IGEM:Stanford/2009/Notebook/Personal Notebook/2009/08/11

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Daily Work


  • Revise diagram breakdowns for Jerome
  • Revise vBOL symbols
  • Either research Th-17 to NO pathway or work on wiki

Project / Accomplishments

  • Looks like transformations worked!!!! Yay! (1.1b and 2.1a)
  • Mini-preps of SoxR/S cultures and pcr on 1.1b and 2.1a
    • Need to sequence 1.2a
  • Made revised constructions for Device 1
  • New schematics for Diagrams (see right)
Overall Device Schematic
right Device 1 Schematic


  • Simple schematic for Device 2....

Alternative Solutions


  • Meeting w/ Jerome for the presentation
    • Show Naive CD4+ cells leading to T-cells?
    • Testing line w/ filtering T-cells
    • Numbers
      • Rough percentage of amounts of T-cells (normal, non-recognizing, self-recognizing...)
    • Why don't some self-recognizing t-cells undergo apoptosis?
    • Circuit diagram
      • Make text bigger, animation,...
      • Take out IDO and dendritic cells?
    • Shorter descriptions
    • More visual support and animation
      • Specifically on slides describing why we need device 2
    • Device 2 parts breakdown- need separate promoter
    • Visual- pyramid w/ age group and
    • Immunology section- still too complicated
      • More pictures
      • Start w/ what the immune system "is" as a definition? Very general
    • Stay away from capital letters
    • Differentiate acquired and innate immune responses- mention vaccines!
      • Talk more about acquired w/ animation (fun can be good)
    • What is an antigen? What is an antibody?
    • Scheme is nice- could be more simple
    • Take away Tc cells
    • Selective filtering- make a factory line and assembly line
    • Define autoimmune diseases w/ respect to Self-recognizing t-cells
    • Start w/ epidemiology then immune response, then back to IBD w/ respect to the immune system
    • Mention system therapy vs. cure
    • Showing the cause of inflammation itself.... b-bells, t-cells, and plasma cells (igE?)-
      • Show transportation- lymph, vs blood, vs epithelial crossing
    • Where are Naïve CD4+ cells? Needs to be in the place of activity!!!
    • email Ariana or Professor Steinman

  • Meeting w/ Christine for Stanford News at 2pm
    • Interviews, vidoes, and revised article
    • Looks good!

  • FAB at 4:00
    • Trp looks better, but not perfect yet...
      • More modeling help needed?
    • IBD Overview
      • Be upfront of assumptions and parameters
        • We assume it is t-cell ratios for inflammation
    • Questions to answer
      • Where are Naive CD4+ cells?
      • What is the "cause" of IBD?
      • Why don't medicines target t-cells?
    • Also,
      • Future- how can we biosynthesize 5MT?


  • Questions to be answered….
    • Genetic component of the disease?
    • Mouse model of IBD to test linear relationship of Th-17 and Treg cells
    • Suicide device?
    • Do people take RA for treatment?
      • The acid form of Vitamin A, all-trans retinoic acid or ATRA, has been made into Tretinoin, which
    • Do people take Il-6 for treatment?
    • Other uses?
    • Where are Naïve CD4+ cells? Needs to be in the place of activity!!!
  • vBOL, are there names for the individual pictures

Weekly Goals