MCB seminars: 11/11/14

Germ cell specification in insects. (Extavour lab)
Taro Nakamura


  • germline markers: Piwi and vasa
  • preformation mode of germ cells — flies, frogs, fish
  • induction mode of germ cells – salamanders + mice
  • most animals use the induction mode. More likely ancesteral
  • Many arthropods do both. Diptera just do preformed mode. Orhoptera just do induction. Cricket just do induction.
  • BMP4 is required for the generation of primordial germ cells in mouse. Blimp is a critical downstream factor.


  • Piwi expressing cells arise de novo during cricket development, mark germ cell precursors
  • blimp1 is co-expresssed with pMad in mesoderm.
  • BMP signaling is also required in cricket for PGC specification. (by knockdown and over-expression)
  • blimp1 is also conserved in cricket germ cell specification.
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Tuesday 11/11/14

9:50 am – 12:20 am

Chromatin Manuscript

Figure work

  • save images of Black-black, blue-other, and black-blue interactions
  • save figure of simulation entanglement results
  • average examples of equilibrated BLUE simulations
  • figures basically done
  • updated all figure captions

A few final revisions to Fig 4

  • Fix fit domain so that scaling fits for the “whole domain” plotted on the intact curves matches

Draft 1 basically complete, ready for Xiaowei

Fly request from Heng

  • send hb-y flies. I think these are still alive(!)
  • only MP02 is still alive. (distal removed)

To add

  • MED31 and H3K4me2 as highly enriched in red, very low in Yellow
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Protected: project 2 update: 11/10/14

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Monday 11/10/14

9:30 am – 1:15 am


  • passage Kc cells
  • working on figures
  • project 2 experiments for Jeff to Image

Cell culture

  • passaged Kc cells
  • density looks good, ready to start new experiments

Project 2

  • see post

Finalize figures!

  • moving more stuff into matlab
  • have Bogdan look at simulation results

Launch new blue simulations

  • not running effectively on Odyssey yet
  • Odyssey still giving trouble
  • running locally.
  • this is going to be extremely slow.
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Saturday 11/08/14

10:00 am – 9:30 pm

Project 2

  • IMR90s, plated and in incubator
  • new L7E1 scratch staining since Thursday night at 37C.
  • stained L8E1 scratch and L7E1 normal in 4C
  • scratch the 2000K density plates Today (11/08)

Chromatin Project Data to Process

Black internal domains

  • 2014-08-15_L4E1
  • 2014-08-16_L4E2
  • 2014-09-17_D08
  • 2014-09-18_D08

Black-Black junctions

  • one of these may already be analyzed. Some of these probably failed
  • 2014-08-17_L4E2-6_E1-7
  • 2014-09-06_D10-6_D11-7
  • 2014-09-09_D10-6_D11-7
  • 2014-09-12_D11-6_D12-7

Yellow-Yellow junctions

  • 2014-09-12_E05-6_E04-7
  • 2014-09-13_E08-6_E07-7

Chromatin Project Figure making

  • Making S3 as a single figure
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Protected: submitted abstract for Fly Meeting 2015

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Thursday 11/06/14

9:45 am – 7:00 pm


  • send Fly Meeting draft abstract to XZ (due Mon)
  • images of small yellow domains for Ting
  • work on manuscript

Oligo secondaries revision planning

  • sent example images of small yellow regions
  • see smallDomainImates_141106.m in OligoSecondaries code

Manuscript revisions

  • re-writing introduction with Bogdan
  • revising body text to account for modifications to figure layout.

Fig 4, modeling: rearrangements

  • combine multiple simulations for black ‘intact’ domains
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Wednesday 11/05/14

9:30 am – 9:50 pm


  • write abstract for fly meeting
  • project 2 experiments with Hao
  • meeting with XZ and Ting
    • discuss Brian’s PAINT experiments
    • discuss revision experiments
  • project 2 team meeting
  • revise figures
  • 2 color image for Ting
  • start up cell culture

server troubleshooting

  • Morgan requires users to be Members of “Remote Desktop Users” (or Domain Admins) in order to log in remotely.
  • now fixed for all users

revising figures

  • finished converting entanglement to bar graph
  • finished splitting fraction overlap by boundary type

Figure 1

  • writing code to visualize domains for figure 1

Chromatin Manuscript

  • Revising text
  • started new google Doc: Super-resolution Imaging of Chromatin Nanostructure
  • writing new intro according to yesterdays outline.

Chromatin experiments

  • start new Kc cell in culture
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Protected: project 2 svd: 11/05/14

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