Monthly Archives: February 2011

Friday 02/04/11

Posted on February 4, 2011 by admin

8:50 A — 7:30P, 10:45 – 12:00 A Confocal: MP05 scan finished and saved Perry’s practice talk. Modeling promoter bursting using GillespieSSA (Gibson-Bruck file center seems buggy).  Estimating burst size, promoter opening rate and promoter closing rate. Clear fog and … Continue reading →

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Protected: Confocal observations

Posted on February 3, 2011 by admin

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Thursday 02/03/11

Posted on February 3, 2011 by admin

10:00A-7:00P, 8:00P-12:00A in situs day 1 pt2 Confocal: endogenous hb-gradient, twist, pMAD, MP05 (set up overnight) Analyzing hb gradient data.  + reading new Holloway paper. collect virgin fog and MG-alpha Flip MP08 plate and flip fly stocks New collection cages: … Continue reading →

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Protected: shadow investigation

Posted on February 3, 2011 by admin

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Wednesday 02/02/11

Posted on February 2, 2011 by admin

10:00 A – 4:00P, 8:00P – 1:00A Requests from ML: in vivo measure of bcd binding constant duration of temporal overlap of the brk shadow and primary (try on Thursday) Confocal: MP10 sna, runs until 1p, 12 embryos (aborted 13th … Continue reading →

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hb-gradient analysis

Posted on February 2, 2011 by admin

Analyzing hb-gradient: anlz_hb_gradient_data.m   (committed to Git). Circular field lines not appropriate (obviously).  Need to compute planes of separation instead. May be better to ensure original data has appropriate left-right planar orientation.  This will not only make segmentation easier, but … Continue reading →

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Improving dot z-segmentation

Posted on February 1, 2011 by admin

Improving z-dot segmentation double checking code: Turning mRNA counts into graphs.  With correcting for cell size variation gradient appears smoothly.  (I plot instead mRNA density per cell, and multiple by the mean cell volume to return to normalized total counts … Continue reading →

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Tuesday 02/01/11

Posted on February 1, 2011 by admin

10:00A — 7:00P, 8:00P-12:00A Mendeley Berkeley Advisors meeting Jen Confocal UAS x Espl-cluster genes affects on snail patterning New slide for ML: median embryo from each population showing multiplicative action. Planning in situs for later this week. Integrating new duplicate … Continue reading →

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Understanding bursty Gal4-LacZ expression

Posted on February 1, 2011 by admin

Researching UAS-LacZ line sequences to probe stochastic expression effects. my UAS-LacZII from flybase stock 3955, From Kathy Matthews, 1998 gift of flybase. contains: P{UAS-NZ}20b — SV40 T NLS-lacZ fusion in pUAST (beta-gal is localized to the nucleus). Insertion on chromosome … Continue reading →

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