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Title: Life with Four Billion Atoms

Today it is commonplace to design and construct single silicon chips with billions of transistors. These are complex systems, difficult (but possible) to design, test, and fabricate. Remarkably, simplmore »e living systems can be assembled from a similar number of atoms, most of them in water molecules. In this talk I will present the current status of our attempts at full understanding and complexity reduction of one of the simplest living systems, the free-living bacterial species Mesoplasma florum. This 400 nm diameter cell thrives and replicates every 40 minutes with a genome of only 800 kilobases. Our recent experiments using transposon gene knockouts identified 354 of 683 annotated genes as inessential in laboratory culture when inactivated individually. While a functional redesigned genome will certainly not remove all of those genes, this suggests that roughly half the genome can be removed in an intentional redesign. I will discuss our recent knockout results and methodology, and our future plans for Genome re-engineering using targeted knock-in/knock-out double recombination; whole cell metabolic models; comprehensive whole cell metabolite measurement techniques; creation of plug-and-play metabolic modules for the simplified organism; inherent and engineered biosafety control mechanisms. This redesign is part of a comprehensive plan to lay the foundations for a new discipline of engineering biology. Engineering biological systems requires a fundamentally different viewpoint from that taken by the science of biology. Key engineering principles of modularity, simplicity, separation of concerns, abstraction, flexibility, hierarchical design, isolation, and standardization are of critical importance. The essence of engineering is the ability to imagine, design, model, build, and characterize novel systems to achieve specific goals. Current tools and components for these tasks are primitive. Our approach is to create and distribute standard biological parts, organisms, assembly techniques, and measurement techniques as a way of enabling this new field.« less
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Title: Life with Four Billion Atoms
Authors:
Publication Date: 2013-04-10
OSTI Identifier: 1087597
DOE Contract Number: AC02-07CH11359
Resource Type: Multimedia
Resource Relation: Conference: Fermilab Colloquia, Fermi National Accelerator Laboratory (FNAL), Batvia, Illinois (United States), presented on April 10, 2013
Research Org: FNAL (Fermi National Accelerator Laboratory (FNAL), Batavia, IL (United States))
Sponsoring Org: USDOE Office of Science (SC)
Subject: 99 GENERAL AND MISCELLANEOUS
Country of Publication: United States
Language: English
Run Time: 1:02:18
System Entry Date: 2016-01-28