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| | {{Team:Groningen/Header}} | | {{Team:Groningen/Header}} |
| - | ='''Lab plan:'''= | + | =='''Lab plan:'''== |
| - | | + | For Basic Cloning strategy and final products see [https://2009.igem.org/Team:Groningen/Project The Project] |
| - | # Clone gvp from BioBrick (BBa_I750016) in vector with inducible promoter (e.g. PAra)
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| - | # Clone a metal ion transporter (CitM and HtmA are planned)
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| - | # Clone a metal accumulating protein.
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| - | # Clone a metal sensitive promoter in front of the gvp cluster.
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| - | # Clone the metal accumulating protein and metal transporter in one vector, possibly on a synthetic operon
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| - | # Transform both vectors in one ''E. coli'' strain
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| - | =='''Wk1'''==
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| - | ==='''Gvp Cluster'''===
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| - | *BBa_I750016 is a construct: E-genR-X-RBS-PART-S-P in vector BBa_J61035.
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| - | *Possibly the AmpR and ColE1 are also still present on the vector, as the part was last checked in 2008 and contained a Amp resistance marker…
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| - | *The part is present in the microtiter plate: Kit Plate 2, Well 11A
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| - | *Quality control was okay, but plasmid length was different than expected. --> should be checked by us.
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| - | *Plan:
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| - | **Get chemically competent ''E. coli''
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| - | **Dilute dry DNA of gvp with 15ul diH2O
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| - | **Transform to ''E. coli'' --> see protocol
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| - | **Plate on LB-A plates with Amp or Gentamicin selection (50/50)
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| - | **Use positive and negative control
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| - | **Grow o/n @ 37 degrees
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| - | **Pick single colony and grow o/n in 5ml LB + correct antibiotic
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| - | ***Make glycerol stocks of the o/n culture
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| - | ***Do DNA isolation
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| - | ***Check the vectors insert by restriction analysis --> ''Pst''I and ''Xba''I (would give 1 band of ~ 3539bp and 1 of 6064bp)
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| - | *Design primers to get rid of restrictionsites
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| - | ==='''CitM'''===
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| - | *SJ transformed ''E. coli'' with pWSK29, a low copy nr vector containing CitM (according to B. Krom this is the best vector for CitM)
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| - | *Get plasmid and possibly the plate with ''E. coli'' transformants.
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| - | **Check expression of CitM while growing on citrate medium with Amp, induce with IPTG
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| - | *Check gene for restriction sites and design primers to get rid of restriction sites.
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| - | *Design primers to introduce a pre/suffix --> ask B. Krom whether this would be feasible
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| - | ==='''HtmA'''===
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| - | * On its way, but hopefully arrives next week
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| - | ==='''Accumulation of metal'''===
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| - | *BioBrick (BBa_K129004) LamB + metal binding domain is not available
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| - | *Find out whether it’s possible to only express the metal binding domain (6AA) and if so, order synthetic DNA with part with pre/suffix
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| - | ==='''To do list'''===
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| - | *Get CitM from the biological centre
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| - | *Finish equipment list --> send to facility manager
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| - | *Design primers
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| - | *Read articles to find [https://2009.igem.org/Team:Groningen/Project modeling parameters] for the different sub-projects and to find testing-phenotype (e.g. metal inport) protocols
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| - | *Start ordering materials like: media, restriction enzymes, kits
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| - | *Talk with Profs for permission to use stuff from the different groups in Haren
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| - | *Check compatibility of different plasmids / promoters / replicons in ''E. coli''--> On Fermentas site about [http://www.fermentas.com/techinfo/nucleicacids/mappuc1819.htm pUC18, pUC19] and about [http://www.fermentas.com/techinfo/nucleicacids/mappacyc184.htm pACYC184]
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| - | *Make a plan for July, concerning:
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| - | **Vector --> how to get the pBS3K1 empty, what kind of vector is pWSK29 (Frans)
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| - | **Primers --> how to remove restrictionsites in gvp, possibly in CitM / HtmA (PstI) (Frans)
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| - | **Promoters (Frans, Michael)
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| - | ***High/moderate/low expression upon induction or constitutive
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| - | ***Metal sensitive promotor
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| - | *[http://partsregistry.org/Featured_Parts:CloningFacilitationTools cloning facilitation tools]
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| - | =='''Wk 2:'''==
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| - | *Get everything in the lab
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| - | *Have BioBricks checked on correct insert
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| - | *Have primers ordered
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| | | | |
| | + | =='''Wk1 / Wk2'''== |
| | + | For weekly of the lab work planning see [https://2009.igem.org/Team:Groningen/Notebook Notebook] --> Mondays |
| | | | |
| | =='''July:'''== | | =='''July:'''== |
| - | | + | For detailed planning of the labwork for different groups see the Construction phases in [https://2009.igem.org/Team:Groningen/Project_Plan Project Plan] for the functions Implementer and Tester (mostly combined for lab work) |
| - | GVP (2 people)
| + | {{Team:Groningen/Footer}} |
| - | #Test insert length of gvp cluster
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| - | #Clone gvp from BBa_J61035 to another vector with p15A vector (pBS3K1)
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| - | #Clone gvp in vector with different promoters; high, moderate, low expression…
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| - | ##
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| - | ##
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| - | ##
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| - | #Silence restriction sites in gvp cluster by PCR (which?)
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| - | #Test phenotype, growth rates E. coli --> which of the promoters is the best one?
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| - | #Check compatibility of gvp expression and CitM expression in E. coli by transforming the organism with both vectors and select on two antibiotics (compatible selection markers and promoters)
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| - | Metal transporters (3 people)
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| - | *CitM
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| - | #Transform E. coli with pWSK29
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| - | #Test phenotype, expression, check growth rate while expressing CitM
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| - | Metal accumulation (3 people)
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For detailed planning of the labwork for different groups see the Construction phases in Project Plan for the functions Implementer and Tester (mostly combined for lab work)
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