Team:Imperial College London/Lab Diaries/Surface protein team
From 2010.igem.org
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'''Report:''' | '''Report:''' | ||
- | * | + | *Analyzing the PCR product with gel electrophoresis, we observed -as expected- a 2kb fragment on the gel. This confirms that the PCR of pSB1C3 was successful as the vector is approximately 2kb long. |
*Having confirmed that the PCR was successful we purified the PCR product from the solution using the ''E.Z.N.A.'' Cycle Pure Kit (Omega bio-tek)'' but used 25µl of ddH2O instead of elusion buffer in the last step. | *Having confirmed that the PCR was successful we purified the PCR product from the solution using the ''E.Z.N.A.'' Cycle Pure Kit (Omega bio-tek)'' but used 25µl of ddH2O instead of elusion buffer in the last step. | ||
*We then did a restriction digestion for: | *We then did a restriction digestion for: | ||
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<ul> | <ul> | ||
<li>Repeat gel electrophoresis of pSB1C3-BOO14 restriction digest | <li>Repeat gel electrophoresis of pSB1C3-BOO14 restriction digest | ||
- | <li>Perform PCR to amlify CWB out of the B. subtilis genome</li> | + | <li>Perform PCR to amlify CWB out of the ''B. subtilis'' genome</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Transformation of E. coli with ligation product pSB1C3-BOO14</li> | + | <li>Transformation of ''E. coli'' with ligation product pSB1C3-BOO14</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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'''Tuesday, 18th-Aug-2010''' | '''Tuesday, 18th-Aug-2010''' | ||
- | * | + | *''E. coli'' was transformed with the pSB1C3-BOO14 ligation using chemical competence and heat shock. We prepared plates with our transformants to be incubated overnight. |
*We reorganized and updated our Lab-Page on the Wiki, including new tables, upload of pictures and result as well as user-interface optimisation. | *We reorganized and updated our Lab-Page on the Wiki, including new tables, upload of pictures and result as well as user-interface optimisation. | ||
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*We repeated the gel electrophoresis but reduced the time it ran for to 10 minutes as BOO14 is very short. However we still only observed a very faint band at 100bp, so we can't be completely sure that the ligation was successful. | *We repeated the gel electrophoresis but reduced the time it ran for to 10 minutes as BOO14 is very short. However we still only observed a very faint band at 100bp, so we can't be completely sure that the ligation was successful. | ||
*Therefore we carried out another restriction digest with AseI (which cuts within B0014) and NcoI (which cuts within pSB1C3). | *Therefore we carried out another restriction digest with AseI (which cuts within B0014) and NcoI (which cuts within pSB1C3). | ||
- | *We also performed a PCR to amplify LytC cell wall binding domain (CWB) from the Bacillus genome. | + | *We also performed a PCR to amplify LytC cell wall binding domain (CWB) from the ''Bacillus'' genome. |
*Analysis of the PCR product with gel electrophoresis showed that lytC had not been amlified properly. There we will do a series of different PCR reaction tomorrow to determine the optimal temperatures. | *Analysis of the PCR product with gel electrophoresis showed that lytC had not been amlified properly. There we will do a series of different PCR reaction tomorrow to determine the optimal temperatures. | ||
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<ul> | <ul> | ||
<li>Midi prep of pSB1C3-BOO14 | <li>Midi prep of pSB1C3-BOO14 | ||
- | <li>PCR of | + | <li>PCR of LytC using Pfu polymerase |
<li>DpnI restriction digest of PCR product</li> | <li>DpnI restriction digest of PCR product</li> | ||
</ul> | </ul> | ||
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<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of | + | <li>Restriction digest of LytC with XbaI</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<ul> | <ul> | ||
<li>Restriction digest of pSB1C3-BOO14 with XbaI and SpeI | <li>Restriction digest of pSB1C3-BOO14 with XbaI and SpeI | ||
- | <li>Gel electrophoresis to measurement of relative concentrations of pSB1C3 and | + | <li>Gel electrophoresis to measurement of relative concentrations of pSB1C3 and LytC after restriction digest |
<li>Dephosphorylation of pSB1C3 | <li>Dephosphorylation of pSB1C3 | ||
- | <li>Ligation of pSB1C3 with | + | <li>Ligation of pSB1C3 with LytC |
- | <li>PCR of promoter | + | <li>PCR of promoter Pveg out of vector using taq</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<ul> | <ul> | ||
