Difference between revisions of "Part:BBa M50437:Experience"

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This experience page is provided so that any user may enter their experience using this part.<BR>Please enter
 
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how you used this part and how it worked out.
 
  
 
===Applications of BBa_M50437===
 
===Applications of BBa_M50437===
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Ideally, this plasmid could be used to speed up synthesis of 2,3-DHB, which would, in turn, solubilize iron.
 
  
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==User Reviews==
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This plasmid was designed to speed up synthesis of 2,3-dihydroxybenzoic acid (2,3-DHB), which would, in turn, theoretically solubilize iron compounds such as iron (III) oxide due to its high affinity for complexation with ferric ions. We found that our device was unable to produce the necessary enzymes for biosynthesis of the small-molecule, although the original concept had potential.
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===User Reviews===
 
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<partinfo>BBa_M50435 AddReview number</partinfo>
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<I>Username</I>
 
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Enter the review inofrmation here.
 
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We transformed ordered this construct from DNA 2.0. We used the pD441-CH plasmid backbone, which encodes for kanamycin resistance, and then transformed this plasmid into "E. coli".
 
We transformed ordered this construct from DNA 2.0. We used the pD441-CH plasmid backbone, which encodes for kanamycin resistance, and then transformed this plasmid into "E. coli".
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We then grew up cells with our plasmid in LB + kanamycin solution with 2 mM IPTG at 37℃ for 2 days, then ran a Western blot assay to see if ahpC and entC were being produced.
 
We then grew up cells with our plasmid in LB + kanamycin solution with 2 mM IPTG at 37℃ for 2 days, then ran a Western blot assay to see if ahpC and entC were being produced.
 
Our western blot results (figure 1) showed that the entC enzyme was not being produced, or at least not being produced in large enough quantities to effect 2,3-DHB synthesis. Possible explanations for our failure to produce entC include, but are not limited to, a failure in plasmid design or production; a degradation of entC within the cell into smaller segments, explaining the light band on our membrane; or an inability of the cell to carry large amounts of the entC enzyme. No matter the cause, because the two genes work together to produce 2,3-DHB, we concluded that 2,3-DHB was not being produced within our cells, meaning they would not have been able to solubilize a statistically different amount of iron (III) than standard E. coli.  
 
Our western blot results (figure 1) showed that the entC enzyme was not being produced, or at least not being produced in large enough quantities to effect 2,3-DHB synthesis. Possible explanations for our failure to produce entC include, but are not limited to, a failure in plasmid design or production; a degradation of entC within the cell into smaller segments, explaining the light band on our membrane; or an inability of the cell to carry large amounts of the entC enzyme. No matter the cause, because the two genes work together to produce 2,3-DHB, we concluded that 2,3-DHB was not being produced within our cells, meaning they would not have been able to solubilize a statistically different amount of iron (III) than standard E. coli.  
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[[File:PLTK_KEL_Western_Blot.png]]
  
