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… our first year at iGEM

… 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.

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… our first year at iGEM

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  1. … our first year at iGEM Dr John Mitchell, on behalf of the St Andrews iGEM team

  2. 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

  3. WhatisiGEM? Undergraduatesspecify, designandbuildbiological systems over 10 weeks. Standard,interchangable parts: BioBricks. BeganatMITin2003. In2010,130teams participated. Our first year at iGEM St Andrews

  4. 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

  5. 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

  6. 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

  7. StandardPartsandtheRegistry Partsflankedbya standardprefixandsuffix, allowingforstandard assemblyprocedure; Agrowingcollectionof partsanddevices; Searchable; Mixandmatch; Varietyofchassis. Our first year at iGEM St Andrews

  8. Our(Second) Project:Tackling Cholera Our first year at iGEM St Andrews

  9. OurProject-TacklingCholera Acutebacterialinfection,often fatal Contaminatedfoodandwater Outbreaksoftenfollownatural disasters Our first year at iGEM St Andrews

  10. VibriocholeraeQuorumSensing Interestingwhen comparedtoother quorumsensingsystems Highcelldensityleadsto highCAI-1concentrations AthighCAI-1 concentrations,virulence factorsarerepressed Our first year at iGEM St Andrews

  11. QuorumSensing Decisionsbasedon populationdensity. Autoinducermoleculesare secretedanddetected promotingfurther autoinducersynthesis. Oftenwhenan autoinducerconcentration thresholdisreached,cells changebehavior. St Andrews Our first year at iGEM

  12. 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

  13. 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

  14. Therefore... IfwecantrickVibriocholeraeintothinkingitisathighcell densityitwillbecomeavirulentandsafe. Our first year at iGEM St Andrews

  15. TheCqsABioBrick CAI-1 Our first year at iGEM St Andrews

  16. Re-engineeringtheLuxOperon Rearrangingthenaturaloperontoproducebistableexpression patterns. We seek to make a switch Our first year at iGEM St Andrews

  17. Modelling Goals TocreateamathematicalrepresentationoftheE. coliHSLQuorum SensingSystem, based on ODEs & written in C++. TounderstandthebistableswitchingmechanismofE. colitoallow theCAI-Iproductionmechanismtobeactivated&deactivatedas appropriate. Our first year at iGEM St Andrews

  18. 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

  19. LuxRQuorumSensingCircuit St Andrews Our first year at iGEM

  20. Model:Pseudo-MultiCell Cellgrowthatadoublingrateof20minutes; Celldeathatahalvingrateof20minutes; Instantaneous diffusionofHSLthroughoutthesystem; HSLdiffusesevenlyacrosstheentiresystem. St Andrews Our first year at iGEM

  21. GFP:High/LowCellDensity Shows bistability (hysteresis) St Andrews Our first year at iGEM

  22. Parameter Scan Findtheparameterspacein whichthesystemswitcheson Investigate∆Celldensity varyingoneparameter Investigate∆Celldensity varyingtheotherparameter Our first year at iGEM St Andrews

  23. 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

  24. 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

  25. WebCrawler Opinionagainsttime Positive Negative Opinions towards synthetic biology change frequently. Our first year at iGEM St Andrews

  26. 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

  27. Team Wiki – don’t write it all on the last evening! Our first year at iGEM St Andrews

  28. Judging form: plan how to tick the boxes! Our first year at iGEM St Andrews

  29. 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

  30. 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

  31. Designing the Optimal RBS Thethermodynamicmodel used to design the 3 RBS quantifiesthestrengthofthemolecular interactionbetweenanmRNAandthe30SribosomecomplexbyGibbs freeenergy. Themodelisbasedontwoseparatedtransitionstates: TheinitialstateisthefoldedmRNAandthefree30Scomplex Thefinalstateistheassembled30ScomplexboundonanmRNA St Andrews Our first year at iGEM

  32. ScientificAchievements ConstructedaBioBricktogeneratethecholeraautoinducer CAI-1. CreatedsystemsofequationstodescribeE.coli,V.cholerae andS.aureusquorumsensingsystems. PredictedRBSstrengthsbasedontheirsequenceand calculatedsecondarystructure. IntroducedtwonewRBSsequenceswithmeasuredrelative strengths … Our first year at iGEM St Andrews

  33. 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

  34. 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

  35. Youarenotalone Our first year at iGEM St Andrews

  36. 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

  37. Advisors Anne Smith Chris Hooley John Mitchell Wim Verleyen Olivia Medivil Our first year at iGEM St Andrews

  38. Sponsors Our first year at iGEM St Andrews

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