All in the Family: Focused Genomic Comparisons

In a study published ahead the week of January 8, 2018 in the Proceedings of the National Academy of Sciences, a team led by researchers at the Technical University of Denmark (DTU), the DOE Joint Genome Institute (JGI), a DOE Office of Science User Facility, and the DOE’s Joint BioEnergy Institute (JBEI), led by Lawrence Berkeley National Laboratory (Berkeley Lab), report the first results of a long-term plan to sequence, annotate and analyze the genomes of 300 Aspergillus fungi. These findings are a proof of concept of novel methods to functionally annotate genomes in order to more quickly identify genes of interest.

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JBEI Partners with LanzaTech in New DOE Technology Commercialization Fund Grant

LanzaTech is looking into new routes to capture carbon capture and biomanufacture new products. In order to accelerate development while at the same time reducing costs and increasing throughput, LanzaTech is partnering with Department of Energy (DOE) laboratories: Berkeley Lab; DOE Joint Genome Institute; Sandia National Laboratories (SNL); the Joint BioEnergy Institute (JBEI), and Oak Ridge National Lab to develop new foundational technologies that will open new frontiers in this space.

Under a Technology Commercialization Fund (TCF) grant by the DOE, LanzaTech, with Berkeley Lab, SNL and JBEI are focusing on microfluidics, as a way to shrink the physical footprint of LanzaTech’s manufacturing facility, and reducing the cost and time needed to test the outcome of each experiment.

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Berkeley Lab researchers demonstrate importance of microbial communities for enzyme stability, Biofuels Digest

Biofuels Digest covered the JBEI recent study demonstrates the importance of microbial communities as a source of stable enzymes that could be used to convert plants to biofuels.

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To Find New Biofuel Enzymes, It Can Take a Microbial Village

A new study led by researchers at the Department of Energy’s Joint BioEnergy Institute (JBEI), based at Lawrence Berkeley National Laboratory (Berkeley Lab), demonstrates the importance of microbial communities as a source of stable enzymes that could be used to convert plants to biofuels. The study, recently published in the journal Nature Microbiology, reports on the discovery of new types of cellulases, enzymes that help break down plants into ingredients that can be used to make biofuels and bioproducts. The cellulases were cultured from a microbiome. Using a microbial community veers from the approach typically taken of using isolated organisms to obtain enzymes.

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Study speeds transformation of biofuel waste into useful chemicals,

JBEI’s Feedstocks Division collaborated with Sandia National Laboratories in a study that looked into efficient ways to turn discarded plant matter into chemicals.

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Genome Research Challenges Previous Understanding of the Origin of Photosynthesis

Patrick Shih, JBEI Post-Doctoral Researcher and the study's co-first author. Photo credit: Majed Abolfazli Patrick Shih, a postdoctoral researcher at JBEI, collaborated with Caltech scientists, to reconstruct the evolutionary history of photosynthesis to provide new insight into the yet-unfolding story of its origins. The recent study titled, “Evolution of the 3-hydroxypropionate bicycle and recent transfer of anoxygenic photosynthesis into the Chloroflexi.” was published in the Proceedings of the National Academy of Sciences. Read more in the Berkeley Lab News Center.

JBEI Researchers Improve Membrane Protein Expression And Function Using Genomic Edits

Development of robust microbial platforms for bioproduction requires strains that have been engineered to have efficient carbon uptake, energy generation, tolerance to biomass pretreatment byproducts and the export of final product. Many of these optimizations require expression and overexpression of native and heterologous membrane proteins. Over the years, scientists at the U.S. Department of Energy’s Joint BioEnergy Institute (JBEI), and others have successfully found many such engineering targets. However, JBEI has also found that expression of membrane proteins is challenging and can also impact the microbial growth, thus negatively limiting the use of these discoveries.

Genome-wide view of single gene disruptions enriched in high GFP populations. Gene disruptions enriched in at least two biological replicates (RHigh/Low, n ≥ 2) are shown for TnLib/gstA-GFP (grey inner band) and all TnLib/IMP tested (green inner bands). The consensus band (blue outer band) represents gene disruptions enriched in at least three replicates across all TnLib/IMP, for which color density increases with instances of enrichment.

In a new paper published in Nature Scientific Reports, Biofuels and Bioproducts Division scientists at JBEI, hypothesized that they could find loci in the genome that could be edited to enhance expression of any given membrane protein of interest.

The hypothesis was tested by using a bar coded gene knockout library in E. coli in conjunction with expression of fluorescent protein tagged membrane proteins. Numerous loci in the genome were identified that when disrupted allowed improved expression, and consequently function, of the proteins of interest. These are host backgrounds that are better suited to serve as the conversion platforms. This study also represents a systematic evaluation of a microbial host genome to improve membrane protein expression.

Published in Nature Scientific Reports, “Improving membrane protein expression and function using genomic edits” is authored by Heather M. Jensen, Thomas Eng, Victor Chubukov, Robin A. Herbert and Aindrila Mukhopadhyay.

Congratulations to JBEI’s Berkeley Lab Director’s Award Recipients

JBEI’s Irina Silva and Patrick Shih are among the 2017 Berkeley Lab Director’s Awards honorees. This annual program recognizes outstanding contributions by employees to all facets of Lab activities. A complete list of winners can be found here.

Irina Silva, Communications & Outreach Manager at JBEI, received an award for Exceptional Achievement in Diversity for her efforts to connect Berkeley Lab science and scientists with local young people to help train a future scientific workforce that truly represents the diversity of the Bay Area.

Patrick Shih, a postdoctoral fellow the Joint BioEnergy Institute, received an award for Exceptional Early Scientific Career Achievement for his work in the fields of plant biology, synthetic biology, and metabolic engineering related to energy, sustainability, and human health.

A ceremony honoring all of the 2017 recipients will be held at 3 pm on November 30 in the Building 50 Auditorium and will be streamed live.

Director of the CA Governor’s Office of Business Visits JBEI

Panorea Avdis, Director of Governor Brown’s Office of Business and Economic Development (GO-Biz), visited the Biosciences Area’s Emery Station Operations Center on September 6 to learn more about the biosciences and bioeconomy related initiatives. GO-Biz was created to serve as California’s single point of contact for economic development and job creation efforts and is an important one-stop shop for companies that want to take advantage of California incentives.

During the visit Director Avdis, who was accompanied by Deputy Director and CA Small Business Advocate, Jesse Torres, met with Mary Maxon, Biosciences Associate Lab Director, Blake Simmons, Division Director, Biological Systems and Engineering, Chief Science & Technology Officer and Vice President for Deconstruction, Joint BioEnergy Institute (JBEI), and Todd Pray, Program Head, Advanced Biofuels Process Development Unit (ABPDU). Avdis also toured the laboratories at JBEI and visited the ABPDU to learn more about how it can be a resource for young biosciences companies seeking to scale up operations.