Team:ETH Zurich/Biology/Journal

From 2011.igem.org

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{{:Team:ETH Zurich/Templates/Header/Biology|currPage=Journal}}
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{| style="width:900px;background:#f5f5f5;text-align:justify;font-family: helvetica, arial, sans-serif; margin-top:25px; border-radius:10px;" cellspacing="15" cellpadding="5"
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{{:Team:ETH Zurich/Templates/SectionStart}}
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|style="font-size:2em;" valign="top" class="biology"|Lab Journal
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= Lab Journal =
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|style="font-family: helvetica, arial, sans-serif;font-size:1.5em; border-radius:10px" align="right" class="biologyTitle"|Week [[#Week 1:  20.6-26.6|1]] [[#Week 2:  27.6-3.7|2]] [[#Week 3:  4.7-10.7|3]] [[#Week 4:  11.7-17.7|4]] [[#Week 5:  18.7-24.7|5]] [[#Week 6:  25.7-31.7|6]] [[#Week 7:  1.8-7.8|7]] [[#Week 8:  8.8-14.8|8]] [[#Week 9:  15.8-21.8|9]] [[#Week 10:  22.8-28.8|10]] [[#Week 11:  29.8-4.9|11]] [[#Week 12:  5.9.-11.9|12]] [[#Week 13:  12.9.-18.9|13]] [[#Week 14:  19.9.-25.9|14]]
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'''Here you can follow the progress of our project as it is coming together.'''
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|-
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{{:Team:ETH Zurich/Templates/SectionEnd}}
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|colspan="2"|'''Here you can follow the progress of our project as it is coming together.'''
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|}
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{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 1:  20.6-26.6''' ==
== '''Week 1:  20.6-26.6''' ==
-
 
* First meeting
* First meeting
-
* Brainstorming
+
* [[Team:ETH_Zurich/Team/Brainstorming|Brainstorming]]
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== ''' Week 2:  27.6-3.7''' ==
== ''' Week 2:  27.6-3.7''' ==
 +
* [[Team:ETH_Zurich/Team/Brainstorming|Brainstorming]]
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
-
* Brainstorming
+
{{:Team:ETH Zurich/Templates/SectionStart}}
-
 
+
== ''' Week 3:  4.7-10.7''' ==
== ''' Week 3:  4.7-10.7''' ==
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</gallery>
</gallery>
-
* Design of several Operons for AlcR and several PCR primer
+
* Design of several Operons for AlcR and several PCR primers
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 4:  11.7-17.7''' ==
== '''Week 4:  11.7-17.7''' ==
-
* Ordering of the LacI<sub>M1</sub> and codonoptimized AlcR gene
+
* Ordering of the LacI<sub>M1</sub> and codon-optimized AlcR gene
* Making of competent DH5-&alpha; cells
* Making of competent DH5-&alpha; cells
* Cloning of the AlcR-testsystem
* Cloning of the AlcR-testsystem
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 5:  18.7-24.7''' ==
== '''Week 5:  18.7-24.7''' ==
* First test of the AlcR-system in 96-well plates
* First test of the AlcR-system in 96-well plates
-
 
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 6:  25.7-31.7''' ==
== '''Week 6:  25.7-31.7''' ==
* Transformation of the parts from the iGEM plates
* Transformation of the parts from the iGEM plates
-
 
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 7:  1.8-7.8''' ==
== '''Week 7:  1.8-7.8''' ==
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* Ligation and Transformation of
* Ligation and Transformation of
-
** &lambda;<sub>P</sub> and luxI
+
** P<sub>R</sub> and luxI
-
** &lambda;<sub>P</sub> and lacI
+
** P<sub>R</sub> and lacI
** P<sub>lac</sub> and GFP<sub>LVA</sub>
** P<sub>lac</sub> and GFP<sub>LVA</sub>
** P<sub>lux</sub> and mCherry
** P<sub>lux</sub> and mCherry
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* First meeting with Dr. Oliver Frey (Bio engineering laboratory, Prof. Andreas Hierlemann, D-BSSE ETHZ) to exchange ideas about microfluidic design
* First meeting with Dr. Oliver Frey (Bio engineering laboratory, Prof. Andreas Hierlemann, D-BSSE ETHZ) to exchange ideas about microfluidic design
-
 
