Team:Wageningen UR/Journal/week6

From 2012.igem.org

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{{Template:Ecoil}}
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{{Template:WUR}}
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= week 5: 4 june - 8 june =
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= week 6: 4 june - 10 june =
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== office work ==
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== Office work ==
'''Wiki page'''
'''Wiki page'''
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Monday:
Monday:
-
*Update notebook and protocols
+
*Update of notebook and protocols
-
*Start to make master-plan for wiki page
+
*Start to design the master-plan for the wiki page
-
*Developing the wiki template further
+
*Designing the wiki template further
This monday we've worked further on updating the wiki, we are now on schedule with the notebook and protocols. We also made a master plan on how the wiki should look like. The first steps are being made to create a prize winning wiki page.
This monday we've worked further on updating the wiki, we are now on schedule with the notebook and protocols. We also made a master plan on how the wiki should look like. The first steps are being made to create a prize winning wiki page.
Line 17: Line 17:
Tuesday:
Tuesday:
 +
 +
*Update of notebook and protocols
 +
*Designing the master-plan for the wiki further
 +
*Creating the wiki homepage
 +
 +
 +
Wednesday:
 +
 +
*Update of notebook and protocols
 +
*Changing every Wensday into Wednesday
 +
 +
 +
Thursday:
 +
*Update notebook and protocols
*Update notebook and protocols
-
*Develop master-plan further
+
 
 +
 
 +
'''Munich'''
 +
 
 +
 
 +
Monday:
 +
 
 +
*Review of the two abstracts
 +
 
 +
 
 +
Tuesday:
 +
 
 +
*Further editing the two abstracts
 +
*Submitting the abstracts
 +
 
 +
 
 +
'''Other'''
 +
 
 +
Tuesday:
 +
*Start designing the WageningenUR clothing
 +
 
[Meeting]
[Meeting]
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written by: Mark
written by: Mark
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== lab work ==
+
== Lab work ==
'''CCMV Bricking:'''
'''CCMV Bricking:'''
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*Check agar plates for colonies
*Check agar plates for colonies
*Grow colonies in LB medium + kanamycin, checked optical density
*Grow colonies in LB medium + kanamycin, checked optical density
-
Colonies:
+
*Colonies:
<ol>
<ol>
<li>CCMV-1</li>
<li>CCMV-1</li>
Line 49: Line 83:
*Checked Greiner tubes
*Checked Greiner tubes
-
Colonies:
+
*Colonies:
<ol>
<ol>
<li>CCMV-1: growth</li>
<li>CCMV-1: growth</li>
Line 58: Line 92:
</ol>
</ol>
*Mini prep the 4 remaining samples
*Mini prep the 4 remaining samples
 +
*Prepare the mini prep samples for agarose gel
 +
*Run the agarose gel (1% w/v agarose)
 +
*Check agarose gel
 +
 +
The gel does not look promissing, as the size seems to be bigger than we expected. However, as we are dealing with plasmids, digestion will give the conclusive outcome, with linearized products on a gel. This will be done tomorrow
 +
 +
 +
Wednesday:
 +
 +
*Minipreps of the 4 remaining samples is digested by Not1, for half an hour in a FastDigest Green buffer (fermentas)
 +
*Digest products are ready to load on an agarose gel without adding loading buffer due to the Green buffer
 +
*Run the agarose gel (1% w/v agarose)
 +
 +
The digestion products were not the expected products. We suspect that the linearized backbone pSB1K3 ligated with itself (suffix to suffix, prefix to prefix), as we get a single result arround 2.2k bp. Conclusion: the bricking failed.
 +
 +
Thursday:
 +
*
*
Line 64: Line 115:
Monday:
Monday:
-
*Followed dialysis protocol
+
*Prepared two samples for dialysis according to the dialysis protocol
-
*Change: instead of sonicator for cell lysis, French press was used
+
*Change: instead of sonicator for cell lysis, French press was used for one of the samples
We've also made two samples of wt CCMV VLP ready for dialysis. There is only one modification applied in the protocol, instead of using the horrible sonicator, we used the French press, which is a great apparatus and easy to use. In the late afternoon we started with the dialysis.
We've also made two samples of wt CCMV VLP ready for dialysis. There is only one modification applied in the protocol, instead of using the horrible sonicator, we used the French press, which is a great apparatus and easy to use. In the late afternoon we started with the dialysis.
-
written by: Mark
+
Tuesday:
 +
 