<li>Screen plates for successful transformation | <li>Screen plates for successful transformation | ||
- | <li>Gel electrophoresis of | + | <li>Gel electrophoresis of Pveg PCR sample 2 and PCR purified sample 1</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Gel electrophoresis of | + | <li>Gel electrophoresis of LytC |
- | <li>Gel purification of | + | <li>Gel purification of LytC |
<li>Midi prep of pSB1C3-BOO14 | <li>Midi prep of pSB1C3-BOO14 | ||
- | <li>Overnight digestion of | + | <li>Overnight digestion of LytC with SpeI</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest with XbaI and SpeI | + | <li>Restriction digest with XbaI and SpeI to confirm BOO14 in pSB1C3 |
<li>Gel purification of restriction product | <li>Gel purification of restriction product | ||
<li>Gel electrophoresis to analyse restriction product</li> | <li>Gel electrophoresis to analyse restriction product</li> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of | + | <li>Restriction digest of Pveg with EcoRI and XbaI</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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*The PCR product was then digested with DpnI to remove template DNA and then gel purified. | *The PCR product was then digested with DpnI to remove template DNA and then gel purified. | ||
*pSB1C3-BOO14 was midi prepped, and the final DNA concentration was measured to be 120ng/µl. | *pSB1C3-BOO14 was midi prepped, and the final DNA concentration was measured to be 120ng/µl. | ||
- | *Overnight digestion of | + | *Overnight digestion of LytC with SpeI was set up because restriction will be inefficient on the PCR product. XbaI will be added to the mixture in the morning making the final volume of the digestion 30µl. |
'''Tuesday, 24th-Aug-2010''' | '''Tuesday, 24th-Aug-2010''' | ||
- | *XbaI was added to the restriction digest of | + | *XbaI was added to the restriction digest of LytC. PCR purification was performed to isolate the CWB. |
- | *Due to problems with our midi-prep of pSB1C3, we only digested the two components but then had to set up another culture of | + | *Due to problems with our midi-prep of pSB1C3, we only digested the two components but then had to set up another culture of ''B. subtilis'' for another round of midi prep. |
'''Wednesday, 25th-Aug-2010''' | '''Wednesday, 25th-Aug-2010''' | ||
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*We performed a restriction digest of pSB1C3-BOO14 with XbaI and SpeI. | *We performed a restriction digest of pSB1C3-BOO14 with XbaI and SpeI. | ||
- | *We then determined the relative concentrations of | + | *We then determined the relative concentrations of LytC and pSB1C3 to prepare ligation. We found that pSB1C3 had a about 4 time higher concentration than LytC. |
*We set up a 10µl dephosphorylation reaction with 2µl of pSB1C3 and incubated for 10min followed by heat deactivation of the T4 alkaline phosphatase. | *We set up a 10µl dephosphorylation reaction with 2µl of pSB1C3 and incubated for 10min followed by heat deactivation of the T4 alkaline phosphatase. | ||
- | *2.5µl of the dephosphorylation reaction were used together with 2µl of | + | *2.5µl of the dephosphorylation reaction were used together with 2µl of LytC for a 10µl ligation reaction. This was split into a 5µl overnight ligation and a 5µl bench ligation reaction. |
- | *After 2 hours incubation at room temperature we transformed | + | *After 2 hours incubation at room temperature we transformed ''E. coli'' with the ligated vector and later plated it. |
- | *We set up a test PCR using taq polymerase to determine the best protocol to get the promoter | + | *We set up a test PCR using taq polymerase to determine the best protocol to get the promoter Pveg out the current vector pSB1AK3. |
*Gel electrophoresis of the PCR products suggested that the following protocol was most suitable: | *Gel electrophoresis of the PCR products suggested that the following protocol was most suitable: | ||
# 5 cycles at 60∞C | # 5 cycles at 60∞C | ||
# 25 cycles at 66∞C | # 25 cycles at 66∞C | ||
- | *We set up another PCR reaction using Pfu for to obtain two identical samples of | + | *We set up another PCR reaction using Pfu for to obtain two identical samples of Pveg with high fidelity |
*Sample 1 was later PCR purified by Kirill and Kyascha (thanks guys!) | *Sample 1 was later PCR purified by Kirill and Kyascha (thanks guys!) | ||
'''Friday, 27th-Aug-2010''' | '''Friday, 27th-Aug-2010''' | ||
- | *Both samples of | + | *Both samples of Pveg were successfully puified and can both be used in the following cloning steps |
