User:Pakpoom Subsoontorn/Notebook/general reading/2008/11/10

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Activity note: 11/30/08

  • Analyze E.coli shape transform movie...the first one, using SICIC

Activity note: 11/27/08

  • Read "Mobile DNA II", invertase chapter

Activity note: 11/26/08

  • E.coli shape transformation time course- doesn't work..cells grow too slow
  • edit cellGrid diagram
  • grading Quiz, the rest of hw2..put score on
  • winscp and image analysis code installation

Activity note: 11/25/08

  • replication termination site for symmetry breaking
  • more reading stuffs on S.pombe mate-type switching

Activity note: 11/24/08

  • finish up cellGrid autocat and submit the design

Activity note: 11/22/08

  • read the review on mate-type switching in S.pombe, download two more papers
  • edit up to paragraph-11 of selfactivating paper

Activity note: 11/21/08

  • edit the second chip design
  • outline plan with KC

Activity note: 11/20/08

  • Meeting with Drew..discuss database, recombinase selection, daisy chain, gated oscillator, lineage tracker
  • New idea about lineage tracker with S.pombe matetype switching mechanism
  • edit the second chip design

Activity note: 11/19/08

  • Finish reading second round of Reshes's 2008, get technical detail about image processing and parameter estimation, set-up meeting time for detailed discussion with KC
  • Note: spending too much time on reading...should get all gist in at most 2 rounds!
  • need to review statistical analysis,...significance..hypothesis testing..etc.
  • Re-contact with Erik, Jongmin...get OZ paper...SA paper must be done soon!

Activity note: 11/18/08

  • Cell cracking/ cell filament experiment on KC's new microscope (see labbook)
  • found, ordered Mobile DNA II, ...read 4 chapters on intro, cre-loxP, Application, tyrosine recombinase
  • load, start reading FimB characterization paper
  • Note: I should spare some time for read/thinking assays instead of just keep reading for more recombinase info
  • Note: Try to get conclusion about characterization goal/library/DB project from the next meeting with Drew..then set-up meeting with Michele to talk about how practicality
  • Note: how much do we want to go into mechanism?

Activity note: 11/17/08

  • re-read Pinho's review for detail about E.coli cell-wall synthesis (note in KC labbook)
  • re-read most of Cell Wall dynamics paper...note that I need to be more specific about studying round/rod dynamics. It seems pretty hard, in the end, to explain whatever we will measure here (note in KC labbook)
  • I need better plan for paper reading: breakdown keywords, question list, new techniques, new results, figure break down
  • Grow cell K-12, 4312, 4312-GFP
  • note that AutoCAD09 has expired

Activity note: 11/14/08

  • EMing e.coli k-12 and 4312

Activity note: 11/13/08

  • Revelation: Optimizing, organizing and automating. Speed up the construction process and evaluation process which will allow us to compare many different machines all at once. This is analogous to directed evolution vs de novo protein design...but at the system level. This will includes text mining, HT-experiment, and HT analysis.
  • Start Organizing info by labs...found new resource for PhC31: Margaret Smith lab, U of Aberdeen. Read their 1998 for in E.coli/invitro assay for PhiC31..Skim through 2008 mutational studies on functional domain
  • Plan to confine the first round paper reading to 2006-
  • start organizing papers by assay..start assay page on oww
  • A flash of thought about large-scale mutagenesis studies of protein activity
  • Grow cells e.coli k-12 and 4312 for EM

Activity note: 11/12/08

  • read KC's paper on E.coli cell wall and supplement in detail, listed all questions for meetings
  • meeting KC, outline plan for cell shape dynamics at different growth phase and cracking experiment and modeling membrane/cell-wall relation
  • might need to edit the latest chip soon
  • review thermo up to Boltzmann factor

Activity note: 11/11/08

  • re-read MP Calos paper 2006 on PhiC31, marked important references, facts
  • Import recombinases studies PhiC31, Cre, R4, TP901-1 from MPC's main research page to papers..Tn3chimeric to Papers
  • I think we need to captures fundamental characterizing assay and then think about large scale thinggy

Activity note: 11/10/08

  • read review paper on bacterial cell wall synthesis, start making gene list/annotation, start bionumber for cell wall

Activity note: 11/09/08

  • Wrote weekly summary note on Genetically Encoding Memory and Bacterial cell-shape determination (see summary note page)
  • Primary organized literature for site-specific recombinartion in Paper...need to know how to remove/cross out



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