Difference between revisions of "Part:BBa K802001"
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<partinfo>BBa_K802001 short</partinfo>
 
<partinfo>BBa_K802001 short</partinfo>
  
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This part associates the <i>Bacillus subtillis</i> <i>Constitutive Promoter</i> (PVeg) with the <i>dispersin B</i> gene (DspB).The DspB gene code for an enzyme which catalyzes the hydrolysis of the extracellular matrix produced by Gram-negative bacteria.
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This part associates the <i>Bacillus subtilis</i> <i>Constitutive Promoter</i> (PVeg) with the <i>dispersin B</i> gene (DspB).The DspB gene code for an enzyme which catalyzes the hydrolysis of the extracellular matrix produced by Gram-negative bacteria.
 
<br/>
 
<br/>
 
== Characterization ==
 
== Characterization ==
 
<html>
 
<html>
  
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<p>Following results show that this part allows <i>B. subtillis</i> 168 strains to scatter the <i>S. aureus</i> and <i>epidermidis</i> cells in a biofilm. </p><br/>
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<p>Following results show that this part allows <i>B. subtilis</i> 168 strains to scatter the <i>S. aureus</i> and <i>epidermidis</i> cells in a biofilm. </p><br/>
  
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<p>In our plasmid collection, this part is named pBK33 in the backbone Chloramphenicol and pBKH41 in the shuttle vector <i>E. coli</i> – <i>B. subtillis</i>. The corresponding negative control is the shuttle vector (pBKH26 in our collection). We worked with the plasmid pBKH41 for the tests and we tried two different genetic backgrounds: the strain NM522 to make test in <i>E. coli</i> and the strain 168 to make test in <i>Bacillus subtillis</i>.</p><br/>
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<p>In our plasmid collection, this part is named pBK33 in the backbone Chloramphenicol and pBKH41 in the shuttle vector <i>E. coli</i> – <i>B. subtilis</i>. The corresponding negative control is the shuttle vector (pBKH26 in our collection). We worked with the plasmid pBKH41 for the tests and we tried two different genetic backgrounds: the strain NM522 to make test in <i>E. coli</i> and the strain 168 to make test in <i>Bacillus subtilis</i>.</p><br/>
  
 
<a href="http://2012.igem.org/Team:Lyon-INSA/protocol"/><font color="grey"><b>In you have any question on the following experiments, don’t forget that all the informations relative to our strains, plasmids and protocols are on our wiki notebook.</b></font></a>
 
<a href="http://2012.igem.org/Team:Lyon-INSA/protocol"/><font color="grey"><b>In you have any question on the following experiments, don’t forget that all the informations relative to our strains, plasmids and protocols are on our wiki notebook.</b></font></a>
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<p>Biofilms are formed by the <i>S. aureus</i> fluorescent strain RN4220 pALC2084 expressing GFP. It is a nonmotile laboratory strain, used to form biofilm in 96-well microscopic-grade microtiter plate.<br><br/>
 
<p>Biofilms are formed by the <i>S. aureus</i> fluorescent strain RN4220 pALC2084 expressing GFP. It is a nonmotile laboratory strain, used to form biofilm in 96-well microscopic-grade microtiter plate.<br><br/>
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<i>Bacillus subtillis</i> 168 transformed by pBKH41 (DspB in in the shuttle vector) and by pBKH26 (the shuttle vector without gene to have a negative control) were grown on LB medium supplemented with erythromycin (15µg/mL).<br>  
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<i>Bacillus subtilis</i> 168 transformed by pBKH41 (DspB in in the shuttle vector) and by pBKH26 (the shuttle vector without gene to have a negative control) were grown on LB medium supplemented with erythromycin (15µg/mL).<br>  
 
After 24h of culture at 30°C without shaking, biofilm were observed under a time-lapse confocal microscope. <b>For each well, two observations were made : one before washing the biofilm and one after washing (i.e. after removing the supernatant).</b><br>  
 
After 24h of culture at 30°C without shaking, biofilm were observed under a time-lapse confocal microscope. <b>For each well, two observations were made : one before washing the biofilm and one after washing (i.e. after removing the supernatant).</b><br>  
 
Cells expressing GFP were excited at 488 nm with an argon laser, and fluorescent emission was collected on a detector in the range of 500-600 nm using an oil-immersion objective with a magnification of 63x. The overall three-dimensional structures of the biofilms were scanned from the solid surface to the interface with the growth medium, using a step of 1 µm.<br>
 
Cells expressing GFP were excited at 488 nm with an argon laser, and fluorescent emission was collected on a detector in the range of 500-600 nm using an oil-immersion objective with a magnification of 63x. The overall three-dimensional structures of the biofilms were scanned from the solid surface to the interface with the growth medium, using a step of 1 µm.<br>

Revision as of 21:20, 22 September 2012

Dispersin generator for B. subtilis

This part associates the Bacillus subtilis Constitutive Promoter (PVeg) with the dispersin B gene (DspB).The DspB gene code for an enzyme which catalyzes the hydrolysis of the extracellular matrix produced by Gram-negative bacteria.