- | *Our transformation was unsuccessful and no background was observed either. We thus used our overnight ligation to transform | + | *Our transformation was unsuccessful and no background was observed either. We thus used our overnight ligation to transform ''E. coli'' again. |
*We decided to digest the promoter with EcoRI and SpeI rather than EcoRI and XbaI as originally planned. Digestion with SpeI was set up overnight but the digestion volume was accidentially made up to a total of 30µl rather than 28.5µl allowing for EcoRI to be added the next day. | *We decided to digest the promoter with EcoRI and SpeI rather than EcoRI and XbaI as originally planned. Digestion with SpeI was set up overnight but the digestion volume was accidentially made up to a total of 30µl rather than 28.5µl allowing for EcoRI to be added the next day. | ||
'''Saturday, 28th-Aug-2010''' | '''Saturday, 28th-Aug-2010''' | ||
- | *Transformation of | + | *Transformation of ''E. coli'' using our overnight digestion was unsuccessful which means we have to restart construction of our LytC vector. |
- | *EcoRI was added to the | + | *EcoRI was added to the Pveg digestion and both samples were incubated for 1 hour |
- | *5µl of sample 1, which is to be PCR purified later, were loaded on a gel and 30µl (all) of sample 2, which is to be gel purified. The electrophoresis confirmed that | + | *5µl of sample 1, which is to be PCR purified later, were loaded on a gel and 30µl (all) of sample 2, which is to be gel purified. The electrophoresis confirmed that Pveg had been digested and the bands of smaple 2 (two lanes in total) were cut out of the gel for gel purification (0.44g). |
|} | |} | ||
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<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Gel Purify | + | <li>Gel Purify Pveg (digested E+S) sample 2</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Run gel electrophoresis | + | <li>Run gel electrophoresis to analyze colony PCR results</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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'''Monday, 30th-Aug-2010''' | '''Monday, 30th-Aug-2010''' | ||
- | *Both sample of | + | *Both sample of Pveg which had been digested with EcoRI and SpeI were purified: Sample 1 was PCR purified (by another team) and sample 2 gel purified. Two methods of purification were used because Pveg is so small that either method posed the risk of loosing our product. |
*Gel electrophoresis later confirmed that both samples were purified successfully. | *Gel electrophoresis later confirmed that both samples were purified successfully. | ||
- | *We also set up a PCR of | + | *We also set up a PCR of LytC for blunt ended ligation as an alternative to our previous cloning strategy. |
'''Tuesday, 31st-Aug-2010''' | '''Tuesday, 31st-Aug-2010''' | ||
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'''Plan:''' | '''Plan:''' | ||
- | * | + | * Restriction digest of pSB1C3 EcoRI and SpeI |
* Gel electrophoresis of digestion product | * Gel electrophoresis of digestion product | ||
* Gel purification of pSB1C3 | * Gel purification of pSB1C3 | ||
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'''Report:''' | '''Report:''' | ||
- | * Restriction digest of pSB1C3-BOO14 was performed with EcoRI and SpeI to remove the terminator and later allow ligation with | + | * Restriction digest of pSB1C3-BOO14 was performed with EcoRI and SpeI to remove the terminator and later allow ligation with Pveg. |
* Gel electrophoresis was used to confirmed that digestion of pSB1C3-BOO14 with EcoRI and SpeI was successful. | * Gel electrophoresis was used to confirmed that digestion of pSB1C3-BOO14 with EcoRI and SpeI was successful. | ||
- | * The digested vector was then gel purified and the relative concentrations of the digested pSB1C3 and | + | * The digested vector was then gel purified and the relative concentrations of the digested pSB1C3 and Pveg were determined. Our samples contained about 30 times as much vector as promoter and the vector is about 20 times larger than the insert. |
- | * therefore we decided to ligate overnight in a ration of 1.5 volumes of | + | * therefore we decided to ligate overnight in a ration of 1.5 volumes of Pveg to 1 volume of dephosphorylated vector. |
* LytC was digested overnight with SpeI. | * LytC was digested overnight with SpeI. | ||
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* We performed another restriction digest of pSB1C3-BOO14 using XbaI and SpeI. | * We performed another restriction digest of pSB1C3-BOO14 using XbaI and SpeI. | ||
- | * XbaI was added to the restriction digestion of | + | * XbaI was added to the restriction digestion of LytC. |