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 8:  8.8-14.8''' ==
== '''Week 8:  8.8-14.8''' ==
 +
[[File:Lab5.jpg|right|300px]]
* Synthesized LacI<sub>M1</sub> Gen arrived
* Synthesized LacI<sub>M1</sub> Gen arrived
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** P<sub>tet</sub> and LacI<sub>M1</sub>
** P<sub>tet</sub> and LacI<sub>M1</sub>
** P<sub>tet</sub>-LacI<sub>M1</sub> and Terminator
** P<sub>tet</sub>-LacI<sub>M1</sub> and Terminator
-
 
* Improving of the testsystem
* Improving of the testsystem
-
** Exchange of same rare codons in AlcR by PCR
+
** Exchange of some rare codons in AlcR by PCR
-
** His-tagging of AlcR
+
** His-tagging of AlcR for detection in Western blot
-
** GFP assam
+
** include sfGFP
-
* Transformation of &lambda;<sub>P</sub>
+
* Transformation of P<sub>R</sub>
-
* Making of competent JM101 cells
+
* Creation of competent JM101 cells
** Check for transformation efficiency
** Check for transformation efficiency
-
 
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 9:  15.8-21.8''' ==
== '''Week 9:  15.8-21.8''' ==
-
 
+
[[File:IMG 6171 Kopie.JPG|right|300px]]
* Growth and repression test of AlcR-system with M9-medium
* Growth and repression test of AlcR-system with M9-medium
* Ligation and Transformation of
* Ligation and Transformation of
-
** &lambda;<sub>P</sub> and lacI
+
** P<sub>R</sub> and lacI
-
** &lambda;<sub>P</sub> and luxI
+
** P<sub>R</sub> and luxI
** P<sub>tet</sub> and CI
** P<sub>tet</sub> and CI
-
** &lambda;<sub>P</sub>-lacI and terminator
+
** P<sub>R</sub>-lacI and terminator
-
** &lambda;<sub>P</sub>-luxI and terminator
+
** P<sub>R</sub>-luxI and terminator
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 10:  22.8-28.8''' ==
== '''Week 10:  22.8-28.8''' ==
* Transformation and Ligation
* Transformation and Ligation
** P<sub>tet</sub>-CI and Terminator
** P<sub>tet</sub>-CI and Terminator
-
*Preparation of chemically competent DH5-α and JM101 cells
+
* Preparation of chemically competent DH5-α and JM101 cells
-
 
+
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 11:  29.8-4.9''' ==
== '''Week 11:  29.8-4.9''' ==
* Transformation and Ligation
* Transformation and Ligation
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* Diffusion test through tube system filled with agarose and cells
* Diffusion test through tube system filled with agarose and cells
* Test of the improved AlcR system
* Test of the improved AlcR system
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
== '''Week 12:  5.9.-11.9''' ==
 +
[[File:Lab6.JPG|right|300px]]
-
== '''Week 12:  5.9.-11.9''' ==
 
