Sunday 05/11/14

12:00p – 5:00p

Finish probe making:

  • E05-E12, F01-F08 p3
  • Run gel
  • Run clean up.

E5-E12_F1-F8_P3

New stains

  • F02-p3, F04-p1
  • F02-p3, F03-p1
  • F03-p3, F04-p1

New Probes to make

  • L3: B02 – B09
  • L2: F03, F04, F05, F06, F07. L3: F09, F10, F11 (all 2 color),
  • alliquoted but lacking dye and not yet run.
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Monday 05/19/14

9:00a – 6:00p

My lab meeting feedback

  • Complement area analysis as Radius of gyration of molecule positions.
  • volume analysis for some loci.
  • log transform spot densities to avoid saturation.
  • Area comparison plots normalized to largest spot
  • fraction of single vs. double dots for different regions. Use steve images. Use
  • tetraploid vs. diploid chromosomes (do karyotyping / metaphase spreads?)

counting spots

  • Double spots: ANTC- 18 of 100 from single-Z mosaic.
  • first pass at radius of gyration using flists.
    Lib3_RgData
Posted in Summaries | Comments Off on Monday 05/19/14

Friday 05/09/14

Goals

  • Project 2
    • relaunch batch analysis
    • troubleshoot output
    • send new writeup to Xiaowei
  • STORM
    • keep rolling.

Samples to Image

  1. L2G06-p1-A647
  2. L2G08-p1-A647

Samples to stain

  • F01 – F06

P3 Probes to finish

  • F01-F08 and E05 – E12
  • F04(EPc) + F02(En) vs F09 (En TAD)
  • Per sample
    • 3.5 uL 100 mM primer
    • 4 uL 5x RT buffer
    • 2 uL dNTPs (10 mM)
    • 1 uL RNAsin inhibitor
    • .2 uL Maxima
    • 10 uL RNA
  • master mix 18x
    • 63 uL primer
    • 72 uL RT buffer
    • 18 uL RNAsin inhibitor
    • 36 uL dNTPs
    • 4 uL Maxima

New Probes to make

  • L3: B02 – B09
  • L2: F03, F04, F05, F06, F07. L3: F09, F10, F11 (all 2 color),
Posted in Summaries | Comments Off on Friday 05/09/14

Tuesday 05/06/14

9:00a – 12:00p

Conference Prep

  • Review speaker list, read up on papers.
  • Travel to Janelia.

Project 2

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Monday 05/05/14

9:00a – 5:00p

Lab Meeting

  • Guest speaker, see post.

Multicolor STORM more trouble-shooting

  • observed that 647 images look particularly weak, especially given the brightness of these spots.
  • 15 min of max 405 completely bleaches the 647 spot. (~50K frames).
  • 561 laser at 10% is .45-5 mW at back objective at 35 mW power source.
  • 405 laser at max power is .45 mW at back objective
  • 40 min of 461 at .45 mW (10% AOTF, 35mW source set), results in about a 2/3rds reduction in brightness of the spots.
  • should test 488.
  • imaging depth — 750 now appears above instead of below the 647 channel? (at least in test image, 750 spot visible in same x-y position when offset is 200 above the 647 position). This is very weird, the beads don’t seem to have this offset. maybe a

Lessons

  • area bleaching is stronger / larger destroyed region in 2 color samples. space out the fields of view more.
  • 647 greatly-greatly diminished after 750 imaging. Long time at max 405 power appears to be the cause.
  • can’t excite simultaneously — too much blead-through.
  • just keep the 405 low and image for longer.

Project 2,

  • see protected post

Data Analysis

  • Start processing of data on Cajal and Tuck for L3F07, L3F08, L3E04, L3E04E05, and L3E06E07

Coding

  • resumed work on integrating new ChromeWarp method into STORMfinder
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lab meeting 05/05/14

Jean-Ju Chung, Spatial Organization of CatSper in Sperm

  • (former collaborator of Sang-He)
  • Clapman lab
  • results now published, to appear soon.

background

  • ejaculated sperm not motile outside female environment. Hence ‘not fertile’.
  • what’s the difference? Bicarbonate rich, Albumin. pH changes sharply from 5 vagina to 8 in cervix / 9 in mouse fallopian tube.
  • consequent ‘capacitation’ of sperm cells. Go from activated motility, to hyperactivated (whip-like motion, believed to function in fusion)
  • sperm require few hours to mature.
  • CatSper — sperm specific Ca channel.

CatSper

- Identified 4 channels in sperm.   
- knockouts are male-specific infertile
- lack hyper-active motility.  
- structurally more similar to K channel than other Ca / Na channels
- stay in the ER, don't become functional ion channels until mature sperm
- then localize in principle piece (main body of the tail).  
- Ca specific conductance abolished in any of the knockouts.  -- heterotetramer.
- progesterone activates human CatSper

How is CatSper organized?

  • Conventional imaging: CatSper is localized to the principle piece. Sometimes 2 lines, sometime 3 lines or apparent helix.
  • 9(doublet microtubules)+2(singlet) microtubule organization + 2 outer layers. ~300nm inner diameter
  • CatSper1 arranged in 4 long parallel lines in two double rows.
  • immunoEM see four doublets flanking each of the longitudinal columns.
  • CatSper is quadralateral before formation of the longitudal column in immature sperm.

How does this organization affect the function of beating?

  • CatSper colocalizes with Ca2+ signaling molecules like P-CaMKII, and PP2B-Ag
  • CatSper still organized in Caviolin knockout.
  • Caviolin not still organized in CatSper knockout.
  • functionally confines tyrosine phosphorylation to the interior of the axonneme – (microtubule bundle)
  • Maybe the clustering of CatSper is important to the signalling.

probing P-Tyr phosphorylation

  • add heavy labels to P-Tyr from Wt and CatSpe1 nulls
  • mix and mass-spec.
  • 62 phosphoylation sites on 45 proteins. (previously only 7 known)
  • 41 sites show 2 fold increase in P-tyr in the knockout.
  • find Src family kinases target CatSper-dependent phosphorylation pathways
  • Calmodulin (Ca binding) concentrated in center.
  • phosphorylated Calmodulin focused in the very center after capactiation, and focused on the perifery in the CatSper1 null.

Model

  • Tyrosine phosphorylation is downstream of PKA in sperm.
  • upregulation of tyrosine phsophorylation in CatSper nulls is also PKA depedent.

relation to swimming

  • Capacitation generates heterogeneous sperm populations — different radial distributions of CatSper1
  • Motility correlative imaging.
    • all hyperactive swimming sperm have intact quadralateral structure of CatSper and focused concentration of pY.
  • use fluorescently labeled sperm to trace migration through female reproductive system in transgenic mice
  • CatSper null sperm don’t exit the uterus (or very few).
Posted in Lab Meeting, Seminars | Comments Off on lab meeting 05/05/14

Sunday 05/04/14

10:30a – 10:00p

Goals

  • Poster revisions as detailed by XZ.
  • Relaunch Oligo-Array analysis — matlab control script killed by Odyssey.
  • Test new 2-clr STORM stains

Questions for RC computing

  • use general queue / infiband to analyze data on Odyssey CPUs and write results to my local hard-drives?
  • better way to dispatch large numbers of genes for analysis?

STORM

  • imaging E04-P3 E05-P1 sample
  • 750 spots faint but visible in all cells.
  • decent switching for first movie. later movies look more questionable.
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Saturday 05/03/14

6:30p – 8:30p

STORM

  • setup imaging of E04
  • high background. Otherwise dyes look very bright, switching looks great.
Posted in Summaries | Comments Off on Saturday 05/03/14