Biodefense in the Age of Synthetic Biology (2018) / Chapter Skim
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Appendix A: Specific Synthetic Biology Concepts, Approaches, and Tools
Appendix A: Specific Synthetic Biology Concepts, Approaches, and Tools
Pages 147-156
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From page 147... ...
Designers must consider the effects of a large array of potential variables, including DNA bases, codons, amino acids, genes and gene segments, regulatory elements, environmental context, empirical and theoretical design rules, and many other elements. Automated biological design, known in the field as bio-design automation, lowers the barrier to designing genetic constructs by automating some decisions and processes that would otherwise require a high level of expertise or a long time to carry out.
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From page 148... ...
Microbiome engineering Building genes Building chromosomes Building genomes Booting genomes High-throughput screening Directed evolution aFor each column, darker shading indicates routine use for that community, lighter shading indicates emerging use, and white background indicates little or no use. Adoption flows from left to right in most cases.
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From page 149... ...
In addition to aiding biological design, automation tools are used in other phases of the DBT cycle, as well. For example, researchers can use automated assembly tools to plan how to physically create their designed constructs most efficiently or to send designs created in silico directly to remote manufacturing facilities.
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From page 150... ...
In parallel, the rise of DNA construction and genome editing technologies could facilitate the construction of multiple variants that involve alterations to multiple genes in an organism. By applying high-throughput screening or selection to these variant libraries, it may be possible to isolate pathogens with dramatically modified phenotypes relevant to their potential weaponization, such as environmental stability, resistance to desiccation, and ability to be mass produced and dispersed.
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From page 151... ...
Considered here are technological capabilities and advances related to specified changes and to the construction of libraries for high-throughput screening or directed evolution. Factors that may impact the level of concern related to Build capabilities include cost, time, and ease of access for DNA construction; the complexity of libraries that can be generated for directed evolution; and the difficulties inherent in rendering the DNA "operable" (i.e., the ability to create a synthetic DNA sequence that actually functions within a living system)
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From page 152... ...
Other researchers are currently pursuing the construction of bacterial and yeast genomes ranging from 4 to 11 megabase pairs in length; these efforts also use an existing close relative, replacing or "patching" the natural genome with large fragments of the synthetic genome (Richardson et al., 2017)
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From page 153... ...
In contrast, genetic engineering and CRISPR/Cas9-based technologies may allow engineering in many new species, providing convenient paths to the further identification of altered phenotypes via either high-throughput screening or directed evolution of organisms with radically new phenotypes and genome-wide sequence changes. Library Construction One of the watershed differences that has been enabled by improvements in DNA construction is the ability to generate large libraries of genetic variants.
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From page 154... ...
TEST Testing is used to determine whether a design or biological product created with synthetic biology tools has the desired properties. Tests are typically performed at many stages of a project; for example, a researcher might use computer models to determine if a design is likely to work, then perform tests to validate that the correct DNA construct has been synthesized, then boot the construct to verify that it is capable of performing the intended biological functions.
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From page 155... ...
Prototypes can vary based on smaller changes -- different DNA bases, codons, or amino acids, for example -- or based on larger-scale differences such as the configuration of multiple genes within a genetic circuit. Like automated biological design, directed evolution is a synthetic biology technique that spans all three phases of the DBT cycle.
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From page 156... ...
156 BIODEFENSE IN THE AGE OF SYNTHETIC BIOLOGY Gibson, D.G., J.I. Glass, C
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