synthetic biology, engineering genetic data storage, logic, and communication systems using phage and integrasesResearch presentation on recent and unpublished work before the MIT Synthetic Biology Working Group on 24 September 2012 in MIT Building 56

Endy, Drew

DSpace@MIT

Drew EndyStanford BioengineeringThe BioBricks Foundation24 September 2012SBWG Cambridge MA1Integrases,          Aliens,               & Bill Joy2Ton & Jerome want 8 bio. bitsAging3Aging3Development4Development45But really we are working on this type of stuff because it challenges us to get better at...(i) composition of molecular parts(ii) reliability of performance     (“noise”, evolution)01010101**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 20126“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 20126“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 20126“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 20126“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 201261“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 201260“flipee”**please see Nash & Pollock (1981, 1983) thru Friedland & Lu et al. (2010+) for prior work on flipping DNA and data storage BONNET et al., PNAS May 201260“flipee”71IntegraseSET “flipper” “flipee”7Non-induced Arabinose WashedCytometerMicroscope020406080100% Cells FlippedInput LevelTimeSET signalPre “O” Switch Hold “1”8Non-induced Arabinose WashedCytometerMicroscope020406080100% Cells FlippedInput LevelTimeSET signalPre “O” Switch Hold “1”8Non-induced Arabinose WashedCytometerMicroscope020406080100% Cells FlippedInput LevelTimeSET signalPre “O” Switch Hold “1”8Non-induced Arabinose WashedCytometerMicroscope020406080100% Cells FlippedInput LevelTimeWe can write one “memory”SET signalPre “O” Switch Hold “1”81“flipee”9Integrase1“flipee”9Integrase1RESET “flipper” Excisionase“flipee”9Integrase0RESET “flipper” Excisionase“flipee”91010100 ~900/cell ~5500/cellNon-induced Arabinose WashedInput LevelTimeRESET signalPre “1” Switch Hold “0”11Non-induced Arabinose WashedInput LevelTimeRESET signalPre “1” Switch Hold “0”11Non-induced Arabinose WashedInput LevelTimeRESET signalPre “1” Switch Hold “0”11Non-induced Arabinose WashedInput LevelTimeRESET signalPre “1” Switch Hold “0”11Non-induced Arabinose WashedInput LevelTimeRESET signalPre “1” Switch Hold “0”11Non-induced Arabinose WashedInput LevelTimeWe can mostly erase a memory!RESET signalPre “1” Switch Hold “0”11Integrase0“flipee”RESET “flipper” ExcisionaseEven bigger problems putting together12Integrase0“flipee”RESET “flipper” Even bigger problems putting together12Integrase1“flipee”RESET “flipper” Even bigger problems putting together    12Integrase0“flipee”RESET “flipper” Even bigger problems putting togetherExcisionase121“flipee”IntegraseSET “flipper” 13Even bigger problems putting together1“flipee”IntegraseSET “flipper” Excisionase13Even bigger problems putting together0“flipee”IntegraseSET “flipper” ExcisionaseRE13Even bigger problems putting together1“flipee”IntegraseSET “flipper” 13Even bigger problems putting together14Switch given sustained input pulses14Switch given sustained input pulsesSwitch & hold given 2000’ input pul es14Switch given sustained input pulsesSwitch & hold given 2000’ input pul esS itch & hold given 200’ input pulses14Switch given sustained input pulsesSwitch & hold given 2000’ input pul esS itch & hold given 200’ input pulses’ input pulses0 20 40 60 80 100 120GenerationsGFP IntensityRESET SET HOLD Input Time:20HFSCShorter Inputs: ~2.5 cell doublings0 20 40 60 80 100 120 140 160 180 200GenerationsGFP Intensity15Inputs: ~10 cell doublings0 20 40 60 80 100 120GenerationsGFP IntensityRESET SET HOLD Input Time:20HFSCShorter Inputs: ~2.5 cell doublings0 20 40 60 80 100 120 140 160 180 200GenerationsGFP Intensity15Inputs: ~10 cell doublings0 20 40 60 80 100 120GenerationsGFP IntensityRESET SET HOLD Input Time:20HFSCShorter Inputs: ~2.5 cell doublings0 20 40 60 80 100 120 140 160 180 200GenerationsGFP Intensity15Inputs: ~10 cell doublings0 20 40 60 80 100 120GenerationsGFP IntensityRESET SET HOLD Input Time:20HFSCShorter Inputs: ~2.5 cell doublings0 20 40 60 80 100 120 140 160 180 200GenerationsGFP Intensity15Inputs: ~10 cell