Trials and Tribulations of a First Year iGEM Team

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What do you do when team members disappear, deadlines are flying by, and the Jamboree is only two days away? Newcastle University answered these questions when they formed an iGEM team for the first …

What do you do when team members disappear, deadlines are flying by, and the Jamboree is only two days away? Newcastle University answered these questions when they formed an iGEM team for the first time in 2008. The team was composed of six students, three instructors and many advisors, all from different backgrounds and with differing motivations in joining the team. Everyone was excited about our project, but a summer of hard work only produced a proof of concept. In this presentation, I will discuss the lessons we learned and how we managed to pull everything together in the end to win a Gold medal at the Jamboree.

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  • First year iGEM – wanted to shoot big! Wanted something awesome, on
  • Methicillin-resistant Staphylococcus aureus MRSA difficult to distinguish from other S. aureus Mostly they just grow up the culture and see if they die in response to methicillin and other antibiotics Not sexy, as one of our advisors called it! It's not big and awesome enough for iGEM. Can be accomplished using traditional biology No computational aspect. Most of instructors were from computing science, with interest in synthetic biology. Therefore, wanted to incorporate in silico with biology
  • 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
  • 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
  • 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
  • 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
  • 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
  • Learned: Be very clear about commitments Communication! Have a contigency plan
  • 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
  • Mostly sandwiches, crisps, fruit Bagels for breakfast – I thought it was great, but some people were less pleased
  • 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 track 2) We didn't make any grandiose claims about curing cancer in order to enhance our presentation – we just told it like it was.

Transcript

  • 1. Trials and Tribulations of a First Year iGEM Team Morgan Taschuk Newcastle University
  • 2. Outline
  • 8. The Team Advisors Instructors Students
  • 9. The Team
    • Four students in Bioinformatics Masters program
      • Require major aspects of project to be computational
    • Two biologists
    • 10. And me
    • 11. Wanted to shoot big!
  • 12. Circle of (Synthetic) Life Feedback Implementation Computational Modelling Bioinformatics Tools Sequence Synthesize Clone Analyze
  • 13. Circle of (Synthetic) Life
    • MRSA diagnostic
      • Difficult to detect
      • 14. Not “sexy”
      • 15. No computational aspect
    • Gram positive diagnostic
    Feedback Implementation Computational Modelling Bioinformatics Tools Sequence Synthesize Clone Analyze
  • 16. Sensing Bacteria
    • Quorum sensing:
      • Gram positive bacteria secrete ‘fingerprints’ of signal peptides
      • 17. Cell-cell communication
  • 18. Sensing Bacteria
    • Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
  • 19. Sensing Bacteria
    • Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
  • 20. Sensing Bacteria ? ?
    • Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
    • 21. Need to discriminate between fingerprints
  • 22. Sensing Bacteria
    • Use quorum sensing in B. subtilis to detect multiple Gram positive bacteria
    • 23. Need to discriminate between fingerprints
    • 24. Limited outputs
  • 25. In Vitro Neural Nets
    • Sexy!
      • Bacteria performing computational tasks
    • Computational
      • Evolutionary algorithms
    • Plenty of potential
  • 26. Where do we start??
  • 27. Good Advice
    • This time, last year:
      • No computational tools ready
      • 28. Wet lab booked from 4 August
      • 29. No DNA designed
    • Modularise the tasks into discrete, achieveable chunks
    • 30. Designed a BioBrick by hand
    • 31. Synthesized it
      • Six weeks! Shipped on 5 August
  • 32. Bad timing May Jun Jul Aug Sept Oct Nov Apr
  • 33. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team
  • 34. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team
  • 35. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team
  • 36. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team Tasks
  • 37. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team Tasks
  • 38. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team Tasks
  • 39. Bad timing May Jun Jul Aug Sept Oct Nov Apr Team Tasks
  • 40. Tally
    • Date: 22 September 2008
    • 41. Number of remaining students: 1
    • 42. Unfinished tasks
      • Wiki
      • 43. T-Shirts
      • 44. Presentation
      • 45. DNA submission
      • 46. Only just about everything we're judged on!
  • 47. Wiki
    • Hard work
      • Internal wiki transferred
      • 48. Ripped several theses apart
      • 49. Organised lab journals
  • 50. T-Shirts David Appleyard and iGEM
  • 51. Part Characterisation
    • One day per part
    • 52. Not all parts need to have DNA, or even work!
  • 53. Poster
    • Finished: 4 November
  • 54. Presentation
    • ...........
    • 55. Practiced with the first version on 4 November
  • 56. Finally on the way
    • 7 November, 4:30am
    • 57. Seven hour layover in Amsterdam
    • 58. Revised the talk (again)
  • 59. Stata Center
  • 60. Jamboree, Day One
  • 61. Lots going on David Appleyard and iGEM
  • 62. People Watching
  • 63. David Appleyard and iGEM
  • 64.  
  • 65.  
  • 66. ?
  • 67.  
  • 68.  
  • 69.  
  • 70.  
  • 71. Lunch
    • Still revising our presentation
  • 72. The Talk
    • No real questions at the end
    David Appleyard and iGEM David Appleyard and iGEM
  • 73. Poster Session David Appleyard and iGEM Don’t let this happen to you!
  • 74. Afters David Appleyard and iGEM
  • 75. Jamboree Day 2 Awards
    • Finalists:
  • 81. Awards David Appleyard and iGEM
  • 82. iGEM from Overhead David Appleyard and iGEM Us!
  • 83. Melee onstage David Appleyard and iGEM
  • 84. Melee David Appleyard and iGEM
  • 85. Awards
  • 86. Like any long-term project
    • Be very clear about commitments from the outset
    • 87. Communication!
    • 88. Have a contingency plan
    • 89. You have less time than you think you have
  • 90. iGEM Specifically
    • Break your project into small, distinct pieces
    • 91. Be ambitious with your goals, but realistic with your claims
      • You probably have not invented the cure for cancer
    • Do not leave all of the documentation until the end
      • Judging happens here!
    • Be creative
    • 92. Bio brick away!
  • 93. Thank you and good luck!