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Team:Stanford/PartsPage
From 2009.igem.org
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<table border CLASS="cell" width=95% height=20% align=center> | <table border CLASS="cell" width=95% height=20% align=center> | ||
<tr> | <tr> | ||
| - | <th> Cloning Step </th><th> Basic Parts </th><th> Detailed Parts | + | <th> Cloning Step </th><th> Basic Parts </th><th> Detailed Parts </th><th> Picture </th> |
</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.1a </th> | <th>Step 1.1a </th> | ||
| - | <td>SoxR/S Promoter + GFP tag </td><td> RBS-SoxR-TT-SoxS Promoter + RBS-GFP-TT | + | <td>SoxR/S Promoter + GFP tag </td><td> RBS-SoxR-TT-SoxS Promoter + RBS-GFP-TT </td><td><a href="http://openwetware.org/images/1/19/1.1a.png"><img src="http://openwetware.org/images/1/19/1.1a.png" alt="1.1a" width="100" height="40"></img></a> |
</td> | </td> | ||
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.1b </th> | <th>Step 1.1b </th> | ||
| - | <td>SoxR/S Promoter + Blh </td><td>RBS-SoxR-TT-SoxS Promoter + RBS-Blh | + | <td>SoxR/S Promoter + Blh </td><td>RBS-SoxR-TT-SoxS Promoter + RBS-Blh </td><td><a href="http://openwetware.org/images/9/92/1.1b.png"> <img src="http://openwetware.org/images/9/92/1.1b.png" alt="1.1b" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.1c </th> | <th>Step 1.1c </th> | ||
| - | <td> Blh + Terminator </td><td> RBS-Blh + TT | + | <td> Blh + Terminator </td><td> RBS-Blh + TT </td><td> <a href="http://openwetware.org/images/a/a5/1.1c.png"><img src="http://openwetware.org/images/a/a5/1.1c.png" alt="1.1c" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.1d </th> | <th>Step 1.1d </th> | ||
| - | <td> Constitutive Promoter + Blh (1.1c) </td><td> Promoter +RBS-Blh-TT | + | <td> Constitutive Promoter + Blh (1.1c) </td><td> Promoter +RBS-Blh-TT </td><td><a href="http://openwetware.org/images/9/92/1.1d.png"> <img src="http://openwetware.org/images/9/92/1.1d.png" alt="1.1d" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.1e </th> | <th>Step 1.1e </th> | ||
| - | <td> Constitutive Promoter + Crt Cluster </td><td> Promoter + RBS-Crt | + | <td> Constitutive Promoter + Crt Cluster </td><td> Promoter + RBS-Crt </td><td> <a href="http://openwetware.org/images/b/b9/1.1e.png"><img src="http://openwetware.org/images/b/b9/1.1e.png" alt="1.1e" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.2a </th> | <th>Step 1.2a </th> | ||
| - | <td> Constitutive Promoter + SoxR/s w/ GFP (1.1a) </td><td> Promoter+ RBS-SoxR-TT-SoxSP-RBS-GFP-TT | + | <td> Constitutive Promoter + SoxR/s w/ GFP (1.1a) </td><td> Promoter+ RBS-SoxR-TT-SoxSP-RBS-GFP-TT </td><td><a href="http://openwetware.org/images/d/d1/1.2a.png"> <img src="http://openwetware.org/images/d/d1/1.2a.png" alt="1.2a" width="100" height="40"></img</a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.2b </th> | <th>Step 1.2b </th> | ||
| - | <td> SoxR/S-Blh (1.1b) + RALDH II </td><td> RBS-SoxR-TT-SoxSP-RBS-Blh + RBS-RALDH II-TT | + | <td> SoxR/S-Blh (1.1b) + RALDH II </td><td> RBS-SoxR-TT-SoxSP-RBS-Blh + RBS-RALDH II-TT </td><td><a href="http://openwetware.org/images/0/0f/1.22b.png"> <img src="http://openwetware.org/images/0/0f/1.22b.png" alt="1.2b" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Step 1.3a </th> | <th>Step 1.3a </th> | ||
| - | <td> Constitutive Promoter + SoxR/S w/ Blh and RaldhII </td><td> Promoter+ RBS-SoxR-TT-SoxSP-RBS-Blh-RBS-RALDH II-TT | + | <td> Constitutive Promoter + SoxR/S w/ Blh and RaldhII </td><td> Promoter+ RBS-SoxR-TT-SoxSP-RBS-Blh-RBS-RALDH II-TT </td><td><a href="http://openwetware.org/images/6/6a/1.32b.png"> <img src="http://openwetware.org/images/6/6a/1.32b.png" alt="1.3a" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Controls W/ PQ (+) </th> | <th>Controls W/ PQ (+) </th> | ||
| - | <td> Constitutive Promoter + GFP tag </td><td> Promoter+ RBS-GFP-TT | + | <td> Constitutive Promoter + GFP tag </td><td> Promoter+ RBS-GFP-TT </td><td> <a href="http://openwetware.org/images/f/fb/1%2BC.png"><img src="http://openwetware.org/images/f/fb/1%2BC.png" alt="1.3a" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Controls W/ PQ (-) </th> | <th>Controls W/ PQ (-) </th> | ||