Characterization

Following results show that this part allows B. subtilis 168 strains to scatter the S. aureus and epidermidis cells in a biofilm.


In our plasmid collection, this part is named pBK33 in the backbone Chloramphenicol and pBKH41 in the shuttle vector E. coli – B. subtilis. The corresponding negative control is the shuttle vector (pBKH26 in our collection). We worked with the plasmid pBKH41 for the tests and we tried two different genetic backgrounds: the strain NM522 to make test in E. coli and the strain 168 to make test in Bacillus subtilis.


In you have any question on the following experiments, don’t forget that all the informations relative to our strains, plasmids and protocols are on our wiki notebook.


Confocal Microscopy


Biofilms are formed by the S. aureus fluorescent strain RN4220 pALC2084 expressing GFP. It is a nonmotile laboratory strain, used to form biofilm in 96-well microscopic-grade microtiter plate.

Bacillus subtilis 168 transformed by pBKH41 (DspB in in the shuttle vector) and by pBKH26 (the shuttle vector without gene to have a negative control) were grown on LB medium supplemented with erythromycin (15µg/mL).
After 24h of culture at 30°C without shaking, biofilm were observed under a time-lapse confocal microscope. For each well, two observations were made : one before washing the biofilm and one after washing (i.e. after removing the supernatant).
Cells expressing GFP were excited at 488 nm with an argon laser, and fluorescent emission was collected on a detector in the range of 500-600 nm using an oil-immersion objective with a magnification of 63x. The overall three-dimensional structures of the biofilms were scanned from the solid surface to the interface with the growth medium, using a step of 1 µm.
The 3D constructions were obtained with IMARIS software.


Three cases are analysed :
    -Blank : it is a S. aureus biofilm not treated (just with growth medium).
    -Negative control : it is a S. aureus biofilm treated by B. subtilis containing the shuttle vector without the DspB gene.
    -Strain with our part : it is a S. aureus biofilm treated by B. subtilis containing the part BBa_K802001 in the shuttle vector.


    S.aureus biofilm not treated (Blank)




    S.aureus biofilm treats by the strain with the shuttle vector without DspB gene (Negativ control)




    S.aureus biofilm treats by the strain with the part


    Conclusion:
    With these observations, we concluded that the part allowed to scatter a S. aureus biofilm after washing. The bindings between the S. aureus cells inside the biofilm are affected, so that the biofilm can be easily eliminate after washing.


    Statistic analysis:
    In order to quantify our results, we made a statistic analysis with the MATLAB software. Different parameters [1] were used to quantify the biofilm, particularly :
      - Total Biovolume (µm3) : it corresponds to the overall volume of the biofilm and also allows to have an estimation of the biomass in the biofilm.
      - Substratum coverage (%) : it corresponds to the area coverage in the first image of the stack (i.e. at the substratum). It is a good mean to estimate how efficiently the substratum is colonized by bacteria of the population.
      The same three cases as previously are analysed.





      Conclusion:
      This statistic results demonstrate that the S. aureus biofilm treated by the B. subtilis with the part is significantly reduced after washing. The blank and the negative control prove that the wash doesn't affect the biofilm when the cells are not first scattered by the dispersin action.

      [1]Quantification of biofilm structures by the novel computer program COMSTAT. Heydorn A, Nielsen AT, Hentzer M, Sternberg C, Givskov M, Ersbøll BK, Molin S.Molecular Microbial Ecology Group, Department of Microbiology, Technical University of Denmark, DK-2800 Lyngby, Denmark.July 2000.



      SDS-PAGE Protein gel





      Usage and Biology

      This part was designed to be used in Bacillus strain in order to scatter a Staphyloccocus aureus biofilm.
      Possible applications include biofilm treatment in medical domain, oil or food-processing industries, using this scattering property to eliminate a harmful biofilm.


      Sequence and Features


      Assembly Compatibility:
      • 10
        COMPATIBLE WITH RFC[10]
      • 12
        COMPATIBLE WITH RFC[12]
      • 21
        COMPATIBLE WITH RFC[21]
      • 23
        COMPATIBLE WITH RFC[23]
      • 25
        INCOMPATIBLE WITH RFC[25]
        Illegal NgoMIV site found at 675
      • 1000
        COMPATIBLE WITH RFC[1000]