Team:Stanford/NotebookPage/11 August 2009

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June
MTWTFSS
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[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/8_June_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/9_June_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/10_June_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/11_June_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/12_June_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/13_June_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/14_June_2009&action=edit 14]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/15_June_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/16_June_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/17_June_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/18_June_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/19_June_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/20_June_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/21_June_2009&action=edit 21]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/22_June_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/23_June_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/24_June_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/25_June_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/26_June_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/27_June_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/28_June_2009&action=edit 28]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/29_June_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/30_June_2009&action=edit 30]
July
MTWTFSS
    [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/1_July_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/2_July_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/3_July_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/4_July_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/5_July_2009&action=edit 5]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/6_July_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/7_July_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/8_July_2009&action=edit 8] [http://2009.igem.org/Team:Stanford/NotebookPage/9_July_2009 9] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/10_July_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/11_July_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/12_July_2009&action=edit 12]
[http://2009.igem.org/Team:Stanford/NotebookPage/13_July_2009 13] [http://2009.igem.org/Team:Stanford/NotebookPage/14_July_2009 14] [http://2009.igem.org/Team:Stanford/NotebookPage/15_July_2009 15] [http://2009.igem.org/Team:Stanford/NotebookPage/16_July_2009 16] [http://2009.igem.org/Team:Stanford/NotebookPage/17_July_2009 17] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/18_July_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/19_July_2009&action=edit 19]
[http://2009.igem.org/Team:Stanford/NotebookPage/20_July_2009 20] [http://2009.igem.org/Team:Stanford/NotebookPage/21_July_2009 21] [http://2009.igem.org/Team:Stanford/NotebookPage/22_July_2009 22] [http://2009.igem.org/Team:Stanford/NotebookPage/23_July_2009 23] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/24_July_2009&action=edit 24] [http://2009.igem.org/Team:Stanford/NotebookPage/25_July_2009 25] [http://2009.igem.org/Team:Stanford/NotebookPage/26_July_2009 26]
[http://2009.igem.org/Team:Stanford/NotebookPage/27_July_2009 27] [http://2009.igem.org/Team:Stanford/NotebookPage/28_July_2009 28] [http://2009.igem.org/Team:Stanford/NotebookPage/29_July_2009 29] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/30_July_2009&action=edit 30] [http://2009.igem.org/Team:Stanford/NotebookPage/31_July_2009 31]
August
MTWTFSS
          [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/1_August_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/2_August_2009&action=edit 2]
[http://2009.igem.org/Team:Stanford/NotebookPage/3_August_2009 3] [http://2009.igem.org/Team:Stanford/NotebookPage/4_August_2009 4] [http://2009.igem.org/Team:Stanford/NotebookPage/5_August_2009 5] [http://2009.igem.org/Team:Stanford/NotebookPage/6_August_2009 6] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/7_August_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/8_August_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/9_August_2009&action=edit 9]
[http://2009.igem.org/Team:Stanford/NotebookPage/10_August_2009 10] [http://2009.igem.org/Team:Stanford/NotebookPage/11_August_2009 11] [http://2009.igem.org/Team:Stanford/NotebookPage/12_August_2009 12] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/13_August_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/14_August_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/15_August_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/16_August_2009&action=edit 16]
[http://2009.igem.org/Team:Stanford/NotebookPage/17_August_2009 17] [http://2009.igem.org/Team:Stanford/NotebookPage/18_August_2009 18] [http://2009.igem.org/Team:Stanford/NotebookPage/19_August_2009 19] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/20_August_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/21_August_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/22_August_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/23_August_2009&action=edit 23]
[http://2009.igem.org/Team:Stanford/NotebookPage/24_August_2009 24] [http://2009.igem.org/Team:Stanford/NotebookPage/25_August_2009 25] [http://2009.igem.org/Team:Stanford/NotebookPage/26_August_2009 26] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/27_August_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/28_August_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/29_August_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/30_August_2009&action=edit 30]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/31_August_2009&action=edit 31]
September
MTWTFSS
  [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/1_September_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/2_September_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/3_September_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/4_September_2009&action=edit 4] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/5_September_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/6_September_2009&action=edit 6]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/7_September_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/8_September_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/9_September_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/10_September_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/11_September_2009&action=edit 11] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/12_September_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/13_September_2009&action=edit 13]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/14_September_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/15_September_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/16_September_2009&action=edit 16] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/17_September_2009&action=edit 17] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/18_September_2009&action=edit 18] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/19_September_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/20_September_2009&action=edit 20]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/21_September_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/22_September_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/23_September_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/24_September_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/25_September_2009&action=edit 25] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/26_September_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/27_September_2009&action=edit 27]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/28_September_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/29_September_2009&action=edit 29] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/30_September_2009&action=edit 30]
October
MTWTFSS
      [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/1_October_2009&action=edit 1] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/2_October_2009&action=edit 2] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/3_October_2009&action=edit 3] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/4_October_2009&action=edit 4]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/5_October_2009&action=edit 5] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/6_October_2009&action=edit 6] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/7_October_2009&action=edit 7] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/8_October_2009&action=edit 8] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/9_October_2009&action=edit 9] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/10_October_2009&action=edit 10] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/11_October_2009&action=edit 11]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/12_October_2009&action=edit 12] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/13_October_2009&action=edit 13] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/14_October_2009&action=edit 14] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/15_October_2009&action=edit 15] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/16_October_2009&action=edit 16] [http://2009.igem.org/Team:Stanford/NotebookPage/17_October_2009 17] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/18_October_2009&action=edit 18]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/19_October_2009&action=edit 19] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/20_October_2009&action=edit 20] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/21_October_2009&action=edit 21] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/22_October_2009&action=edit 22] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/23_October_2009&action=edit 23] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/24_October_2009&action=edit 24] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/25_October_2009&action=edit 25]
[http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/26_October_2009&action=edit 26] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/27_October_2009&action=edit 27] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/28_October_2009&action=edit 28] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/29_October_2009&action=edit 29] [http://2009.igem.org/Team:Stanford/NotebookPage/30_October_2009 30] [http://2009.igem.org/wiki/index.php?title=Team:Stanford/NotebookPage/31_October_2009&action=edit 31]

Daily Work

Goals

  • 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
  • vBOL symbols revised


Problems

  • Simple schematic for Device 2....

Alternative Solutions

Events

  • 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?

Comments

  • 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