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Team:Lyon-INSA-ENS/Realisation/Week13
From 2011.igem.org
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<h1 style="color: white;"> Week 13 </h1> | <h1 style="color: white;"> Week 13 </h1> | ||
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| - | <p style="text-align : center"> <small> From Monday the 12th of September to | + | <p style="text-align : center"> <small> From Monday the 12th of September to Sunday the 18th of September 2011 </small> </p> |
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<h6 style="text-align :left"> Monday </h6> <HR> | <h6 style="text-align :left"> Monday </h6> <HR> | ||
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<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
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Inserts of pIG34 200µl clone 1 and pIG34 800µl clone 1 are good so the ligation went well. We’re keeping in collection the pIG34 200µl clone 1 as pIG34 in the plasmids’ collection and MC400+pIG34 as S32 in the strains’ collection.<br/><br/> | Inserts of pIG34 200µl clone 1 and pIG34 800µl clone 1 are good so the ligation went well. We’re keeping in collection the pIG34 200µl clone 1 as pIG34 in the plasmids’ collection and MC400+pIG34 as S32 in the strains’ collection.<br/><br/> | ||
| - | Cloning and transformation of rcn-ompR234 + pSB1C3 in MC4100<br/><br/> | + | Cloning and transformation of rcn-ompR234 + pSB1C3 in MC4100.<br/><br/><br/> |
</p> | </p> | ||
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<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
<FONT COLOR="blue"><b>Plasmid and strain Collection</b></FONT> <br/><br/> | <FONT COLOR="blue"><b>Plasmid and strain Collection</b></FONT> <br/><br/> | ||
| - | Plating of S17 from the collection to extract a bigger quantity of pIG25 ( pSB1C3 containing rcn-csgBAEFG )<br/><br/> | + | Plating of S17 from the collection to extract a bigger quantity of pIG25 (pSB1C3 containing rcn-csgBAEFG).<br/><br/> |
Storage of the correct clone of:<br/> | Storage of the correct clone of:<br/> | ||
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MC4100 + pIG34 (S32) <br/><br/> | MC4100 + pIG34 (S32) <br/><br/> | ||
| - | Storage of rcn-OmpR in psB1K3 (pIG34) from the previous miniprep. <br/><br/> | + | Storage of rcn-OmpR in psB1K3 (pIG34) from the previous miniprep. <br/><br/><br/> |
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<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
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Sterilization of microscope cover slips in ethanol during a few minutes, then rinsed in sterilized water. <br/><br/> | Sterilization of microscope cover slips in ethanol during a few minutes, then rinsed in sterilized water. <br/><br/> | ||
| - | <b>Test</b | + | <b>Test</b> <br/> |
Preparation of plates for the following strains (one repetition):<br/> | Preparation of plates for the following strains (one repetition):<br/> | ||
-PHL1414/piG3 AmpR = negative control without Co and with Co 25µM<br/> | -PHL1414/piG3 AmpR = negative control without Co and with Co 25µM<br/> | ||
| - | -PHL1414/ | + | -PHL1414/piG16 AmpR without Co, Co 10µM, Co 25µM, Co 50µM and Co 100µM<br/><br/> |
Incubation at 30°C overnight (during 16 hours).<br/><br/><br/> | Incubation at 30°C overnight (during 16 hours).<br/><br/><br/> | ||
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</p> | </p> | ||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="orange"> <b> Others </b></FONT> <br/><br/> | ||
| + | Pouring of 9 LB+Amp plates<br/><br/> | ||
