Difference between revisions of "Team:Freiburg/Production Nanocillus"
| Line 14: | Line 14: | ||
<font color="#FFCCAC"> | <font color="#FFCCAC"> | ||
To combine our targeting and the drug delivery system, we used the spores of | To combine our targeting and the drug delivery system, we used the spores of | ||
| − | Bacillus subtilis as a carrier. The finished product is called Nanocillus. <br><br> | + | <i>Bacillus subtilis</i> as a carrier. The finished product is called Nanocillus. <br><br> |
But before any experiments with the Nanocillus can be performed, they need to be produced!<br> | But before any experiments with the Nanocillus can be performed, they need to be produced!<br> | ||
| Line 40: | Line 40: | ||
<div class="para_center_20"> | <div class="para_center_20"> | ||
<font color="#c2e8ea"> | <font color="#c2e8ea"> | ||
| − | To start with the production of the Nanocillus, competent cells of B. subtilis are needed.<br><br> | + | To start with the production of the Nanocillus, competent cells of <i>B. subtilis</i> are needed.<br><br> |
| − | The Bacillus subtilis WT and the different knock outs: dCotZ, dCotB, dCotG and CgeA were inoculated in 4 ml of LB medium to grow overnight at 37°C at 200 rpm . The next day, the samples were diluted in 10 ml of minimal medium (MNGE) to an Optical Density (OD600) of around 0.1/ml and the incubation was continued. The OD was measured every 20 minutes until the samples reached an OD600 of around 1.0-1.3/ml, which takes around 4 hours depending on the different strains and the status of the original culture. <br><br> | + | The <i>Bacillus subtilis</i> WT and the different knock outs: dCotZ, dCotB, dCotG and CgeA were inoculated in 4 ml of LB medium to grow overnight at 37°C at 200 rpm . The next day, the samples were diluted in 10 ml of minimal medium (MNGE) to an Optical Density (OD600) of around 0.1/ml and the incubation was continued. The OD was measured every 20 minutes until the samples reached an OD600 of around 1.0-1.3/ml, which takes around 4 hours depending on the different strains and the status of the original culture. <br><br> |
</font> | </font> | ||
</div> | </div> | ||
| Line 70: | Line 70: | ||
If not used directly, glycerol was added to each tube to a final concentration of 10% and the samples were frozen in -80°C. | If not used directly, glycerol was added to each tube to a final concentration of 10% and the samples were frozen in -80°C. | ||
<br><br> | <br><br> | ||
| − | For the transformation of the constructs into the host B.subtilis, 600 ng of the construct DNA, which was originally isolated from transformed E. coli, is added to each tube. The negative controls were left untreated. All the samples were incubated for 1 hour at 37°C at 200 rpm and then 100 µl of the expression mix (see protocol) was added to each sample, followed by another incubation for one more hour.<br><br> | + | For the transformation of the constructs into the host <i>B.subtilis</i>, 600 ng of the construct DNA, which was originally isolated from transformed E. coli, is added to each tube. The negative controls were left untreated. All the samples were incubated for 1 hour at 37°C at 200 rpm and then 100 µl of the expression mix (see protocol) was added to each sample, followed by another incubation for one more hour.<br><br> |
To check if the transformation was successful, 400 µl the samples were plated on selective plates. Since the inserted backbone includes an antibiotic resistance for chloramphenicol, the plates were made with 5000 ng of chloramphenicol. | To check if the transformation was successful, 400 µl the samples were plated on selective plates. Since the inserted backbone includes an antibiotic resistance for chloramphenicol, the plates were made with 5000 ng of chloramphenicol. | ||
<br><br> | <br><br> | ||
| Line 102: | Line 102: | ||
<div class="para_center_20"> | <div class="para_center_20"> | ||
<font color="#c2e8ea"> | <font color="#c2e8ea"> | ||
| − | To purify the cultures of spores from remaining vegetative cells, they were treated with the enzyme lysozyme. The lysozyme affects the freely accessible peptidoglycan of the gram-positive vegetative cells of B. subtilis. In contrast the stable spores aren't affected or harmed.The samples were centrifuged, resuspended in 1x PBS and the lysozyme (15 mg/ml) was added at a dilution of 1:6. After the spores were inoculated at room temperature ( RT) with vicious shaking, all the vegetative cells should be lysed.Repeated washing and centrifugation of the samples for 6 times separated the spores from the redundant cell fragments. <br> | + | To purify the cultures of spores from remaining vegetative cells, they were treated with the enzyme lysozyme. The lysozyme affects the freely accessible peptidoglycan of the gram-positive vegetative cells of <i>B. subtilis</i>. In contrast the stable spores aren't affected or harmed.The samples were centrifuged, resuspended in 1x PBS and the lysozyme (15 mg/ml) was added at a dilution of 1:6. After the spores were inoculated at room temperature (RT) with vicious shaking, all the vegetative cells should be lysed. Repeated washing and centrifugation of the samples for 6 times separated the spores from the redundant cell fragments. <br> |
To set a norm for the following experiments, the remaining spores were counted in the Neubauer improved counting chamber and aliquots were made for an easier storage at -80°C. | To set a norm for the following experiments, the remaining spores were counted in the Neubauer improved counting chamber and aliquots were made for an easier storage at -80°C. | ||
Revision as of 13:19, 19 October 2016
Nanocillus Production
To combine our targeting and the drug delivery system, we used the spores of Bacillus subtilis as a carrier. The finished product is called Nanocillus.But before any experiments with the Nanocillus can be performed, they need to be produced!