 +
*Changed the buffer 3 times according to the dialysis protocol
 +
*Made an appointment for DLS
 +
 
 +
 
 +
Wednesday:
 +
 
 +
*Changed the buffer 3 times according to the dialysis protocol
 +
 
 +
 
 +
Thursday:
 +
 
 +
*Stopped dialysis
 +
*Prepare samples for ultracentrifuge according to protocol
 +
*Run ultracentrifuge, 4 degree Celcius 3 hours
 +
*prepare samples for DLS
 +
 
 +
 
 +
written by: Mark and Jeroen
 +
----
 +
[[https://2012.igem.org/Team:Wageningen_UR/Journal/week5 previous week]]          [[https://2012.igem.org/Team:Wageningen_UR/Journal/week7 next week]]

Latest revision as of 22:53, 26 September 2012

week 6: 4 june - 10 june

Office work

Wiki page

Monday:

  • Update of notebook and protocols
  • Start to design the master-plan for the wiki page
  • Designing the wiki template further

This monday we've worked further on updating the wiki, we are now on schedule with the notebook and protocols. We also made a master plan on how the wiki should look like. The first steps are being made to create a prize winning wiki page.


Tuesday:

  • Update of notebook and protocols
  • Designing the master-plan for the wiki further
  • Creating the wiki homepage


Wednesday:

  • Update of notebook and protocols
  • Changing every Wensday into Wednesday


Thursday:

  • Update notebook and protocols


Munich


Monday:

  • Review of the two abstracts


Tuesday:

  • Further editing the two abstracts
  • Submitting the abstracts


Other

Tuesday:

  • Start designing the WageningenUR clothing


[Meeting]


written by: Mark

Lab work

CCMV Bricking:

Monday:

  • Check agar plates for colonies
  • Grow colonies in LB medium + kanamycin, checked optical density
  • Colonies:
  1. CCMV-1
  2. CCMV-2
  3. d26-CCMV-1
  4. d26-CCMV-2
  5. d26-CCMV-3
  • overnight in shaker 37 degree Celcius

The monday morning of this week started with a bit of a shock: our plates with our transformed E.coli we're almost completely empty. Luckely there was at least one colony on both of the plates with transformed E.coli containing bricks. We put them in Greiner tubes with LB-medium and a antibiotic and after a few hours checked their optical density. In the afternoon we prepared the samples for a PCR to validate the bricks.


Tuesday:

  • Checked Greiner tubes
  • Colonies:
  1. CCMV-1: growth
  2. CCMV-2: no growth
  3. d26-CCMV-1: growth
  4. d26-CCMV-2: growth
  5. d26-CCMV-3: growth
  • Mini prep the 4 remaining samples
  • Prepare the mini prep samples for agarose gel
  • Run the agarose gel (1% w/v agarose)
  • Check agarose gel

The gel does not look promissing, as the size seems to be bigger than we expected. However, as we are dealing with plasmids, digestion will give the conclusive outcome, with linearized products on a gel. This will be done tomorrow


Wednesday:

  • Minipreps of the 4 remaining samples is digested by Not1, for half an hour in a FastDigest Green buffer (fermentas)
  • Digest products are ready to load on an agarose gel without adding loading buffer due to the Green buffer
  • Run the agarose gel (1% w/v agarose)

The digestion products were not the expected products. We suspect that the linearized backbone pSB1K3 ligated with itself (suffix to suffix, prefix to prefix), as we get a single result arround 2.2k bp. Conclusion: the bricking failed.

Thursday:

CCMV test protocol:

Monday:

  • Prepared two samples for dialysis according to the dialysis protocol
  • Change: instead of sonicator for cell lysis, French press was used for one of the samples

We've also made two samples of wt CCMV VLP ready for dialysis. There is only one modification applied in the protocol, instead of using the horrible sonicator, we used the French press, which is a great apparatus and easy to use. In the late afternoon we started with the dialysis.


Tuesday:

  • Changed the buffer 3 times according to the dialysis protocol
  • Made an appointment for DLS


Wednesday:

  • Changed the buffer 3 times according to the dialysis protocol


Thursday:

  • Stopped dialysis
  • Prepare samples for ultracentrifuge according to protocol
  • Run ultracentrifuge, 4 degree Celcius 3 hours
  • prepare samples for DLS


written by: Mark and Jeroen

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