Endy, Alpha, June 2004 1 Atrophy time SRM Physical Performance (short) SRM Adapt & Learn (medium) SRM Evolve or Persist (long) SRM Encoding Design of Self-Replicating.

Slides:

Advertisements

Similar presentations

Eau d’e coli igem 2006: mit. meet the team The Undergrads: Kate Broadbent Biological Engineering Andre Green Biology / Physics Stephen Payne Biological.

Advertisements

Harvard iGEM 2006 Cyanobacterial Oscillator Hetmann Hsieh Jeff Lau Dave Ramos Zhipeng Sun Harvard iGEM 2006 Creating a robust biological oscillating biobrick.

Science, Technology, Engineering, and Math all rolled up into iGEM Ung.igem.org/High_School_Division.

Synthetic Biology Lecture 2: Fundamentals of Synthetic Biology.

Endy, BIOS, June Atrophy time SRM Physical Performance (short) SRM Adapt & Learn (medium) SRM Evolve or Persist (long) SRM Encoding Design of Self-Replicating.

Programming Biological Cells Ron Weiss, George Homsy, Radhika Nagpal Tom Knight, Gerald Sussman, Nick Papadakis MIT Artificial Intelligence Laboratory.

CS 374, Algorithms in Biology. Florian Buron Transforming cells into automata Genetic Circuit Building Blocks for Cellular Computation (Gardner, Cantor.

IGEM2009 SHORT COURSE Lesson1 Introduction to iGEM and Synthetic Biology.

Endy, MIT April Drew Endy  file here [.ppt]  Registry of Standard Biological.

1 8 Bit ALU EE 166 Design Project San Jose State University Roger Flores Brian Silva Chris Tran Harizo Yawary Advisor: Dr. Parent May 2006.

Programmed cells: Interfacing natural and engineered gene networks Kobayashi, Kærn, Araki, Chung, Gardner, Cantor & Collins,( PNAS 2004). You, Cox, Weiss.

Problems at the interface between statistics, biomathematics and bioinformatics Chris Glasbey Biomathematics & Statistics Scotland.

Synthetic Biology and iGEM Cambridge iGEM2007 team 27 July 2007.

The Alpha Project - Stepping Towards Predictive Biology Michael B. Gonzales Senior Research Fellow Molecular Sciences Institute Berkeley, CA.

But is it art? Brandeis University Panel of artists…. and their art… Will the real artist please stand up?

Error-Corrected DNA Synthesis Peter Carr MIT Media Laboratory.

Harvard iGEM 2006 Cyanobacterial Oscillator From cyanobacteria......to E. coli Photosynthetic Circadian rhythm Evolved over billions of years Model organism.

Biotechnology & Genomics. DNA Cloning  Producing identical copies through asexual means.

Breaking Down Practices v1.0: Applications Megan Palmer May 10th 2011.

Genetic Engineering and Recombinant DNA

Higher copy (pSB3K3) Abstract We are working to enable the engineering of integrated biological systems. Specifically, we would like to be able to build.

Synthetic biology: New engineering rules for emerging discipline Andrianantoandro E; Basu S; Karig D K; Weiss R. Molecular Systems Biology 2006.

Abstraction Lesson 2 presented by Dr. Natalie Kuldell.

Building Biological Systems from Standard Parts Tom Knight MIT Computer Science and Artificial Intelligence Laboratory IGEM Headquarters Ginkgo Bioworks.

IGEM and The Registry Synthetic Biology Genopole Randy Rettberg, Dec. 16, 2010.

Experience Bioengineering Professor Richard L. Magin.

Genetic Technologies Manipulating & Cloning DNA.

2007 Synthetic Biology Team Challenge March 19-23, 26 Instructors: Howard Salis, Jeff Tabor.

UTACCEL 2010 Adventures in Biotechnology Graham Cromar.

Endy, MIT BE, 20 May Application Struggle, Limited Success, Struggle… System?? Devices? Design & Fabrication.

Genome Navigator Patrick Mar and Jennifer Maurer.

Genetic Circuit Challenge Workshop Thursday 24 Nov 2011 Bentham seminar room 1.

Why synthetic Biology? Reverse Engineering vs. Forward engineering: »Synthetic replicas of natural genetic circuits.

Endy, DB May Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)

Synthetic Biology Risks and opportunities of an emerging field Constructing Life.

Berkeley Lab scientists open electrical link to living cells The Terminator. The Borg. The Six Million Dollar Man. Science fiction is ripe with biological.

