uOttawa’s 2013 Project Pulse generator
uOttawa’s 2013 Project Primer designer
uOttawa’s 2013 Project Children’s book
Accomplishments Constructed the first synthetic pulse generator in yeast Collaborated with the University of Waterloo Mathematically modeled the synthetic network Produced numerous novel functional BioBricks Created a primer-generating web application Wrote the first ever iGEM children’s book uOttawa 2013
Synthetic pulse generator
The incoherent feedforward loop uOttawa 2013
Temporal pulse generation Concentration uOttawa 2013
Temporal pulse generation Concentration uOttawa 2013
Temporal pulse generation Concentration uOttawa 2013
Temporal pulse generation Concentration uOttawa 2013
Network Design uOttawa 2013
Network Design uOttawa 2013
No temporal pulse is observed uOttawa 2013
Sigmoidal gene activation • Sigmoidal response uOttawa 2013
Sigmoidal gene activation • Sigmoidal response TIME uOttawa 2013
Negative autoregulation linearizes dose response • Sigmoidal response TIME uOttawa 2013
Negative autoregulation linearizes dose response • Sigmoidal response • Linear response TIME TIME uOttawa 2013
Mechanism of negative autoregulation uOttawa 2013
Mechanism of negative autoregulation uOttawa 2013
Mechanism of negative autoregulation uOttawa 2013
Collaboration with uWaterloo uOttawa 2013
Model shows pulse generation Concentration Time (min) uOttawa 2013
Experimental data exhibits a transient pulse in sfGFP in both cases uOttawa 2013
Experimental data exhibits a transient pulse in sfGFP in both cases uOttawa 2013
Linearization is observed 4 1.2 3.5 1.1 sfGFP Fluoresecnce (AU) 3 1 BFP Fluorescence (AU) 2.5 0.9 2 0.8 BFP 1.5 0.7 sfGFP 1 0.6 2.5 3 3.5 4 4.5 5 5.5 6 6.5 7 7.5 Time (h) uOttawa 2013
Fold-change response uOttawa 2013
Model exhibits functional fold-change response Variation in rate of production Concentration Time (mins) uOttawa 2013
Network versatility uOttawa 2013
Toxic molecule detection uOttawa 2013
BBa_K1164004: pTRE-LX uOttawa 2013
BBa_K1164004: pTRE-LX Characterization 4 3.5 GFP Fluorescence (AU) 3 2.5 2 1.5 1 0.5 0 0 2 4 6 8 10 IPTG (mM) uOttawa 2013
BBa_K1164004: pTRE-LX Characterization 1.6 1.4 GFP Fluorescence (AU) 1.2 1 0.8 0.6 0.4 0.2 0 0 25 50 75 100 ATc (ng/mL) uOttawa 2013
Bricklayer Web Application
Bricklayer Application PCR based assembly means designing primers. Lots of primers. uOttawa 2013
Early Version of Primer Generator uOttawa 2013
uOttawa 2013
uOttawa 2013
Bricklayer Application uOttawa 2013
Bricklayer Application uOttawa 2013
Bricklayer Application uOttawa 2013
Bricklayer Application uOttawa 2013
Bricklayer Application Spend less time designing primers. Spend more time designing networks. uOttawa 2013
Children’s Book
Human Practices Developing a Foundation: uOttawa 2013
Human Practices Our Approach: Create a foundation based on knowledge Provide accurate information Engage today’s youth How do we complete this?... uOttawa 2013
Human Practices A Children’s Book! Mr. Cool’s Microscopic Adventures uOttawa 2013
uOttawa 2013
Human Practices Scalability: • Global audience • Digital avenues for cross- platform sharing – High resolution audiovisual book – Audiobook • Registered ISBN • Available at three Ottawa Public Library locations uOttawa 2013
Human Practices So, how do we target our initial audience, children? uOttawa 2013
Human Practices In-class Workshops: • Students in grades 3-4 (n=24) • DNA, protein function, and applications of synthetic biology uOttawa 2013
Human Practices Workshop Results: What is DNA? uOttawa 2013
Human Practices Workshop Results: What is Synthetic Biology? uOttawa 2013
Human Practices Summary: • Wrote, illustrated, and published Mr. Cool’s Microscopic Adventures • Demonstrated scalability of project • Provided workshops on synthetic biology to youth • Created a foundation of knowledge that is statistically supported uOttawa 2013
Thank you! Thanks to the members of the Kærn Lab: - Dr. Mads Kærn - Afnan Azizi - Daniel Charlebois - Daniel Jedrysiak - Hilary Phenix - Ian Roney - Mila Tepliakova Thanks to: - Dr. Gábor Balázsi (University of Texas) - Dr. David Eide (University of Wisconsin- Madison) - Dr. Tom Ellis (Imperial College) - Dr. Michael Knop (ZMBH University of Heidelberg) uOttawa 2013
Questions? uOttawa 2013
Supplementary Materials • - Ctrl in IPTG & ATc gradient 1.4 sfGFP Fluorescence (AU) 1.2 1 0.8 1.4-1.5 1.2-1.4 0.6 1-1.2 0.4 0.8-1 0.2 0.6-0.8 105 0 0.4-0.6 90 0.2-0.4 75 60 0-0.2 45 30 9 ATc (ng/mL) 6 15 3 0 IPTG (mM) uOttawa 2013
Supplementary Figures • - Ctrl in IPTG & ATc gradient Concentration Time (mins) uOttawa 2013
Transcription formulas uOttawa 2013
Transcription formulas uOttawa 2013
Translation formula uOttawa 2013
Protein in nucleus uOttawa 2013
Control equations uOttawa 2013
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