Team:Cambridge/LabBook/Week5

From 2010.igem.org

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The experiment was performed twice in a row and both times luminescence was observed with the CCD camera (though not by eye in the dark room).
The experiment was performed twice in a row and both times luminescence was observed with the CCD camera (though not by eye in the dark room).
 +
==Tuesday==
===33. Experiment: In vitro assay for luciferase activity using CHBT as substrate (Theo and Anja)===
===33. Experiment: In vitro assay for luciferase activity using CHBT as substrate (Theo and Anja)===
2ml of TOP10 with promoter, rbs and luc were spun at 13000rpm for 5 mins. Supernatant was discarded and cell pellet was resuspended in 500μl fresh LB to which 1 drop of chloroform was added. The cells were subjected to three rounds of freeze (-80°C) and thaw (37°C) treatment.  
2ml of TOP10 with promoter, rbs and luc were spun at 13000rpm for 5 mins. Supernatant was discarded and cell pellet was resuspended in 500μl fresh LB to which 1 drop of chloroform was added. The cells were subjected to three rounds of freeze (-80°C) and thaw (37°C) treatment.  
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EXPERIMENT WAS CANCELLED!
EXPERIMENT WAS CANCELLED!
-
===34. Preparation of Photobacterium Broth (Theo and Anja)===
+
===34. Experiment: Preparation of Photobacterium Broth (Theo and Anja)===
35.2g broth promoter was dissolved in 500ml water by warming/boiling. Broth was filter sterilised.  
35.2g broth promoter was dissolved in 500ml water by warming/boiling. Broth was filter sterilised.  
-
===35. Ampoule of Photobacterium (extracted by Theo and Peter)===
+
===35. Experiment: Ampoule of Photobacterium (extracted by Theo and Peter)===
 +
Ampoule was broken, 500μl LB broth added and 100μl added to each of 5 falcons containing broth.
 +
==Wednesday==
 +
Theo added 5g agar to 250ml broth and placed for autoclaving.
 +
 +
After autoclaving the medium was turbid. It was poured into 9 empty, sterile dishes and left to set on the bench.
 +
 +
==Thursday==
 +
===36. Experiment: Renewed colonies of TOP10/pHK555 & pHK724 (Will)===
 +
*Inoculated 2x5ml LB with 1 colony for each
 +
*Streaked out cells on Amp + Chl plate (*)
 +
*Incubated both at 30°C overnight.
 +
 +
Results:
 +
*1 LB glow very faintly, other not at all
 +
*Poor growth from streaking, but strong glow
 +
 +
==Friday==
 +
===36. Experiment: Transformation of TOP10 competent cells with luxR from registry (Bill)===
 +
*Followed transformation protocol from 02/08/10
 +
*Transformed with BBa_I0462 from distribution from distribution Kit Plate 1 Well 80
 +
*Plated out on 2 ampicillin plates the transformation, (amp is resistance marker of plasmid)
 +
*Also cultured in 2 LB + Amp plates
 +
 +
Results (Hannah):
 +
{| class="wikitable"
 +
|-
 +
! Plate/Broth
 +
! Contains
 +
! Growth
 +
|-
 +
| Plate (Amp)
 +
| TOP10 LuxR
 +
| Yes
 +
|-
 +
| Plate (Amp)
 +
| TOP10 Only
 +
| No
 +
|-
 +
| Plate (No Amp)
 +
| TOP10 LuxR
 +
| Yes
 +
|-
 +
| Broth (LB + Amp)
 +
| TOP10 LuxR
 +
| No
 +
|}
 +
 +
===37. Experiment: Plating out of registry stabs (Theo)===
 +
Theo plated out BBa_K216007 and 08 on A plates
 +
 +
===38. Experiment: Inoculated growth media for extraction of plasmid pHK555 for use in oligos (Will)===
 +
*5ml SOB + 2.5μl Chloramphenicol + 1 colony Invitrogen 10 with pHK555 (from plate 5/8/10)
 +
*5ml SOB + 2.5μl Chloramphenicol + 10μl of glycerol stock of Slock10/pHK555 cells
 +
*5ml LB + 2.5μl Chloramphenicol + 1 colony Invitrogen 10 with pHK555 (from plate 5/8/10)
 +
 +
===39. Experiment: Restreaked TOP10/pHK555+pHK724 (Will)===
 +
Using poorly grown strain from yesterday (*) restreaked onto LB agar+Chl+Amp (hope to select for strong growth).
 +
 +
===40. Experiment: Streaked out Invitrogen 10 pHK555 (from plate 5/8/10) (Will)===
 +
On Chl plate, for colony PCR of pHK555 Plasmid
 +
 +
==Saturday==
 +
===41. Experiment: Culturing in broth of TOP10+LuxR from registry (Hannah)===
 +
*Took single colony from plate, added to LB+Amp broth
 +
*2 days later took them out and put in fridge
 +
 +
==Sunday==
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Latest revision as of 11:52, 27 August 2010

Contents

Monday

31. Experiment: Diagnostic gel to test for luciferase insertion (Theo & Anja)

Took overnight culture of TOP10 transformed with plasmid (potentially) containing promoter + rbs and luciferase

