• < home >
• < team >
  • → members
  • → attributions
  • → freiburg
• < project >
  • → description
  • → results
  • → modeling
  • → notebook
  • → sample data
• < human practices >
  • → oath
  • → ethics
  • → safety
• < gallery >
• < sponsors >
• < to the forums >

Sample Data

How Our System Works

Our Favorite New Parts

1. [http://partsregistry.org/Part:BBa_K608408 BBa_K608408] GST

The GST-tag was PCR amplified from a pGEX vector with overhang primers including the iGEM restriction sites and then pasted into the iGEM vector. To verify the functionality of the construct we cloned it before a GFP sequence and expressed it with an IPTG inducible vector. Results see partsregistry page. The submitted sequence was partially confirmed by sequencing.

2. [http://partsregistry.org/Part:BBa_K608406 BBa_K608406] Precipitator

The Precipitator is a new artificially designed LRR protein. It is meant as protein that binds Nickel ions with Histidines grouped on its surface. The bound Nickel can then precipitate His-tagged proteins. In our Lab in a Cell it should function as an adaptor between the plastic surface of pipettes and the His-tagged protein. Please look at our detailed description of the design layout in our modeling section. The sequence was synthesised and cloned into the iGEm vector. The submitted sequence was fully confirmed by sequencing.

3. [http://partsregistry.org/Part:BBa_K608404 BBa_K608404] IPTG-inducible Promoter with plastic binding domain-tagged GFP

Also new parts

[http://partsregistry.org/Part:BBa_K608101 BBa_K608101] CcaR, green light response regulator

[http://partsregistry.org/Part:BBa_K608102 BBa_K608102] CcaS, green light receptor

Pre-existing Parts

[http://partsregistry.org/Part:BBa_K608151 BBa_K608151] translational unit of pcyA

We designed this composite in order to gain the enzyme pcyA (phycocyanobilin-ferredoxin oxidoreductase),
this design is essential if the part is going be integrated into an assembly of various genes.
The enzyme plays an important role in the production of the PCB chromophore (phycocyanobilin)
which is essential for the green and red light receptor system.
Sequencing confirmed that the part is correct in the pSB1C3 vector.
All physical DNA samples used for this composite come from the [http://partsregistry.org/Main_Page registry of standart biological parts]
For PCB chromophore production the enzyme ho1 (heme oxygenase) in a similar design is needed
because both enzymes are necessary to convert heme into PCB chromophore.

We've Also Characterized the Following Parts

[http://partsregistry.org/Part:BBa_K608351 BBa_K608351] (correct) temperature sensitive promoter

[http://partsregistry.org/Part:BBa_K608352 BBa_K608352] Bacteriophage Lysis Cassette with RBS

[http://partsregistry.org/Part:BBa_K608002 BBa_K608002] strong Promotor and strong RBS

[http://partsregistry.org/Part:BBa_K608003 BBa_K608003] strong Promotor , medium RBS

[http://partsregistry.org/Part:BBa_K608004 BBa_K608004] strong Promotor , weak RBS

[http://partsregistry.org/Part:BBa_K608005 BBa_K608005] medium Promotor , strong RBS

[http://partsregistry.org/Part:BBa_K608006 BBa_K608006] medium Promotor , medium RBS

[http://partsregistry.org/Part:BBa_K608007 BBa_K608007] medium Promotor , weak RBS

Precipitator

Green light receptor

Lysis cassette

The Concept

The idea behind our lysis cassette was to be able to achieve cell lysis by simply heating the bacteria to 42°C for a short period of time. This was to be accomplished by combining the biobricks BBa_K098995 (temperature sensitive promoter) and BBa_K124017 (Bacteriophage λ lysis genes). Sequencing of these parts (carried out by GATC Biotech GmbH) showed some fundamental inconsistencies leading to a lot of time spent on fixing them.
The sequences were corrected and the new biobricks were sent to the registry, although the novel temperature sensitive lysis cassette composite's sequence was verified some 18 hours before the Wiki-freeze, so that it could not be sent to the registry on time.

The temperature sensitive lysis cassette

The much anticipated part that we frustratingly could not clone in time to send to the registry.

Theoretically 28°C - 30°C incubation should repress the lysis genes, while a shift to 42°C would lead to their expression and finally cell lysis.

[File:Freiburg11_LysisCassetteODmeasurement.jpg|900px]

frame|caption|The lysis genes seem to work as expected, though the preliminary results hint that the temperature sensitive promoter might be quite leaky at 30°C. More testing is necessary to be able to propose the exact functionality of the]