- | * Correct digestion of | + | * Correct digestion of LytC and pSB1C3-BOO14 was confirmed using gel electrophoresis and pSb1C3 as well as LytC were then gel purified. All planned steps worked and overnight ligation of pSB1C3 and LytC were set up. |
* We also prepared some LB agar today and had a meeting with the supervisors. | * We also prepared some LB agar today and had a meeting with the supervisors. | ||
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'''Friday, 3rd-Sep-2010''' | '''Friday, 3rd-Sep-2010''' | ||
- | *We finally measured the concentration of DNA in the midi | + | *We finally measured the concentration of DNA in the midi preps (of plasmids containing synthesis products). The concentrations varied between 78ng/µl and 230ng/µl and one will have to be repeated as the yield was too low. |
*The transformation of the LytC-pSB1C3 was had produced many colonies. 20 colony PCRs were set up and a replica plate made. | *The transformation of the LytC-pSB1C3 was had produced many colonies. 20 colony PCRs were set up and a replica plate made. | ||
*Unfortunately gel electrophoresis suggested that the ligation was not successful, so another round of gel electrophoresis will be performed on monday to confirm these results. | *Unfortunately gel electrophoresis suggested that the ligation was not successful, so another round of gel electrophoresis will be performed on monday to confirm these results. | ||
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<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li> | + | <li>Mini preps from overnight cultures. </li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Amplification of | + | <li>Amplification of Pveg using PCR from pSB1AK3 |
- | <li>Gel electrophoresis to confirm correct amplification of | + | <li>Gel electrophoresis to confirm correct amplification of Pveg |
- | <li>Excision and gel purification of | + | <li>Excision and gel purification of Pveg</li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>XbaI was added to overnight digestion of | + | <li>XbaI was added to overnight digestion of Pveg with SpeI |
- | <li>Gel electrophoresis to analyse | + | <li>Gel electrophoresis to analyse Pveg restrcition digest |
- | <li>Because | + | <li>Because Pveg was lost during the last steps PCR amlification of Pveg from PSB1AK3 was repeated. |
- | <li>PCR purification of | + | <li>PCR purification of Pveg</li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Mini prep using overnight cultures of pSB1C3- | + | <li>Mini prep using overnight cultures of pSB1C3-LytC |
- | <li>Restriction digest with EcoRI and SpeI as well as XbaI and SpeI for all 23 mini preps of pSB1C3- | + | <li>Restriction digest with EcoRI and SpeI as well as XbaI and SpeI for all 23 mini preps of pSB1C3-LytC |
- | <li>Culture of K5 for midi prep failed: New | + | <li>Culture of K5 for midi prep failed: New culture was set up</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of pSB1C3- | + | <li>Restriction digest of pSB1C3-LytC mini preps with XbaI and SpeI |
<li>Gel electrophoresis to analyse restriction fragments</li> | <li>Gel electrophoresis to analyse restriction fragments</li> | ||
</ul> | </ul> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of | + | <li>Restriction digest of Pveg with XbaI and SpeI |
<li>Gel electrophoresis of restriction fragments for analysis | <li>Gel electrophoresis of restriction fragments for analysis | ||
- | <li>Diagnostic digest of | + | <li>Diagnostic digest of Pveg was repeated with SpeI overnight </li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of | + | <li>Restriction digest of LytC in blunt-ended ligation vector |
<li>Set up of midi prep cultur from K5 | <li>Set up of midi prep cultur from K5 | ||
- | <li>Set up 23 mini prep cultures of pSB1C3- | + | <li>Set up 23 mini prep cultures of pSB1C3-LytC |
<li>Test culture was set up to test new chloramphenicol aliquot</li> | <li>Test culture was set up to test new chloramphenicol aliquot</li> | ||
</ul> | </ul> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Repeat of digest of | + | <li>Repeat of digest of Pveg with SpeI overnight (EcoRI will be added tomorrow)</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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'''Monday, 6th-Sep-2010''' | '''Monday, 6th-Sep-2010''' | ||
- | * We repeated the gel electrophoresis for the 7th colony PCR, because it showed a faint band around 1kb, indicating that | + | * We repeated the gel electrophoresis for the 7th colony PCR, because it showed a faint band around 1kb, indicating that LytC was present in pSB1C3. |
