trials and tribulations of a first year igem team
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Trials and Tribulations of a First Year iGEM Team
Morgan Taschuk
Newcastle University
Outline
Team composition
Ambitious project
Potholes
The Jamboree
Happy Ending
Questions
The Team
AdvisorsInstructorsStudents
The Team
Four students in Bioinformatics Masters programRequire major aspects of project to be computational
Two biologists
And me
Wanted to shoot big!
First year iGEM wanted to shoot big! Wanted something awesome, on
Sequence
Feedback
Synthesize
Clone
Analyze
ImplementationCircle of (Synthetic) Life
Computational Modelling
Bioinformatics Tools
Sequence
Feedback
Synthesize
Clone
Analyze
ImplementationCircle of (Synthetic) Life
Computational Modelling
Bioinformatics ToolsMRSA diagnosticDifficult to detect
Not sexy
No computational aspect
Gram positive diagnostic
Methicillin-resistant Staphylococcus aureusMRSA difficult to distinguish from other S. aureusMostly they just grow up the culture and see if they die in response to methicillin and other antibioticsNot sexy, as one of our advisors called it! It's not big and awesome enough for iGEM. Can be accomplished using traditional biologyNo computational aspect. Most of instructors were from computing science, with interest in synthetic biology. Therefore, wanted to incorporate in silico with biology
Sensing Bacteria
Quorum sensing:Gram positive bacteria secrete fingerprints of signal peptides
Cell-cell communication
Quorum sensing
Fingerprints: unique to species or even the strain
Cell-to-cell communication, determine friend or foe
Multiple detection
Pull quorum self-sensing systems out of multiple bacteria and place it into a single B. subtilis genome
Fingerprints can be very similar. Related strains may release the same signal peptides, but at different relative levels
Limited outputs
Practical consideration: only 3-4 fluorescent proteins can be used with any chance of detecting by eye
Sensing Bacteria
Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
Quorum sensing
Fingerprints: unique to species or even the strain
Cell-to-cell communication, determine friend or foe
Multiple detection
Pull quorum self-sensing systems out of multiple bacteria and place it into a single B. subtilis genome
Fingerprints can be very similar. Related strains may release the same signal peptides, but at different relative levels
Limited outputs
Practical consideration: only 3-4 fluorescent proteins can be used with any chance of detecting by eye
Sensing Bacteria
Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
Quorum sensing
Fingerprints: unique to species or even the strain
Cell-to-cell communication, determine friend or foe
Multiple detection
Pull quorum self-sensing systems out of multiple bacteria and place it into a single B. subtilis genome
Fingerprints can be very similar. Related strains may release the same signal peptides, but at different relative levels
Limited outputs
Practical consideration: only 3-4 fluorescent proteins can be used with any chance of detecting by eye
Sensing Bacteria
?
?
Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
Need to discriminate between fingerprints
Quorum sensing
Fingerprints: unique to species or even the strain
Cell-to-cell communication, determine friend or foe
Multiple detection
Pull quorum self-sensing systems out of multiple bacteria and place it into a single B. subtilis genome
Fingerprints can be very similar. Related strains may release the same signal peptides, but at different relative levels
Limited outputs
Practical consideration: only 3-4 fluorescent proteins can be used with any chance of detecting by eye
Sensing Bacteria
Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
Need to discriminate between fingerprints
Limited outputs
Quorum sensing
Fingerprints: unique to species or even the strain
Cell-to-cell communication, determine friend or foe
Multiple detection
Pull quorum self-sensing systems out of multiple bacteria and place it into a single B. subtilis genome
Fingerprints can be very similar. Related strains may release the same signal peptides, but at different relative levels
Limited outputs
Practical consideration: only 3-4 fluorescent proteins can be used with any chance of detecting by eye
In Vitro Neural Nets
Sexy!Bacteria performing computational tasks
ComputationalEvolutionary algorithms
Plenty of potential
Where do we start??
Learned:Be very clear about commitmentsCommunication!Have a contigency plan
Good Advice
This time, last year:No computational tools ready
Wet lab booked from 4 August
No DNA designed
Modularise the tasks into discrete, achieveable chunks
Designed a BioBrick by hand
Synthesized itSix weeks! Shipped on 5 August
No computational tools were ready:Masters projects ran until beginning of August. Wet lab booked at the beginning of August. While this timetable initially seemed reasonable, there is an additional step between BioBrick design and testing it in the bacteria: DNA production.
Since we were using B. subtilis, and our brick wasn't in the repository, opted to have it synthesized
Designed a Brick by hand
Bad timing
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Bad timing
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
Tasks
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
ComputationalWet lab
Tasks
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
ComputationalWet labWiki
T-shirts, Presentation,Part docs, etc
Tasks
Bad timing
Me
Masters Students
Biologists
May
Jun
Jul
Aug
Sept
Oct
Nov
Apr
Team
ComputationalWet labWiki
T-shirts, Presentation,Part docs, etc
Tasks
Tally
Date: 22 September 2008
Number of remaining students: 1
Unfinished tasks
Wiki
T-Shirts
Presentation
DNA submission
Only just about everything we're judged on!
Wiki
Hard work
Internal wiki transferred
Ripped several theses apart
Organised lab journals
T-Shirts
David Appleyard and iGEM
Part Characterisation
One day per part
Not all parts need to have DNA, or even work!
Poster
Finished: 4 November
Presentation
...........
Practiced with the first version on 4 November
Finally on the way
7 November, 4:30am
Seven hour layover in Amsterdam
Revised the talk (again)
Stata Center
Jamboree, Day One
Mostly sandwiches, crisps, fruitBagels for breakfast I thought it was great, but some people were less pleased
Lots going on
David Appleyard and iGEM
People Watching
David Appleyard and iGEM
?
Lunch
Still revising our presentation
The Talk
No real questions at the end
David Appleyard and iGEM
David Appleyard and iGEM
Although we considered the lack of real questions at the end a vicopry, we suspected it had to do with two things:1) Our project was mostly a software project, but we tried hard to make it fit into another track2) We didn't make any grandiose claims about curing cancer in order to enhance our presentation we just told it like it was.
Poster Session
Dont let this happen to you!David Appleyard and iGEM
Afters
David Appleyard and iGEM
Jamboree Day 2 Awards
Finalists:
NYMU-Taipei
Caltech
Slovenia
Freiburg
Harvard
UC Berkeley
Awards
David Appleyard and iGEM
iGEM from Overhead
Us!David Appleyard and iGEM
Melee onstage
David Appleyard and iGEM
Melee
David Appleyard and iGEM
Awards
Like any long-term project
Be very clear about commitments from the outset
Communication!
Have a contingency plan
You have less time than you think you have
iGEM Specifically
Break your project into small, distinct pieces
Be ambitious with your goals, but realistic with your claimsYou probably have not invented the cure for cancer
Do not leave all of the documentation until the endJudging happens here!
Be creative
Bio brick away!
Thank you and good luck!