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    A vertical tree stump outdoors with about a dozen shiitake mushrooms sprouting from its surface.
    Tracing the Evolution of Shiitake Mushrooms
    Understanding Lentinula genomes and their evolution could provide strategies for converting plant waste into sugars for biofuel production. Additionally, these fungi play a role in the global carbon cycle.

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    Soil Virus Offers Insight into Maintaining Microorganisms
    Through a collaborative effort, researchers have identified a protein in soil viruses that may promote soil health.

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    Data yielded from RIViT-seq increased the number of sigma factor-gene pairs confirmed in Streptomyces coelicolor from 209 to 399. Here, grey arrows denote previously known regulation and red arrows are regulation identified by RIViT-seq; orange nodes mark sigma factors while gray nodes mark other genes. (Otani, H., Mouncey, N.J. Nat Commun 13, 3502 (2022). https://doi.org/10.1038/s41467-022-31191-w)
    Streamlining Regulon Identification in Bacteria
    Regulons are a group of genes that can be turned on or off by the same regulatory protein. RIViT-seq technology could speed up associating transcription factors with their target genes.

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    The switchgrass diversity panel growing at the Kellogg Biological Station in Michigan. (David Lowry)
    Mapping Switchgrass Traits with Common Gardens
    The combination of field data and genetic information has allowed researchers to associate climate adaptations with switchgrass biology.

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    Artist rendering of genome standards being applied to deciphering the extensive diversity of viruses. (Illustration by Leah Pantea)
    Expanding Metagenomics to Capture Viral Diversity
    Along with highlighting the viruses in a given sample, metagenomics shed light on another key aspect of viruses in the environment — their sheer genetic diversity.

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    Photograph of a stream of diatoms beneath Arctic sea ice.
    Polar Phytoplankton Need Zinc to Cope with the Cold
    As part of a long-term collaboration with the JGI Algal Program, researchers studying function and activity of phytoplankton genes in polar waters have found that these algae rely on dissolved zinc to photosynthesize.

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    Silver Age of GOLD Introduces New Features
    The Genomes OnLine Database makes curated microbiome metadata that follows community standards freely available and enables large-scale comparative genomics analysis initiatives.

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    Graphical overview of the RNA Virus MetaTranscriptomes Project. (Courtesy of Simon Roux)
    A Better Way to Find RNA Virus Needles in the Proverbial Database Haystacks
    Researchers combed through more than 5,000 data sets of RNA sequences generated from diverse environmental samples around the world, resulting in a five-fold increase of RNA virus diversity.

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    HPCwire Editor's Choice Award (logo crop) for Best Use of HPC in the Life Sciences
    JGI Part of Berkeley Lab Team Awarded Best Use of HPC in Life Sciences
    The HPCwire Editors Choice Award for Best Use of HPC in Life Sciences went to the Berkeley Lab team comprised of JGI and ExaBiome Project team, supported by the DOE Exascale Computing Project for MetaHipMer, an end-to-end genome assembler that supports “an unprecedented assembly of environmental microbiomes.”

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    Digital ID card with six headshots reads: Congratulations to our 2022 Function Genomics recipients!
    Final Round of 2022 CSP Functional Genomics Awardees
    Meet the final six researchers whose proposals were selected for the 2022 Community Science Program Functional Genomics call.

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    CSP New Investigators FY23 R1
    JGI Announces First Round of 2023 New Investigator Awardees
    Twice each year we look for novel research projects aligned with DOE missions and from PIs who have not led any previously-accepted proposals through the CSP New Investigator call.

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    screencap from Amundson and Wilkins subsurface microbiome video
    Digging into Microbial Ecosystems Deep Underground
    JGI users and microbiome researchers at Colorado State University have many questions about the microbial communities deep underground, including the role viral infection may play in other natural ecosystems.

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    2022 JGI-UC Merced interns (Thor Swift/Berkeley Lab)
    Exploring Possibilities: 2022 JGI-UC Merced Interns
    The 2022 UC Merced intern cohort share how their summer internship experiences have influenced their careers in science.

