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


  • 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


  • 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


  • 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


  • 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