Tuesday 03/26/13

10:30 A – 7:30 P, 8:30 P – 10:30 P


  • working on literature references, laying out introduction.
  • Stinchcombe model

    • write out probability mass function of discrete mRNA arrivals in terms of the random differential equation for the continuous mRNA Y(t), where only the promoter switching is stochastic. Can study the effect of different waiting time distributions on statistical properties of the mRNA production. Stinchcombe_model
  • Istrail 2007, Ben-Tabou 2009 model non-cooperative multi-imputs as separate regulation with same max synthesis rate

    • literally I_{max}/2 (S(Y_A) + S(Y_B)) where S(Y) is a sigmoid in Y and Y_A is the enhancer site occupancy of enhancer A.
    • This seems bad for a few reasons: why should the gene not be able to reach max synthesis when only one input is present. Certainly why is this half, but it is also not clear they should be restricted to sum to I_{max}, I thought the max was supposed to be set by saturation.
  • Zinzen 2006 changes the site occupancy function to be the probability that any one of all possible sites is bound.
    • They then stitch together homotypic and heterotypic cooperative interactions along with non-cooperative binding sites. This is actually pretty good.
    • However, this model does not allow for individual sites to influence transcription and be cooperative. Transcriptional activity may be x with just one site and y with just the other site, and if both are left in tact it may be larger than max(x,y). In this model if sites interact, transcription is proportional to KcAB, which is zero if A or B is missing, and if they don’t interact, transcription is just sigmoid of P(A or B) which is no bigger when both are bound than when just one is bound.

Genomics discussion: To look up

  • Poopular trends: “topologically associated domains” (from HiC data). Dickson 2012 Nature (Bing Ren’s group). Also Decker’s group.


  • Imaging cy5-405 on STORM3 O/N. STORM3 back-optics need some alignment tuning — TIRF field does not provide uniform illumination
  • STORM2 512 x 512 field of view is strongly clipped by the final iris at the end of the beam sizing column.
  • STORM2 focus lock doesn’t get much signal anymore?
This entry was posted in Summaries and tagged , , . Bookmark the permalink.