In the following video, you can see how the cells are cultured, made competent, transformed and then sporulated. The spores are lyophilized and filled into capsules. Finished is our Nanocillus!
To validate that the spores are expressing our constructs, western blots and flow cytometry analyses were performed. In doing so, it is confirmed that the Nanocillus is expressing our constructs and can be used for the spore production and in further applications.
Video Production
To start with the production of the Nanocillus, competent cells of B. subtilis are needed.
The Bacillus subtilis WT and the different knock outs: dCotZ, dCotB, dCotG and CgeA were inoculated in 4 ml of LB medium to grow overnight at 37°C at 200 rpm . The next day, the samples were diluted in 10 ml of minimal medium (MNGE) to an Optical Density (OD600) of around 0.1/ml and the incubation was continued. The OD was measured every 20 minutes until the samples reached an OD600 of around 1.0-1.3/ml, which takes around 4 hours depending on the different strains and the status of the original culture.
The Bacillus subtilis WT and the different knock outs: dCotZ, dCotB, dCotG and CgeA were inoculated in 4 ml of LB medium to grow overnight at 37°C at 200 rpm . The next day, the samples were diluted in 10 ml of minimal medium (MNGE) to an Optical Density (OD600) of around 0.1/ml and the incubation was continued. The OD was measured every 20 minutes until the samples reached an OD600 of around 1.0-1.3/ml, which takes around 4 hours depending on the different strains and the status of the original culture.
Growth Curves + Video
The competence was checked under the microscope (the cells should be very motile) and 400 µl were filled in different tubes. Each tube equals one transformation.
If not used directly, glycerol was added to each tube to a final concentration of 10% and the samples were frozen in -80°C.
For the transformation of the constructs into the host B.subtilis, 600 ng of the construct DNA, which was originally isolated from transformed E. coli, is added to each tube. The negative controls were left untreated. All the samples were incubated for 1 hour at 37°C at 200 rpm and then 100 µl of the expression mix (see protocol) was added to each sample, followed by another incubation for one more hour.
To check if the transformation was successful, 400 µl the samples were plated on selective plates. Since the inserted backbone includes an antibiotic resistance for chloramphenicol, the plates were made with 5000 ng of chloramphenicol.
After growing for 14 hours, the plates were checked and colonies could be picked. Another test was performed to make sure that the DNA was inserted in the right locus. For the amyE- locus, the picked colonies were put on starch plates to grow. The next day lugol’s iodide was dropped on each colony. The WT and wrong inserted DNA colonies were still able to express the a-amylase and consequently can reduce the starch and decolourize the area around them. Only colonies with positively inserted DNA stay coloured from the lugol’s iodide and therefore are used for further experiments.
Another approach with cells, DNA was inserted in the thrC- locus. The positive colonies no longer own the threonine synthase and are not able to grow on minimal medium without threonine. Picked colonies were then plated on two different minimal mediums. One with threonine and one without the threonine to determine which colonies have the correct integrated DNA. Additionally, for the sacA- and lacA- locus a colony PCR was performed to confirm the right integration.