- | * Simultaneously we set up another 20 colony PCRs for colonies from the pSB1C3- | + | * Simultaneously we set up another 20 colony PCRs for colonies from the pSB1C3-LytC ligation/transformation and made a replica plate. |
- | * We also set up mini prep cultures from (a) the blunt-ended ligation of | + | * We also set up mini prep cultures from (a) the blunt-ended ligation of LytC and a vector and (b) numbers 5, 7, 18 and 19 of pSB1C3-lytC from the original colony PCR. |
* The second colony PCR products were analysed using gel electrophoresis, but we think the primers may not be annealing because the bands at 1kb were not observed. | * The second colony PCR products were analysed using gel electrophoresis, but we think the primers may not be annealing because the bands at 1kb were not observed. | ||
'''Tuesday, 7th-Sep-2010''' | '''Tuesday, 7th-Sep-2010''' | ||
- | * We used the overnight cultures to make mini preps of both blunt-ended ligation of | + | * We used the overnight cultures to make mini preps of both blunt-ended ligation of LytC and pSB1C3-LytC. |
- | * We then performed a restriction digest of the pSB1C3- | + | * We then performed a restriction digest of the pSB1C3-LytC mini preps with XbaI and SpeI to confirm that: |
#The LytC cell wall binding domain is in the plasmid | #The LytC cell wall binding domain is in the plasmid | ||
#The CWB is in the correct orientation | #The CWB is in the correct orientation | ||
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'''Wednesday, 8th-Sep-2010''' | '''Wednesday, 8th-Sep-2010''' | ||
- | * We used PCR to amplify | + | * We used PCR to amplify Pveg from pSB1AK3 again. |
- | * Gel electrophoresis confirmed that PCR of | + | * Gel electrophoresis confirmed that PCR of Pveg was successful although a big, strong band appeared far above the expected length of Pveg as well. |
- | * | + | * Pveg was cut out of the gel and purified. |
- | * A restriction digest of | + | * A restriction digest of Pveg with XbaI and SpeI was performed. |
* When analysing the restriction fragments using gel electrophoresis it appeared to have failed ''(it turned out later that one of the settings of the UV-box had been changed so not enough light was detected) | * When analysing the restriction fragments using gel electrophoresis it appeared to have failed ''(it turned out later that one of the settings of the UV-box had been changed so not enough light was detected) | ||
* pVEG was then digested with SpeI ovenight | * pVEG was then digested with SpeI ovenight | ||
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'''Thursday, 9th-Sep-2010''' | '''Thursday, 9th-Sep-2010''' | ||
- | * XbaI was added to overnigh digestion of | + | * XbaI was added to overnigh digestion of Pveg with SpeI. |
- | * The XbaI and SpeI restriction digestion of | + | * The XbaI and SpeI restriction digestion of Pveg was analysed using gel electrophoresis but it Pveg had been lost. |
* Therefore the PCR amlification from pSB1AK3 was repeated. | * Therefore the PCR amlification from pSB1AK3 was repeated. | ||
* This was followed by PCR purification which was then used for an overnight digestion with SpeI. Unlike last time, the gel purification was not used because it decreased our yield too much. | * This was followed by PCR purification which was then used for an overnight digestion with SpeI. Unlike last time, the gel purification was not used because it decreased our yield too much. | ||
- | * A restriction digest of | + | * A restriction digest of LytC in the blunt-ended vector was performed. |
* Subsequent analysis by gel electrophoresis showed a possible candidate from Kirsten's blunt ended ligations (K5). | * Subsequent analysis by gel electrophoresis showed a possible candidate from Kirsten's blunt ended ligations (K5). | ||
* A midi prep culture for K5 was set up. | * A midi prep culture for K5 was set up. | ||
- | * 23 mini prep cultures from our ligation plate of pSB1C3- | + | * 23 mini prep cultures from our ligation plate of pSB1C3-LytC were set up. |
* A test culture was set up to check if a new aliquot of chloramphenicol works. | * A test culture was set up to check if a new aliquot of chloramphenicol works. | ||
'''Friday, 10th-Sep-2010''' | '''Friday, 10th-Sep-2010''' | ||
- | * | + | *Pveg was set up in a restriction digest with SpeI |
*The overnight culture of K5 failed because the wrong antibiotic was used. A new culture was set up with the correct antibiotic. | *The overnight culture of K5 failed because the wrong antibiotic was used. A new culture was set up with the correct antibiotic. | ||
- | *23 Mini preps of | + | *23 Mini preps of LytC-pSB1C3 ligation were made. |