| + | |||
| + | Dilution of 5µL pIG25 (371.4 ng/µL) into 25µL water to obtain 3 additional tubes at concentration of about 50ng/µL for sequencing. <br/> | ||
| + | Sequencing (pIG25 and pIG27) sent. <br/><br/> | ||
| + | |||
| + | </p> | ||
<br/> <br/> | <br/> <br/> | ||
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Extraction of piG33 800µl 1 and 2, and pIG33 200µl 1 and 2.<br/> | Extraction of piG33 800µl 1 and 2, and pIG33 200µl 1 and 2.<br/> | ||
| - | Digestion by EcoR1, Pst1 and gel electrophoresis for verification.<br/> | + | Digestion by EcoR1, Pst1 and gel electrophoresis for verification.<br/><br/><br/> |
</p> | </p> | ||
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<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
<FONT COLOR="blue"><b>Plasmid and strain Collection</b></FONT> <br/><br/> | <FONT COLOR="blue"><b>Plasmid and strain Collection</b></FONT> <br/><br/> | ||
| - | Start of a 5mL liquid culture of S17 in LB+Cm medium<br/> | + | Start of a 5mL liquid culture of S17 in LB+Cm medium.<br/> |
Minipreps of this culture to extract pIG25 in larger quantity. Digestion (E+P) and electrophoresis for control : the insert of pIG25 is not good so there was a mistake the first time it was controlled. More or less 500bp are missing. Back to the lab, let’s try to built it again to have it on time.<br/> | Minipreps of this culture to extract pIG25 in larger quantity. Digestion (E+P) and electrophoresis for control : the insert of pIG25 is not good so there was a mistake the first time it was controlled. More or less 500bp are missing. Back to the lab, let’s try to built it again to have it on time.<br/> | ||
The inserts pIG33 800µl 1 and 200µl 2 are good. pIG33 800µl 1 becomes pIG33 and is put in the plasmids’ collection.<br/> | The inserts pIG33 800µl 1 and 200µl 2 are good. pIG33 800µl 1 becomes pIG33 and is put in the plasmids’ collection.<br/> | ||
| - | MC4100+pIG33 = S33 is stored. | + | MC4100+pIG33 = S33 is stored. |
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<h6 style="text-align :left"> Wednesday </h6> <HR> | <h6 style="text-align :left"> Wednesday </h6> <HR> | ||
| - | <br/> | + | <br/><br/> |
<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
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Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3 (pIG25) <br/> | Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3 (pIG25) <br/> | ||
Plating of PHL916 on LB ( sureE strain that should not recombine DNA ) in case the transformation of pIG25 into MC4100 fails. <br/><br/> | Plating of PHL916 on LB ( sureE strain that should not recombine DNA ) in case the transformation of pIG25 into MC4100 fails. <br/><br/> | ||
| - | Digestion of pIG20 with E and P<br/> | + | Digestion of pIG20 with E and P.<br/> |
Gel electrophoresis for control of the insert → good<br/><br/> | Gel electrophoresis for control of the insert → good<br/><br/> | ||
| - | Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3 | + | Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3.<br/><br/><br/> |
</p> | </p> | ||
| - | < | + | <div style="border:1px solid black;float:left;margin-left:3%; width : 180px"> |
| - | < | + | <img src="https://static.igem.org/mediawiki/2011/c/c2/2011-03-17_10-23-03.jpg" width="180px"/> |
| + | </div> | ||
| - | + | <p style=" line-height : 1.5em;margin-left:30%"> | |
| - | + | <FONT COLOR="purple"><b> Adherence Test - pRcn-OmpR234 Characterization </b></FONT> <br/><br/> | |
| - | + | ||
| - | <p style=" line-height : 1.5em"> | + | |