Core members iGEM Web of registries Based on MIT Registry of Standard Biological Parts (parts.mit.edu)parts.mit.edu Well-characterized, community-rated,

Winston Retreat June 2006 S. cerevisiae 2.0. Engineered Biological Systems Nature has optimized biology (“artifacts”) Technologies exist to optimize differently.

Anita Nguyen & Harriet Gliddon.  A good characterisation for a part is: “The minimum amount of information someone needs to reuse the part without any.

A Genetic Differential Amplifier: Design, Simulation, Construction and Testing Seema Nagaraj and Stephen Davies University of Toronto Edward S. Rogers.

Engineered Gene Circuits Jeff Hasty. How do we predict cellular behavior from the genome? Sequence data gives us the components, now how do we understand.

Abstraction Hierarchy and PoPS  Engineers fabricate things but things sometimes are just too complicated  Engineers like to hide things  In Engineering.

GAMES camp Synthetic Biology and iGEM (International Genetically Engineered Machines)

Key Concepts of Synthetic Biology & The Central Dogma IGEM Presentation 1 7 th July 09 Dineka Khurmi James magA Field.

Harvard iGEM 2006 Cyanobacterial Oscillator From cyanobacteria......to E. coli Photosynthetic Circadian rhythm Evolved over billions of years Model organism.

Bio-Design Automation EE5393 – University of Minnesota Brian’s Automated Modular Biochemical Instantiator.

Addressable Conjugation in Bacterial Networks High School Matt Fleming Kaitlin A. Davis Undergrads Bryan HernandezFreshman Jennifer LuFreshman Samantha.

Bistable and Oscillatory Systems. Bistable Systems Systems which display two stable steady states with a third unstable state are usually termed bistable.

WELCOME TO BOSTON LEADERSHIP INSTITUTE Biological Research Biotechnology and Synthetic Biology.

Center for Genomic Experimentation and Computation Orna Resnekov Molecular Sciences Institute Berkeley, CA.

Combinatorial Synthesis of Genetic Networks Calin C. Guet, Michael B. Elowitz, Weihong Hsing, Stanislas Leibler Amit Meshulam Bioinformatics Seminar Technion,

Directed Evolution of a Genetic Circuit 15 February 2008 George McArthur This presentation is primarily based on content taken from the paper “Directed.

Synthetic Biology Genetic Engineering. What is it?

Synthetic Biology: A Brief Survey

Synthetic Biology Sergio Peisajovich Lim Lab June 2007.

… a few words about Synthetic Biology.

Eau d’e coli igem 2006: mit.

What is Synthetic Biology?

Standard biological parts for synthetic biology

Standard biological parts for synthetic biology

Standard biological parts for synthetic biology

Jeffrey C. Way, James J. Collins, Jay D. Keasling, Pamela A. Silver

Subhayu Basu et al. , DNA8, (2002) MEC Seminar Su Dong Kim

Definitions and Measures of Performance for Standard Biological Parts

Wendell A. Lim, Connie M. Lee, Chao Tang Molecular Cell

Molecular Biotechnology

Trajectories of Quality of Life after Hematopoietic Cell Transplantation: Secondary Analysis of Blood and Marrow Transplant Clinical Trials Network 0902.

Engineering Biological Systems with Synthetic RNA Molecules

Diagram of the workflow (related to Fig 1)‏

Presentation transcript:

Endy, Alpha, June Atrophy time SRM Physical Performance (short) SRM Adapt & Learn (medium) SRM Evolve or Persist (long) SRM Encoding Design of Self-Replicating Machines

Endy, Alpha, June Yeast Consider a Cell Signaling Pathway Cell Cycle

Endy, Alpha, June Yeast Cell Cycle Consider a Different Cell Signaling Pathway Budding Metabolism Yet Another Signaling Pathway

Endy, Alpha, June

5 Atrophy SRM T7 Encoding What does T7 know?

Endy, Alpha, June F. William Studier, Science 176:403 (1972) Deletion Amber/Enzyme Amber/Essential

Endy, Alpha, June Previous Page Sequence (BNL) Dunn & Studier, J. Mol. Bio. 166:477 (1983)

Endy, Alpha, June Atrophy SRM T7 What We Know What We Need To Know Encoding What do we know?

