Difference between revisions of "Part:BBa J100534:Design"

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===Design Notes===
 
===Design Notes===
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We decided not to order the AHL chemical because there is no lux cassette in the E. coli cultures that we will use (not possible for the lux gene to be expressed). This lux R gene is typically expressed in the bio Therefore, we are allowing it to function as a constitutive promoter. We have two experimental groups that will be compared to a negative control, which contains water instead of the diluted oligo solution, and a positive control, which contains neither water nor the oligo solution. Spectrophotometry will be used to compare the optical density of each E. coli population and to create a ratio of red to optical density for the purpose of measuring the amount of red in each cell. This will tell us how effective the promoter is. We will alter several variables, including temperature, to se if they effect our results. We are currently looking into whether or not there is a gene that is similar to the lux R gene that is naturally expressed in E. coli that our promoter might be able to affect/function with. The bacteria in which this promoter is usually found also undergoes growth sue to density-based quorum sensing. To see if E. coli altered with this promoter can divide in the same way, we will take a dense cell colony, dilute it, and centrifuge it down. We will take an aliquot from the top of the centrifuged sample, which should theoretically contain some chemical that induces quorum sensing division. We will then spread that on another cell colony of the same dilution and see if it promotes growth.
+
We decided not to order the AHL chemical because there is no lux cassette in the E. coli cultures that we will use (not possible for the lux gene to be expressed). This lux R gene is typically expressed in the bio Therefore, we are allowing it to function as a constitutive promoter. We have two experimental groups that will be compared to a negative control, which contains water instead of the diluted oligo solution, and a positive control, which contains neither water nor the oligo solution. Spectrophotometry will be used to compare the optical density of each E. coli population and to create a ratio of red to optical density for the purpose of measuring the amount of red in each cell. This will tell us how effective the promoter is. We hypothesize that allowing the bacteria to incubate for one hour at a temperature of 42 degrees Celsius will act as an inducer for the specific promoter. We incubated samples for each of our experimental groups and then ran them in the spectrophotometer to compare the amount of fluorescence produced with the optic density of both the incubated and non-incubated groups.
 +
In moving forwards, we are currently looking into whether or not there is a gene that is similar to the lux R gene that is naturally expressed in E. coli that our promoter might be able to affect/function with. The bacteria in which this promoter is usually found also undergoes growth sue to density-based quorum sensing. To see if E. coli altered with this promoter can divide in the same way, we will take a dense cell colony, dilute it, and centrifuge it down. We will take an aliquot from the top of the centrifuged sample, which should theoretically contain some chemical that induces quorum sensing division. We will then spread that on another cell colony of the same dilution and see if it promotes growth.
  
 
===Source===
 
===Source===

Revision as of 19:55, 27 February 2020


Constitutive RFP Promoter in E. coli


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 35
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

We decided not to order the AHL chemical because there is no lux cassette in the E. coli cultures that we will use (not possible for the lux gene to be expressed). This lux R gene is typically expressed in the bio Therefore, we are allowing it to function as a constitutive promoter. We have two experimental groups that will be compared to a negative control, which contains water instead of the diluted oligo solution, and a positive control, which contains neither water nor the oligo solution. Spectrophotometry will be used to compare the optical density of each E. coli population and to create a ratio of red to optical density for the purpose of measuring the amount of red in each cell. This will tell us how effective the promoter is. We hypothesize that allowing the bacteria to incubate for one hour at a temperature of 42 degrees Celsius will act as an inducer for the specific promoter. We incubated samples for each of our experimental groups and then ran them in the spectrophotometer to compare the amount of fluorescence produced with the optic density of both the incubated and non-incubated groups. In moving forwards, we are currently looking into whether or not there is a gene that is similar to the lux R gene that is naturally expressed in E. coli that our promoter might be able to affect/function with. The bacteria in which this promoter is usually found also undergoes growth sue to density-based quorum sensing. To see if E. coli altered with this promoter can divide in the same way, we will take a dense cell colony, dilute it, and centrifuge it down. We will take an aliquot from the top of the centrifuged sample, which should theoretically contain some chemical that induces quorum sensing division. We will then spread that on another cell colony of the same dilution and see if it promotes growth.

Source

This promoter sequence came from an article published on NCBI: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4444344/


References