Imperial College/14 August 2008

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=14 August 2008=
==Wet Lab==
==Wet Lab==
 +
 +
=== Cloning ===
 +
 +
*Parts taken from the registry and transformed by electroporation into XL1-Blue ''E.coli'' along with XL1-Blue controls and grown on Kanamycin and Ampicillin plates. Parts taken:
 +
**C0012 (LacI)
 +
**J31005 (Chloraphemicol acetyltransferase)
 +
**B0015 (Double terminator)
 +
**J04630 (GFP and Double Terminator)
 +
**I13401 (mRFP and Double Terminator)
 +
 +
===''B.subtilis''===
 +
*The transformation protocol 2 was carried out today, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_4#Transformation_Protocol_2| Click link here for protocol]
 +
*The basic principle of this protocol is that competent cells are prepared by growing a culture to a high O.D.<sub>600</sub> and then performing electroporation on these competent cells.
 +
*Today we grew the competent cells, we used an O.D.<sub>600</sub> of 1.5 before we harvested them. In addition electroporation was carried out using the plasmid pDR110. Previously we had mini-preped this to give a stock of 40ng/ul. We transformed with 40ng, 120ng, 200ng and 400ng in a volume of 10ul (water was used to make up to 10ul).
 +
*Transformed cells were plated out and placed into the 30<sup>o</sup>C incubator.
==Dry Lab==
==Dry Lab==
-
*Completed ''A More Complex Example of Bayesian Parameter Estimation'' of Tutorial 2. Helped Yanis to source for good tracking software, found SpotTracker which is more accurate than ParticleTracker. Went for microscope training, obtained 2 x videos on ''B.Subtilis'' motility, stored on server with James.
+
*Completed ''A More Complex Example of Bayesian Parameter Estimation'' of Tutorial 2.  
 +
*Sourced for better tracking algorithm, found SpotTracker which is more accurate than ParticleTracker.  
 +
*Went for microscope training, obtained 2 x videos on ''B.Subtilis'' motility, stored on server with James.
 +
*Discussion with Dr. Suhail ( from Structural Bioinformatics Group,Imperial College London) on the computing requirements to analyse the cells motility. We will be allocated a linux 64-bit workstation, that we will be able to access remotely via SSH.
 +
 
 +
==Microscope==
 +
 
 +
*Chris, Clinton, James and Prudence received microscope training on Widefield 1, recording two 60s videos of ''B.subtilis'' swimming for analysis
 +
*Determined that best results would be obtained by bringing a ''B.subtilis'' overnight culture to the microscope facility and diluting 100 fold.
 +
<br>
 +
{{Imperial/EndPage|Notebook|Notebook}}

