Synthetic Bio- Communication 1 S YNTHETIC B IO -C OMMUNICATION 1. A - PowerPoint PPT Presentation

O RIGIN OF L IFE : C YS E R ESULTS 0.23 0.18 0.18 OD OD 0.13 0.13 0.08 0.08 0 10000 20000 30000 40000 50000 60000 70000 0 10000 20000 30000 40000 50000 60000 70000 Time (secs) Time (secs) Vmax Points = 21 Vmax Points = 21 Well H1 H2 H3 H4 H5 H6 Well E1 E2 E3 E4 E5 E6 Vmax 0.085 0.078 0.059 0.067 0.049 0.073 Vmax 0.159 0.104 0.085 0.078 0.082 0.090 R^2 0.770 0.850 0.905 0.883 0.891 0.906 R^2 0.557 0.769 0.727 0.629 0.659 0.776 Positive Control (Trento 2012) Ancestral Gene

O RIGIN OF L IFE : H IS C R ESULTS 0.28 0.23 0.23 0.18 OD OD 0.18 0.13 0.13 0.08 0.08 0 10000 20000 30000 40000 50000 60000 70000 0 10000 20000 30000 40000 50000 60000 70000 Time (secs) Time (secs) Vmax Points = 21 Vmax Points = 21 Well F1 F2 F3 F4 F5 F6 Well C1 C2 C3 C4 C5 C6 Vmax 0.142 0.164 0.107 0.105 0.115 0.117 Vmax 0.138 0.117 0.102 0.132 0.107 0.130 R^2 0.762 0.949 0.965 0.744 0.933 0.937 R^2 0.811 0.862 0.828 0.847 0.871 0.904 Positive Control Ancestral Gene

A PPLICATION : C RISPR Target: CasA • CASCADE Complex • Mechanism • Protein Modeling Testing • Test functionality - purified proteins • Compare to modern sequences

D OES THE M ODEL W ORK ? A-1 A- E. coli Thanks to Rich Lenski (MSU) we can validate the model A+ A+6

D OES THE M ODEL W ORK ? L ENSKI D ATA The Experiment • E coli evolution • 25 years • 12 strains • 40,000 generations Our Goals • Ancestral Reconstruction • Whole Genome • Proof of Concept • Modeling Evolution

P ROOF OF C ONCEPT : L ENSKI D ATA Results • Lazarus ~90% • Consensus ~99% Implications • Timeline too short? • Problems with model? • Not enough strains?

F UTURE A IMS Proof of Concept • Alternative Models: ML, Bayes, MP • Selective Pressure Application • Biochemical Assay • Functional Assay

D E -E XTINCTION : B IO B RICKS 7 BioBricks: Ancestral HisC Modern HisC 3 characterized AroE Ancestral CysE 4 currently being tested Ancestral CasA Modern CasA CasBCDE

D E -E XTINCTION : E THICS

D E -E XTINCTION : A CCOMPLISHMENTS ✓ Predicted Ancestral Genes ✓ Successfully Tested Ancestral Gene Function ✓ Modeled Ancestral Proteins ✓ Collaborated with Dr. Rich Lenski to Model and Tested Reconstruction Methods ✓ Submitted 7 BioBricks!

S YNTHETIC B IO -C OMMUNICATION B IO W IRES 1. A TOMIC C RISPR -C AS 2. I NTERCELLULAR 3. T IME D E -E XTINCTION E U :CROPIS 4. S PACE

E U :CROPIS Euglena Combined Regenerative Organic Food Production A German satellite In mission scheduled to Space launch in 2016

E U :CROPIS Brown-Stanford iGEM team pioneers PowerCell for in situ resource utilization on Mars 2011 2016

P OWER C ELL Goal Develop a universal, sustainable energy source to power biological tools Application Feed the biological tools that will transform raw materials into fuel, food, drugs, and other products useful to settlers Brown-Stanford 2011

E U :CROPIS We create a chromogenic biosensor for PowerCell in B. subtilis 2011 2016 2013

E U :CROPIS Load microfluidics chip into satellite 2011 2015

E U :CROPIS Launch! Activate first gravity level and ground controls. 2011 2016

Eu:CROPIS Microfluidics Chip

Anabaena Bacillus subtilis (Brown-Stanford 2011) (Stanford-Brown 2013)

P ROGRESS

P ROGRESS We identified genes associated with regulation of sucrose metabolism (sacY) sporulation (spo0A)

P ROGRESS We identified genes associated with regulation of sucrose metabolism (sacY) sporulation (spo0A) Used oligos to construct gene promoters

P ROGRESS We identified genes associated with regulation of sucrose metabolism (sacY) sporulation (spo0A) Used oligos to construct gene promoters Assembled 2 plasmids containing: sucrose metabolism promoter, a ribosome binding site, and a red chromoprotein/RFP

P ROGRESS We identified genes associated with regulation of sucrose metabolism (sacY) sporulation (spo0A) Used oligos to construct gene promoters Assembled 2 plasmids containing: sucrose metabolism promoter, a ribosome binding site, and a red chromoprotein/RFP Synthesized the equivalent construct for sporulation