 
===Iron Toxicity Assay===
 
===Iron Toxicity Assay===
  
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In order to test iron solubility due to our construct, we decided to grow up our construct in different iron chloride concentrations. We hypothesized that cells creating ahpC and entC without feedback regulation (i.e. with our plasmid) would die due to iron toxicity.
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In order to test iron solubility due to our construct, we decided to grow up our construct in different iron (III) chloride concentrations. We hypothesized that cells creating ahpC and entC without feedback regulation (i.e. with our plasmid) would die due to iron toxicity.
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In order to test cell viability, we grew up two cultures in LB and kanamycin media at 37℃ for 2 days. For our negative control, the cells were grown up solely in LB and kanamycin. Our experimental cells were grown up in a media that consisted of LB, kanamycin, and 2 mM IPTG in order to fully induce the promoter. After two days, we measured the OD600 of each culture.  
+
In order to test cell viability, we grew up two cultures in LB and kanamycin media at 37℃ for 2 days. For our negative control, the cells were grown up solely in LB and kanamycin. Our experimental cells were grown up in a media that consisted of LB, kanamycin, and 2 mM IPTG in order to fully induce the promoter. After two days, we measured the OD<sub>600</sub> of each culture.  
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We tested ten concentrations of FeCl3: 10 mM of FeCl3, 5 mM of FeCl3, 2.5 mM of FeCl3, 1.25 mM of FeCl3, 1 mM of FeCl3, 0.625 mM of FeCl3, 0.5 mM of FeCl3, 0.25 mM of FeCl3, 0.125 mM of FeCl3, 0.0625 mM of FeCl3, and 0 mM of FeCl3 in media. For each concentration of FeCl3, we used two conditions, one where we added cells that had been induced with IPTG and two microliters of IPTG, and one where we added cells that had not been induced with IPTG. All cells were diluted to an OD600 of 0.01 in the well plate. Each test (+/- IPTG with a certain concentration of iron) was performed in triplicate wells, with an additional well for a blank, which contained solely media, IPTG or water, and iron without cells. This plate was then left to grow for two days at 37℃.
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We tested ten concentrations of FeCl<sub>3</sub>: 10 mM of FeCl<sub>3</sub>, 5 mM of FeCl<sub>3</sub>, 2.5 mM of FeCl<sub>3</sub>, 1.25 mM of FeCl<sub>3</sub>, 1 mM of FeCl<sub>3</sub>, 0.625 mM of FeCl<sub>3</sub>, 0.5 mM of FeCl<sub>3</sub>, 0.25 mM of FeCl<sub>3</sub>, 0.125 mM of FeCl<sub>3</sub>, 0.0625 mM of FeCl<sub>3</sub>, and 0 mM of FeCl<sub>3</sub> in media. For each concentration of FeCl<sub>3</sub>, we used two conditions, one where we added cells that had been induced with IPTG and two microliters of IPTG, and one where we added cells that had not been induced with IPTG. All cells were diluted to a starting OD<sub>600</sub> of 0.01 in the well plate. Each test (+/- IPTG with a certain concentration of iron) was performed in triplicate wells, with an additional well for a blank, which contained solely media, IPTG or water, and iron without cells. This plate was then left to grow for two days at 37℃.
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We then measured the OD600 of the cells after two days to test for growth. A higher OD600 would indicate more growth. The amount of iron remaining in the media was verified with semi-quantitative iron test strips (usage instructions obtained from the manufacturer), which change color in response to Fe2+ and Fe3+ ions, with the resulting color indicative of the approximate concentration range.  
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We then measured the OD<sub>600</sub> of the cells after two days to test for growth. A higher OD<sub>600</sub> would indicate more growth.
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[[File: PLTK_KEL_irontox2.png]]
  
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Using a t-test comparing our +IPTG results to an expected value of the -IPTG average, we determined that there was only a statistically significant difference at 5 mM. We used two controls: a blank, which controlled for interference in  OD600 from media and iron, and a control measurement of cell growth with no IPTG and therefore no construct expression. However, precipitation of iron (III) chloride led to cloudiness of media, interfered with OD600 measurements at concentrations greater than 2.5 mM FeCl3 likely meaning that our statistical significance at 5 mM was simply an experimental error. Overall, our results indicate that there is no significant difference in cell growth for our control and experimental conditions. Therefore, our cells are not suffering from iron toxicity, and are likely not solubilizing iron at high enough levels to die.
+
Using a t-test comparing our +IPTG results to an expected value of the -IPTG average, we determined that there was only a statistically significant difference at 5 mM. We used two controls: a blank, which controlled for interference in  OD<sub>600</sub> from media and iron, and a control measurement of cell growth with no IPTG and therefore no construct expression. However, precipitation of iron (III) chloride led to cloudiness of media, interfered with OD<sub>600</sub> measurements at concentrations greater than 2.5 mM FeCl<sub>3</sub> likely meaning that our statistical significance at 5 mM was simply an experimental error. Overall, our results indicate that there is no significant difference in cell growth for our control and experimental conditions. Therefore, our cells are not suffering from iron toxicity, and are likely not solubilizing iron at high enough levels to die.
  
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Overall, it appears that our construct is not functioning as planned
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Overall, it appears that our construct is not functioning as planned.
  