- | *A restriction digest of | + | *A restriction digest of LytC-pSB1C3 was performed with EcoRI and SpeI as well as XbaI and SpeI for the next day. |
- | *Another restriction digest of | + | *Another restriction digest of Pveg was set up using EcoRI and SpeI this time (EcoRI will be added on the next morning). |
'''Saturday, 11th-Sep-2010''' | '''Saturday, 11th-Sep-2010''' | ||
- | *EcoRI was added to the | + | *EcoRI was added to the Pveg restriction digest. |
- | *Gel electrophoresis of the restriction digest of the mini preps indicated that restriction did not work as expected, maybe because one of the enzymes did not cut as a result of a wrong insert. Another possibility is that | + | *Gel electrophoresis of the restriction digest of the mini preps indicated that restriction did not work as expected, maybe because one of the enzymes did not cut as a result of a wrong insert. Another possibility is that LytC is in pSB1C3 in the wrong direction, thus disrupting the restriction sites. |
*Gel electrophoresis was used to analyse the restriction fragments of pVeg, which indicated that pVeg had been cut correctly. | *Gel electrophoresis was used to analyse the restriction fragments of pVeg, which indicated that pVeg had been cut correctly. | ||
- | * | + | *Pveg was cut out of the gel to be gel purified for ligation with pSB1C3. |
*The K5 midi prep was started and paused after step 13 of the protocol. | *The K5 midi prep was started and paused after step 13 of the protocol. | ||
'''Sunday, 12th-Sep-2010''' | '''Sunday, 12th-Sep-2010''' | ||
- | *Digested | + | *Digested Pveg was gel purified and ligated with digested, dephosphorylated pSB1C3. |
- | *Restriction digest of pSB1C3- | + | *Restriction digest of pSB1C3-LytC with EcoRI and SpeI as well as EcoRI only was performed. |
* Gel electrophoresis showed that SpeI did not cut the vector, probably as a result of incorrect ligation. | * Gel electrophoresis showed that SpeI did not cut the vector, probably as a result of incorrect ligation. | ||
*The midi prep of K5 was completed | *The midi prep of K5 was completed | ||
Line 710: | Line 710: | ||
<ul> | <ul> | ||
<li>Screen plates for transformed colonies | <li>Screen plates for transformed colonies | ||
- | <li>Set up mini prep cultures of pSB1C3- | + | <li>Set up mini prep cultures of pSB1C3-LytC and pSB1C3-Pveg |
<li>Wiki meeting</li> | <li>Wiki meeting</li> | ||
</ul> | </ul> | ||
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<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Mini preps of pSB1C3- | + | <li>Mini preps of pSB1C3-LytC (7) were made but the pSB1C3-Pveg (4) mini preps failed |
- | <li>New cultures for mini preps of pSB1C3- | + | <li>New cultures for mini preps of pSB1C3-Pveg were set up</li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Mini preps of pSB1C3- | + | <li>Mini preps of pSB1C3-Pveg were successfully made</li> |
</ul> | </ul> | ||
</td> | </td> | ||
Line 735: | Line 735: | ||
<li>Gel electrophoresis to determine concentrations of purified fragments | <li>Gel electrophoresis to determine concentrations of purified fragments | ||
<li>Dephosphorylation of pSB1C3 | <li>Dephosphorylation of pSB1C3 | ||
- | <li>Ligation of pSB1C3 with | + | <li>Ligation of pSB1C3 with LytC overnight |
- | <li>Transform ''E. coli'' with | + | <li>Transform ''E. coli'' with Pveg ligations (has to be repeated)</li> |
</ul> | </ul> | ||
</td> | </td> | ||
<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Transform | + | <li>Transform ''E. coli'' with the ligated pSB1C3-LytC (from K5 culture) |
- | <li>Transform | + | <li>Transform ''E. coli'' with the ligated pSB1C3-Pveg |
- | <li>Repeat PCR amplification of | + | <li>Repeat PCR amplification of Pveg from pSB1AK3 with the shorter extension time</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of pSB1C3- | + | <li>Restriction digest of pSB1C3-LytC with |
1) XbaI and SpeI | 1) XbaI and SpeI | ||
2) AccI | 2) AccI | ||
Line 761: | Line 761: | ||
<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Restriction digest of pSB1C3- | + | <li>Restriction digest of pSB1C3-Pveg, pSB1C3-LytC and linker sequences in pSB1C3 with EcoRI and SpeI. |
<li>Gel electrophoresis of digests</li> | <li>Gel electrophoresis of digests</li> | ||
</ul> | </ul> | ||
Line 779: | Line 779: | ||
* After gel purification the relative concentration of vector to insert were determined by gel electrophoresis. | * After gel purification the relative concentration of vector to insert were determined by gel electrophoresis. | ||
* After dephosphorylation of pSB1C3, overnight ligation was set up. | * After dephosphorylation of pSB1C3, overnight ligation was set up. | ||