doublings16~3 years and ~750 attempts...171718Note, not a formally bistable systemWorks b/c we have two relatively nice A-to-D converters.What else could you make with A-to-D converters?Gate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoter BTP PTPBB PBTerm.INTBBonnet & Yin, unpublishedBoolean Integrase Logic: ORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoter BTP PTPBB PBTerm.INTBBonnet & Yin, unpublishedBoolean Integrase Logic: ORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoter BTP PTPBB PBTerm.INTBBonnet & Yin, unpublishedBoolean Integrase Logic: ORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoterINTBBTP PTPBB PBTerm.Bonnet & Yin, unpublishedBoolean Integrase Logic: XORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoterINTBBTP PTPBB PBTerm.Term.Bonnet & Yin, unpublishedBoolean Integrase Logic: NORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoterINTBBTP PTPBB PBTerm.Bonnet & Yin, unpublishedBoolean Integrase Logic: XNORGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoter BTP PTPBB PBTerm.INTBTerm.Bonnet & Yin, unpublishedBoolean Integrase Logic: ANDGate Source[Battery, here]PoPSOUTPoPSConditional Output SignalPoPSIN-1PoPS1N-2 TerminatorRBS TP901 IntTerminatorRBS BxbI IntINTTPConditional Input SignalsPromoter BTP PTPBB PBINTBTerm.Bonnet & Yin, unpublishedPromoterBoolean Integrase Logic: NANDBonnet & Yin, unpublishedBoolean Integrase Logic GatesBonnet & Yin, unpublishedBoolean Integrase Logic GatesBonnet & Yin, unpublishedBoolean Integrase Logic Gates2626272727293030303131Hmm....~1E31 phage per Earth...3232DNA replication32ScaffoldDNA replication32ScaffoldDNA replication3333Could you code...343435Jaschke et al., in press36Jaschke et al., in press37øX174 is known to have 11 CDSs.  However, analysis suggests ~82 ORFs of length 30+ codons with putative RBSs...Going to try exploring “reverse negative” genomics.38http://www.andyross.net/bill_joy.htm“No matter who you are, most of the smartest people work for someone else” - Bill Joy (?)39“No matter who you are, most of the smartest biological engineers work for someone else” 39“No matter who you are, most of the smartest biological engineers work for someone else” “No matter who you are, most of the smartest biologists work for someone else” 39“No matter who you are, most of the smartest biological engineers work for someone else” “No matter who you are, most of the smartest biologists work for someone else” “No matter who you are, most of the best bio. parts you need will be engineered by someone else” 39“No matter who you are, most of the smartest biological engineers work for someone else” “No matter who you are, most of the smartest biologists work for someone else” “No matter who you are, most of the best bio. parts you need will be engineered by someone else” “No matter who you are, most of the opportunities for what you can engineer will exist somewhere else” 39“No matter who you are, most of the smartest biological engineers work for someone else” “No matter who you are, most of the smartest biologists work for someone else” “No matter who you are, most of the best bio. parts you need will be engineered by someone else” “No matter who you are, most of the opportunities for what you can engineer will exist somewhere else” “No matter who you are, most of the issues arising from what you engineer will ramify somewhere else” 39“No matter who you are, most of the smartest biological engineers work for someone else” “No matter who you are, most of the smartest biologists work for someone else” “No matter who you are, most of the best bio. parts you need will be engineered by someone else” “No matter who you are, most of the opportunities for what you can engineer will exist somewhere else” “No matter who you are, most of the issues arising from what you engineer will ramify somewhere else” “No matter who you are, most of the best biotechnology ideas will be imagined and made true by someone else” 40So what do you (we) do about it?

Integrases, Aliens, & Bill Joy

http://dspace.mit.edu/bitstream/1721.1/78009/1/Endy_SBWG_v2.pdf

Integrases, Aliens, & Bill Joy

Abstract

Similar works

Full text

Available Versions

DSpace@MIT