P ROGRESS We identified genes associated with regulation of sucrose metabolism (sacY) sporulation (spo0A) Used oligos to construct gene promoters Assembled 2 plasmids containing: sucrose metabolism promoter, a ribosome binding site, and a red chromoprotein/RFP Synthesized the equivalent construct for sporulation Transformed into B. subtilis using an integration vector

R ESULTS Bacillus with sucrose metabolism promoter + RFP (Phase Contrast)

R ESULTS B. subtilis with sucrose inducer Bacillus with sucrose inducer promoter + fluorescent promoter + RFP chromoprotein eForRed (Fluorescence) (Fluorescence)

F UTURE A IMS

F UTURE A IMS Fall 2013: Isolate colonies containing our construct and characterize promoters

F UTURE A IMS Fall 2013: Isolate colonies containing our construct and characterize promoters Winter 2013: Helium balloon test

F UTURE A IMS Fall 2013: Isolate colonies containing our construct and characterize promoters Winter 2013: Helium balloon test 2014: Biocompatibility tests with microfluidics chip

F UTURE A IMS Fall 2013: Isolate colonies containing our construct and characterize promoters Winter 2013: Helium balloon test 2014: Biocompatibility tests with microfluidics chip 2015: Prepare for mission

F UTURE A IMS Fall 2013: Isolate colonies containing our construct and characterize promoters Winter 2013: Helium balloon test 2014: Biocompatibility tests with microfluidics chip 2015: Prepare for mission 2016: EuCROPIS Satellite Mission

E U :CROPIS - A CCOMPLISHMENTS Constructed and synthesized prototype prototype chromogenic biosensors to detect sucrose induction and sporulation 5 BioBricks: BBa_K1218020 BBa_K1218021 BBa_K1218001 BBa_K1218025 BBa_K1218023

E U :CROPIS - A CCOMPLISHMENTS Constructed and synthesized prototype prototype chromogenic biosensors to detect sucrose induction and sporulation 5 BioBricks: BBa_K1218020 Contributed on project to validate PowerCell on the EuCROPIS BBa_K1218021 BBa_K1218001 satellite mission and send synthetic biology into outer space BBa_K1218025 BBa_K1218023

O UTREACH

C ALIFORNIA A CADEMY OF S CIENCES

Synthetic Bio- Communication 1 S YNTHETIC B IO -C OMMUNICATION 1. A - PowerPoint PPT Presentation

Stanford-Brown 2013 Synthetic Bio- Communication 1 S YNTHETIC B IO -C OMMUNICATION 1. A TOMIC 2. I NTERCELLULAR 3. T IME 4. S PACE S YNTHETIC B IO -C OMMUNICATION B IO W IRES 1. A TOMIC 2. I NTERCELLULAR 3. T IME 4. S PACE S YNTHETIC B IO -C

Interactions between textchat and audio modalities for L2 communication in the synthetic world

SK Telecom 1 U U U U U U U- U - - communication - - - - - communication

Synthetic Bio-Communication S YNTHETIC B IO -C OMMUNICATION 1. A TOMIC 2. I NTERCELLULAR 3. T IME

PHONICS 101 A PA R E N T S G U I D E SYSTEMATIC SYNTHETIC PHONICS Systematic synthetic

Modular Synthetic Receptor System Interfaced with Nano Breadboard Synthetic receptor scheme

What are synthetic drugs and how do we combat them? How to deal with the current trends of

Feature FIGURE 2 : Partially funded synthetic CDO structure protection buyer will apply the posted

Synthetic Biology and Rational Design Keith Shearwin University of Adelaide Synthetic biology

SYNTHETIC DATA GENERATION FOR AN ALL-IN-ONE DMS Sagar Bhokre NEED FOR SYNTHETIC DATA Where does

Building with Biology Todays activities Introduction to Synthetic Biology Building 4

CSCI 2570 Introduction to Nanocomputing Synthetic Biology John E Savage What is Synthetic

4D Topological Physics with Synthetic Dimensions Hannah Price University of Birmingham, UK

The Semi Synthetic Artemisinin Project Industrialization of a Synthetic Biology derived product

Synthetic Biology Synthetic Biology Christian KRASSNIG 2005 Specific Activities covering a

A synthetic aperture microphone array for the meeting room TNO TPD Synthetic aperture microphone

Stabilisation/solidification of synthetic drill cuttings Stabilisation/solidification of synthetic

Synthetic Aperture Radar Image Compression By Magesh Valliappan Guner Arslan 1 Synthetic

Page 1 Synthetic aperture photography Synthetic aperture photography Computational

Synthetic biology Arnold Driessen Molecular Microbiology, University of Groningen

The 18 th International Electronic Conference on Synthetic Organic Chemistry 130 November 2014

Science with synthetic stellar surveys Robyn Sanderson Caltech UPenn/Flatiron CCA OMG

DNA-based synthetic DNA-based synthetic lectins lectins to inv to investigate estigate clathrin

Session 12 Assessing and Developing Communication SECTION 4: 1 Communication Communication

Using Synthetic Coverage Information to Evaluate Test Suite Prioritizers Gregory M. Kapfhammer