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    Using Team Science to Build Communities Around Data
    As the data portals grow and evolve, the research communities further expand around them. But with two projects, communities are forming to generate high quality genomes to benefit researchers.

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    Cow Rumen and the Early Days of Metagenomics
    Tracing a cow rumen dataset from the lab to material for a hands-on undergraduate research course at CSU-San Marcos that has since expanded into three other universities.

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Home › Our Science › Science Programs & Platforms Leads › Yasuo Yoshikuni

Yasuo Yoshikuni

Yasuo Yoshikuni

Yasuo Yoshikuni, DOE Joint Genome Institute

Dr. Yasuo Yoshikuni has been head of the DNA Synthesis Science Program since 2015. The mission of this program is to harness the power of DNA synthesis, strain engineering, and biosystems design for DOE-mission-relevant discovery and applications. This program has supported over 250 projects since it started. In the JGI, Dr. Yoshikuni also manages the Synthetic Biology Pathway Engineering group. His research focus includes engineering of non-model yeasts for production of biofuels and renewable chemicals, developing genome engineering tools for non-model organisms, modulating microbe-microbe and plant-microbe interactions in various environments to improve crop yield, and developing a platform for building composite materials. Before joining the JGI, Dr. Yoshikuni was co-founder and chief science officer at a clean technology startup, Bio Architecture Lab, Inc. (BAL), where his significant achievement was using systems and synthetic biology to discover novel pathways assimilating unique sugar polymers in macroalgae and developing the first microbial platform technologies unlocking the potential of macroalgae as an environmentally sustainable and cost-effective biomass for production of renewable fuels and chemicals. The development of this technology allowed the company to build a strong IP proposition and to raise ~$40 million from venture capitalists, receive prestigious national grants (ARPA-E, CORFO), and build a commercial partnership with leading companies in the oil and chemical industries (e.g., Statoil, DuPont).

Education

  • B.E. in Biological Science and Technology, Tokyo University of Science, Japan (summa cum laude)
  • Ph.D. in Bioengineering, University of California, Berkeley
  • Postdoctoral training in Biochemistry, University of Washington

Awards

  • R&D100 Award finalist 2019
  • SIMB Young Investigator Award 2013
  • Sustainable Biofuels Awards, Green Shoots Award 2012
  • Jane Coffin Childs Memorial Fund, Fellow 2007-2008
  • Editorial board member of Synthetic Biology (Oxford Journal)
  • Review committee member of International Journal of Molecular Sciences and Frontiers in Chemical Engineering

Selected Publications

  1. Ke et al., 2021 CRISPR-CRAGE enables rapid activation of secondary metabolite biosynthetic gene clusters in bacteria, Cell Chemical Biology, accepted
  2. K. Bowman et al., 2020, Bidirectional titration of yeast gene expression using a pooled CRISPR guid RNA approach, PNAS 117, 18424-18430
  3. Wang et al. GRAGE enables rapid activation of biosynthetic gene clusters in undomesticated bacteria, Nature Microbiology,12:2498-2510
  4. M. M. Stoffel et al. 2019, Four amino acids define the CO2 binding pocket of enoyl-coA carboxylases/reductases, PNAS 2019, 116:13964-13969
  5. Mukherjee e. al. 2017, 1003 reference genomes of bacterial and archaeal isolates expand coverage of the tree of life, Nature Biotechnology 35, 676-683
  6. B. Siegel et al. 2015. Computational protein design enables a novel one-carbon assimilation pathway, PNAS 112, 11, 3704-3709.
  7. Enquist-Newman et al. 2014. Efficient ethanol production from brown macroalgae sugars by a synthetic yeast platform, Nature 505, 239-243.
  8. N. S. Santos et al. 2013. Implementation of stable and complex biological systems through recombinase-assisted genome engineering Nature Communications, 4, 2503.
  9. Wargacki et al. 2012. An engineered microbial platform for direct biofuel production from brown macroalgae, Science 335, 308-313.
  10. Yoshikuni et al. 2006. Designed divergent evolution of enzyme function, Nature 440, 1078-1082.
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