… our first year at
Download
1 / 38

… our first year at iGEM - PowerPoint PPT Presentation


  • 101 Views
  • Uploaded on

… our first year at iGEM. Dr John Mitchell, on behalf of the St Andrews iGEM team. What is iGEM? i nternational G enetically E ngineered M achine competition (iGEM). Synthetic Biology competition between U/G teams representing universities worldwide.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' … our first year at iGEM' - imaran


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

… our first year at iGEM

Dr John Mitchell, on behalf of the St Andrews iGEM team


WhatisiGEM?

international Genetically Engineered Machine competition (iGEM).

Synthetic Biology competition between U/G teams representing universities worldwide.

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.

Our first year at iGEM

St Andrews


WhatisiGEM?

Undergraduatesspecify,

designandbuildbiological

systems over 10 weeks.

Standard,interchangable

parts: BioBricks.

BeganatMITin2003.

In2010,130teams

participated.

Our first year at iGEM

St Andrews


Spirit of iGEM

Open: parts made freely available for future use.

Ambitious: projects typically visionary but unfinished!

Cooperative: teams may help one another.

Interdisciplinary

A

… and requires funding!

Our first year at iGEM

St Andrews iGEM

St Andrews


OurTeam

Aninterdisciplinaryeffort

9Undergraduates

2 Biologists

2 Physicists

2 Medics

1 Chemist

1 ComputerScientist

1 Biochemist

5Advisors

(3 Faculty: Biology, Chemistry, Physics; 2 PG)

Our first year at iGEM

St Andrews


OurTeam

Aninterdisciplinaryeffort

9Undergraduates

2 Biologists

2 Physicists

2 Medics

1 Chemist

1 ComputerScientist

1 Biochemist

5Advisors

(3 Faculty: Biology, Chemistry, Physics; 2 PG)

Don’t take your team photograph outside in pouring rain!

Our first year at iGEM

St Andrews


StandardPartsandtheRegistry

Partsflankedbya

standardprefixandsuffix,

allowingforstandard

assemblyprocedure;

Agrowingcollectionof

partsanddevices;

Searchable;

Mixandmatch;

Varietyofchassis.

Our first year at iGEM

St Andrews


Our(Second) Project:Tackling Cholera

Our first year at iGEM

St Andrews


OurProject-TacklingCholera

Acutebacterialinfection,often

fatal

Contaminatedfoodandwater

Outbreaksoftenfollownatural

disasters

Our first year at iGEM

St Andrews


VibriocholeraeQuorumSensing

Interestingwhen

comparedtoother

quorumsensingsystems

Highcelldensityleadsto

highCAI-1concentrations

AthighCAI-1

concentrations,virulence

factorsarerepressed

Our first year at iGEM

St Andrews


QuorumSensing

Decisionsbasedon

populationdensity.

Autoinducermoleculesare

secretedanddetected

promotingfurther

autoinducersynthesis.

Oftenwhenan

autoinducerconcentration

thresholdisreached,cells

changebehavior.

St Andrews

Our first year at iGEM


LowCellDensity

P

CqsS

LuxO

Repressor

HapR

LuxU

P

CAI-1

CqsA

CqsA is an enzyme that makes CAI-1

Our first year at iGEM

St Andrews


HighCellDensity

P

CAI-1

CAI-1

P

P

CAI-1

CqsS

LuxO

LuxU

CAI-1

Repressor

CAI-1

CqsA

CAI-1

MasterRegulator

HapR

CAI-1

CqsA is an enzyme that makes CAI-1

Our first year at iGEM

St Andrews


Therefore...

IfwecantrickVibriocholeraeintothinkingitisathighcell

densityitwillbecomeavirulentandsafe.

Our first year at iGEM

St Andrews


TheCqsABioBrick

CAI-1

Our first year at iGEM

St Andrews


Re-engineeringtheLuxOperon

Rearrangingthenaturaloperontoproducebistableexpression

patterns.

We seek to make a switch

Our first year at iGEM

St Andrews


Modelling Goals

TocreateamathematicalrepresentationoftheE. coliHSLQuorum

SensingSystem, based on ODEs & written in C++.

TounderstandthebistableswitchingmechanismofE. colitoallow

theCAI-Iproductionmechanismtobeactivated&deactivatedas

appropriate.

Our first year at iGEM

St Andrews


Advising the Modellers

With hindsight, we would have given more direction earlier in the modelling team’s work.

Only at the third attempt did we produce a really useful model.