*Design of a system to characterize our new biobrick LacI<sub>M1</sub>
*Design of a system to characterize our new biobrick LacI<sub>M1</sub>
**Transformation and Ligation
**Transformation and Ligation
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***P<sub>const</sub> and TetR<sub>LVA</sub>
***P<sub>const</sub> and TetR<sub>LVA</sub>
-
*Growth-test of ''E.coli'' in M9 with reduced Ampicillin concentration
+
*Growth-test of ''E. coli'' in M9 with reduced Ampicillin concentration
*AlcR test with reduced Ampicillin concentration
*AlcR test with reduced Ampicillin concentration
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*Alternative Sensor system: Xylene system
*Alternative Sensor system: Xylene system
 +
**Transformation and Ligation
 +
*** P<sub>const</sub> and XylR
 +
*** P<sub>Xyl</sub> and CI
 +
*** P<sub>Xyl</sub> and LacI <sub>M1</sub>
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 13:  12.9.-18.9''' ==
== '''Week 13:  12.9.-18.9''' ==
 +
[[File:IMG 6442.JPG|right|300px]]
 +
* PCR of the pBR322 Ori
 +
* PCR of the gen cluster for the upper TOL pathway
 +
* first test of cell printing
 +
*Transformation and Ligation of
 +
** P<sub>const</sub>-TetR- P<sub>Tet</sub>-LacI<sub>M1</sub> and  P<sub>R</sub>-GFPassam
 +
* Western Blot of AlcR
 +
* Making of competent DH5-α cells
 +
* Design and construction of Psb6A5
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
== '''Week 14:  19.9.-25.9''' ==
== '''Week 14:  19.9.-25.9''' ==
 +
* Characterization of LacI<sub>M1</sub>
 +
* Cloning of all biobricks into pSB1C3
 +
* PCR of LacI and CI
 +
* wiki
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
== '''Week 15:  26.9.-02.10''' ==
 +
[[File:IMG 6649.JPG|right|300px]]
 +
* design of Pu promoter
 +
* test of Pu promoter
 +
* test for indol degradation
 +
* Poster
 +
* Preparing the presentation
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
 +
== '''European Jamboree 30.9-2.10''' ==
 +
* Sightseeing and having fun in Amsterdam
 +
* Gold Medal
 +
* Honorable Mention in category ''Best Model''
 +
* [https://2011.igem.org/Jamborees Jamboree]
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
 +
== '''Week 16:  03.10.-09.10''' ==
 +
* proof of concept with an arabinose inducable system
 +
* cloning for the xylene system
 +
* cloning of the lac-testsystem to compaire LacI<sub>M1</sub>
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
== '''Week 17:  10.10.-16.10''' ==
 +
* cloning of the alarm-test system
 +
* cloning the final system with xylene
 +
* cloning the arabinose system
 +
* cloning the AlcR (codon optimized) system
 +
* building a channel out of different materials
 +
* Design a assay for testing the alarm system
 +
* Sender receiver test on plates
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
 +
== '''Week 18:  17.10.-23.10''' ==
 +
* Cloning
 +
* inactivating of the kanamycin casette of BW27749 to get BW27783
 +
* Make competent BW27783 and DH5-&alpha; cells
 +
* Sender receiver test on plates with sterile filtrated supernatant
 +
* Sender an receiver test in tube
 +
* Dose response experiment for xylene
 +
* Dose response experiment for acetaldehyde
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/SectionStart}}
 +
 +
== '''Week 19: 24.10-30.10''' ==
 +
* Cloning
 +
* Microscope experiments of the channel with and without degradation
 +
* Alarm test with AHL
 +
* Dose response experiment for acetaldehyde
 +
* Dose response experiment for arabinose
 +
{{:Team:ETH Zurich/Templates/SectionEnd}}
 +
{{:Team:ETH Zurich/Templates/HeaderNewEnd}}

Latest revision as of 19:50, 27 October 2011

Can you feel the smoke tonight?
 

Contents

Lab Journal

Here you can follow the progress of our project as it is coming together.

Week 1: 20.6-26.6

  • First meeting


Week 2: 27.6-3.7


Week 3: 4.7-10.7

  • Working on the design of the system
IMG 5009.JPG
IMG 5010.jpg
  • Design of several Operons for AlcR and several PCR primers


Week 4: 11.7-17.7

  • Ordering of the LacIM1 and codon-optimized AlcR gene
  • Making of competent DH5-α cells
  • Cloning of the AlcR-testsystem


Week 5: 18.7-24.7

  • First test of the AlcR-system in 96-well plates


Week 6: 25.7-31.7

  • Transformation of the parts from the iGEM plates


Week 7: 1.8-7.8

  • Growth test of DH5-α with AlcR-system in flasks
  • Ligation and Transformation of
    • PR and luxI
    • PR and lacI
    • Plac and GFPLVA
    • Plux and mCherry
    • Ptet and CI -had to be redone because of point mutation in the primer (week 9)
    • Pconst and luxR
  • First meeting with Dr. Oliver Frey (Bio engineering laboratory, Prof. Andreas Hierlemann, D-BSSE ETHZ) to exchange ideas about microfluidic design


