Bacterial Relay Race 09 An illustration of a cell-to-cell - PowerPoint PPT Presentation

The TUDelft iGEM team presents: Bacterial Relay Race ‘09 An illustration of a cell-to-cell communication device Calin , Daniel, Saeed, Sriram, Tim and Tim

The TUDelft iGEM team Bacterial Relay Race ‘09 2|24 Cell-to-cell communication

Cell-to-cell communication Overview • Principles of cellular communication • Propagation of a set of instructions Conjugation • Bacterial relay race Self-destruction Time-delay • Conjugation system Ethics • Self-destructive plasmid • Time-delay device Achievements • Quorum sensing is limited to binary signals Bacterial Relay Race ‘09 3|24 Cell-to-cell communication

System Overview Overview Conjugation Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 4|24 Cell-to-cell communication

Conjugation • Stop entry exclusion Overview • Knockout trbK Conjugation • Stop conjugative transfer of Self-destruction helper plasmid Time-delay • Knockout oriTR Ethics • Address lethal zygosis Achievements • Knockout trbC • λ -red knockouts Bacterial Relay Race ‘09 5|24 Cell-to-cell communication

Conjugation Overview Conjugation testing plasmids Conjugation Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 6|24 Cell-to-cell communication

Conjugation Entry exclusion expression blocks incoming transfers Overview Conjugation Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 7|24 Cell-to-cell communication

Modeling Overview Conjugation Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 8|24 Cell-to-cell communication

Modeling Overview Conjugation Two modes of propagation Self-destruction 1. Conjugation Time-delay • 8 to 20 μ m / hr 2. Cell division Ethics • > 20 μ m / hr Achievements Bacterial Relay Race ‘09 9|24 Cell-to-cell communication

Self-destructive plasmid Overview • IPTG inducible destruction Conjugation • I-SceI homing endonuclease Self-destruction • 30 bp cut site Time-delay • Induction stops GFP expression Ethics Achievements Bacterial Relay Race ‘09 10|24 Cell-to-cell communication

Self-destructive plasmid • Cut site biobricked Overview • Successful assembly Conjugation • In vivo testing unsuccessful Self-destruction • Undocumented Time-delay degradation tag Ethics Achievements Bacterial Relay Race ‘09 11|24 Cell-to-cell communication

Time-delay device Overview • Two approaches: Conjugation • synthetic transcriptional cascade Self-destruction • biosynthetic AND gate Time-delay Ethics Achievements Bacterial Relay Race ‘09 12|24 Cell-to-cell communication

Time-delay device Overview Two level negative cascade Conjugation Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 13|24 Cell-to-cell communication

Modeling the Time-delay Overview • Stability Conjugation • Sensitivity • Design Self-destruction Recommendations Time-delay Ethics too short Achievements AWESOME! infinite delay Bacterial Relay Race ‘09 14|24 Cell-to-cell communication

Time-delay device • Plasmids assembled successfully Overview • Tunable delay for future teams Conjugation • Delay time agrees with predicted value Self-destruction Time-delay Ethics Achievements Bacterial Relay Race ‘09 15|24 Cell-to-cell communication

Time-delay device Overview Conjugation Self-destruction Key Time-delay Ethics Achievements Lock Bacterial Relay Race ‘09 16|24 Cell-to-cell communication

Issues in synthetic biology Overview Conjugation Self-destruction Time-delay Ethics ~ Reductionism Achievements ~ Building Bacterial Relay Race ‘09 17|24 Cell-to-cell communication

Concepts of life Overview Reductionism Bottom up Conjugation Understanding? Building? Self-destruction Time-delay LIFE “Research” LIFE?? traditional scientific Ethics Time Achievements Concepts Process Questions Bacterial Relay Race ‘09 18|24 Cell-to-cell communication

Methods Overview • Literature review • Survey Conjugation • 242 participants from Self-destruction iGEM community • Analysis Time-delay • Quantitative Ethics • Qualitative Achievements • Raise awareness on ethical issues • Gain insight in opinions and perceptions Bacterial Relay Race ‘09 19|24 Cell-to-cell communication

Survey Results Will the reductionist approach lead to an understanding of life? Overview Conjugation Self-destruction Time-delay No, living systems are too complex. Ethics Achievements Yes, we will eventually No, biological phenomena are fully understand life. fundamentally special. Bacterial Relay Race ‘09 20|24 Cell-to-cell communication

Survey results A complex living system is Life is physical and can be Overview more than the sum of its explained materialistically biological components Conjugation 65% Self-destruction 40% 40% Time-delay Ethics 23% 19% 13% Achievements Not Agree Agree Not Agree Agree For all results see : http://2009.igem.org/Team:TUDelft/Ethics Bacterial Relay Race ‘09 21|24 Cell-to-cell communication

Major Achievements • Engineered a tunable delay device Overview • Characterized and submitted 21 new BioBricks • Characterized several exisiting BioBricks Conjugation • New toolbox for modeling conjugation systems Self-degradation • Lock and Key generation algorithm Time-delay • An extensive study on Human Practice Ethics Achievements Bacterial Relay Race ‘09 22|24 Cell-to-cell communication

Acknowledgements • Supervisors Sponsors: • Emrah Nikerel • Domenico Bellomo • Janine Kiers • Advisors • Esengül Y ı ld ı r ı m • Steven Flipse Bacterial Relay Race ‘09 23|24 Cell-to-cell communication

For more information: http://2009.igem.org/Team:TUDelft Bacterial Relay Race ‘09 An illustration of a cell-to-cell communication device Calin, Daniel, Saeed, Sriram, Tim and Tim