… our first year at igem dr john mitchell, on behalf of the st andrews igem team
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… … our first year at iGEMour first year at iGEM
Dr John Mitchell, on behalf of the St Andrews iGEM team
Synthetic Biology competition between U/G teams representing universities worldwide.
Our first year at iGEM
What is iGEM?
international Genetically Engineered Machine competition (iGEM).
Standard biological parts are designed, grown in cells, & characterised.
Suitable parts (“BioBricks”) are chosen and assembled into a machine, ideally to solve some significant scientific or environmental problem.
St Andrews
Our first year at iGEM
What is iGEM?
Undergraduates specify,design and build biologicalsystems over 10 weeks.
Standard, interchangableparts: BioBricks.
Began at MIT in 2003.
In 2010, 130 teamsparticipated.
St Andrews
A
Our first year at iGEM
Spirit of iGEM
Open: parts made freely available for future use.
Ambitious: projects typically visionary but unfinished!
Cooperative: teams may help one another.
Interdisciplinary
… and requires funding!
St Andrews iGEMSt Andrews
Our first year at iGEM
Our TeamAn interdisciplinary effort
9 Undergraduates
2 Biologists2 Physicists2 Medics1 Chemist1 Computer Scientist1 Biochemist
5 Advisors
(3 Faculty: Biology, Chemistry, Physics; 2 PG)
St Andrews
Our first year at iGEM
Our TeamAn interdisciplinary effort
9 Undergraduates
2 Biologists2 Physicists2 Medics1 Chemist1 Computer Scientist1 Biochemist
5 Advisors
(3 Faculty: Biology, Chemistry, Physics; 2 PG)
Don’t take your team photograph outside in pouring rain!
St Andrews
Our first year at iGEM
Standard Parts and the Registry
Parts flanked by astandard prefix and suffix,allowing for standardassembly procedure;
A growing collection ofparts and devices;
Searchable;
Mix and match;
Variety of chassis.
St Andrews
Our (Second) Project: Tackling Cholera
St Andrews Our first year at iGEM
Our first year at iGEM
Our Project - Tackling Cholera
Acute bacterial infection, oftenfatal
Contaminated food and water
Outbreaks often follow naturaldisasters
St Andrews
Vibrio cholerae Quorum Sensing
Interesting whencompared to otherquorum sensing systemsHigh cell density leads tohigh CAI-1 concentrationsAt high CAI-1concentrations, virulencefactors are repressed
St Andrews Our first year at iGEM
Quorum Sensing
Decisions based onpopulation density.
Autoinducer molecules aresecreted and detectedpromoting furtherautoinducer synthesis.
Often when anautoinducer concentrationthreshold is reached, cellschange behavior.
St Andrews Our first year at iGEM
Low Cell Density
CqsS LuxU LuxO
Repressor
HapR
CqsACAI-1
P
P
Our first year at iGEMSt Andrews
CqsA is an enzyme that makes CAI-1
CqsS LuxU LuxO
PP
Master Regulator
HapR
High Cell Density
PCAI-1
CAI-1
CAI-1
RepressorCAI-1
CqsA
CAI-1
CAI-1
Our first year at iGEMSt Andrews
CAI-1
CqsA is an enzyme that makes CAI-1
Therefore...
If we can trick Vibrio cholerae into thinking it is at high celldensity it will become avirulent and safe.
St Andrews Our first year at iGEM
The CqsA BioBrick
St Andrews Our first year at iGEM
CAI-1
Re-engineering the Lux Operon
Rearranging the natural operon to produce bistable expressionpatterns.
St Andrews Our first year at iGEM
We seek to make a switch
To create a mathematical representation of the E. coli HSL QuorumSensing System, based on ODEs & written in C++.To understand the bistable switching mechanism of E. coli to allowthe CAI-I production mechanism to be activated & deactivated asappropriate.
Modelling Goals
Our first year at iGEMSt Andrews
With hindsight, we would have given more direction
earlier in the modelling team’s work.
Advising the Modellers
Our first year at iGEMSt Andrews
Only at the third attempt did we produce a really useful model.
LuxR Quorum Sensing Circuit
Our first year at iGEMSt Andrews
Cell growth at a doubling rate of 20 minutes;Cell death at a halving rate of 20 minutes;Instantaneous diffusion of HSL throughout the system;HSL diffuses evenly across the entire system.