- | * ''E. coli'' were transformed with pSB1C3- | + | * ''E. coli'' were transformed with pSB1C3-Pveg but could not be plated so transformation will have to repeated. |
'''Tuesday, 14th-Sep-2010''' | '''Tuesday, 14th-Sep-2010''' | ||
*The meeting with Prof Fenwick and Dr Harrison from the Schistosoma Control Initiative (SCI) was very rewarding. Feedback can be found on the Human Practices page. | *The meeting with Prof Fenwick and Dr Harrison from the Schistosoma Control Initiative (SCI) was very rewarding. Feedback can be found on the Human Practices page. | ||
- | *We performed two transformations of | + | *We performed two transformations of ''E. coli'' with: |
- | #the ligated pSB1C3- | + | #the ligated pSB1C3-LytC (from K5 culture) |
- | #the ligated pSB1C3- | + | #the ligated pSB1C3-Pveg |
- | *We also repeated the PCR amplification of | + | *We also repeated the PCR amplification of Pveg from pSB1AK3 with the shorter extension time, which produced a much higher concentration of pveg so it will be easier to ligate it with pSB1C3. |
'''Wednesday, 15th-Sep-2010''' | '''Wednesday, 15th-Sep-2010''' | ||
- | *Transformations of | + | *Transformations of ''E. coli'' with pSB1C3-Pveg and pSB1C3-LytC was successful. |
- | *Mini prep cultures were set up for both pSB1C3- | + | *Mini prep cultures were set up for both pSB1C3-LytC (7) and pSB1C3-Pveg (5). |
*The team had a meeting to discuss the wiki. | *The team had a meeting to discuss the wiki. | ||
'''Thursday, 16th-Sep-2010''' | '''Thursday, 16th-Sep-2010''' | ||
- | *The mini preps of pSB1C3- | + | *The mini preps of pSB1C3-LytC were successful, however the mini preps of pSB1C3-pveg failed. |
*Restriction digest of pSB1C3-lytC with XbaI and SpeI for the double digest, as well as AccI for the single digest were performed. | *Restriction digest of pSB1C3-lytC with XbaI and SpeI for the double digest, as well as AccI for the single digest were performed. | ||
*Cultures for new pSB1C3-pVeg mini preps were set up. | *Cultures for new pSB1C3-pVeg mini preps were set up. | ||
- | *Unfortunately gel electrophoresis of the digestion of pSb1C3- | + | *Unfortunately gel electrophoresis of the digestion of pSb1C3-LytC were not conclusive because Either XbaI or SpeI did not cut, nor did AccI. Therefore the digest will be repeated tomorrow with EcoRI rather than XbaI. |
'''Friday, 17th-Sep-2010''' | '''Friday, 17th-Sep-2010''' | ||
- | *Mini preps of | + | *Mini preps of Pveg were successfully made |
- | *Restriction digest of pSB1C3- | + | *Restriction digest of pSB1C3-Pveg, pSB1C3-LytC and several linker sequences also in pSB1C3 were set up using EcoRI and SpeI. |
- | *Gel electrophoresis was used to analyse the restriction digest. It showed that pSB1C3- | + | *Gel electrophoresis was used to analyse the restriction digest. It showed that pSB1C3-Pveg as well as the linkers had been ligated and transformed into ''E. coli'' successfully. However we most likely did not succeed in construction pSB1C3-LytC yet. |
|} | |} | ||
{| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20" | {| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif;color:#555555;margin-top:5px;" cellspacing="20" | ||
Line 834: | Line 834: | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Prepare K5M3 ( | + | <li>Prepare K5M3 (LytC in blunt ended ligation vector) as well as H2 and H3 for sequencing |
<li>Analysed digestion of H2 and H3 with AseI </li> | <li>Analysed digestion of H2 and H3 with AseI </li> | ||
</ul> | </ul> | ||
Line 845: | Line 845: | ||
<td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;height:100px;width:150px;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Midi prep cultures set up yesterday were used to make successful midi preps of pSB1C3- | + | <li>Midi prep cultures set up yesterday were used to make successful midi preps of pSB1C3-Pveg</li> |
</ul> | </ul> | ||
</td> | </td> | ||
Line 870: | Line 870: | ||
<li>Restriction digest of the linkers with EcoRI and SpeI as well as AccI | <li>Restriction digest of the linkers with EcoRI and SpeI as well as AccI | ||
<li>Gel electrophoresis | <li>Gel electrophoresis | ||
- | <li>Set up midi prep cultures for pSB1C3- | + | <li>Set up midi prep cultures for pSB1C3-Pveg (H2,H3)</li> |
</ul> | </ul> | ||
</td> | </td> | ||
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<td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | <td style="background-color:#e7e7e7;text-align:left;font-family: helvetica, arial, sans-serif;color:#555555;"> | ||
<ul> | <ul> | ||
- | <li>Determine concentration of DNA in pSB1C3- | + | <li>Determine concentration of DNA in pSB1C3-Pveg midi prep |