 
===Stanford Location===
 
===Stanford Location===

Latest revision as of 06:14, 12 June 2018


Applications of BBa_M50437

This plasmid was designed to speed up synthesis of 2,3-dihydroxybenzoic acid (2,3-DHB), which would, in turn, theoretically solubilize iron compounds such as iron (III) oxide due to its high affinity for complexation with ferric ions. We found that our device was unable to produce the necessary enzymes for biosynthesis of the small-molecule, although the original concept had potential.

User Reviews

UNIQc02de6407dadeb8b-partinfo-00000000-QINU UNIQc02de6407dadeb8b-partinfo-00000001-QINU

We transformed ordered this construct from DNA 2.0. We used the pD441-CH plasmid backbone, which encodes for kanamycin resistance, and then transformed this plasmid into "E. coli".

Western Blot

We then grew up cells with our plasmid in LB + kanamycin solution with 2 mM IPTG at 37℃ for 2 days, then ran a Western blot assay to see if ahpC and entC were being produced. Our western blot results (figure 1) showed that the entC enzyme was not being produced, or at least not being produced in large enough quantities to effect 2,3-DHB synthesis. Possible explanations for our failure to produce entC include, but are not limited to, a failure in plasmid design or production; a degradation of entC within the cell into smaller segments, explaining the light band on our membrane; or an inability of the cell to carry large amounts of the entC enzyme. No matter the cause, because the two genes work together to produce 2,3-DHB, we concluded that 2,3-DHB was not being produced within our cells, meaning they would not have been able to solubilize a statistically different amount of iron (III) than standard E. coli.

PLTK KEL Western Blot.png

Iron Toxicity Assay

In order to test iron solubility due to our construct, we decided to grow up our construct in different iron (III) chloride concentrations. We hypothesized that cells creating ahpC and entC without feedback regulation (i.e. with our plasmid) would die due to iron toxicity. In order to test cell viability, we grew up two cultures in LB and kanamycin media at 37℃ for 2 days. For our negative control, the cells were grown up solely in LB and kanamycin. Our experimental cells were grown up in a media that consisted of LB, kanamycin, and 2 mM IPTG in order to fully induce the promoter. After two days, we measured the OD600 of each culture. We tested ten concentrations of FeCl3: 10 mM of FeCl3, 5 mM of FeCl3, 2.5 mM of FeCl3, 1.25 mM of FeCl3, 1 mM of FeCl3, 0.625 mM of FeCl3, 0.5 mM of FeCl3, 0.25 mM of FeCl3, 0.125 mM of FeCl3, 0.0625 mM of FeCl3, and 0 mM of FeCl3 in media. For each concentration of FeCl3, we used two conditions, one where we added cells that had been induced with IPTG and two microliters of IPTG, and one where we added cells that had not been induced with IPTG. All cells were diluted to a starting OD600 of 0.01 in the well plate. Each test (+/- IPTG with a certain concentration of iron) was performed in triplicate wells, with an additional well for a blank, which contained solely media, IPTG or water, and iron without cells. This plate was then left to grow for two days at 37℃. We then measured the OD600 of the cells after two days to test for growth. A higher OD600 would indicate more growth.

PLTK KEL irontox2.png

Using a t-test comparing our +IPTG results to an expected value of the -IPTG average, we determined that there was only a statistically significant difference at 5 mM. We used two controls: a blank, which controlled for interference in OD600 from media and iron, and a control measurement of cell growth with no IPTG and therefore no construct expression. However, precipitation of iron (III) chloride led to cloudiness of media, interfered with OD600 measurements at concentrations greater than 2.5 mM FeCl3 likely meaning that our statistical significance at 5 mM was simply an experimental error. Overall, our results indicate that there is no significant difference in cell growth for our control and experimental conditions. Therefore, our cells are not suffering from iron toxicity, and are likely not solubilizing iron at high enough levels to die.

Overall, it appears that our construct is not functioning as planned.

Stanford Location

Plasmid name: pLysisToKill
DNA2.0 Gene Construct: pD441-CH, customized
Organism: E. coli
Device type: Actuator
Glycerol stock barcode: 0133024475, 0133024500, 0133027012
Box label: BioE44 S18
Physical location: Room 114, Uytengsu Teaching Lab, Shriram Center