Latest revision as of 20:36, 28 October 2008

July
MTWTFSS
  [http://2008.igem.org/wiki/index.php?title=Imperial_College/1_July_2008&action=edit 1] [http://2008.igem.org/wiki/index.php?title=Imperial_College/2_July_2008&action=edit 2] [http://2008.igem.org/wiki/index.php?title=Imperial_College/3_July_2008&action=edit 3] [http://2008.igem.org/wiki/index.php?title=Imperial_College/4_July_2008&action=edit 4] [http://2008.igem.org/wiki/index.php?title=Imperial_College/5_July_2008&action=edit 5] [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_July_2008&action=edit 6]
[http://2008.igem.org/Imperial_College/7_July_2008 7] [http://2008.igem.org/Imperial_College/8_July_2008 8] [http://2008.igem.org/Imperial_College/9_July_2008 9] [http://2008.igem.org/wiki/index.php?title=Imperial_College/10_July_2008&action=edit 10] [http://2008.igem.org/Imperial_College/11_July_2008 11] [http://2008.igem.org/wiki/index.php?title=Imperial_College/12_July_2008&action=edit 12] [http://2008.igem.org/wiki/index.php?title=Imperial_College/13_July_2008&action=edit 13]
[http://2008.igem.org/wiki/index.php?title=Imperial_College/14_July_2008&action=edit 14] [http://2008.igem.org/Imperial_College/15_July_2008 15] [http://2008.igem.org/Imperial_College/16_July_2008 16] [http://2008.igem.org/wiki/index.php?title=Imperial_College/17_July_2008&action=edit 17] [http://2008.igem.org/Imperial_College/18_July_2008 18] [http://2008.igem.org/wiki/index.php?title=Imperial_College/19_July_2008&action=edit 19] [http://2008.igem.org/wiki/index.php?title=Imperial_College/20_July_2008&action=edit 20]
[http://2008.igem.org/Imperial_College/21_July_2008 21] [http://2008.igem.org/Imperial_College/22_July_2008 22] [http://2008.igem.org/Imperial_College/23_July_2008 23] [http://2008.igem.org/Imperial_College/24_July_2008 24] [http://2008.igem.org/Imperial_College/25_July_2008 25] [http://2008.igem.org/wiki/index.php?title=Imperial_College/26_July_2008&action=edit 26] [http://2008.igem.org/wiki/index.php?title=Imperial_College/27_July_2008&action=edit 27]
[http://2008.igem.org/Imperial_College/28_July_2008 28] [http://2008.igem.org/Imperial_College/29_July_2008 29] [http://2008.igem.org/Imperial_College/30_July_2008 30] [http://2008.igem.org/wiki/index.php?title=Imperial_College/31_July_2008&action=edit 31]
August
MTWTFSS
        [http://2008.igem.org/Imperial_College/1_August_2008 1] [http://2008.igem.org/Imperial_College/2_August_2008 2] [http://2008.igem.org/wiki/index.php?title=Imperial_College/3_August_2008&action=edit 3]
[http://2008.igem.org/Imperial_College/4_August_2008 4] [http://2008.igem.org/Imperial_College/5_August_2008 5] [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_August_2008&action=edit 6] [http://2008.igem.org/Imperial_College/7_August_2008 7] [http://2008.igem.org/Imperial_College/8_August_2008 8] [http://2008.igem.org/wiki/index.php?title=Imperial_College/9_August_2008&action=edit 9] [http://2008.igem.org/Imperial_College/10_August_2008 10]
[http://2008.igem.org/Imperial_College/11_August_2008 11] [http://2008.igem.org/Imperial_College/12_August_2008 12] [http://2008.igem.org/Imperial_College/13_August_2008 13] [http://2008.igem.org/Imperial_College/14_August_2008 14] [http://2008.igem.org/Imperial_College/15_August_2008 15] [http://2008.igem.org/Imperial_College/16_August_2008 16] [http://2008.igem.org/Imperial_College/17_August_2008 17]
[http://2008.igem.org/Imperial_College/18_August_2008 18] [http://2008.igem.org/Imperial_College/19_August_2008 19] [http://2008.igem.org/Imperial_College/20_August_2008 20] [http://2008.igem.org/Imperial_College/21_August_2008 21] [http://2008.igem.org/Imperial_College/22_August_2008 22] [http://2008.igem.org/wiki/index.php?title=Imperial_College/23_August_2008&action=edit 23] [http://2008.igem.org/Imperial_College/24_August_2008 24]
[http://2008.igem.org/Imperial_College/25_August_2008 25] [http://2008.igem.org/Imperial_College/26_August_2008 26] [http://2008.igem.org/Imperial_College/27_August_2008 27] [http://2008.igem.org/Imperial_College/28_August_2008 28] [http://2008.igem.org/Imperial_College/29_August_2008 29] [http://2008.igem.org/wiki/index.php?title=Imperial_College/30_August_2008&action=edit 30] [http://2008.igem.org/Imperial_College/31_August_2008 31]
September
MTWTFSS
[http://2008.igem.org/Imperial_College/1_September_2008 1] [http://2008.igem.org/Imperial_College/2_September_2008 2] [http://2008.igem.org/Imperial_College/3_September_2008 3] [http://2008.igem.org/Imperial_College/4_September_2008 4] [http://2008.igem.org/Imperial_College/5_September_2008 5] [http://2008.igem.org/wiki/index.php?title=Imperial_College/6_September_2008&action=edit 6] [http://2008.igem.org/Imperial_College/7_September_2008 7]
[http://2008.igem.org/Imperial_College/8_September_2008 8] [http://2008.igem.org/Imperial_College/9_September_2008 9] [http://2008.igem.org/Imperial_College/10_September_2008 10] [http://2008.igem.org/Imperial_College/11_September_2008 11] [http://2008.igem.org/Imperial_College/12_September_2008 12] [http://2008.igem.org/wiki/index.php?title=Imperial_College/13_September_2008&action=edit 13] [http://2008.igem.org/wiki/index.php?title=Imperial_College/14_September_2008&action=edit 14]
[http://2008.igem.org/Imperial_College/15_September_2008 15] [http://2008.igem.org/Imperial_College/16_September_2008 16] [http://2008.igem.org/Imperial_College/17_September_2008 17] [http://2008.igem.org/Imperial_College/18_September_2008 18] [http://2008.igem.org/Imperial_College/19_September_2008 19] [http://2008.igem.org/wiki/index.php?title=Imperial_College/20_September_2008&action=edit 20] [http://2008.igem.org/wiki/index.php?title=Imperial_College/21_September_2008&action=edit 21]
[http://2008.igem.org/Imperial_College/22_September_2008 22] [http://2008.igem.org/Imperial_College/23_September_2008 23] [http://2008.igem.org/Imperial_College/24_September_2008 24] [http://2008.igem.org/Imperial_College/25_September_2008 25] [http://2008.igem.org/Imperial_College/26_September_2008 26] [http://2008.igem.org/wiki/index.php?title=Imperial_College/27_September_2008&action=edit 27] [http://2008.igem.org/wiki/index.php?title=Imperial_College/28_September_2008&action=edit 28]
[http://2008.igem.org/Imperial_College/29_September_2008 29] [http://2008.igem.org/Imperial_College/30_September_2008 30]