| - | <FONT COLOR="purple"><b> | + | |
Start of a rcn-OmpR234 24 well plate with :<br/> | Start of a rcn-OmpR234 24 well plate with :<br/> | ||
| - | S27 ( rcn in pSB1C3 ) without cobalt and with cobalt (25µM) <br/> | + | S27 ( rcn in pSB1C3 ) without cobalt and with cobalt (25µM). <br/> |
| - | S33 ( rcn-OmpR234 in pSB1C3 ) with increasing concentration of cobalt (0, 10, 25 and 100 µM) | + | S33 ( rcn-OmpR234 in pSB1C3 ) with increasing concentration of cobalt (0, 10, 25 and 100 µM).<br/><br/><br/> |
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<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
<FONT COLOR="orange"> <b> Others </b></FONT> <br/><br/> | <FONT COLOR="orange"> <b> Others </b></FONT> <br/><br/> | ||
| - | Plating of PHL644, PHL1256, PHL628 to be sent to other research teams, on request. | + | Plating of PHL644, PHL1256, PHL628 to be sent to other research teams, on request. |
</p> | </p> | ||
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<FONT COLOR="red"> <b>Strain construction </b> </FONT> <br/><br/> | <FONT COLOR="red"> <b>Strain construction </b> </FONT> <br/><br/> | ||
| - | None of the transformation of the day before has grown. Let’s try it again.<br/><br/> | + | None of the transformation of the day before has grown. Let’s try it again.<br/><br/><br/> |
</p> | </p> | ||
<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
| - | <FONT COLOR="purple"><b> | + | <FONT COLOR="purple"><b> Fluorescence Test - rcn Characterization </b></FONT> <br/><br/> |
| - | + | Characterization of rcn-gfp with the kinetic studie.<br/> | |
3 people are repeating the same 4 erlen of culture with the M63G medium:<br/> | 3 people are repeating the same 4 erlen of culture with the M63G medium:<br/> | ||
- NM522/p157 + spc + 25µM Co<br/> | - NM522/p157 + spc + 25µM Co<br/> | ||
| - | - NM522/p157<br/> | + | - NM522/p157 + spc<br/> |
- NM522/p115 + spc + 25µM Co<br/> | - NM522/p115 + spc + 25µM Co<br/> | ||
- NM522/p115 + spc<br/> | - NM522/p115 + spc<br/> | ||
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</p> | </p> | ||
| + | |||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="purple"><b> Adherence Test - 18A-0mpR234 Characterization</b></FONT> <br/><br/> | ||
| + | |||
| + | Start a 24 well plates in M63G medium + Amp with PHL1414/piG3 (negative control) and PHL1414/piG16.<br/> | ||
| + | Incubation at 30°C for 48h.<br/><br/> | ||
| + | |||
<br/> <br/> | <br/> <br/> | ||
| - | <h6 style="text-align :left"> Friday </h6><HR> | + | <h6 style="text-align :left"> Friday </h6><HR><br/><br/> |
<p style=" line-height : 1.5em"> | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="red"> <b>Strain construction</b> </FONT> <br/><br/> | ||
| + | The transformations from Wednesday have grown : selection of 5 clones for pIG36 and Ptrc +Cm, 10 for pIG25.<br/><br/> | ||
| - | + | Miniprep (QIAGen), digestion (Fermentas E+P) and electrophoresis of all clones for pIG25, 4 for pIG36, 2 for Ptrc-Cm ( the other cultures had not grown ). One correct clone is found for pIG25 and pIG36, none is correct for Ptrc-Cm.<br/><br/> | |
| + | <div style="border:1px solid black;float:left;margin-left:25%; width : 300px"> | ||
| + | <img src="https://static.igem.org/mediawiki/2011/1/19/Gelwiki13.JPG" width="300px"/> | ||
| + | </div> | ||
| + | </p> | ||
| + | |||
| + | <br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/><br/> | ||
| + | |||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="purple"> <b> Adherence Test - pRcn-OmpR234 Characterization </b> </FONT> <br/><br/> | ||
