Friday 01/23/15

9:00 am – 8:00 pm

Experiments and Training

  • teaching ultra-cryo sectioning
  • first two section broke off block — not good enough pyramid / contact area. Better to use trimming knife to carve pyramid
  • third mounted section cut well, had good natural pyramidal shape.
  • section quality with -45C knife, -50C sample and -52C chamber seemed to cut very well — samples in green box downstairs.

Writing

U01

  • working on new methods section
  • working on description of results section
  • finished writing both sections
  • integrated figures, wrote captions
  • proofread document, sent to Xiaowei

K99

  • troubleshooting how to submit requests for letter writers
  • got registered as a PI on eRA commons
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Thursday 01/22/15

9:20 am – 6:30 pm,

K99

Working on Training Plan

  • completed draft of training plan
  • completed draft on training in responsible conduct of research
  • working on Specific Aims document

U01

  • working on text for my sections

Experiments

  • cleaned and coated coverglass with GS
  • hydrated some 2-14 hr yw embryos, embedded in 12% gelatin
  • equilibrated embryos in 30% sucrose then 70% sucrose.

Lab stuff

  • software install for Laptop and Monet, 1pm
  • lab safety meeting, 2pm
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lab safety meeting

Notes

  • where labcoats
  • lab will stop stocking latex
  • hazardous waste disposal
    • must pick a hazard
    • only 4 most common components
    • hefty fines for unlabeled bottles
    • last inspection was surprise
  • Lasers
    • goggles and supervision for alignment
  • Laser microscope training records
    • require reading manual
    • require signature
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Wednesday 01/21/15

9:00 am – 11:00 pm

Working on U01

  • drafting figure 1 describing paper results
  • drafting figure 2 describing methods

Presentation for Kingston group

  • went well, hope this strengthens our collaboration
  • should touch base with Nicole about paper
  • discussed MNase with Michael
  • discussed HiC 5C and mouse hox genes with Patrick

Discussion with Mirny group

Notes

  • remember to get google-hangouts or skype setup in advance of meeting and charge PC
  • skype now supports multiple video chat (though I think hangouts will interface the slides better)
  • action plans below

Geoff will handle

  1. images of the Hi-C data from all the domains, with the domains labeled (I gave them little names like L2D03, just the genome coordinates will also be fine).
  2. categorize the domains into “TAD” or “Linker” (or whatever breakdown you think might be interesting. Then I can pick out just these domains and see how they scale for radius of gyration and also compute eccentricities / gyration tensors and all that and look for patterns.
  3. label the different scaling trends you see in each chromatin type. It would be great to know which blue domains are the ones which show mostly short range contacts vs. more long range contacts. If you just label all the curves, or make a table of scaling coefficients from Hi-C for all domains, that would be very helpful.
  4. Bogdan and I were talking, and decided it would be nice to use the Hi-C data to look at interaction between neighboring domains. Maybe we could just sum the average number of normalized contacts per 10kb for 50 kb upstream and downstream of the boundary, and compare that the to global average contact frequency.

I will handle

  • gyration tensor computations
  • comparisons of gyration tensor eigenvalue ratios with Hi-C scaling groups
  • comparisons of scaling coefficient fits with Hi-C scaling groups
  • incorporation of Hi-C data into figure 3 and main text
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Tuesday 01/20/14

9:45 am – 8:00 pm

K99

working on Biosketch

  • Section A: wrote draft of personal statement
  • Section B: completed positions/honors/service
  • Section C: NIH substantially revised section C: now asks for a description of top 5 contributions to science, with Figures, and 4 citations each.
  • Biosketch now also hosted online by NIH: https://www.ncbi.nlm.nih.gov/myncbi/alistairboettiger/cv/17656/#sectionFunding

working on Career Objectives

  • first draft complete
  • maybe too long (over one page) – check limits

Working on Training Plan

  • finished experimental training part
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Monday 01/19/15

8:45 am – 6:15 pm, 7:00 pm – 11:40 pm

Lab tasks

  • Flipped fly stocks. – a bit too late, several stocks expired. My chr2/3 marked double-balancer lines will hopefully still make it.
  • discussion with Jeff about project 2. Meeting Friday. Promised analysis of code and thresholds before then.
  • trying to schedule meeting with Mirny and team to discuss paper
  • check in with Georgia about probe making. Proposed embryo sectioning later this week.
  • discussion with Bogdan about primer design for oligo libraries. Confirmed plus sequence is sequence of mRNA (so RC a + strand gene to get probes against it). Mentioned BB should discuss project plans with JM.
  • contacted IT about software for laptop. (Should have asked about install on Monet as well).
  • ordered adapter for alternate battery.

K99 application

  • sent request with updated CV and talking points to GO
  • sent request with updated CV and talking points to SYS
  • sent request with updated CV and talking points to ML
  • Moved letters onto Morgan — LibreOffice .docx files don’t open in Word on Morgan, so it might be a problem
  • resent letters with copy of research proposal (BWF version).
  • sent talking points with CV and research proposal to BK
  • sent talking points with CV and research proposal to AS
  • sent talking points with CV and research proposal to CW
  • sent talking points with CV and research proposal to LM
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Protected: Stochastic Physics in Biology Day 4

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Protected: Gordon Conference Wed

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Protected: Gordon Conference: opening session

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