

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New Advance in Biofuel Production

Joint BioEnergy Institute Researchers Develop Enzyme-free Ionic Liquid Pre-treatment

Advanced biofuels – liquid fuels synthesized from the sugars in cellulosic biomass – offer a clean, green and renewable alternative to gasoline, diesel and jet fuels. Bringing the costs of producing these advanced biofuels down to competitive levels with petrofuels, however, is a major challenge. Researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a bioenergy research center led by Berkeley Lab, have taken another step towards meeting this challenge with the development of a new technique for pre-treating cellulosic biomass with ionic liquids – salts that are liquids rather than crystals at room temperature. This new technique requires none of the expensive enzymes used in previous ionic liquid pretreatments, and makes it easier to recover fuel sugars and recycle the ionic liquid. (more…)

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Making Do with More: Joint BioEnergy Institute Researchers Engineer Plant Cell Walls to Boost Sugar Yields for Biofuels

When blessed with a resource in overwhelming abundance it’s generally a good idea to make valuable use of that resource. Lignocellulosic biomass is the most abundant organic material on Earth. For thousands of years it has been used as animal feed, and for the past two centuries has been a staple of the paper industry. This abundant resource, however, could also supply the sugars needed to produce advanced biofuels that can supplement or replace fossil fuels, providing several key technical challenges are met. One of these challenges is finding ways to more cost-effectively extract those sugars. Major steps towards achieving this breakthrough are being taken by researchers at the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI).

“Through the tools of synthetic biology, we have engineered healthy plants whose lignocellulosic biomass can more easily be broken down into simple sugars for biofuels,” says Dominique Loque, who directs the cell wall engineering program for JBEI’s Feedstocks Division. “Working with the model plant, Arabidopsis, as a demonstration tool, we have genetically manipulated secondary cell walls to reduce the production of lignin while increasing the yield of fuel sugars.” (more…)

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Biofuels Blend Right In

Researchers Show Ionic Liquids Effective for Pre-Treating Mixed Blends of Biofuel Feedstocks

Winemakers have long known that blending different grape varietals can favorably balance the flavor characteristics of the wine they produce. In the future, makers of advanced biofuels might use a similar strategy, blending different feedstock varieties to balance the energy characteristics of the transportation fuel they produce.

A collaborative study by researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a bioenergy research center led by Berkeley Lab, and the Idaho National Laboratory (INL) has shown that an ionic liquid proven to be effective for pre-treating individual biofuel feedstocks is also effective at pre-treating multiple different feedstocks that have been mixed and densified into a blend. (more…)

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A Better Route to Xylan

Joint BioEnergy Institute Researchers Find New Access to Abundant Biomass for Advanced Biofuels

After cellulose, xylan is the most abundant biomass material on Earth, and therefore represents an enormous potential source of stored solar energy for the production of advance biofuels. A major roadblock, however, has been extracting xylan from plant cell walls. Researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI) have taken a significant step towards removing this roadblock by identifying a gene in rice plants whose suppression improves both the extraction of xylan and the overall release of the sugars needed to make biofuels.

The newly identified gene – dubbed XAX1 – acts to make xylan less extractable from plant cell walls. JBEI researchers, working with a mutant variety of rice plant – dubbed xax1 – in which the XAX1 gene has been “knocked-out” found that not only was xylan more extractable, but saccharification – the breakdown of carbohydrates into releasable sugars – also improved by better than 60-percent. Increased saccharification is key to more efficient production of advanced biofuels. (more…)

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Latest JBEI Startup to Speed Up Biotech Industry

TeselaGen’s DNA construction technology makes genetic engineering cheaper and faster.

Sequencing, splicing and expressing DNA may seem to be the quintessence of cutting-edge science—indeed DNA manipulation has revolutionized fields such as biofuels, chemicals and medicine. But in fact, the actual process can still be tedious and labor-intensive, something Lawrence Berkeley National Laboratory (Berkeley Lab) scientist Nathan Hillson learned the hard way.

After struggling for two days to design a protocol to put together a genetic circuit with 10 pieces of DNA—using a spreadsheet as his primary tool—he was dismayed to discover that an outside company could have done the whole thing, including parts and labor, for lower cost than him ordering the oligonucleotides himself. “I learned two things: one, I never wanted to go through that process again, and two, it’s extremely important to do the cost-effectiveness calculation,” said Hillson, a biochemist who also directs the synthetic biology program at the Berkeley Lab-led Joint BioEnergy Institute (JBEI). “So that was the genesis of the j5 software. This is the perfect thing to teach a computer to do.” (more…)

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Microbe That Can Handle Ionic Liquids

New Find From Joint BioEnergy Institute Could Help Reduce Biofuel Production Costs

In the search for technology by which economically competitive biofuels can be produced from cellulosic biomass, the combination of sugar-fermenting microbes and ionic liquid solvents looks to be a winner save for one major problem: the ionic liquids used to make cellulosic biomass more digestible for microbes can also be toxic to them. A solution to this conundrum, however, may be in the offing.

Researchers with the U.S. Department of Energy (DOE)’s Joint BioEnergy Institute (JBEI), a multi-institutional partnership led by Berkeley Lab, have identified a tropical rainforest microbe that can endure relatively high concentrations of an ionic liquid used to dissolve cellulosic biomass. The researchers have also determined how the microbe is able to do this, a discovery that holds broad implications beyond the production of advanced biofuels. (more…)

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