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Revision as of 01:54, 4 October 2013 (view source) JuliaS1992 (Talk | contribs) (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...") ← Older edit		Revision as of 01:55, 4 October 2013 (view source) JuliaS1992 (Talk | contribs) Newer edit →
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	==Lab Update ==		==Lab Update ==
-	#Delftibactin:	+	===Delftibactin===
	#* Del H		#* Del H
	#** problems with 1B bands		#** problems with 1B bands
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	#*** for DelOP		#*** for DelOP
-	#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
-	#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
-	#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

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Revision as of 01:55, 4 October 2013

Contents 1 Cooperation with Freiburg(Hanna) 2 Lyon (Hanna, Philipp, Tania) 3 Human Practice 4 Financing, Karl Steinbruch Stiftung, Software Project 5 Lab Update 5.1 Delftibactin 5.2 Indigoidine 5.3 Tyrocidine 5.4 Methyl-malonyl CoA 6 NRPS

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

1. • 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

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

Indigoidine

1. • 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

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

Methyl-malonyl CoA

1. • 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