Endy, Alpha, June Atrophy What We Make SRM T7-SB Encoding Genome Domestication

Endy, Alpha, June A0 TR/ SRL ø OLA1A2 R0.3 BoxA R0.50.6A/B0.7 C R11 ø 1.1A ø 1.1B R ø 1.3 R1.31.3TE ø 1.5 ø 1.6 A2 NsiIPciIMfeISpeIBclI B

Endy, Alpha, June A0 63 TR/ SRL ø OL 35 A1 88 A2 316 R0.3 BoxA R A/B C R ø 1.1A ø 1.1B R ø 1.3 R TE ø ø A NsiIPciIMfeISpeIBclI

Endy, Alpha, June A0 63 TR/ SRL ø OL 35 A1 88 A2 316 R0.3 BoxA R A/B C R ø 1.1A ø 1.1B R ø 1.3 R TE ø ø A NsiIPciIMfeISpeIBclISacINheIApaLISapI

Endy, Alpha, June

Endy, Alpha, June

Endy, Alpha, June T7 + Rebuild [1-8311] :T7 +

Endy, Alpha, June

Endy, Alpha, June D23L AvrII D24L EcoRI D26L BamHI D27L EagI D28L SacII D30L SalI D22L BstEII D22RD23RD24RD26RD27RD28RD30R ø ø R3.8 D25L XmaI D25R 2.5 D29L PciI D29R 1.82 BglII FspIAvrII D50L BsiWI D51L PvuI D53L SacII D54L BamHI D55L XmaI D57L HindIII D50RD51RD53RD54RD55RD57R ø9 10ATøTø12 D52L EcoRI D52R 9 D56L ApaI D56R 8 PacI ø10 11 DraIRsrII XbaI BssHIIAatIIAvaIBspHIEciINsiI NdeI AseI D57L HindIII D59L EcoRI D58L PfoI D57R D58R 1213 PacI ø13 R13 D60L BsiWI D62L EagI D59RD60RD62R 16 D61L PvuI D61R 15 ApaLI NciI ScaI BstBIAvaI D64L HindIII D65L BamHI D67L ApaI D68L EcoRI D69L BsiWI D71L SalI D63L SacII D63RD64RD65RD67RD68RD69RD71R ø / E 19/19.2/ R18.5 D66L XmaI D66R 17.5 D70L PstI D70R øOR SRR/TR 160 KasIBspDIFspI BglI BlpIDraIIIAcvIAciIKpnI

Endy, Alpha, June E.colibrator, IAP 2004

Endy, Alpha, June Application Struggle, Limited Success, Struggle… System?? Devices? Design & Fabrication

Endy, Alpha, June Application Struggle, Success, Predictable Success Systems Parts & Fabrication Design Applications Tools Registries Synthesis Measurement

Endy, Alpha, June Standardization of Components –Predictable performance –Off-the-shelf –ME, 1800s Abstraction –Insulate relevant characteristics from overwhelming detail –Simple artifacts that can be used in combination –From Physics to EE, 1900s Decoupling Design & Fabrication –Rules insulating design process from details of fabrication –Enable parts, device, and system designers to work together –VLSI electronics, 1970s Enabling Biological Engineering

Endy, Alpha, June Abstraction Hierarchy Devices Parts Systems

Endy, Alpha, June Parts Zif268, Paveltich & Pabo c. 1991

Endy, Alpha, June Devices cI-857 O Lac RBS T CI LacI CI

Endy, Alpha, June Devices LacI  CI inverter CI LacI

Endy, Alpha, June Systems Inverter.2Inverter.3Inverter.1

Endy, Alpha, June Interfaces Devices Parts Systems Inv.2Inv.3Inv.1 Zif268, Paveltich & Pabo c LacI  CI inverter CI LacI

Endy, Alpha, June Parts/Device Interface Devices Parts Zif268, Paveltich & Pabo c LacI  CI inverter CI LacI XX A  B inverter B A

Endy, Alpha, June Device/System Interface Devices Systems Inv.2Inv.3Inv.1 A  B inverter B A C  D inverter D C E  F inverter F E

Endy, Alpha, June Device/System Interface Devices Systems E  FC  DA  B inverter B A C  D inverter D C E  F inverter F E X X X

Endy, Alpha, June Device/System Interface Devices Systems E  FC  DA  B inverter B A C  D inverter D C E  F inverter F E A  D X X X

Endy, Alpha, June Device/System Interface cI-857 O Lac RBS T cI LacI cI-857 RBS T cI O PoPS in PoPS out LacI cI PoPS out PoPS in

Endy, Alpha, June cI RBS T O PoPS OUT PoPS IN cI PoPS OUT INVERTER PoPS OUT PoPS IN Polymerase Per Second = PoPS!

