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Virginia Commonwealth/9 June 2009
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==Tuesday 09 June 2009== | ==Tuesday 09 June 2009== | ||
===Results=== | ===Results=== | ||
| + | * n/a | ||
---- | ---- | ||
| + | |||
===Tasks=== | ===Tasks=== | ||
| - | |||
*Discussion: gel electrophoresis, BioBrick assembly, and the engineering design process | *Discussion: gel electrophoresis, BioBrick assembly, and the engineering design process | ||
**Gel electrophoresis is a type of size variation chromatography. DNA is pulled through the gel plate via a voltage and current. Used to verify the length of BioBricks. | **Gel electrophoresis is a type of size variation chromatography. DNA is pulled through the gel plate via a voltage and current. Used to verify the length of BioBricks. | ||
| - | + | *BioBrick assembly | |
| - | [[Image:Biobrick_assembly. | + | [[Image:Biobrick_assembly.jpg|none|thumb|600px|3A BioBrick assembly]] |
| - | + | *Engineering design process | |
| - | [[Image: | + | [[Image:Biological engineering work flow.png|none|thumb|600px|Work flow diagram]] |
| - | + | ||
*Literature discussion (especially relating to systems biology) | *Literature discussion (especially relating to systems biology) | ||
| + | ---- | ||
====Drylab==== | ====Drylab==== | ||
*Characterizing promoters: Characterize the same seven promoter from "Measuring the activity of BioBrick promoters using an in vivo reference standard" and characterizing seven more. | *Characterizing promoters: Characterize the same seven promoter from "Measuring the activity of BioBrick promoters using an in vivo reference standard" and characterizing seven more. | ||
| - | + | *Process variables | |
{|border="1" | {|border="1" | ||
|E. coli strains||Reporters||Backbone||Carbon source||Growth time||Temp | |E. coli strains||Reporters||Backbone||Carbon source||Growth time||Temp | ||
| Line 58: | Line 59: | ||
|stock strains and W3110||BBa_E0240||pSB3K3||LB and Glycerol||1-12 hours||30 C | |stock strains and W3110||BBa_E0240||pSB3K3||LB and Glycerol||1-12 hours||30 C | ||
|} | |} | ||
| - | + | *Promoters to be tested | |
{|border="1" | {|border="1" | ||
|Characterized||Not characterized | |Characterized||Not characterized | ||
| Line 78: | Line 79: | ||
-- | -- | ||
{|border="1" | {|border="1" | ||
| - | |Reference promoter|| | + | |Reference promoter||BBa_J23101 |
|} | |} | ||
*The reporter sequence codes for an RBS, GFP, and a terminator. | *The reporter sequence codes for an RBS, GFP, and a terminator. | ||
*We need to somehow take into account the degradation rate of the GFP. I suspect that other reporters such as RFP or luciferases will have different degradation rates. I also suspect that these degradation rates are not constant and might possibly skew the results of the test. For example, as the concentration of the reporter protein increases in concentration the degradation rate of might increase. In order to characterize and standardize the promoters we must be sure that no other variable is affecting florescence of the reporter. If we can refine the method from the paper and improve upon or confirm the results might be able to publish the results. This would give a solid leg up at the iGEM competition and significantly contribute to the field. | *We need to somehow take into account the degradation rate of the GFP. I suspect that other reporters such as RFP or luciferases will have different degradation rates. I also suspect that these degradation rates are not constant and might possibly skew the results of the test. For example, as the concentration of the reporter protein increases in concentration the degradation rate of might increase. In order to characterize and standardize the promoters we must be sure that no other variable is affecting florescence of the reporter. If we can refine the method from the paper and improve upon or confirm the results might be able to publish the results. This would give a solid leg up at the iGEM competition and significantly contribute to the field. | ||
-[[User:Bussingkm|Bussingkm]] 23:56, 9 June 2009 (UTC) | -[[User:Bussingkm|Bussingkm]] 23:56, 9 June 2009 (UTC) | ||
Latest revision as of 14:42, 5 August 2009
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Contents |
Tuesday 09 June 2009
Results
- n/a
Tasks
- Discussion: gel electrophoresis, BioBrick assembly, and the engineering design process
- Gel electrophoresis is a type of size variation chromatography. DNA is pulled through the gel plate via a voltage and current. Used to verify the length of BioBricks.
- BioBrick assembly
- Engineering design process
- Literature discussion (especially relating to systems biology)
Drylab
- Characterizing promoters: Characterize the same seven promoter from "Measuring the activity of BioBrick promoters using an in vivo reference standard" and characterizing seven more.
- Process variables
| E. coli strains | Reporters | Backbone | Carbon source | Growth time | Temp |
| stock strains and W3110 | BBa_E0240 | pSB3K3 | LB and Glycerol | 1-12 hours | 30 C |
- Promoters to be tested
| Characterized | Not characterized |
| BBa_J23113 | BBa_J23100 |
| BBa_J23116 | BBa_J23103 |
| BBa_J23150 | BBa_J23104 |
| BBa_J23151 | BBa_J23105 |
| BBa_J23102 | BBa_J23106 |
| BBa_R0040 | BBa_J23107 |
| BBa_R0011 | BBa_J23108 |
--
| Reference promoter | BBa_J23101 |
- The reporter sequence codes for an RBS, GFP, and a terminator.
- We need to somehow take into account the degradation rate of the GFP. I suspect that other reporters such as RFP or luciferases will have different degradation rates. I also suspect that these degradation rates are not constant and might possibly skew the results of the test. For example, as the concentration of the reporter protein increases in concentration the degradation rate of might increase. In order to characterize and standardize the promoters we must be sure that no other variable is affecting florescence of the reporter. If we can refine the method from the paper and improve upon or confirm the results might be able to publish the results. This would give a solid leg up at the iGEM competition and significantly contribute to the field.
-Bussingkm 23:56, 9 June 2009 (UTC)