Model: Pseudo-Multi Cell
Our first year at iGEMSt Andrews
GFP: High/Low Cell Density
Our first year at iGEMSt Andrews
Shows bistability (hysteresis)
Find the parameter space inwhich the system switches on
Investigate ∆ Cell densityvarying one parameter
Investigate ∆ Cell densityvarying the other parameter
Parameter Scan
Our first year at iGEMSt Andrews
Crawler Design
BBC News
NY TimesCNN
Blog
Parse Pages and ExtractLinks
Journal
InitialInput
Queue ofLinks
A new discovery insynthetic biology….New field of syntheticbiology requiresregulation….Disaster ahead withsynthetic biology …
Synthetic biology bringshope to millions…
Blog Link
News LinkPaper Link
“SyntheticBiology”
“Synbio”
Opinion Finder
Positive
Synthetic biologybrings hope tomillions
Negative
Disaster aheadwith syntheticbiology
Human practices: Web Crawler
Our first year at iGEMSt Andrews
Synthetic biology grant awards made …
Web CrawlerPercent of total discussion against time
St Andrews Our first year at iGEM
There is very little synthetic biology web content when compared to other sciences and even less compared to elements of popular culture.
Web CrawlerOpinion against time
St Andrews Our first year at iGEM
Positive
Negative
Opinions towards synthetic biology change frequently.
Web Crawler
St Andrews Our first year at iGEM
Positive
Negative
This was a really inventive piece of technology. However, we could probably have done more rigorous research with it.
Team Wiki – don’t write it all on the last evening!
St Andrews Our first year at iGEM
Judging form: plan how to tick the boxes!
St Andrews Our first year at iGEM
St Andrews
Thus, we designed and built three RBS ...
mRNA sequence which ribosome binds to, initiating translation.RBS sequence affects the rate of translation …… via (1) ribosome attachment rate & (2) mRNA stability.We used existing software to design two fast & one slow RBS.Successfully used these to express GFP & measure fluorescence.
BioBricks: Ribosome Binding Sites
Our first year at iGEM
St Andrews
Thus, we designed and built three RBS ...
mRNA sequence which ribosome binds to, initiating translation.RBS sequence affects the rate of translation …… via (1) ribosome attachment rate & (2) mRNA stability.We used existing software to design two fast & one slow RBS.Successfully used these to express GFP & measure fluorescence.Results agreed with our predictions!
BioBricks: Ribosome Binding Sites
Our first year at iGEM
The thermodynamic model used to design the 3 RBS quantifies the strength of the molecular interaction between an mRNA and the 30 S ribosome complex by Gibbs free energy.
The model is based on two separated transition states:The initial state is the folded mRNA and the free 30S
complexThe final state is the assembled 30S complex bound on
an mRNA
Designing the Optimal RBS
Our first year at iGEM St Andrews
Scientific Achievements
Constructed a BioBrick to generate the cholera autoinducerCAI-1.Created systems of equations to describe E. coli, V. choleraeand S. aureus quorum sensing systems.Predicted RBS strengths based on their sequence andcalculated secondary structure.Introduced two new RBS sequences with measured relativestrengths …
St Andrews Our first year at iGEM
Scientific Achievements
Constructed a BioBrick to generate the cholera autoinducerCAI-1.Created systems of equations to describe E. coli, V. choleraeand S. aureus quorum sensing systems.Predicted RBS strengths based on their sequence andcalculated secondary structure.Introduced two new RBS sequences with measured relativestrengths …
… and a gold medalgold medal!
St Andrews Our first year at iGEM
W
St Andrews Our first year at iGEM
Students gained experience of real research, project planning, teamwork, teaching one another, interdisciplinary links, approaching sponsors, coping with failure & success, presenting their work etc. etc.
Academics gained experience of new areas of research, potential new collaborators, research themes & possible sponsors or suppliers.
Began the summer with very little knowledge of
synthetic biology.
Had to come up with a new project idea
Learn and debug standard lab protocols.
Our team’s experience
You are not alone
St Andrews Our first year at iGEM
Students
Our first year at iGEMSt Andrews
Rachael Blackburn
Lukas Ly
Alasdair Morton
David Owen
Patrick Olden
Fatemeh Salimi
Sarah Shapiro
Jonathan Ward
James Taylor
Advisors
Our first year at iGEMSt Andrews
Anne Smith Chris Hooley John Mitchell Wim Verleyen Olivia Medivil
Sponsors
St Andrews Our first year at iGEM