| + | Revealing of the plate : no effect from rcn-ompR234 is visible compared to the controls. <br/><br/> | ||
| + | |||
| + | </p> | ||
| + | |||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="orange"> <b> Others </b></FONT> <br/><br/> | ||
| + | Dissolution of 0.11g of Ampiciline sodium salt ( Sigma A0166-5G) into 10mL water and filtration to obtain a solution of Amp at 10mg/mL. | ||
| + | </p> | ||
<br/> <br/> | <br/> <br/> | ||
<br/> <br/> | <br/> <br/> | ||
| + | <h6 style="text-align :left"> Saturday </h6><HR><br/><br/> | ||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="blue"><b>Plasmid and strain Collection</b></FONT> <br/><br/> | ||
| + | Storage of the correct clones and extracted plasmids from the previous day : S34 (NM522 + pIG25), S35 (NM522+pIG36), pIG25, pIG37 (=pIG36 after transformation and extraction ).<br/><br/> | ||
| + | </p> | ||
| + | |||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="purple"> <b> Adherence Test - 18A-OmpR234 Characterization </b> </FONT> <br/><br/> | ||
| + | Revealing of the plate : ompR234 doubles the adherence compared to negative controls.<br/><br/> | ||
| + | |||
| + | </p> | ||
| + | |||
| + | <br/> <br/> | ||
| + | <br/> <br/> | ||
| + | |||
| + | <h6 style="text-align :left"> Sunday </h6><HR> | ||
| + | |||
| + | <br/><br/> | ||
| + | <p style=" line-height : 1.5em"> | ||
| + | <FONT COLOR="red"> <b>Strain construction</b> </FONT> <br/><br/> | ||
| + | Miniprep (QIAGen), digestion (Fermentas E+P) and electrophoresis of the last 3 clones for Ptrc-Cm.<br/><br/> | ||
| + | </p> | ||
| + | |||
| + | <br/> <br/> | ||
| + | <br/> <br/> | ||
| + | |||
| + | <br/> <br/> | ||
| + | <p> | ||
| + | <a href="https://2011.igem.org/Team:Lyon-INSA-ENS/Realisation/Week12"/><font color="grey"><b>Previous Week</b></font></a> | ||
| + | <a style = "float : right"; href="https://2011.igem.org/Team:Lyon-INSA-ENS/Realisation/Week17"/><font color="grey"><b>Next Week</b></font></a> | ||
| + | <br/> | ||
| + | </p> | ||
| + | <br/> <br/> | ||
</div> | </div> | ||
Latest revision as of 18:50, 27 October 2011
Week 13
From Monday the 12th of September to Sunday the 18th of September 2011
Monday
Strain construction
Extraction of PHL1414+pIG3, PHL1414+pIG16 (clone 1,2,3) , MC4100+piG34 200µl (clone 1,2), MC4100+pIG34 800µl (clone 1, 2).
Digestion by EcoRI and PstI.
Gel electrophoresis to verify the ligations. Inserts have the good length for pIG3, pIG16 so the transformation went well.
Inserts of pIG34 200µl clone 1 and pIG34 800µl clone 1 are good so the ligation went well. We’re keeping in collection the pIG34 200µl clone 1 as pIG34 in the plasmids’ collection and MC400+pIG34 as S32 in the strains’ collection.
Cloning and transformation of rcn-ompR234 + pSB1C3 in MC4100.
Plasmid and strain Collection
Plating of S17 from the collection to extract a bigger quantity of pIG25 (pSB1C3 containing rcn-csgBAEFG).
Storage of the correct clone of:
PHL1414 + pIG3 (S30)
PHL1414+pIG16 (S31)
MC4100 + pIG34 (S32)
Storage of rcn-OmpR in psB1K3 (pIG34) from the previous miniprep.
Microscopy Test
Preparation
Sterilization of microscope cover slips in ethanol during a few minutes, then rinsed in sterilized water.
Test
Preparation of plates for the following strains (one repetition):
-PHL1414/piG3 AmpR = negative control without Co and with Co 25µM
-PHL1414/piG16 AmpR without Co, Co 10µM, Co 25µM, Co 50µM and Co 100µM
Incubation at 30°C overnight (during 16 hours).
Others
Pouring of 9 LB+Amp plates
Dilution of 5µL pIG25 (371.4 ng/µL) into 25µL water to obtain 3 additional tubes at concentration of about 50ng/µL for sequencing.