| - | <td> GFP tag w/ No Promoter </td><td> RBS-GFP-TT | + | <td> GFP tag w/ No Promoter </td><td> RBS-GFP-TT</td><td> <a href="http://openwetware.org/images/e/e0/1-C.png"><img src="http://openwetware.org/images/e/e0/1-C.png" alt="1.3a" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Controls Blh and Raldh II (+) </th> | <th>Controls Blh and Raldh II (+) </th> | ||
| - | <td> Constitutive Promoter + Blh and RaldhII </td><td> Promoter+ RBS-Blh-TT-RBS-RALDH II-TT | + | <td> Constitutive Promoter + Blh and RaldhII </td><td> Promoter+ RBS-Blh-TT-RBS-RALDH II-TT </td><td> <a href="http://openwetware.org/images/4/4f/1%2BC2.png"><img src="http://openwetware.org/images/4/4f/1%2BC2.png" alt="1.3a" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
<tr> | <tr> | ||
<th>Controls Blh and Raldh II (-) </th> | <th>Controls Blh and Raldh II (-) </th> | ||
| - | <td> Blh and RaldhII w/ no Promoter</td><td> RBS-Blh-TT-RBS-RALDH II-TT | + | <td> Blh and RaldhII w/ no Promoter</td><td> RBS-Blh-TT-RBS-RALDH II-TT </td><td> <a href="http://openwetware.org/images/3/37/1-C2.png"><img src="http://openwetware.org/images/3/37/1-C2.png" alt="1.3a" width="100" height="40"></img></a> </td> |
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</tr> | </tr> | ||
</table> | </table> | ||
Revision as of 01:52, 19 October 2009
| Home | Project | Modeling | Parts | Notebook | Team | SBOL-V |
<center>
Contents |
Stanford iGEM 2009 Registered Parts
[http://partsregistry.org/cgi/partsdb/search.cgi Stanford in the Parts Registry]
Table of Registered Parts
| Part # | Name | Part Description | Type |
|---|---|---|---|
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223040 BBa_K223040] | SoxR Gene | This part produces the SoxR protein, which in the presence of oxidative stresses, such as paraquat and nitric oxide, binds with high affinity to the SoxS promoter. The SoxR generator, when coupled with the SoxS promoter, can be utilized as an inducible sensor for oxidative stress. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223041 Bba_K223041] | SoxS promoter | The SoxS promoter is activated by the SoxR protein in the presence of oxidative stress, such as Paraquat or Nitric Oxide. It has a high affinity binding with the SoxR protein. It can be used in conjunction with the SoxR gene as an inducible sensor for oxidative stress. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223042 Bba_K223042] | Blh Gene | The Blh gene cleaves beta-carotene into retinal. It can be used in the pathway for the production of retinoic acid from beta-carotene in conjunction with the RALDH II genes. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223043 Bba_K223043] | RALDH II Gene | The Raldh II gene converts retinal into retinoic acid. It is helpful if used in conjunction with the Blh gene for the entire process of converting beta-carotene into retinoic acid. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223044 Bba_K223044] | SoxR-SoxS System | This entire system works as a superoxide sensor. Superoxides activate the SoxR protein to bind with the SoxS Promoter and begin transcription of downstream genes. It is an inducible sensor. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223045 Bba_K223045] | RALDH II Intermediate | Working composite part with a ribosome binding site and terminator. | Intermediate |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223046 Bba_K223046] | SoxR/SoxS- GFP | SoxR - SoxS Promoter System with downstream GFP production. This was used to characterize the inducible oxidative stress signal when activating the SoxR-SoxS promoter system. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223047 Bba_K223047] | Lacl Promoter-SoxR/SoxS-GFP | This is the SoxR-SoxS inducible promoter system with downstream production of GFP in order to characterize the device. We used the lacl regulated promoter. