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Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists

Author

Listed:
  • Ashty S. Karim

    (Northwestern University
    Northwestern University)

  • Dylan M. Brown

    (Northwestern University
    Northwestern University)

  • Chloé M. Archuleta

    (Northwestern University
    Northwestern University)

  • Sharisse Grannan

    (Northwestern University
    Independent Evaluator)

  • Ludmilla Aristilde

    (Northwestern University
    Northwestern University)

  • Yogesh Goyal

    (Northwestern University
    Northwestern University
    Northwestern University Feinberg School of Medicine)

  • Josh N. Leonard

    (Northwestern University
    Northwestern University)

  • Niall M. Mangan

    (Northwestern University
    Northwestern University)

  • Arthur Prindle

    (Northwestern University
    Northwestern University
    Northwestern University)

  • Gabriel J. Rocklin

    (Northwestern University
    Northwestern University)

  • Keith J. Tyo

    (Northwestern University
    Northwestern University)

  • Laurie Zoloth

    (Northwestern University
    University of Chicago)

  • Michael C. Jewett

    (Northwestern University
    Northwestern University
    Stanford University)

  • Susanna Calkins

    (Northwestern University
    Northwestern University
    Rosalind Franklin University of Medicine and Science)

  • Neha P. Kamat

    (Northwestern University
    Northwestern University
    Biomedical Engineering Northwestern University)

  • Danielle Tullman-Ercek

    (Northwestern University
    Northwestern University)

  • Julius B. Lucks

    (Northwestern University
    Northwestern University)

Abstract

Synthetic biology allows us to reuse, repurpose, and reconfigure biological systems to address society’s most pressing challenges. Developing biotechnologies in this way requires integrating concepts across disciplines, posing challenges to educating students with diverse expertise. We created a framework for synthetic biology training that deconstructs biotechnologies across scales—molecular, circuit/network, cell/cell-free systems, biological communities, and societal—giving students a holistic toolkit to integrate cross-disciplinary concepts towards responsible innovation of successful biotechnologies. We present this framework, lessons learned, and inclusive teaching materials to allow its adaption to train the next generation of synthetic biologists.

Suggested Citation

  • Ashty S. Karim & Dylan M. Brown & Chloé M. Archuleta & Sharisse Grannan & Ludmilla Aristilde & Yogesh Goyal & Josh N. Leonard & Niall M. Mangan & Arthur Prindle & Gabriel J. Rocklin & Keith J. Tyo & L, 2024. "Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-49626-x
    DOI: 10.1038/s41467-024-49626-x
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    References listed on IDEAS

    as
    1. Dae-Kyun Ro & Eric M. Paradise & Mario Ouellet & Karl J. Fisher & Karyn L. Newman & John M. Ndungu & Kimberly A. Ho & Rachel A. Eachus & Timothy S. Ham & James Kirby & Michelle C. Y. Chang & Sydnor T., 2006. "Production of the antimalarial drug precursor artemisinic acid in engineered yeast," Nature, Nature, vol. 440(7086), pages 940-943, April.
    2. C. J. Paddon & P. J. Westfall & D. J. Pitera & K. Benjamin & K. Fisher & D. McPhee & M. D. Leavell & A. Tai & A. Main & D. Eng & D. R. Polichuk & K. H. Teoh & D. W. Reed & T. Treynor & J. Lenihan & H., 2013. "High-level semi-synthetic production of the potent antimalarial artemisinin," Nature, Nature, vol. 496(7446), pages 528-532, April.
    3. Scott L. Greer & Benjamin Trump, 2019. "Regulation and regime: the comparative politics of adaptive regulation in synthetic biology," Policy Sciences, Springer;Society of Policy Sciences, vol. 52(4), pages 505-524, December.
    4. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    5. Ribeiro, Barbara & Shapira, Philip, 2020. "Private and public values of innovation: A patent analysis of synthetic biology," Research Policy, Elsevier, vol. 49(1).
    6. Christopher A. Voigt, 2020. "Synthetic biology 2020–2030: six commercially-available products that are changing our world," Nature Communications, Nature, vol. 11(1), pages 1-6, December.
    7. Arthur Prindle & Jintao Liu & Munehiro Asally & San Ly & Jordi Garcia-Ojalvo & Gürol M. Süel, 2015. "Ion channels enable electrical communication in bacterial communities," Nature, Nature, vol. 527(7576), pages 59-63, November.
    8. H. Jeong & B. Tombor & R. Albert & Z. N. Oltvai & A.-L. Barabási, 2000. "The large-scale organization of metabolic networks," Nature, Nature, vol. 407(6804), pages 651-654, October.
    9. Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
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