Our first year at iGEM

St Andrews


LuxRQuorumSensingCircuit

St Andrews

Our first year at iGEM


Model:Pseudo-MultiCell

Cellgrowthatadoublingrateof20minutes;

Celldeathatahalvingrateof20minutes;

Instantaneous diffusionofHSLthroughoutthesystem;

HSLdiffusesevenlyacrosstheentiresystem.

St Andrews

Our first year at iGEM


GFP:High/LowCellDensity

Shows bistability (hysteresis)

St Andrews

Our first year at iGEM


Parameter Scan

Findtheparameterspacein

whichthesystemswitcheson

Investigate∆Celldensity

varyingoneparameter

Investigate∆Celldensity

varyingtheotherparameter

Our first year at iGEM

St Andrews


Humanpractices: WebCrawler

CrawlerDesign

“Synthetic

Biology”

“Synbio”

NYTimes

CNN

Blog

Twitter

Facebook

BBCNews

Initial

Input

Anewdiscoveryin

syntheticbiology….

Newfieldofsynthetic

biologyrequires

regulation….

Disasteraheadwith

syntheticbiology…

ParsePagesandExtract

Links

Synthetic biology grant

awards made …

Syntheticbiologybrings

hopetomillions…

BlogLink

OpinionFinder

Journal

Queueof

Links

NewsLink

PaperLink

Positive

Syntheticbiology

bringshopeto

millions

Negative

Disasterahead

with synthetic

biology

Our first year at iGEM

St Andrews


WebCrawler

Percentoftotaldiscussionagainsttime

There is very little synthetic biology web content when compared to other sciences and even less compared to elements of popular culture.

Our first year at iGEM

St Andrews


WebCrawler

Opinionagainsttime

Positive

Negative

Opinions towards synthetic biology change frequently.

Our first year at iGEM

St Andrews


WebCrawler

Positive

Negative

This was a really inventive piece of technology. However, we could probably have done more rigorous research with it.

Our first year at iGEM

St Andrews


Team Wiki – don’t write it all on the last evening!

Our first year at iGEM

St Andrews


Judging form: plan how to tick the boxes!

Our first year at iGEM

St Andrews


BioBricks: Ribosome Binding Sites

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.

St Andrews

Our first year at iGEM


BioBricks: Ribosome Binding Sites

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!

St Andrews

Our first year at iGEM


Designing the Optimal RBS

Thethermodynamicmodel used to design the 3 RBS quantifiesthestrengthofthemolecular interactionbetweenanmRNAandthe30SribosomecomplexbyGibbs freeenergy.

Themodelisbasedontwoseparatedtransitionstates:

TheinitialstateisthefoldedmRNAandthefree30Scomplex

Thefinalstateistheassembled30ScomplexboundonanmRNA

St Andrews

Our first year at iGEM


ScientificAchievements

ConstructedaBioBricktogeneratethecholeraautoinducer

CAI-1.

CreatedsystemsofequationstodescribeE.coli,V.cholerae

andS.aureusquorumsensingsystems.

PredictedRBSstrengthsbasedontheirsequenceand

calculatedsecondarystructure.

IntroducedtwonewRBSsequenceswithmeasuredrelative

strengths …

Our first year at iGEM

St Andrews


ScientificAchievements

ConstructedaBioBricktogeneratethecholeraautoinducer

CAI-1.

CreatedsystemsofequationstodescribeE.coli,V.cholerae

andS.aureusquorumsensingsystems.

PredictedRBSstrengthsbasedontheirsequenceand

calculatedsecondarystructure.

IntroducedtwonewRBSsequenceswithmeasuredrelative

strengths …

… and a gold medal!

Our first year at iGEM

St Andrews


W

Our team’s experience

Beganthesummerwithverylittleknowledgeof

synthetic biology.

Hadtocomeupwithanewprojectidea

Learnanddebugstandardlabprotocols.

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.

Our first year at iGEM

St Andrews


Youarenotalone

Our first year at iGEM

St Andrews


Students

Sarah Shapiro

Fatemeh Salimi

Jonathan Ward

James Taylor

David Owen

Patrick Olden

Alasdair Morton

Rachael Blackburn

Lukas Ly

Our first year at iGEM

St Andrews


Advisors

Anne Smith

Chris Hooley

John Mitchell

Wim Verleyen

Olivia Medivil

Our first year at iGEM

St Andrews


Sponsors

Our first year at iGEM

St Andrews


ad