Team:Lyon-INSA/notebook

From 2012.igem.org

(Difference between revisions)
 
(7 intermediate revisions not shown)
Line 2,223: Line 2,223:
<jour nb="10">
<jour nb="10">
-
<date>Wednesday, October 10th 2012</date>
+
                        <date>Wednesday, October 10th 2012</date>
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
-
 
+
<ul>
 +
<li>Ligation of the part pBK14 containing the <i>gfp</i> gene with the part pBK7 (containing a <i>B. subtilis</i> RBS).</li>
 +
<li>Ligation of the part pBK13 containing the <i>rfp</i> gene with the part pBK7 (containing a <i>B. subtilis</i> RBS).</li>
 +
<li>Transformation of the NM522 <i>E. coli</i> strain with the two ligations.</li>
 +
</ul>
</description>
</description>
<titre>Stick</titre>
<titre>Stick</titre>
-
<description>
+
<description>Ligation of the PCR product <i>xylR</i> gene with the part pBK9 (P<sub><i>lac</i></sub> gene)and NM522 transformation.
-
 
+
</description>
</description>
</jour>
</jour>
 +
<jour nb="11">
<jour nb="11">
<date>Thursday, October 11th 2012</date>
<date>Thursday, October 11th 2012</date>
Line 2,239: Line 2,243:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Screening of 15 clones per transformation (antibiotic resistance test).
</description>
</description>
<titre>Stick</titre>
<titre>Stick</titre>
<description>
<description>
-
Inoculate 5 mL of LB medium with chloramphenicol with 1 colony of <i>Bacillus subtilis</i> 168 <i>ΔabrB</i> and 5 mL of LB medium with 1 colony of <i>Bacillus subtilis</i> 168. Incubate overnight at 37°C. (This is for the 48h positive <i>Bacillus subtilis</i> biofilm test plate)
+
Inoculation of 5 mL of LB medium with chloramphenicol with 1 colony of <i>Bacillus subtilis</i> 168 <i>ΔabrB</i> and 5 mL of LB medium with 1 colony of <i>Bacillus subtilis</i> 168. Incubation overnight at 37°C. (This is for the 48h positive <i>Bacillus subtilis</i> biofilm test plate)
</description>
</description>
</jour>
</jour>
Line 2,251: Line 2,256:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
-
To test the surfactant properties of the surfactin produced by the <i>B. subtilis</i> BK52 strain, a biofilm test was made in a 24 well plate. Liquid cultures are seeded with BK52 and BK49.
+
Liquid cultures are inoculated with colonies having the expected antibiotic phenotype.
 +
</br>
 +
To test the surfactant properties of the surfactin produced by the <i>B. subtilis</i> BK52 strain, a biofilm test was made in a 24-well plate. Liquid cultures are seeded with BK52 and BK49.
</description>
</description>
<titre>Stick</titre>
<titre>Stick</titre>
<description>
<description>
-
(24h plate)The same inoculation as previously is prepared.
+
<ul>
-
(48h plate)<i>Bacillus subtilis</i> 168 <i>ΔabrB</i> or <i>Bacillus subtilis</i> 168 are added in the 12 well plate with MgSO4  1mM and Glucose 0.1 %.
+
<li>(24h plate)The same inoculation as previously is prepared.</li>
 +
<li>(48h plate)<i>Bacillus subtilis</i> 168 <i>ΔabrB</i> or <i>Bacillus subtilis</i> 168 are added in the 12 well plate with MgSO4  1mM and Glucose 0.1 %.</li>
 +
</ul>
The plate is incubated at 37°C for 48h
The plate is incubated at 37°C for 48h
-
(For both)Inoculate 5 mL of LB medium with 1 colony of <i>E coli</i> (<i>ompR++</i> GFP, curlis overproduction).Incubate overnight at 37°C.  
+
(For both) Inoculation of 5 mL of LB medium with 1 colony of <i>E coli</i> (<i>ompR++</i> GFP, curlis overproduction). Incubation overnight at 37°C.  
</description>
</description>
</jour>
</jour>
Line 2,268: Line 2,277:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Miniprep of the screened clones. Unfortunately, the gel electrophoresis was disappointing and the extracted plasmids did not contain the ligated genes.
 +
</br>
A 24-well plate is incubated with filtered supernatant of the saturated cultures with BK52 and BK49 at room temperature for 24 hours.
A 24-well plate is incubated with filtered supernatant of the saturated cultures with BK52 and BK49 at room temperature for 24 hours.
Line 2,274: Line 2,285:
<titre>Stick</titre>
<titre>Stick</titre>
<description>
<description>
-
(24h plate)<i>Bacillus subtilis</i> 168 <i>ΔabrB</i> or <i>Bacillus subtilis</i> 168 are added in the 12 well plate with MgSO4  1mM and Glucose 0.1 %.
+
(24h plate)<i>Bacillus subtilis</i> 168 <i>ΔabrB</i> or <i>Bacillus subtilis</i> 168 are added in a 12-well plate with MgSO4  1mM and Glucose 0.1 %.
The plate is incubated at 37°C for 48h.
The plate is incubated at 37°C for 48h.
</description>
</description>
Line 2,284: Line 2,295:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
The wells are carefully rinsed with M63 medium two times after having previously discarded the supernatant. Then, each well is inoculated with a saturated adherent <i>E. coli</i> strain diluted 100 times in LB medium diluted 2 times.</br>
 +
Moreover, another 24-well plate assay was made using the same supernatant, but this time the plate was incubated only 4 hours before <i>E. coli</i> inoculation.
</description>
</description>
<titre>Stick</titre>
<titre>Stick</titre>
<description>
<description>
-
(For both)The supernatant is removed, wells are washed and LB is added.To see if <i>E coli</i> forms a biofilm over the Bacillus subtilis biofilm the overnight culture of <i>E coli</i> is added into each wells.
+
(For both) The supernatant is removed, wells are washed and LB is added.To see if <i>E coli</i> forms a biofilm over the <i>Bacillus subtilis</i> biofilm, the overnight culture of <i>E coli</i> is added into each well.
Plates are incubated for 36h at 30°C.
Plates are incubated for 36h at 30°C.
</description>
</description>
Line 2,298: Line 2,311:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Unfortunately, the observation of the plates under confocal microscope is not possible, so the experiment must be repeated. The only difference is that this time 12-well plates  with glass lamellae are used so the observation of the biofilm would be possible.
</description>
</description>
<titre>Stick</titre>
<titre>Stick</titre>
<description>
<description>
-
(For both)Now let's observe the Confocal microscopy !
+
(For both) Now let's observe using the confocal microscope !
Results : It works ! Our positive <i>Bacillus subtilis</i> biofilm inhibits the stick of other bacteria !
Results : It works ! Our positive <i>Bacillus subtilis</i> biofilm inhibits the stick of other bacteria !
</description>
</description>
Line 2,311: Line 2,325:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
-
 
