IGEM:Stanford/2009/Notebook/Personal Notebook/2009/08/06

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Daily Work


  • Morning:
    • vBOL tutorial polishing
    • purchase omnigraffle
    • possible wiki template work
  • Afternoon
    • Red papers for NO/SoxR affinity and Th-17 to NO pathway

Project / Accomplishments

  • Long review of entire cloning process
  • Learned to check sequences w/ Ape and order form (fwd and rev)
  • Broke down project steps
  • Finished new draft of presentation and went over it w/Jerome
    • Now contact physician and clinician
  • Finished vBOL presentation
  • Grew liquid cultures of B0015 and B0034, and part 53 and glycerol stock 9
  • Started ligation for 1.1b (device one, first round of cloning, part b)
    • Right cycle on PCR?


  • A little unsure about ligation protocol.... which PCR cycle? We chose ligation...

Alternative Solutions


  • 3pm meeting w/ Jerome about updated presentation... Feedback
    • More clear about age groups- is this when it starts?
    • Why industrial countries targeted? Sterile environments....
    • Where does it take place?
    • Genetic component of the disease?
    • Mouse model of IBD to test linear relationship of Th-17 and Treg cells
    • Colon slide- show parts w/ larger picture and then transition into video by itself
      • Naive cd4+ cells do not show up in the video on the screen
      • Positive feedback between t-cells and differentiation of naive cd4+ cells
    • Trp analog levels
    • Device one diagram: sensor will end at SoxS, then generator is entire sequence
    • Constitutive export system..
      • Constitutively expressing everything besides il-6
    • Missing consistent background of T-cells... larger description of immunology and mediated immune cells
    • Simple, fun animation... like the french cartoons
    • Take out th1 and th2 cells in picture
    • th-17 to t-reg cells stemming from Immune System
      • Go straight to the problem
    • Explain T-cells- what do they do? Like a detector....
      • Signal another cell to kill the pathogen...
      • talk about the recruitment of b-cells
    • Cartoon is not a system level diagram
    • New system level diagram- simple but w/ external features like b-cells and dendritic cells
    • Also, upstream of inflammation and immunosuppression symbols in diagram... disease...
    • Reuse presentation diagrams
    • Missing level between box pictures and basic parts diagram
      • Maybe boxes such as SoxR/S system= NO sensor
    • Introduce vBOL later, but not too much time
    • suicide device?
    • schematics w. numbers/letters
    • Other questions... do people take RA for treatment? Il-6? Methyl tryptophans for IDO
      • Check out other uses for the products

  • From here
    • Contact clinician from here
    • Presentation works from here


Weekly Goals