Team:SDU-Denmark/Notebook

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=Project management notebook=
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=Project task-management notebook=
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==Week 1 - BioBricks, primers, protocols and more ==
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== Todo ==
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===Plasmid backbone===
 
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We found a plasmid backbone, that works in both e. coli and b. subtilis (that is, both in gram negative and gram positive bacteria). It has a quality star.
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===Create biobrick RIP in registry===
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The plasmid backbone is called BBa_I742123, and can be found here: http://partsregistry.org/wiki/index.php/Part:BBa_I742123
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===Create biobrick RIP+Export in registry===
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It seems that the backbone works with all e. coli type, both we're not a 100%.
 
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The backbone is resistant to the following antibiotics: chloramphenicol, neomycin & gentamicin. 
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== Doing ==
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Ordering: we've written HQ, requesting the part since we cant figuar out how to get it via the registry.
 
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===E. coli type===
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== Done ==
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===Find Plasmid backbone===
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'''Task:''' Find a backbone for both e.coli and b. subtilis
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'''People:''' Helle and Mike
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 +
 
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''July 7th 2009:''
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We found the backbone, [http://partsregistry.org/wiki/index.php/Part:BBa_I742123 BBa_I742123], which other teams have found to be compatible with both both gram positive and gram negative bacteria, such as e. coli.
 +
 
 +
After talking to HQ, it turns out that the quality of their stock is bad, and they will try to get some home from older teams. Furthermore, it might simply be better to use a more specifik backbone for e. coli and for b. subtilis.
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 +
(mike)
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 +
 
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''July 8th 2009:''
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We decided to start working with [http://partsregistry.org/Part:pSB1A3 pSB1A3] instead, which is a high-output e. coli backbone.
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Output: 100-300 number pr. cell.
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Resistance: ampicillin (we're going with 50 µg/mL first)
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(mike)
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===E. coli strain===
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'''Task:''' Find a e.coli strain
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'''People:''' Mike
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 +
 
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''July 7th 2009''
The plasmid seems to be working in most types (no need for ccdB)
The plasmid seems to be working in most types (no need for ccdB)
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Jacob suggests E. coli KG22, which can turns on the operon by adding IPTG.
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==Week 2 - ? ==
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''July 8th 2009''
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We'll use Top10 e.coli strain first.
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===Promoter for e.coli===
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'''Task:''' Find a constitutive and inducible promoter
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'''People:''' Anna and Kir
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 +
 
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''July 7th 2009''
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 +
 
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'''Constitutive promoter'''
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We'll use [http://partsregistry.org/Part:BBa_J23100 BBa_J23100] as constitutive promoter. Its located in QC09 Kit Plate 1, Well C18.
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 +
 
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'''Inducible promoter'''
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We'll use [http://partsregistry.org/Part:BBa_R0011 BBa_R0011] as an inducible promoter. It's located in: QC09 Kit Plate 1, Well 6G, Plasmid: pSB1A2
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Use:
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To induce this promoter region, generally add 1mM of IPTG to a plate (amount will vary by cell strain). That is, total volume of stuff in plate (usually around 0.025 liters) * 0.001 = X amount of liters that you will add to the solution.
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 +
 
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===RBS===
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'''Task:''' Find a RBS
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'''People:''' John and Julius
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 +
 
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''July 7th 2009''
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We'll use [http://partsregistry.org/wiki/index.php?title=Part:BBa_B0034 BBa_B0034]. The sequence is: 5'-AAAGAGGAGAAA-3'. It's located in: Kit plate 1, well 2M.
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Binding to the site is not regulated, and it has been reported to be very effective.
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 +
 
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===Terminator===
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'''Task:''' Find a terminator
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'''People:''' Marc
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''July 7th 2009''
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We'll use [http://partsregistry.org/wiki/index.php?title=Part:BBa_B0015 BBa_B0015]. This is a double terminator consisting of BBa_B0010 and BBa_B0012. This is the most commonly used terminator. It seems to be reliable.
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Note, however, that BBa_B0014 is a better part for forward and reverse termination.
 +
 
 +
It's located in: QC09 Plate 669, Well 41811.
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 +
 
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== Done Done ==

Latest revision as of 09:07, 9 July 2009

Home The Team The Project Parts Submitted to the Registry Modeling Notebook


Contents

Project task-management notebook

Todo

Create biobrick RIP in registry

Create biobrick RIP+Export in registry

Doing

Done

Find Plasmid backbone

Task: Find a backbone for both e.coli and b. subtilis

People: Helle and Mike


July 7th 2009: We found the backbone, [http://partsregistry.org/wiki/index.php/Part:BBa_I742123 BBa_I742123], which other teams have found to be compatible with both both gram positive and gram negative bacteria, such as e. coli.

After talking to HQ, it turns out that the quality of their stock is bad, and they will try to get some home from older teams. Furthermore, it might simply be better to use a more specifik backbone for e. coli and for b. subtilis.

(mike)


July 8th 2009: We decided to start working with [http://partsregistry.org/Part:pSB1A3 pSB1A3] instead, which is a high-output e. coli backbone.

Output: 100-300 number pr. cell. Resistance: ampicillin (we're going with 50 µg/mL first)

(mike)


E. coli strain

Task: Find a e.coli strain

People: Mike


July 7th 2009

The plasmid seems to be working in most types (no need for ccdB) Jacob suggests E. coli KG22, which can turns on the operon by adding IPTG.


July 8th 2009

We'll use Top10 e.coli strain first.


Promoter for e.coli

Task: Find a constitutive and inducible promoter

People: Anna and Kir


July 7th 2009


Constitutive promoter

We'll use [http://partsregistry.org/Part:BBa_J23100 BBa_J23100] as constitutive promoter. Its located in QC09 Kit Plate 1, Well C18.


Inducible promoter

We'll use [http://partsregistry.org/Part:BBa_R0011 BBa_R0011] as an inducible promoter. It's located in: QC09 Kit Plate 1, Well 6G, Plasmid: pSB1A2

Use:

To induce this promoter region, generally add 1mM of IPTG to a plate (amount will vary by cell strain). That is, total volume of stuff in plate (usually around 0.025 liters) * 0.001 = X amount of liters that you will add to the solution.


RBS

Task: Find a RBS

People: John and Julius


July 7th 2009

We'll use [http://partsregistry.org/wiki/index.php?title=Part:BBa_B0034 BBa_B0034]. The sequence is: 5'-AAAGAGGAGAAA-3'. It's located in: Kit plate 1, well 2M.

Binding to the site is not regulated, and it has been reported to be very effective.


Terminator

Task: Find a terminator

People: Marc


July 7th 2009

We'll use [http://partsregistry.org/wiki/index.php?title=Part:BBa_B0015 BBa_B0015]. This is a double terminator consisting of BBa_B0010 and BBa_B0012. This is the most commonly used terminator. It seems to be reliable. Note, however, that BBa_B0014 is a better part for forward and reverse termination.

It's located in: QC09 Plate 669, Well 41811.


Done Done

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