14 August 2008

Wet Lab

Cloning

  • Parts taken from the registry and transformed by electroporation into XL1-Blue E.coli along with XL1-Blue controls and grown on Kanamycin and Ampicillin plates. Parts taken:
    • C0012 (LacI)
    • J31005 (Chloraphemicol acetyltransferase)
    • B0015 (Double terminator)
    • J04630 (GFP and Double Terminator)
    • I13401 (mRFP and Double Terminator)

B.subtilis

  • The transformation protocol 2 was carried out today, [http://openwetware.org/wiki/IGEM:IMPERIAL/2008/Prototype/Wetlab/Transformation_protocol_4#Transformation_Protocol_2| Click link here for protocol]
  • The basic principle of this protocol is that competent cells are prepared by growing a culture to a high O.D.600 and then performing electroporation on these competent cells.
  • Today we grew the competent cells, we used an O.D.600 of 1.5 before we harvested them. In addition electroporation was carried out using the plasmid pDR110. Previously we had mini-preped this to give a stock of 40ng/ul. We transformed with 40ng, 120ng, 200ng and 400ng in a volume of 10ul (water was used to make up to 10ul).
  • Transformed cells were plated out and placed into the 30oC incubator.

Dry Lab

  • Completed A More Complex Example of Bayesian Parameter Estimation of Tutorial 2.
  • Sourced for better tracking algorithm, found SpotTracker which is more accurate than ParticleTracker.
  • Went for microscope training, obtained 2 x videos on B.Subtilis motility, stored on server with James.
  • Discussion with Dr. Suhail ( from Structural Bioinformatics Group,Imperial College London) on the computing requirements to analyse the cells motility. We will be allocated a linux 64-bit workstation, that we will be able to access remotely via SSH.

Microscope

  • Chris, Clinton, James and Prudence received microscope training on Widefield 1, recording two 60s videos of B.subtilis swimming for analysis
  • Determined that best results would be obtained by bringing a B.subtilis overnight culture to the microscope facility and diluting 100 fold.



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