<li>Set up midi prep cultures of the linkers that were sucessfully tested | <li>Set up midi prep cultures of the linkers that were sucessfully tested | ||
<li>Make replica plate and set up mini prep cultures of pSB1C3-ComD</li> | <li>Make replica plate and set up mini prep cultures of pSB1C3-ComD</li> | ||
Line 899: | Line 899: | ||
'''Monday, 20th-Sep-2010''' | '''Monday, 20th-Sep-2010''' | ||
- | *Samples of | + | *Samples of LytC in the blunt-ended vector (K5M3) as well as Pveg (H2, H3) were send off for sequencing. No primer had to be added to K5M3 because it is avaliable at the company. |
- | *We analysed the restriction digest from yesterday using gel electrophoresis. AseI did not cut either sample of | + | *We analysed the restriction digest from yesterday using gel electrophoresis. AseI did not cut either sample of Pveg which is a positive result because AseI does not cut Pveg but BOO14, allowing us to say with some confidence that we have got Pveg. Sequencing will give us certainty soon. |
*Replica plate and mini prep cultures for the linker Gly-X Com AB were set up | *Replica plate and mini prep cultures for the linker Gly-X Com AB were set up | ||
Line 912: | Line 912: | ||
'''Wednesday, 21st-Sep-2010''' | '''Wednesday, 21st-Sep-2010''' | ||
- | *Overnight cultures (H2,H3) of pSB1c3- | + | *Overnight cultures (H2,H3) of pSB1c3-pveg were used to make midi preps. |
*Another 3 mini preps of the linker Flex Com CDE were anaysed with a restriction digest using EcoRI and SpeI for the double and AccI for the single digest. | *Another 3 mini preps of the linker Flex Com CDE were anaysed with a restriction digest using EcoRI and SpeI for the double and AccI for the single digest. | ||
*Gel electrophoresis of the restriction fragements showed that the ligation/transformation has not been successful, so it will be repeated. | *Gel electrophoresis of the restriction fragements showed that the ligation/transformation has not been successful, so it will be repeated. | ||
- | *Sequencing results confirmed, that pSB1C3- | + | *Sequencing results confirmed, that pSB1C3-Pveg has the correct sequence. Midi preps concentration will be measured tomorrow. |
'''Thursday, 22nd-Sep-2010''' | '''Thursday, 22nd-Sep-2010''' | ||
- | *Determine concentration of DNA in midi prep of pSB1C3- | + | *Determine concentration of DNA in midi prep of pSB1C3-Pveg: |
#Concentration of DNA in H2 was ~950ng/µl | #Concentration of DNA in H2 was ~950ng/µl | ||
#Concentration of DNA in H3 was ~430ng/µl | #Concentration of DNA in H3 was ~430ng/µl |
Revision as of 02:56, 28 October 2010
Lab Diaries | Overview | Surface Protein Team | XylE Team | Vectors Team | Modelling Team |
Here are the technical diaries for our project. We've split them up into three lab teams and the modelling team. We think it's really important that absolutely anyone can find out what we've been doing. For a really detailed look at what we did, and when, you've come to the right place! |
Surface Protein Team |
Our aim was to assemble the surface protein construct, consisting of the LytC cell wall binding domain, CWBD), the linker containing a protease cleavage site and the autoinducing peptide (AIP). This protein would be under the control of the pVeg promoter.
Here's a picture of the final construct: |
Week 6 | ||||||||||||||||||
Plan:
Report:
Saturday, 14th-Aug-2010 Plan:
Report:
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Week 7 | ||||||||||||||||||
Monday, 17th-Aug-2010
Tuesday, 18th-Aug-2010
Wednesday, 19th-Aug-2010
Thursday, 20th-Aug-2010
Friday, 21st-Aug-2010
Sunday, 22nd Aug 2010
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Week 8 | ||||||||||||||||||
Monday, 23rd Aug 2010
Tuesday, 24th-Aug-2010
Wednesday, 25th-Aug-2010
Thursday, 26th-Aug-2010
Friday, 27th-Aug-2010
Saturday, 28th-Aug-2010
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Week 9 | ||||||||||||||||||
Tuesday, 31st-Aug-2010
Report:
Wednesday, 1st-Sep-2010
Thursday, 2nd-Sep-2010
Friday, 3rd-Sep-2010
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Week 10 | ||||||||||||||||||
Tuesday, 7th-Sep-2010
Wednesday, 8th-Sep-2010
Thursday, 9th-Sep-2010
Friday, 10th-Sep-2010
Saturday, 11th-Sep-2010
Sunday, 12th-Sep-2010
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Week 11 | ||||||||||||||||||
Monday, 13th-Sep-2010
Tuesday, 14th-Sep-2010
Wednesday, 15th-Sep-2010
Thursday, 16th-Sep-2010
Friday, 17th-Sep-2010
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Week 12 | ||||||||||||||||||
Monday, 20th-Sep-2010
Tuesday, 21st-Sep-2010
Wednesday, 21st-Sep-2010
Thursday, 22nd-Sep-2010
Friday, 23rd-Sep-2010
|