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Team:Newcastle University/Constraints Repository
From 2008.igem.org
Newcastle University
GOLD MEDAL WINNER 2008
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Home >> Aim >> Constraints Repository
Constraints Repository
Aim:
Develop a system that will be a repository of constraints that specify the way biological components can be assembled, and the parameters that describe their interactions.
Components of a biological circuit can only be combined in ways which make biological sense. Much of this information is available in publications and public databases, but these are distributed worldwide and do not necessarily have compatible formats. The information therefore needs to be stored and described somewhere which is accessible to the rest of the projects, in a single, coherent form.
Contributors:
Lead: Nina Nielsen-Dzumhur
The matrix.
To populate the compatibility matrix I used three methods.
- literature searching (google the parts and look through journals for conformation that they can interact/control gene expression of the connecting part)
- Look at homologous structures of parts that have been confirmed to interact. If the structure is the same, they may also be compatible.
- use blast of the DNA sequence two parts together to see the sequence exists at all. This would confirm compatibility.
| LacI | LacO | XylR | TetR | ssrA | ComK | PcomG | Pspank | Phi29 | mCherry | GFP | |
| LacI | 0 | 1 | 1 | 1 | 1 | 0 | 0 | 1 | 0 | 1 | 1 |
| LacO | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| XylR | 0 | 0 | 0 | 1 | 0 | 1 | 1 | 0 | 1 | 1 | 1 |
| TetR | 1 | 0 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 |
| ssrA | 0 | 0 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 1 |
| ComK | 0 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 0 | 0 | 1 |
| PcomG | 0 | 0 | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 1 |
| Pspank | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 | 0 | 1 | 1 |
| phi29 | 1 | 0 | 1 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
| mcherry | 1 | 0 | 0 | 1 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| GFP | 1 | 0 | 0 | 1 | 1 | 1 | 0 | 1 | 0 | 0 | 0 |
References
- Abo et al. 2000 - SsrA-mediated tagging and proteolysis of LacI and its role in its regulation of lac operon
- Hahn et al. 1996 - Regulatory inputs for the synthesis of ComK, the competence transcription factor of Bacillus subtilis.
- Hansen et al. 2001 - The Use of Whole-Cell Biosensors to Detect and Quantify Compounds or Conditions Affecting Biological Systems.
- Kap et al. 2007 – http://www.diss.fu-berlin.de/2007/653/kap2.pdf
- Kim et al. 2003 - Limitations of Quantitative Gene Regulation Models: A Case Study
- Kolkmann et al. 2004 - The fate of extracellular proteins tagged by the SsrA system of Bacillus subtilis.
- Lee et al. 2007 - Identification of the Origin of Transfer (oriT) and DNA Relaxase Required for Conjugation of the Integrative and Conjugative Element ICEBs1 of Bacillus subtilis.
- Lee and Auchtung et al. 2007 - Identification and characterization of int (integrase), xis (excisionase) and chromosomal attachment sites of the integrative and conjugative element ICEBs1 of Bacillus subtilis.
- Nankano et al. 2003 - A regulatory protein that interferes with activator stimulated transcription in bacteria.
- Nishihara et al. 1998 - Chaperone Coexpression Plasmids: Differential and Synergistic Roles of DnaK-DnaJ GrpE and GroEL-GroES in Assisting Folding of an Allergen of Japanese Cedar Pollen, Cryj2, in Escherichia coli.
- Oguara et al. 1999 - Positive regulation of Bacillus subtilis sigD by C-terminal truncated LacR at translational level.
- Smits et al. 2005 - Stripping Bacillus: ComK auto-stimulation is responsible for the bistable response in competence development.
- Suel et al. 2007 - Tunability and Noise Dependence in Differentiation Dynamics.
- Susannsa et al. 2004 - Mechanism of Transcription Activation at the comG Promoter by the Competence Transcription Factor ComK of Bacillus subtilis.
- Wiegert et al. 2001 - SsrA-Mediated Tagging in Bacillus subtilis.