Sequencing (pIG25 and pIG27) sent.
Tuesday
Strain construction
Purification and culture of 2 clones from each Petri dish of the transformation of rcn-ompR234 + pSB1C3 in MC4100.
Extraction of piG33 800µl 1 and 2, and pIG33 200µl 1 and 2.
Digestion by EcoR1, Pst1 and gel electrophoresis for verification.
Plasmid and strain Collection
Start of a 5mL liquid culture of S17 in LB+Cm medium.
Minipreps of this culture to extract pIG25 in larger quantity. Digestion (E+P) and electrophoresis for control : the insert of pIG25 is not good so there was a mistake the first time it was controlled. More or less 500bp are missing. Back to the lab, let’s try to built it again to have it on time.
The inserts pIG33 800µl 1 and 200µl 2 are good. pIG33 800µl 1 becomes pIG33 and is put in the plasmids’ collection.
MC4100+pIG33 = S33 is stored.
Wednesday
Strain construction
The Ptrc strong promoter has been received from Genecust in pBluescriptIISK+: transformation in MC4100 and plating on LB+Amp medium.
Digestion by E+P of this plasmid and ligation into pSB1C3 overnight
Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3 (pIG25)
Plating of PHL916 on LB ( sureE strain that should not recombine DNA ) in case the transformation of pIG25 into MC4100 fails.
Digestion of pIG20 with E and P.
Gel electrophoresis for control of the insert → good
Cloning of rcn-csgBAEFG in pSB1C3, transformation in pSB1C3.
Adherence Test - pRcn-OmpR234 Characterization
Start of a rcn-OmpR234 24 well plate with :
S27 ( rcn in pSB1C3 ) without cobalt and with cobalt (25µM).
S33 ( rcn-OmpR234 in pSB1C3 ) with increasing concentration of cobalt (0, 10, 25 and 100 µM).
Others
Plating of PHL644, PHL1256, PHL628 to be sent to other research teams, on request.
Thursday
Strain construction
None of the transformation of the day before has grown. Let’s try it again.
Fluorescence Test - rcn Characterization
Characterization of rcn-gfp with the kinetic studie.
3 people are repeating the same 4 erlen of culture with the M63G medium:
- NM522/p157 + spc + 25µM Co
- NM522/p157 + spc
- NM522/p115 + spc + 25µM Co
- NM522/p115 + spc
1 ml of spc (spectinomycine) is added
The culture is sed by 0,5mL of a overnight preculture.
Adherence Test - 18A-0mpR234 Characterization
Start a 24 well plates in M63G medium + Amp with PHL1414/piG3 (negative control) and PHL1414/piG16.
Incubation at 30°C for 48h.
Friday
Strain construction
The transformations from Wednesday have grown : selection of 5 clones for pIG36 and Ptrc +Cm, 10 for pIG25.
Miniprep (QIAGen), digestion (Fermentas E+P) and electrophoresis of all clones for pIG25, 4 for pIG36, 2 for Ptrc-Cm ( the other cultures had not grown ). One correct clone is found for pIG25 and pIG36, none is correct for Ptrc-Cm.
Adherence Test - pRcn-OmpR234 Characterization
Revealing of the plate : no effect from rcn-ompR234 is visible compared to the controls.
Others
Dissolution of 0.11g of Ampiciline sodium salt ( Sigma A0166-5G) into 10mL water and filtration to obtain a solution of Amp at 10mg/mL.
Saturday
Plasmid and strain Collection
Storage of the correct clones and extracted plasmids from the previous day : S34 (NM522 + pIG25), S35 (NM522+pIG36), pIG25, pIG37 (=pIG36 after transformation and extraction ).
Adherence Test - 18A-OmpR234 Characterization
Revealing of the plate : ompR234 doubles the adherence compared to negative controls.
Sunday
Strain construction
Miniprep (QIAGen), digestion (Fermentas E+P) and electrophoresis of the last 3 clones for Ptrc-Cm.