The positive colonies were picked and incubated in 4 ml LB to grow overnight at 37°C at 200 rpm. To induce the sporulation of vegetative cells, the samples were once again diluted in 10 ml LB to an OD600 of 0.1 - 0,.2/ml and let grown till an OD600 of 0.8-1.0/ml. At that point the samples had reached their exponential growth phase. They were washed once with 1x PBS (Phosphate-buffered saline) and resuspended in 5 ml of DSM (Difco sporulation medium ) to incubate for 24 hours at 37°C at 200 rpm.
If not used directly, glycerol was added to each tube to a final concentration of 10% and the samples were frozen in -80°C.
For the transformation of the constructs into the host B.subtilis, 600 ng of the construct DNA, which was originally isolated from transformed E. coli, is added to each tube. The negative controls were left untreated. All the samples were incubated for 1 hour at 37°C at 200 rpm and then 100 µl of the expression mix (see protocol) was added to each sample, followed by another incubation for one more hour.
To check if the transformation was successful, 400 µl the samples were plated on selective plates. Since the inserted backbone includes an antibiotic resistance for chloramphenicol, the plates were made with 5000 ng of chloramphenicol.
After growing for 14 hours, the plates were checked and colonies could be picked. Another test was performed to make sure that the DNA was inserted in the right locus. For the amyE- locus, the picked colonies were put on starch plates to grow. The next day lugol’s iodide was dropped on each colony. The WT and wrong inserted DNA colonies were still able to express the a-amylase and consequently can reduce the starch and decolourize the area around them. Only colonies with positively inserted DNA stay coloured from the lugol’s iodide and therefore are used for further experiments.
Another approach with cells, DNA was inserted in the thrC- locus. The positive colonies no longer own the threonine synthase and are not able to grow on minimal medium without threonine. Picked colonies were then plated on two different minimal mediums. One with threonine and one without the threonine to determine which colonies have the correct integrated DNA. Additionally, for the sacA- and lacA- locus a colony PCR was performed to confirm the right integration.
The positive colonies were picked and incubated in 4 ml LB to grow overnight at 37°C at 200 rpm. To induce the sporulation of vegetative cells, the samples were once again diluted in 10 ml LB to an OD600 of 0.1 - 0,.2/ml and let grown till an OD600 of 0.8-1.0/ml. At that point the samples had reached their exponential growth phase. They were washed once with 1x PBS (Phosphate-buffered saline) and resuspended in 5 ml of DSM (Difco sporulation medium ) to incubate for 24 hours at 37°C at 200 rpm.
Video SPores
To purify the cultures of spores from remaining vegetative cells, they were treated with the enzyme lysozyme. The lysozyme affects the freely accessible peptidoglycan of the gram-positive vegetative cells of B. subtilis. In contrast the stable spores aren't affected or harmed.The samples were centrifuged, resuspended in 1x PBS and the lysozyme (15 mg/ml) was added at a dilution of 1:6. After the spores were inoculated at room temperature (RT) with vicious shaking, all the vegetative cells should be lysed. Repeated washing and centrifugation of the samples for 6 times separated the spores from the redundant cell fragments.
To set a norm for the following experiments, the remaining spores were counted in the Neubauer improved counting chamber and aliquots were made for an easier storage at -80°C.
To set a norm for the following experiments, the remaining spores were counted in the Neubauer improved counting chamber and aliquots were made for an easier storage at -80°C.
To verify the expression of the constructs, flow cytometry and western blot analyses were performed. By including a hemagglutinin epitope tag to the introduced protein the detection can be verified via Western Blot. Verification, that the introduced protein is located on the surface of the endospores and is accessible can be tested by conjugated anti-HA antibodies. Staining of the spores with said antibodies can be used for flow cytometry analyses to demonstrate proper surface localization.
In figure 2 it can be seen that the transformed spores containing the part BBa_K2114001 (anti-GFP nanobody fused to the coat protein CotZ and a HA tag) were successfully transformed and display the HA tag on the surface.
Chemical decoating of endospores enabled the analysis of extracted surface proteins.
Spore coat lysates were analyzed using Western Blots. Figure 3 shows that spores containing the construct BBa_K2114001 (anti-GFP nanobody fused to the coat protein CotZ and a HA tag) was detected in the spore coat lysate.
After these verification, the bacteria were lyophilized and the capsules were filled with the final product: the Nanocillus.