Endy, Alpha, June Device/System Interface Devices Systems BCA A B C PoPS IN PoPS OUT X

Endy, Alpha, June Interfaces Devices Parts Systems PoPS Inv.2 PoPS Inv.3 PoPS Inv.1 Zif268, Paveltich & Pabo c PoPS Inv.1 PoPS

Endy, Alpha, June E.colibrator, IAP 2004

Endy, Alpha, June Device-Level System Diagram

Endy, Alpha, June Parts- and Device-Level System Diagram

Endy, Alpha, June DNA Layout

Endy, Alpha, June System-Level Timing Diagram

Endy, Alpha, June Population-Level Simulations

Endy, Alpha, June Trigger Test Circuit Characterization and Debug

Endy, Alpha, June MIT Registry of Standard Biological Parts

Endy, Alpha, June Acknowledgements Lab: Jennifer Braff, Barry Canton, Leon Chan, Caitlin Conboy, Jeffrey Gritton, Alison Hearn, Heather Keller, Jason Kelly, Sriram Kosuri, Maia Mahoney, Sara Neves, Sylvain Olier, Jose Pacheco, Francois St-Pierre, Samantha Sutton, Ilya Sytchev, and Ty Thomson Others: Adam Arkin, Frances Arnold, Ralph Baric, Roger Brent, Jehoshua Bruck, Carlos Bustamante, Rob Carlson, Austin Che, Jim Collins, Lynn Conway, Ron Davis, Mita Desai, Eric Eisenstadt, Michael Elowitz, Felice Frankel, Stephanie Forrest, Timothy Gardner, Seth Goldstein, Homme Hellinga, George Homsy, Joe Jacobsen, Tom Kalil, Jay Keasling, Doug Kirkpatrick, Tom Knight, Sri Kosuri, Patrick Lincoln, John Mulligan, Richard Murray, Radhika Nagpal, Richard Newton, Carl Pabo, Randy Rettberg, Pamela Silver, Brad Smith, Christina Smolke, Gerry Sussman, Samantha Sutton, Claire Tomlin, Jeffrey Way, Chris Webb, Ron Weiss, Scot Wolfe, Aarne Vesilind, the members of the MIT Synthetic Biology Working Group, and the students of the 2003 and 2004 MIT IAP Synthetic Biology Labs

Endy, Alpha, June DNA Synthesis Year Bases of DNA Per Person Day Carlson, Pace & Proliferation of Biological Technologies, Biosec. & Bioterror. 1(3):1 (2003)

Endy, Alpha, June Hacking the Living World?

Endy, Alpha, June Risk Biological Risk: Background Technology Classes Relevant to Biological Risk (current relative capabilities) Manipulation Analysis Response Detection

Endy, Alpha, June Biological Risk: Tactics as “Strategy” Maginot Line France, 1940 Ciprofloxacin Smallpox vaccine Anthrax vaccine SARS assay VHF therapy (under construction) Plague vaccine (under construction)

Endy, Alpha, June Biological Risk: Future Strategy Risk Technology Classes Relevant to Future Biological Risk (needed capabilities) Detection Analysis Response Manipulation

Endy, Alpha, June Biological Risk: Suite of Solutions Number of Individuals Individual’s Intent honorable dishonorable Bin Laden Genetics, Inc. Disgruntled Researcher Garage Bio-Hacker Basic Researcher

Endy, Alpha, June A Constructive Society

Endy, Alpha, June D23L AvrII D24L EcoRI D26L BamHI D27L EagI D28L SacII D30L SalI D22L BstEII D22RD23RD24RD26RD27RD28RD30R ø ø R3.8 D25L XmaI D25R 2.5 D29L PciI D29R 1.82 BglII FspIAvrII D50L BsiWI D51L PvuI D53L SacII D54L BamHI D55L XmaI D57L HindIII D50RD51RD53RD54RD55RD57R ø9 10ATøTø12 D52L EcoRI D52R 9 D56L ApaI D56R 8 PacI ø10 11 DraIRsrII XbaI BssHIIAatIIAvaIBspHIEciINsiI NdeI AseI D57L HindIII D59L EcoRI D58L PfoI D57R D58R 1213 PacI ø13 R13 D60L BsiWI D62L EagI D59RD60RD62R 16 D61L PvuI D61R 15 ApaLI NciI ScaI BstBIAvaI D64L HindIII D65L BamHI D67L ApaI D68L EcoRI D69L BsiWI D71L SalI D63L SacII D63RD64RD65RD67RD68RD69RD71R ø / E 19/19.2/ R18.5 D66L XmaI D66R 17.5 D70L PstI D70R øOR SRR/TR 160 KasIBspDIFspI BglI BlpIDraIIIAcvIAciIKpnI

Endy, Alpha, June Kuroda-Kawaguchi et al., Nature Genetics 29:279 (2001)

Endy, Alpha, June Responsibility “Men have forgotten this truth,” said the fox. “But you must not forget it. You become responsible, forever, for what you have tamed.” Saint-Exupéry, Le Petit Prince (1943)