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Team:Groningen/Project Plan/Construction
From 2009.igem.org
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**#If needed add promoter (constitutive promoter --> <partinfo>BBa_J23119</partinfo>) to do initial phenotype testing. | **#If needed add promoter (constitutive promoter --> <partinfo>BBa_J23119</partinfo>) to do initial phenotype testing. | ||
**'''Metal transporters (Jolanda, SJ, Nienke (?))''' | **'''Metal transporters (Jolanda, SJ, Nienke (?))''' | ||
| - | **#Transform E. coli with construct | + | **#Transform E. coli with construct (HmtA first, get GlpF either by ordering or by genome PCR. Then order primers + pre/suffix and RBS in prefix). |
**#Test insert length. | **#Test insert length. | ||
**#Silence restrictionsites in gvp cluster by PCR (2x PstI) and add BioBrick pre/suffix. | **#Silence restrictionsites in gvp cluster by PCR (2x PstI) and add BioBrick pre/suffix. | ||
**#Clone the RBS and the terminator in to the construct. | **#Clone the RBS and the terminator in to the construct. | ||
**'''Metal accumulation (Wilfred, Paul, Nienke (?))''' | **'''Metal accumulation (Wilfred, Paul, Nienke (?))''' | ||
| - | **#Transform E. coli with construct / synthetic gene | + | **#Transform E. coli with construct / synthetic gene. |
**#Test insert length. | **#Test insert length. | ||
**#''(If needed)'' Silence restrictionsites in gvp cluster by PCR (2x PstI in HmtA, unknown in GlpF). | **#''(If needed)'' Silence restrictionsites in gvp cluster by PCR (2x PstI in HmtA, unknown in GlpF). | ||
Revision as of 23:01, 2 July 2009
[http://2009.igem.org/Team:Groningen http://2009.igem.org/wiki/images/f/f1/Igemhomelogo.png]
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| Risk List | Tools and Documentation | Inception | Elaboration | Construction | Transition | |||||||||||||||||
| 1 | 2 | 1 | 2 | 1 | 2 | 3 | 1 | 2 | ||||||||||||||
| apr. 20 | may 18 | jun. 01 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | okt. 15 | ||||||||||
This is the iteration plan for the Construction iteration(s). See [http://www.upedu.org/upedu/process/artifact/ar_itpln.htm the UPEDU artifact description] for information on what this is and what it contains (including a template).
Milestone
These are the major [http://www.upedu.org/upedu/process/itrwkfls/ms_ioc.htm milestone objectives] for the Construction phase:
- TODO Our wonderful buoyant, metal filtering bacteria should be alive and kicking!
- TODO (?) The lab/plan cloning strategy should be fully worked out at the end of the phase to reflect our final decisions on which parts/protocols/procedures/? to use. (I think this roughly corresponds to the Implementation Model in UPEDU. --Jaspervdg 11:09, 23 June 2009 (UTC))
- TODO The Iteration plan for the transition phase completed and reviewed.
- TODO (?) Design Model (and all constituent artifacts) updated with new design elements identified during the completion of all requirements. (I think this can roughly be seen as fleshing out all the device designs and parts, or in other words: making sure The Project is up-to-date. --Jaspervdg 11:09, 23 June 2009 (UTC))
- TODO More?
Resources
- Note that we're opting to do this for the entire phase instead of each iteration as in UPEDU as this seems more natural (our needs change little over the course of one phase). --Jaspervdg 11:01, 23 June 2009 (UTC)
[Resources needed for the phase — material, human, financial, and so on.]
Construction 1
Plan
End date: 2009-07-21
Overall objective:
- The basic model should be ready
- The seperate part of the labwork should be known and working or almost working
- modellers should know which parameters they need so the labworkers can prepare providing these
- The tickets and hostel should be booked
Tasks per role:
- Analyst
- Change Control Manager
- Role not used (yet).
- Configuration Manager
- Designer
- Facility Manager
- Implementer
- Have genes as BioBricks in the vector, together with all DNA elements needed for expression (RBS, term etc).
- Work on the final parts should have been started.
- Try to find protocols for the characterization, to check feasibility.
- Keep record of the labwork on the Notebook site
- GVP (Michael and Paul)
- Test insert length of gvp cluster (E-genR-X-RBS-PART-S-P in vector , Figure 1)
- (Needed?) Silence restrictionsites in gvp cluster by PCR (BamHI, XhoI, BglII --> used in other BBa standard assemblies)and remove repeat in gvpL.
- Add the terminator to the construct
- If needed add promoter (constitutive promoter --> ) to do initial phenotype testing.
- Metal transporters (Jolanda, SJ, Nienke (?))
- Transform E. coli with construct (HmtA first, get GlpF either by ordering or by genome PCR. Then order primers + pre/suffix and RBS in prefix).
- Test insert length.
- Silence restrictionsites in gvp cluster by PCR (2x PstI) and add BioBrick pre/suffix.
- Clone the RBS and the terminator in to the construct.
- Metal accumulation (Wilfred, Paul, Nienke (?))
- Transform E. coli with construct / synthetic gene.
- Test insert length.
- (If needed) Silence restrictionsites in gvp cluster by PCR (2x PstI in HmtA, unknown in GlpF).
- Add BioBrick pre/suffix by PCR.