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223048 Bba_K223048] | Blh and RALDH II | This is the RBS- Blh- RBS- RALDH II- TT generator. Both of these parts are important in the cleaving of beta carotene into retinoic acid. | Intermediate |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223049 Bba_K223049] | SoxR - SoxS- Blh and RALDH II | This is the superoxide inducible SoxR-SoxS promoter system coupled with the production of Blh and RALDH II genes for the cleaving of beta carotene into retinoic acid. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223050 Bba_K223050] | Lacl Promoter-SoxR - SoxS -Blh and RALDH II | Same as BBa_K223049 with the addition of an inducible lacl promoter. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223051 Bba_K223051] | 5MT operon (promoter-operator) | This is a modified trp operon, promoter and operator site, that recognizes and binds to a doubly mutant repressor and its corepressor, 5-methyl-L-tryptophan. In conjunction with the mutant tryptophan repressor, this modified operon functions as an inverter, converting decreasing levels of 5MT into a PoPs output signal for downstream transcription. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223052 Bba_K223052] | 5MT Mutant TrpR gene | The 5 methyl-L-tryptophan aporepressor gene is a mutant version of the regular TrpR gene involved in sensing levels of synthetic compound, 5 MT. It works by binding to its corepressor, 5 MT, and then to its corresponding promoter operator, BBa_K223051, repressing downstream transcription. In the presence of low corepressor levels, the 5MT aporepressor will not bind allowing for downstream transcription. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223053 Bba_K223053] | hIL-6 Generator (Freiburg-compatible) | This gene generates Interleukin 6, an important cell signaling molecule that acts as both a pro- and anti-inflammatory cytokine | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223054 Bba_K223054] | HlyA Signal Sequence (Freiburg-compatible) | The Hemolysin A signal sequence is generally fused with a second protein. Together with the Hly complex (HlyR, HlyC, HlyB and HlyD) and TolC, HlyAs can be used to take large proteins out of the cell. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223055 Bba_K223055] | TolC Gene | TolC, along with HemolysinB, C, and D, for a channel in the cellular membrane to allow for the extracellular transport of HlyAs-fused protein sequences. The TolC receptor, in conjunction to the Hly genes, can serve as channel for transporting large proteins. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223056 Bba_K223056] | Front Flanking Sequence (HlyR, IS1, HlyC) | This front flanking sequence has three of the hemolysin parts - HlyR, Is1 and HlyC. In conjunction with rear flanking sequence, containing HlyB and HlyD, and TolC (part K223055), this part creates a channel protein to facilitate the extracellular export HlyAs-fused proteins. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223057 Bba_K223057] | Rear Flanking Sequence (HlyB and HlyD) | Along with parts BBa_K223055 and K223056, this part helps form the channel protein for the extracellular transport of HlyAs-fused protein. | Basic |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223058 Bba_K223058] | RBS+mutTrpR+TT+mutTrp Operator | This part is a combination of K223051 and K223052. It is an inverter that is sensitive to concentration decreases in 5-methyl-L-tryptophan and converts this to a PoPs output signal used for downstream transcription. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223059 Bba_K223059] | mutTrp (5MT) Inverter with GFP Biobrick part | A modification to Biobrick part BBa_K223058. It has a GFP biobrick part, BBa_I13504, at the end of the sequence and functions as a reporter. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223060 Bba_K223060] | 5MT Inverter-GFP Reporter and Lac Promoter | Identical to part BBa_K223059 except with a Lac promoter. This part can be used to test the efficiency of the 5MT inverter system. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223061 Bba_K223061] | hIL-6 + HlyAs Fusion protein (Freiburg Compatible) | This sequence when coupled with TolC (BBa_K223055), Front Flanking (BBa_K223056) and Rear Flanking (BBa_K223057) sequences, allows for the extracellular export of hIL-6. This particular part only forms the signal sequence for export. | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223062 Bba_K223062] | TolC and Hemolysin B, C and D gene complex | This a composite part of BBa_K223055, BBa_K223056, BBa_K223057 that provides all necessary genes to create a channel protein in the extra cellular membrane of a prokaryotic cell. This channel can be used to export large organic molecules fused to a signal sequence, HlyAs | Composite |
