Difference between revisions of "Part:BBa K2365048:Experience"

(→‎Applications of BBa_K2365048)
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<b> <font size="4">Characterization of BAX: Genomic integration vs. plasmid expression</font> </b>
 
<b> <font size="4">Characterization of BAX: Genomic integration vs. plasmid expression</font> </b>
  
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We further characterized the Bax protein under the expression of an inducible promoter, pGAL1 (<partinfo>BBa_K3190050</partinfo>). We have characterized the apoptotic potential of Bax protein, when the BAX gene is integrated into the yeast genome, as compared to when it is expressed on a high copy plasmid.  
+
We further characterized the Bax protein under the expression of an inducible promoter, pGAL1 (<partinfo>BBa_K3190050</partinfo>). We chose to use this part, as it is Team NAU China 2017's improved version of the original part of Team Debrecen-Hungary 2010 (<partinfo>BBa_K364202</partinfo>).  
  
 +
We have characterized the apoptotic potential of Bax protein under the expression of pGAL1, when the BAX gene is integrated into the yeast genome, as compared to when it is expressed on a high copy plasmid. Furthermore, we have also characterized the neccesary concentration of inducer (galactose) needed in order for high enough expression of BAX to kill the cells.
 +
 +
<br>
 
Using USER ligation, we assembled the BAX gene with pGAL1 on a plasmid backbone compatible with multiplex integration cassette. The backbone used contains a URA selection marker, and will integrate the construct in the yeast genome at chromosome 11, site 2.
 
Using USER ligation, we assembled the BAX gene with pGAL1 on a plasmid backbone compatible with multiplex integration cassette. The backbone used contains a URA selection marker, and will integrate the construct in the yeast genome at chromosome 11, site 2.
  
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For the genomically integrated strain, the positive transformants were confirmed by performing yeast colony PCR. We used 2 primers, one in the forward direction for the backbone and one in the reverse direction for the yeast chromosome 11. In the presence of our construct, we expect to see a band at around 1000 bp as, that is the size of the fragment between the two primer regions. In the absence of the constructs, we expect to see the bands at around 1500 bp, as this is the size of site 2 of chromosome 11.  
 
For the genomically integrated strain, the positive transformants were confirmed by performing yeast colony PCR. We used 2 primers, one in the forward direction for the backbone and one in the reverse direction for the yeast chromosome 11. In the presence of our construct, we expect to see a band at around 1000 bp as, that is the size of the fragment between the two primer regions. In the absence of the constructs, we expect to see the bands at around 1500 bp, as this is the size of site 2 of chromosome 11.  
  
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<b> [INSERT GEL IMAGE of yeast colony PCR] </b>
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[[File:GI_pGAL1-BAX_Yeast_PCR.jpeg|300px]]
  
 
<small> <b> Figure 1: Yeast colony PCR of genomically integrated transformants</b> | The positive colony of yeast is confirmed by the expected band size of around 1000 bp.</small>  
 
<small> <b> Figure 1: Yeast colony PCR of genomically integrated transformants</b> | The positive colony of yeast is confirmed by the expected band size of around 1000 bp.</small>  
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<b> <font size="4">Galactose induction assay</font> </b>
 