Plasmid DNA purification

following "QIAprep Spin Miniprep Kit using a Microcentrifuge" protocol

Gel electrophoresis

E-gel EX Agarose 1% mounted on transilluminator Nanodrop readings:

  • Plasmid with promoter + rbs + luciferase: 18.5ng/μl => 5μl gives 100ng
  • Plasmid with promoter + rbs only: 64.9ng/μl => 2μl gives 100ng

Gel loading mixture:

promoter + rbs + luciferase promoter + rbs only
6X orange loading Dye 3μl 3μl
plasmid DNA 5μl 2μl
deionised H2O 12μl 12μl

Supercoiled DNA ladder loading mixture

  • 1μl Supercoiled DNA ladder (NEB)
  • 3μl 6X orange loading Dye
  • 16μl deionised H2O

Gel was loaded following scheme below:

Supercoiled DNA ladder promoter + rbs only promoter + rbs + luciferase
20μl 20μl 20μl

Empty wells were filled with 200μl deionised H2O. Gell was run and a clear band around 2kb was visible for promoter + rbs, a very faint band was observed around 4kb for promoter + rbs + luciferase.

Gel electrophoresis

was repeated with increased promoter + rbs + luciferase plasmid concentration

Gel loading mixture for promoter + rbs + luciferase

(others as above)

  • 3μl 6X orange LD
  • 15μl plasmid DNA
  • 2μl deionised H2O

Gel was run and the same bands were observed as above, with the ~4kb promoter + rbs + luciferase more clearly than before

32. Experiment: In vitro assay for luciferase activity (Theo & Anja)

50μl of TOP10 cells transformed with plasmid containing promoter + rbs + luc were transferred to an Eppendorf tube and subjected to three rounds of freeze (-80°C) and thaw (37°C) treatement. 50μl of 2mg/ml luciferin were added tot he lysed bacteria and luminescence was tested using a CCD camera. The experiment was performed twice in a row and both times luminescence was observed with the CCD camera (though not by eye in the dark room).

Tuesday

33. Experiment: In vitro assay for luciferase activity using CHBT as substrate (Theo and Anja)

2ml of TOP10 with promoter, rbs and luc were spun at 13000rpm for 5 mins. Supernatant was discarded and cell pellet was resuspended in 500μl fresh LB to which 1 drop of chloroform was added. The cells were subjected to three rounds of freeze (-80°C) and thaw (37°C) treatment.

EXPERIMENT WAS CANCELLED!

34. Experiment: Preparation of Photobacterium Broth (Theo and Anja)

35.2g broth promoter was dissolved in 500ml water by warming/boiling. Broth was filter sterilised.

35. Experiment: Ampoule of Photobacterium (extracted by Theo and Peter)

Ampoule was broken, 500μl LB broth added and 100μl added to each of 5 falcons containing broth.

Wednesday

Theo added 5g agar to 250ml broth and placed for autoclaving.

After autoclaving the medium was turbid. It was poured into 9 empty, sterile dishes and left to set on the bench.

Thursday

36. Experiment: Renewed colonies of TOP10/pHK555 & pHK724 (Will)

  • Inoculated 2x5ml LB with 1 colony for each
  • Streaked out cells on Amp + Chl plate (*)
  • Incubated both at 30°C overnight.

Results:

  • 1 LB glow very faintly, other not at all
  • Poor growth from streaking, but strong glow

Friday

36. Experiment: Transformation of TOP10 competent cells with luxR from registry (Bill)

  • Followed transformation protocol from 02/08/10
  • Transformed with BBa_I0462 from distribution from distribution Kit Plate 1 Well 80
  • Plated out on 2 ampicillin plates the transformation, (amp is resistance marker of plasmid)
  • Also cultured in 2 LB + Amp plates

Results (Hannah):

Plate/Broth Contains Growth
Plate (Amp) TOP10 LuxR Yes
Plate (Amp) TOP10 Only No
Plate (No Amp) TOP10 LuxR Yes
Broth (LB + Amp) TOP10 LuxR No

37. Experiment: Plating out of registry stabs (Theo)

Theo plated out BBa_K216007 and 08 on A plates

38. Experiment: Inoculated growth media for extraction of plasmid pHK555 for use in oligos (Will)

  • 5ml SOB + 2.5μl Chloramphenicol + 1 colony Invitrogen 10 with pHK555 (from plate 5/8/10)
  • 5ml SOB + 2.5μl Chloramphenicol + 10μl of glycerol stock of Slock10/pHK555 cells
  • 5ml LB + 2.5μl Chloramphenicol + 1 colony Invitrogen 10 with pHK555 (from plate 5/8/10)

39. Experiment: Restreaked TOP10/pHK555+pHK724 (Will)

Using poorly grown strain from yesterday (*) restreaked onto LB agar+Chl+Amp (hope to select for strong growth).

40. Experiment: Streaked out Invitrogen 10 pHK555 (from plate 5/8/10) (Will)

On Chl plate, for colony PCR of pHK555 Plasmid

Saturday

41. Experiment: Culturing in broth of TOP10+LuxR from registry (Hannah)

  • Took single colony from plate, added to LB+Amp broth
  • 2 days later took them out and put in fridge

Sunday

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