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    Screencap of green algae video for PNAS paper
    Green Algae Reveal One mRNA Encodes Many Proteins
    A team of researchers has found numerous examples of polycistronic expression – in which two or more genes are encoded on a single molecule of mRNA – in two species of green algae.

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    Advances in Rapidly Engineering Non-model Bacteria
    CRAGE is a technique for chassis (or strain)-independent recombinase-assisted genome engineering, allowing scientists to conduct genome-wide screens and explore biosynthetic pathways. Now, CRAGE is being applied to other synthetic biology problems.

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    Maize can produce a cocktail of antibiotics with a handful of enzymes. (Sam Fentress, CC BY-SA 2.0)
    How Maize Makes An Antibiotic Cocktail
    Zealexins are produced in every corn variety and protect maize by fending off fungal and microbial infections using surprisingly few enzymes.

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    Poplar (Populus trichocarpa and P. deltoides) grow in the Advanced Plant Phenotyping Laboratory (APPL) at Oak Ridge National Laboratory in Tennessee. Poplar is an important biofuel feedstock, and Populus trichocarpa is the first tree species to have its genome sequenced — a feat accomplished by JGI. (Image courtesy of Oak Ridge National Laboratory, U.S. Dept. of Energy)
    Podcast: Xiaohan Yang on A Plantiful Future
    Building off plant genomics collaborations between the JGI and Oak Ridge National Laboratory, Xiaohan Yang envisions customizing plants for the benefit of human society.

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    Expansin complex with cell wall in background. (Courtesy of Daniel Cosgrove)
    Synthesizing Microbial Expansins with Unusual Activities
    Expansin proteins from diverse microbes have potential uses in deconstructing lignocellulosic biomass for conversion to renewable biofuels, nanocellulosic fibers, and commodity biochemicals.

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    High oleic pennycress. (Courtesy of Ratan Chopra)
    Pennycress – A Solution for Global Food Security, Renewable Energy and Ecosystem Benefits
    Pennycress (Thlaspi arvense) is under development as a winter annual oilseed bioenergy crop. It could produce up to 3 billion gallons of seed oil annually while reducing soil erosion and fertilizer runoff.

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    Artistic interpretation of CheckV assessing virus genome sequences from environmental samples. (Rendered by Zosia Rostomian​, Berkeley Lab)
    An Automated Tool for Assessing Virus Data Quality
    CheckV can be broadly utilized by the research community to gauge virus data quality and will help researchers to follow best practices and guidelines for providing the minimum amount of information for an uncultivated virus genome.

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    Unicellular algae in the Chlorella genus, magnified 1300x. (Andrei Savitsky)
    A One-Stop Shop for Analyzing Algal Genomes
    The PhycoCosm data portal is an interactive browser that allows algal scientists and enthusiasts to look deep into more than 100 algal genomes, compare them, and visualize supporting experimental data.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Podcast: A Primer on Genome Mining
    In Natural Prodcast: the basics of genome mining, and how JGI researchers conducted it in IMG/ABC on thousands of metagenome-derived genomes for a Nature Biotechnology paper.

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    Image of Octopus Springs for the CSP annual call
    Letters of Intent are due April 12, 2021 for the annual Community Science Program (CSP) call focused on large-scale genomic science projects that address specific areas of special emphasis and exploit the diversity of JGI capabilities.

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    “SIP technologies at EMSL and JGI” Webinar
    The concerted stable isotope-related tools and resources of the JGI and the Environmental Molecular Sciences Laboratory (EMSL) may be requested by applying for the annual “Facilities Integrating Collaborations for User Science” (FICUS) call.

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    CSP Functional Genomics Call Ongoing
    The CSP Functional Genomics call helps users translate genomic information into biological function. Proposals submitted by July 31, 2021 will be part of the next review.

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    Aerial photo of the switchgrass diversity panel late in the 2020 season at the Kellogg Biological Station in Michigan. (Robert Goodwin)
    A Team Effort Toward Targeted Crop Improvements
    A multi-institutional team has produced a high-quality reference sequence of the complex switchgrass genome. Building off this work, researchers at three DOE Bioenergy Research Centers have expanded the network of common gardens and are exploring improvements to switchgrass.

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    Artistic interpretation of how microbial genome sequences from the GEM catalog can help fill in gaps of knowledge about the microbes that play key roles in the Earth's microbiomes. (Rendered by Zosia Rostomian​, Berkeley Lab)
    Uncovering Novel Genomes from Earth’s Microbiomes
    A public repository of 52,515 microbial draft genomes generated from environmental samples around the world, expanding the known diversity of bacteria and archaea by 44%, is now available .

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    Green millet (Setaria viridis) plant collected in the wild. (Courtesy of the Kellogg lab)
    Shattering Expectations: Novel Seed Dispersal Gene Found in Green Millet
    In Nature Biotechnology, a very high quality reference Setaria viridis genome was sequenced, and for the first time in wild populations, a gene related to seed dispersal was identified.

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Home › Our Science › Scientists at JGI › Yasuo Yoshikuni – Synthetic Biology-Pathway Engineering

Yasuo Yoshikuni – Synthetic Biology-Pathway Engineering

Yasuo Yoshikuni

Yasuo Yoshikuni, DOE Joint Genome Institute

Prior to joining the JGI, Yasuo was a co-founder and Chief Science Officer at a clean technology start-up, Bio Architecture Lab, Inc. (BAL) where his significant achievement was using synthetic biology to develop the first microbial platform technologies enabling to unlock the potential of macroalgae as highly environmentally sustainable and cost-effective biomass for the production of renewable fuels and chemicals. The development of this technology allowed the company to raise $40 million from private funding sources, receive prestigious national grants and build a commercial partnership with leading companies in the oil and chemical industries. The work also led to several high impact scientific publications.  Yasuo’s research focus is to discover novel secondary metabolites and to study their roles in microbial-microbial and plant-microbial communications in various environments. He is currently developing design principles, tools, and methodologies to mine and characterize novel secondary metabolite biosynthetic pathways and component enzymes by leveraging on the JGI’s unique resources and capabilities.

  • DNA Synthesis Science Program Head
  • Synthetic Biology-Pathway Engineering Group Lead
  • Staff Scientist, Lawrence Berkeley National Laboratory

Education

  • B.E. in Biological Science and Technology, Tokyo University of Science, Japan (summa cum laude)
  • Ph.D. in Bioengineering, University of California, Berkeley, CA (with Jay Keasling)
  • Postdoctoral training in Biochemistry, University of Washington, WA (HHMI and Jane Coffin Childs Memorial Fellow)

Awards

  • SIMB Young Investigator Award 2013
  • Sustainable Biofuels Awards, Green Shoots Award 2012
  • Jane Coffin Childs Memorial Fund, Fellow 2007-2008

Selected Publications

  1. C. N. S. Santos et. al., Engineering complex biological systems in bacteria through recombinase-assisted genome engineering. Nature Protocols, 9, 1320-1336 (2014)
  2. M. Enquist-Newman et al, Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform, Nature, 505, 239-243 (2014)
  3. C. N. S. Santos et al., Implementation of stable and complex biological systems through recombinase-assisted genome engineering, Nature Communications, 4, 2503 (2013)
  4. A. J. Wargacki et. al., An engineered microbial platform for direct biofuel production from brown macroalgae, Science, 335, 308-313 (2012)
  5. Y. Yoshikuni et. al., Designed divergent evolution of enzyme function, Nature, 440, 1078-1082, (2006)
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