<b> <font size="4">Galactose induction assay</font> </b>
  
−
As plasmids are transposable elements, we wanted to see wether there is an advantage of using genomic integration to express the bax toxin in yeast. For this purpose, we used our constructs having bax under the inducible promoter GAL1. Cultures of yeast containing pGAL1-BAX, both expressed on a plasmid (PWUS) and genome integrated, were grown O/N and diluted to an OD<sub>600nm</sub> of 0.5. Cultures with the respective empty vectors served as controls. On plates with different galactose concentrations (0%, 0.025%, 0.05%, 0.1% and 0.2%), 10 µl of culture were spotted in increasing dilutions (10<sup>-1</sup> to 10<sup>-4</sup>) along with the control. Due to the equalised cell density of the cultures, the expression rate of the genome integrated and plasmid-expressed bax could then be compared among each other and with the controls after an incubation of three days at 30 °C.
+
As plasmids are transposable elements, we wanted to see wether there is an advantage of using genomic integration to express the Bax toxin in yeast. For this purpose, we used our constructs having BAX under the inducible promoter GAL1. Cultures of yeast containing pGAL1-BAX, both expressed on a high copy plasmid with a URA marker, and genomically integrated, were grown O/N and diluted to an OD<sub>600nm</sub> of 0.5. Cultures with the respective empty vectors served as controls. On plates with different galactose concentrations (0%, 0.025%, 0.05%, 0.1% and 0.2%), 10 µl of culture were spotted in increasing dilutions (10<sup>-1</sup> to 10<sup>-4</sup>) along with the control. Due to the equalised cell density of the cultures, the expression rate of the genome integrated and plasmid-expressed bax could then be compared among each other and with the controls after an incubation of three days at 30 °C.
 +
 
 +
<b> [Insert discussion of plates/results here] </b>
 +
 
 +
[[File:UCopenhagen placeholder.jpeg|500px]]
 +
 
 +
<small><b>Figure 3: BLABLABLA</b> | Even more blablabla </small>
 +
 
 +
<br>
  
 
<b> <font size="4">Quantitative galactose induction assay</font> </b>
 
<b> <font size="4">Quantitative galactose induction assay</font> </b>
  
−
To quantify the effect of bax on our yeast under different expression levels, we have conducted a quantitative galactose induction assay with the genome integrated pGAL1-BAX using varying concentrations galactose. For this, an O/N culture of yeast with pGAL1-BAX was diluted to an OD<sub>600nm</sub> of 0.5. Subsequently, 100 µl of the culture were spread on plates with 0%, 0.05%, 0.1%, 0.3% and 1% galactose, respectively. To obtain countable amounts of colonies, the culture was spread in 10<sup>-3</sup> and 10<sup>-4</sup> dilutions. Yeast containing the corresponding empty vector served as a control. After incubation for three days at 30 °C, the CFU/ml were calculated and compared to the control.
+
To quantify the effect of bax on our yeast under different expression levels, we have conducted a quantitative galactose induction assay with the genome integrated pGAL1-BAX using varying concentrations galactose. For this, an O/N culture of yeast with pGAL1-BAX was diluted to an OD<sub>600nm</sub> of 0.5. Subsequently, 100 µl of the culture were spread on plates with 0%, 0.05%, 0.1%, 0.3% and 1% galactose, respectively. To obtain countable amounts of colonies, the culture was spread in 10<sup>-3</sup> and 10<sup>-4</sup> dilutions. Yeast containing the corresponding empty vector served as a control. After incubation for three days at 30 °C, the CFU/ml were calculated and compared to the control.  
 +
 
 +
<b> [Discussion of below graph] </b>
 +
 
 +
[[File:QGAL-induction.png|600px]]
 +
 
 +
<small><b>Figure 4: BLABLABLA</b> | Even more blablabla </small>
 +
 
  
 
===User Reviews===
 
===User Reviews===

Revision as of 14:08, 17 October 2019


This experience page is provided so that any user may enter their experience using this part.
Please enter how you used this part and how it worked out.

Applications of BBa_K2365048


Submission by Team UCopenhagen 2019:

Characterization of BAX: Genomic integration vs. plasmid expression

We further characterized the Bax protein under the expression of an inducible promoter, pGAL1 (BBa_K3190050). We chose to use this part, as it is Team NAU China 2017's improved version of the original part of Team Debrecen-Hungary 2010 (BBa_K364202).

We have characterized the apoptotic potential of Bax protein under the expression of pGAL1, when the BAX gene is integrated into the yeast genome, as compared to when it is expressed on a high copy plasmid. Furthermore, we have also characterized the neccesary concentration of inducer (galactose) needed in order for high enough expression of BAX to kill the cells.


