Team:Heidelberg/Templates/M-12-07-13

From 2013.igem.org

(Difference between revisions)
(Created page with " == Cooperation with Freiburg(Hanna) == * arrive on Monday(14.7.) want to show us Gibbson Assembly * accomodation: Philipp, Julia, Hanna/Ralf * Would go out for Dinner at Schmidt...")
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==Lab Update ==
==Lab Update ==
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#Delftibactin:
+
===Delftibactin===
#* Del H  
#* Del H  
#** problems with 1B bands
#** problems with 1B bands
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#*** for DelOP
#*** for DelOP
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#Indigoidine
+
===Indigoidine===
#*pptase could be amplified, but not indigoidine synthetase  
#*pptase could be amplified, but not indigoidine synthetase  
#**brainstorming
#**brainstorming
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#*primer strategy with BPSA
#*primer strategy with BPSA
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#Tyrocidine
+
===Tyrocidine===
#*Stamm come from Marahije (?)
#*Stamm come from Marahije (?)
#*Glycerol stocks,colony PCRs
#*Glycerol stocks,colony PCRs
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#*ordering of primers by end of the week
#*ordering of primers by end of the week
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#Methyl-malonyl CoA
+
===Methyl-malonyl CoA===
#* want genomic integration of substrate synthesis complex for DelF
#* want genomic integration of substrate synthesis complex for DelF
#* got the insert from the USA
#* got the insert from the USA

Revision as of 01:55, 4 October 2013

Contents

Cooperation with Freiburg(Hanna)

  • arrive on Monday(14.7.) want to show us Gibbson Assembly
  • accomodation: Philipp, Julia, Hanna/Ralf
  • Would go out for Dinner at Schmidt's, Hanna is going to send an Email
  • we should take away all the things in the lab indicating our actual project with Delftibactin

Lyon (Hanna, Philipp, Tania)

  • hotel: 7x 3 people in one room
  • train to Lyon is booked, need to book the ride back on 15.7. (Monday)

Human Practice

  • Konrad offered to take care of the soil samples to send to the UK (?)
    • want to get some info on Streptomycces from them.
  • Fanny and bts take care of the discussion round

Financing, Karl Steinbruch Stiftung, Software Project

  • Anja: we need three people's CVs that have worked in Bioinfomatics and have more than 120 ECTS
  • they want to know about where we spent the money
  • max ammount is app. 830 €/month
  • dead line is 31.7.

Lab Update

Delftibactin

    • Del H
      • problems with 1B bands
        • new amplification worked
        • were digested and purified today
        • are going to be ligated tomorrow

Dominiks suggestion:

  • divide ligation after 1 hour into two, one is kept at -20°C the other is let continue over night at 4°C
    • pool both together and electroporate this batch
  • gibbson primers arrived today; this will be the new approach, if ligation is unsuccessful
    • parallel gibbson does not make sense, to expensive

---> gel is running right now and will influence decision on further proceeding

    • Del Rest
      • 7-8 fragments of 32 are still missing
      • backbone has been amplified
      • Flo designed new primers
        • for DelOP

Indigoidine

    • pptase could be amplified, but not indigoidine synthetase
      • brainstorming
        • maybe the gene is not in this sub-species?
    • plamsid from UTAH arrived
    • want to write to other labs if they can send us the plasmid
    • there is a different Streptomyces (Stamm) that has this enzyme but need to finde the correct name
    • burocracy discussion.. MTA, Hauspost, Eils signature
    • primer strategy with BPSA

Tyrocidine

    • Stamm come from Marahije (?)
    • Glycerol stocks,colony PCRs
    • new strategy has be developed
    • ordering of primers by end of the week

Methyl-malonyl CoA

    • want genomic integration of substrate synthesis complex for DelF
    • got the insert from the USA
    • just need to amplify the insert with appropritate primers with some extra DNA
    • first tries didn't work
    • has several primers for accurate testing/screening
    • if integration worked only one resistance gene copy
    • gets fragment PLUS other bands of something else...
    • did electroporation and purification this week
      • some altered conditions
    • some good colonies
    • screening

NRPS

  • primary goals of the NRPS etc
  • NRPS are modulary
  • three domains, CA-T-optional
  • flexible linkers between domains
  • can be put into different orders
  • wetlab:
    • goal: library of physical DNA of single modules to be able to put into different orders
    • start with tyrocidine pathway
  • software:
  • tell what you want
  • has info on different pathways and domains
  • tells me how to ligate everything together etc
  • specifity is dependent on CA domain
  • look at what is most probable to work later

--> calculate evolutionary distance according to the taxon ids in the database

  • 4 nodes:
    • b.brevis
    • e.coli.
    • p. aeruginosa
    • b.subtilis
  • Discussion about Linkers:
    • should they be standardized?
    • how should they look like?
    • domains are highly conserved among species and linkers are NOT conserved at all