+
Liquid cultures were inoculated with the strains BK49 and BK52 and then incubated at 37C for 48 hours.
-
</description>
+
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
</description>
</description>
 +
</jour>
</jour>
-
<jour nb="18">
 
-
<date>Thursday, October 18th 2012</date>
 
-
 
-
<titre>Surfactant</titre>
 
-
<description>
 
-
</description>
 
-
<titre>Stick</titre>
 
-
<description>
 
-
</description>
 
-
</jour>
 
<jour nb="19">
<jour nb="19">
<date>Saturday, October 19th 2012</date>
<date>Saturday, October 19th 2012</date>
Line 2,335: Line 2,336:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
The supernatant from the plate is discarded. Each well is inoculated with an <i>E. coli</i> saturated culture diluted 50 times in LB medium diluted 2 times.
-
</description>
 
-
<titre>Stick</titre>
 
-
<description>
 
</description>
</description>
 +
</jour>
</jour>
Line 2,348: Line 2,348:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Ligation of pBK40 and pBK16 followed by transformation into the NM522 strain.
</description>
</description>
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
-
</description>
+
</jour>
</jour>
Line 2,361: Line 2,359:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
The surfactin pre-treated glass lamellae are observed under the confocal microscope. The negative control has a thick biofilm whereas the treated lamella has a few isolated colonies.
</description>
</description>
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
-
</description>
+
</jour>
</jour>
Line 2,374: Line 2,370:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Screening of 12 clones.
</description>
</description>
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
-
</description>
+
</jour>
</jour>
Line 2,387: Line 2,381:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
Miniprep of the transformed clones. The gel electrophoresis confirmed the expected insert. (<i>abrB</i> gene in pSB1C3 backbone)
</description>
</description>
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
-
</description>
+
</jour>
</jour>
Line 2,400: Line 2,392:
<titre>Surfactant</titre>
<titre>Surfactant</titre>
<description>
<description>
 +
The plasmids pBK42 and pBK46 were submitted to the Registry.
</description>
</description>
-
<titre>Stick</titre>
+
-
<description>
+
-
 
+
-
</description>
+
</jour>
</jour>

Latest revision as of 00:15, 27 October 2012

The Notebook


July
August
September
October


Previous day

Next day
Watch us in action !

Our collections

Strains collection
Plasmids collection

Retrieved from "http://2012.igem.org/Team:Lyon-INSA/notebook"