Week 8: 8.8-14.8

Lab5.jpg
  • Synthesized LacIM1 Gen arrived
  • Ligation and Transformation of
    • Plac-GFPLVA and Terminator
    • Plux-mCherry and Terminator
    • Pconst-luxR and Terminator
    • Plac-GFPLVA-Terminator and Plux-mCherry-Terminator on one plasmid
    • Ptet and LacIM1
    • Ptet-LacIM1 and Terminator
  • Improving of the testsystem
    • Exchange of some rare codons in AlcR by PCR
    • His-tagging of AlcR for detection in Western blot
    • include sfGFP
  • Transformation of PR
  • Creation of competent JM101 cells
    • Check for transformation efficiency


Week 9: 15.8-21.8

IMG 6171 Kopie.JPG
  • Growth and repression test of AlcR-system with M9-medium
  • Ligation and Transformation of
    • PR and lacI
    • PR and luxI
    • Ptet and CI
    • PR-lacI and terminator
    • PR-luxI and terminator


Week 10: 22.8-28.8

  • Transformation and Ligation
    • Ptet-CI and Terminator
  • Preparation of chemically competent DH5-α and JM101 cells


Week 11: 29.8-4.9

  • Transformation and Ligation
    • Ptet-CI and Terminator
  • Diffusion test through tube system filled with agarose and cells
  • Test of the improved AlcR system


Week 12: 5.9.-11.9

Lab6.JPG
  • Design of a system to characterize our new biobrick LacIM1
    • Transformation and Ligation
      • PTet and LacI
      • PLac and GFP assam
  • Design of an additional construct to test the band pass filter
    • Transformation and Ligation
      • Pconst and TetRLVA
  • Growth-test of E. coli in M9 with reduced Ampicillin concentration
  • AlcR test with reduced Ampicillin concentration
  • Testdigest of λP-luxI-Terminator
  • Alternative Sensor system: Xylene system
    • Transformation and Ligation
      • Pconst and XylR
      • PXyl and CI
      • PXyl and LacI M1


Week 13: 12.9.-18.9

IMG 6442.JPG
  • PCR of the pBR322 Ori
  • PCR of the gen cluster for the upper TOL pathway
  • first test of cell printing
  • Transformation and Ligation of
    • Pconst-TetR- PTet-LacIM1 and PR-GFPassam
  • Western Blot of AlcR
  • Making of competent DH5-α cells
  • Design and construction of Psb6A5


Week 14: 19.9.-25.9

  • Characterization of LacIM1
  • Cloning of all biobricks into pSB1C3
  • PCR of LacI and CI
  • wiki


Week 15: 26.9.-02.10

IMG 6649.JPG
  • design of Pu promoter
  • test of Pu promoter
  • test for indol degradation
  • Poster
  • Preparing the presentation


European Jamboree 30.9-2.10

  • Sightseeing and having fun in Amsterdam
  • Gold Medal
  • Honorable Mention in category Best Model
  • Jamboree


Week 16: 03.10.-09.10

  • proof of concept with an arabinose inducable system
  • cloning for the xylene system
  • cloning of the lac-testsystem to compaire LacIM1


Week 17: 10.10.-16.10

  • cloning of the alarm-test system
  • cloning the final system with xylene
  • cloning the arabinose system
  • cloning the AlcR (codon optimized) system
  • building a channel out of different materials
  • Design a assay for testing the alarm system
  • Sender receiver test on plates


Week 18: 17.10.-23.10

  • Cloning
  • inactivating of the kanamycin casette of BW27749 to get BW27783
  • Make competent BW27783 and DH5-α cells
  • Sender receiver test on plates with sterile filtrated supernatant
  • Sender an receiver test in tube
  • Dose response experiment for xylene
  • Dose response experiment for acetaldehyde


Week 19: 24.10-30.10

  • Cloning
  • Microscope experiments of the channel with and without degradation
  • Alarm test with AHL
  • Dose response experiment for acetaldehyde
  • Dose response experiment for arabinose


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Retrieved from "http://2011.igem.org/Team:ETH_Zurich/Biology/Journal"