| [http://partsregistry.org/wiki/index.php/Part:BBa_K223063 Bba_K223063] | RBS+BLH | Identical to BBa_K223042 but with RBS (B0034) prior to the sequence. | Composite |
</center>
Device 1 Cloning Plan with Proper Sequences
<center>Device 1 Cloning Plan with Proper Suffix</center>
| Cloning Step | Basic Parts | Detailed Parts | Picture |
|---|---|---|---|
| Step 1.1a | SoxR/S Promoter + GFP tag | RBS-SoxR-TT-SoxS Promoter + RBS-GFP-TT | 
|
| Step 1.1b | SoxR/S Promoter + Blh | RBS-SoxR-TT-SoxS Promoter + RBS-Blh |  |
| Step 1.1c | Blh + Terminator | RBS-Blh + TT |  |
| Step 1.1d | Constitutive Promoter + Blh (1.1c) | Promoter +RBS-Blh-TT |  |
| Step 1.1e | Constitutive Promoter + Crt Cluster | Promoter + RBS-Crt |  |
| Step 1.2a | Constitutive Promoter + SoxR/s w/ GFP (1.1a) | Promoter+ RBS-SoxR-TT-SoxSP-RBS-GFP-TT |  |
| Step 1.2b | SoxR/S-Blh (1.1b) + RALDH II | RBS-SoxR-TT-SoxSP-RBS-Blh + RBS-RALDH II-TT |  |
| Step 1.3a | Constitutive Promoter + SoxR/S w/ Blh and RaldhII | Promoter+ RBS-SoxR-TT-SoxSP-RBS-Blh-RBS-RALDH II-TT |  |
| Controls W/ PQ (+) | Constitutive Promoter + GFP tag | Promoter+ RBS-GFP-TT |  |
| Controls W/ PQ (-) | GFP tag w/ No Promoter | RBS-GFP-TT |  |
| Controls Blh and Raldh II (+) | Constitutive Promoter + Blh and RaldhII | Promoter+ RBS-Blh-TT-RBS-RALDH II-TT |  |
| Controls Blh and Raldh II (-) | Blh and RaldhII w/ no Promoter | RBS-Blh-TT-RBS-RALDH II-TT |  |
Device 2 Cloning Plan with Proper Sequences
<center>Device 2 Cloning Plan with Proper Suffix</center>
| Cloning Step | Basic Parts | Detailed Parts | Antibiotics | Enzymes | Vector & Size (kb) | Insert & Size (kb) | Current Cloner | Picture |
|---|---|---|---|---|---|---|---|---|
| Step 2.1a | hIl-6-HlyAs + Terminator | hIl-6-HlyAs + TT | Ant. | enzymes | Vector | ----Insert---- | Cloner | 
|
| Progress Notes | ||||||||
| Step 2.1b | hIl-6-HlyAs + YFP | hIl-6-HlyAs + YFP | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.1c | RBS + TolC | RBS+ TolC | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.1d | Terminator + HlyR | TT + HlyR | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.1e | Forward Flanking Sequence (FFS) + RBS | Hly-C + RBS | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.1f | Rear Flanking Sequence (RFS) + Terminator | HlyB,D + TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.2a | RBS + hIL-6-HlyAs (2.1a) | RBS + hIL-6-HlyAs-TT | Ant. | enzymes | Vector| | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.2b | hIl-6-HlyAs-YFP(2.1b) + Terminator | hIl-6-HlyAs-YFP+ TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | Step 2.2c | TolC (2.1c) + HlyR Promoter Element (2.1d) | RBS-TolC + TT-HlyR | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | Step 2.2d | FFS-RBS (2.1e) + RFS-TT (2.1f) | FFS-RBS + RFS-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.3a | Trp Operator + hIL-6-HlyAs (2.2a) | Trp Op + RBS-hIL-6-HlyAs-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.3b | RBS + hIL-6-HlyAs-YFP-TT (2.2b) | RBS + hIL-6-HlyAs-YFP-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.3c | TolC-HlyR (2.2c) + FFS-RFS (2.2d) | RBS-TolC-TT-HlyR + FFS-RBS-RFS-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.4a | Trp Operator + HIl-6-HlyAs-YFP (2.3b) | Trp Op + RBS-HIl-6-HlyAs-YFP-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
| Step 2.4b | Const. Promoter + TolC-HlyR-FFS-RFS (2.3c) | Const. Promoter + RBS-TolC-TT-HlyR-FFS-RBS-RFS-TT | Ant. | enzymes | Vector | Insert | Cloner |  |
| Progress Notes | ||||||||