- Clone the RBS and the terminator in to the construct.
- Vectors (Sven, Frans (Modelling aswell?)):
- Transform E. coli TOP10 with pSB3K3 and E. coli DB3.1 with pSB1AC3.
- pSB3K3 contains a p15A ORI and Kan resistance.
- pSB1AC3 contains Amp + Cam resistance markers, a ccdB death gene and a pMB1 ORI.
- Add different promoters to the vectors:
- Inducible are: pBAD-AraC in pSB2K3 and the Lac promoter in pSB1A2.
- Constitutive are: High expected expression yield, and Low expected expression yield, Lac promoter with mutated operator . For these promoter sequences are too small, oligo's have to be ordered + BBa pre/suffix !!without RBS!!
- Metal sentitive are possibly copA (order oligo's) and ??
- Clone in such a way that they are nicely -10 / -30 in front of the start codon.
- Test functionality of the promoters by cloning GFP + RBS + Terminator behind the promoter (BioBrick??).
- Transform E. coli TOP10 with pSB3K3 and E. coli DB3.1 with pSB1AC3.
- Integrator
- Modeller
- Project Manager
- Have both modellers and labworkers up and running.
- Labworkers have choosen the parts and tested those. The bouyancy, metal intake and accumulation should be tested and working seperatly.
- Have a start-up model and make sure the labworkers know which parameters the modellers need and can or already have provided these.
- Have choosen a tester, a "testplan" should have been made, the necessary equipment should be at least ordered.
- the tickets and hostel should be booked, so plans for jamboree or thereafter should be known roughly.
- Public Relations Officer
- Get in contact with papers, magazines and other media for possible publications.
- Keep in contact with other teams on progress during the summer.
- Reviewer
- Scribe
- Stakeholder
- Tester
- Treasurer
- Tickets and hostel should be booked by now.
- All the money should be coming.
- Marketing for next year should be discussed with PR
Use Cases
[List the use cases and scenarios that are being developed for this iteration.]
Evaluation Criteria
[Functionality, performance, capacity, quality measures, quality goals, and so forth.]
Construction 2
Plan
End date: yyyy-mm-dd
Overall objective:
Tasks per role:
- Analyst
- Change Control Manager
- Role not used (yet).
- Configuration Manager
- Designer
- Facility Manager
- Implementer and Tester
- GVP (1 pers):
- Initial testing of phenotype, growth rates E. coli
- Clone gvp from BBa_J61035 to the high / low copy number vector
- (If the vectors do not already contain one) Clone gvp in vector with different promoters; high, moderate, low expression.
- Metal transporters (2 pers):
- Initial testing of phenotype, growth rates E. coli.
- Clone HtmA to the high / low copy number vector.
- (If the vectors do not already contain one) Clone gvp in vector with different promoters; high, moderate, low expression (see GVP). --> do not use constitutive promoter before a combined construct with a metal accumulator has been made!
- Metal accumulation (2 pers):
- Initial testing of phenotype, growth rates E. coli.
- Clone the gene to the high / low copy number vector.
- (If the vectors do not already contain one) Clone gvp in vector with different promoters; high, moderate, low expression (see GVP).
- Vectors (1pers):
- Add different promoters to the vectors--> in such a way that they are nicely -10 / -30 in front of the start codon.
- Test functionality of the promoters by cloning GFP + RBS + Terminator behind the promoter.
- GVP (1 pers):
- Integrator
- Modeller
- Project Manager
- Public Relations Officer
- Reviewer
- Scribe
- Stakeholder
- Tester
- Treasurer
- All money should be in (except for those received afterwards)
- Bills should be paid
- Plane tickets should be in
Use Cases
[List the use cases and scenarios that are being developed for this iteration.]
Evaluation Criteria
[Functionality, performance, capacity, quality measures, quality goals, and so forth.]
Construction 3
Plan
End date: yyyy-mm-dd
Overall objective:
Tasks per role:
- Analyst
- Change Control Manager
- Role not used (yet).
- Configuration Manager
- Designer
- Facility Manager
- Implementer and Tester
- GVP (1 pers):
- Test phenotype, growth rates E. coli again.
- Transform E. coli with both vectors
- Check compatibility of gvp expression and metal transport / accumulation system expression in E. coli by transforming the organism with both vectors and select on two antibiotics (compatible selection markers and promoters)
- Make final buoyancy tests.
- Metal transporters (2 pers):
- Test phenotype, growth rates E. coli again.
- Transform E. coli with both vectors.
- Check compatibility of gvp expression and metal transport / accumulation system expression in E. coli by transforming the organism with both vectors and select on two antibiotics (compatible selection markers and promoters)
- Make final metal importing tests.
- Metal accumulation (2 pers):
- Test phenotype, growth rates E. coli again.
- Transform E. coli with both vectors.
- Check compatibility of gvp expression and metal transport / accumulation system expression in E. coli by transforming the organism with both vectors and select on two antibiotics (compatible selection markers and promoters)
- Make final metal accumulation tests.
- GVP (1 pers):
- Integrator
- Modeller
- Project Manager
- Public Relations Officer
- Reviewer
- Scribe
- Stakeholder
- Tester
- Treasurer
Use Cases
[List the use cases and scenarios that are being developed for this iteration.]
