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  • Bruno Vellutini 18:24 on 2013/03/25 Permalink
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    Starting a Terebratalia RNAseq CLC assembly with the following parameters:

    Automatic word size = ON
    Automatic bubble size = ON
    Minimum contig length = 170
    Auto-detect paired distances = ON
    Perform scaffolding = OFF
    
    Map reads back = ON
    mismatch = 2
    insertion = 3
    deletion = 3
    length = 0.5
    similarity = 0.8
    Colorspace alignment = ON
    Global alignment = OFF
    Update contigs = ON
    Create list of un-mapped = OFF
    
    Create report = ON
    Result handling = Save
    Make log = ON
    
     
  • Bruno Vellutini 17:10 on 2013/03/25 Permalink
    Tags: , , , , , , ,   

    Cloning of Terebratalia wnt2 and other Meara RNA binding proteins 


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    Started a PCR with Terebratalia wnta, wnt2; and Meara ago a, ago b, ago c, bru a, bru b, mago, mex3, orb2.

    2013-03-26 11.47.59 2013-03-28 15.23.26

    12/04/13

    Put colonies to grow.

    Colony T7
    Ago a c1 BV235
    Ago a c2 BV236
    Ago a c3 BV237
    Ago b c1 BV238
    Ago b c2 BV239
    Ago b c4 BV240
    Bru a c1 BV241
    Bru a c2 BV242
    Bru a c3 BV243
    Mago c1 BV244
    Mago c2 BV245
    Mago c3 BV246
    Orb2 c1 BV247

     
  • Bruno Vellutini 11:09 on 2013/03/25 Permalink
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    Warning: preg_match_all(): Compilation failed: invalid range in character class at offset 7 in /home/customer/www/phd.organelas.com/public_html/wp-content/themes/p2/inc/mentions.php on line 77

    After last Lineus collection I rearranged the worms collected a year ago to a small glass bowl. Some time in the last week they laid two egg cases which I found today. I transferred the two egg cases to a small glass bowl with clean sea water.

    So apparently we can keep these worms in the facility with irregular and scarce food supply and they still manage to lay eggs.

    Recently collected worms did not lay anything yet.

     
  • Bruno Vellutini 15:54 on 2013/03/24 Permalink
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    Starting a Isodiametra RNAseq CLC assembly with the following parameters:

    Automatic word size = ON
    Automatic bubble size = ON
    Minimum contig length = 170
    Auto-detect paired distances = ON
    Perform scaffolding = OFF
    
    Map reads back = ON
      mismatch = 2
      insertion = 3
      deletion = 3
      length = 0.5
      similarity = 0.8
    Colorspace alignment = ON
    Global alignment = OFF
    Update contigs = ON
    Create list of un-mapped = OFF
    
    Create report = ON
    Result handling = Save
    Make log = ON
    

    It started at 16h and finished 01h00. ~9h running with 24 cores.

     
  • Bruno Vellutini 13:24 on 2013/03/23 Permalink
    Tags: , Xenoturbella   


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    Starting a Xenoturbella RNAseq CLC assembly with the following parameters:

    Automatic word size = ON
    Automatic bubble size = ON
    Minimum contig length = 170
    Auto-detect paired distances = ON
    Perform scaffolding = OFF
    
    Map reads back = ON
      mismatch = 2
      insertion = 3
      deletion = 3
      length = 0.5
      similarity = 0.8
    Colorspace alignment = ON
    Global alignment = OFF
    Update contigs = ON
    Create list of un-mapped = OFF
    
    Create report = ON
    Result handling = Save
    Make log = ON
    

    It started at 13h30 and finished 23h00. ~12h running with 24 cores.

     
  • Bruno Vellutini 18:31 on 2013/03/22 Permalink
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    More confocal of en+wnt doubles 


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    Took some lateral views of en+wnt1 and a few scans of en+wnt5. The latter is quite noisy for wnt5 probe unfortunately…

    MAX_Ttra_en+wnt5.lif - Series000

     
  • Bruno Vellutini 23:42 on 2013/03/16 Permalink
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    Terebratalia en+wnt1 confocal images 


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    Began confocalling and they look good :)

    MAX_Ttra_en+wnt1.lif - Series004

     
  • Bruno Vellutini 19:30 on 2013/03/14 Permalink
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    Warning: preg_match_all(): Compilation failed: invalid range in character class at offset 7 in /home/customer/www/phd.organelas.com/public_html/wp-content/themes/p2/inc/mentions.php on line 77

    Sorted the collected nemerteans. It looks like there are two main morphotypes that could be Lineus. A more reddish as we use to call Lineus ruber and a more greenish/yellowish. The latter can have a gradient from red to green in the A/P axis. Also there are thin ones that might be different or juvenile stages.

    A different morphotype is whiteish with 2 distinct pink brain areas. Finally there is a similar to Lineus above, but in dark green.

     
  • Bruno Vellutini 19:19 on 2013/03/14 Permalink
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    Probe synthesis for Terebratalia engrailed 


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    Set a transcription reaction to synthesize more DNP probe for Ttra engrailed. Making 4 tubes and initiated precipitation at 18h.

    15/03/13

    Tt en DNP

     
  • Bruno Vellutini 20:00 on 2013/03/13 Permalink
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    Lineus sp. collection 


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    Collected a bunch of nemertines with Henrike and Aina at Aina’s beach.

     
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