Using USER ligation, we assembled the BAX gene with pGAL1 on a plasmid backbone compatible with multiplex integration cassette. The backbone used contains a URA selection marker, and will integrate the construct in the yeast genome at chromosome 11, site 2.

Furthermore, we also transformed yeast with a dual plasmid system. Using USER ligation, we assembled pGAL1 and BAX on a high copy plasmid backbone (200 copies/cell) containing a URA selection marker.

Yeast transformation

After cloning and purifying the pGAL1-BAX constructs in E. coli, we confirmed the sequences of these, prior to transforming into S. cerevisiae.

For the genomically integrated strain, the positive transformants were confirmed by performing yeast colony PCR. We used 2 primers, one in the forward direction for the backbone and one in the reverse direction for the yeast chromosome 11. In the presence of our construct, we expect to see a band at around 1000 bp as, that is the size of the fragment between the two primer regions. In the absence of the constructs, we expect to see the bands at around 1500 bp, as this is the size of site 2 of chromosome 11.

GI pGAL1-BAX Yeast PCR.jpeg

Figure 1: Yeast colony PCR of genomically integrated transformants | The positive colony of yeast is confirmed by the expected band size of around 1000 bp.

For the plasmid expressing strain, we transformed the yeast with two plasmid: the GAL1-BAX cloned in a high copy plasmid (200 copies/cell) with a URA marker, and an empty vector plasmid with a TRP marker. After transforming the yeast, we grew the colonies on plates without URA and TRP, thus selecting for positive transformants. To further confirm the functionality of the GAL1 promoter, we also plated the transformed yeast on a plate with 1 % galactose. As expected, we did not see any growth on the galactose positive plate.

PGAL1-BAX A.jpeg PGAL1-BAX B.jpeg

Figure 2: Transformant plates of dual plasmid transformed S. cerevisiae | Both transformed with pGAL1-BAX (URA marker) and an empty vector (TRP marker). A: plate with no galactose. B: plate with 1 % galactose.


Galactose induction assay

As plasmids are transposable elements, we wanted to see wether there is an advantage of using genomic integration to express the Bax toxin in yeast. For this purpose, we used our constructs having BAX under the inducible promoter GAL1. Cultures of yeast containing pGAL1-BAX, both expressed on a high copy plasmid with a URA marker, and genomically integrated, were grown O/N and diluted to an OD600nm of 0.5. Cultures with the respective empty vectors served as controls. On plates with different galactose concentrations (0%, 0.025%, 0.05%, 0.1% and 0.2%), 10 µl of culture were spotted in increasing dilutions (10-1 to 10-4) along with the control. Due to the equalised cell density of the cultures, the expression rate of the genome integrated and plasmid-expressed bax could then be compared among each other and with the controls after an incubation of three days at 30 °C.

[Insert discussion of plates/results here]

UCopenhagen placeholder.jpeg

Figure 3: BLABLABLA | Even more blablabla


Quantitative galactose induction assay

To quantify the effect of bax on our yeast under different expression levels, we have conducted a quantitative galactose induction assay with the genome integrated pGAL1-BAX using varying concentrations galactose. For this, an O/N culture of yeast with pGAL1-BAX was diluted to an OD600nm of 0.5. Subsequently, 100 µl of the culture were spread on plates with 0%, 0.05%, 0.1%, 0.3% and 1% galactose, respectively. To obtain countable amounts of colonies, the culture was spread in 10-3 and 10-4 dilutions. Yeast containing the corresponding empty vector served as a control. After incubation for three days at 30 °C, the CFU/ml were calculated and compared to the control.

[Discussion of below graph]

QGAL-induction.png

Figure 4: BLABLABLA | Even more blablabla


User Reviews

UNIQf5d7c7700e20dc19-partinfo-00000002-QINU UNIQf5d7c7700e20dc19-partinfo-00000003-QINU