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Team:Heidelberg/Templates/M-12-07-13
From 2013.igem.org
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==Lab Update == | ==Lab Update == | ||
===Delftibactin=== | ===Delftibactin=== | ||
| - | + | * Del H | |
| - | + | ** problems with 1B bands | |
| - | + | *** new amplification worked | |
| - | + | *** were digested and purified today | |
| - | + | *** are going to be ligated tomorrow | |
Dominiks suggestion: | 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 | * divide ligation after 1 hour into two, one is kept at -20°C the other is let continue over night at 4°C | ||
| Line 33: | Line 33: | ||
---> gel is running right now and will influence decision on further proceeding | ---> 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=== | ===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=== | ===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=== | ===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== | ==NRPS== | ||
Latest revision as of 01:56, 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
- problems with 1B bands
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?
- brainstorming
- 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
