Paris/PROTOCOLS

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Revision as of 14:04, 19 July 2007

For newcomers in wetlab: see also the course by D. Endy Laboratory Fundamentals of Biological Engineering.

Getting started

This topic is adressed to all our informatics-physics-I'm-afraid-of-the-bench fellows. So, if you finally found the courage to dare the pipettes, PCRs and nicely smelling bacteria, welcome!

What a pipette is?

Pipettes dispense various volumes. The plunger button indicates the maximum volume (microliters) that the pipette is designed to handle. For example, P-20 will handle up to 20 microliters.
The digital volume indicator is read from top to bottom. For P-2, P-10, P-20, P-100, and P-200, black digits indicate microliters and red digits tenths and hundredths of microliters. For P-1000, red digits indicate milliliters and black digits microliters.

What to do when you have it in you hand?

-Hold the pipette in one hand (it doesn't bite...). With the other hand, turn the volume adjustment knob counterclockwise so the volume indicator is 1/3 revolution above the desired setting, then slowly turn clockwise until the indicator shows the desired volume.
-Attach a new disposable tip to the pipette shaft.
-Press the plunger to the FIRST stop. This part of the stroke is the volume displayed by the indicator.
-Holding the pipette vertically, immerse the tip a few millimeters into the sample.
-Allow the pushbutton to return slowly to the UP position. Avoid to blurt out the plunger button abruptly : there are bulls appearing and your volume is false...
-Ensure that the full volume of sample was properly drawn into the tip.
-Withdraw the tip from the sample.
-To dispense the liquid, gently touch the tip to the side of the receiving vessel, immersing the tip into liquid within the vessel. Press the plunger to the SECOND stop.
-With the plunger fully pressed, withdraw the tip carefully, wiping residual drops against the vessel wall.
-Allow plunger to return to the UP position.
-Discard the tip by depressing the tip ejector button.

Note down that different tips exist : ensure that you have the right one (labels will indicate you the size, etc.). It's better to use filter tips.
To train, you can simply pipette water : it's important to know how much 1 µl is...

To be continued...

Growing bacteria in liquid medium

-Light the Bunsen burner. It permits you to keep a 10 cm perimeter sterile et thus not to contaminate your future colonies.
-Get a 50mL Falcon tube and put into 5 mL of LB medium. Add supplementary stuff if needed (antibiotics, metabolites, etc.).
-Pick up a sterile toothpick. Use it to gather a single colony of cells (you know, a white point on your Petri dish...).
-Place the toothpick with the colony into the solution.
-Incubate overnight at 37°C with shaking (at about 200 rpm).

Next morning, after a cup of coffee and a croissant, you can check up .
<<home

Strains

Here you can find the list of strains we have.

E. Coli MG1655

WT

E. Coli w121

We got the w121 strain from a lab in Pasteur Institute. This strain is [DapA-; Erythromycin R], but also has a couple of other mutations we are not interested in.

E. Coli Ftsz -TS84

Three clones are available : 121.1, 121.2, 121.3. More details soon

Acinetobacter

Transduction with P1 bacteriophage

Preparation of the P1 stock on the w121 strain.

Step of Tuesday, July 3

To be completed...

Transduction to MG1655 using the P1 stock made on w121.

Step of Wednesday, July 4

To be completed...

Titration of bacteriophages

Take your stock of bacteriophage
make several dilution of your stock, for example :
- 10µL of stock in 990µL MgSO₄ 0.1M -> d2
- 10µL of former solution in 990µL MgSO₄ 0.1M ->d4
- 10µL of former solution in 990µL MgSO₄ 0.1M ->d6
- 10µL of former solution in 990µL MgSO₄ 0.1M ->d8
In a petri dish containing LB, spread a solution of 100µL of E. Coli MG1655 in stationnary phase + warm top agar 900µL (TA,7)
Spread this mix over a petri dish
add droplets (7µL) of your phages dilution on the petri dish, mark the places where you put these droplets
Incubate ON at 37°C
check for lyse plaque

Preparation of DAP solution from the powder (50mM)

Step of Friday, July 6

M(DAP)=190.2g/mol
I put 0.285g of DAP in 30ml water
Aliquoted by 15ml
Stored in the freezer at -20°C
the stock is 166x

Preparing growth media

Making 10 petri dish (LB+tet+citrate+DAP)

take 250ml of LB
warm it up in the microwave for ~ 6min
wait until you can handle the bottle for 2sec
add 5ml of citrate 1M
add 1.5ml of DAP
add 250µL of tetracycline (stored in freezer at 1000x)
spread the medium in about 10 petri dish

Making 10 petri dish (LB+erythromycin+citrate+DAP)

take 250ml of LB
warm it up in the microwave for ~ 6min
wait until you can handle the bottle for 2sec
add 5ml of citrate 1M
add 1.5ml of DAP
add 1.9mL of erythromycin (stored in the freezer at 133x)
spread the medium in about 10 petri dish

Fluorescent single cells visualisation

Slide preparation

Make LB-agarose : 0.15g of agarose in 10ml LB
warm it up in the microwave (a lot!!, to avoid cristal of agarose that could remain in the gel => ugly over microscope)
wash the slide (special slide with "two holes" with ethanol)
put ~80µL of LB-agarose in each hole
spread the gel with another slide and wait for ~2 min
remove extra gel with a cutter
put a droplet on the gel:

if you have a solid culture:

- pick up some colonies

- suspend within 100µL liquid medium (M9)

- put 1-2 µL on the gel

if you have an avernight liquid culture:

- take 1mL of the culture

- centrifugate 1000 rpm 1 min

- resuspend into 150 µL of medium (M9)

- put 1-2 µL on the gel slide

spread it by moving the slide
wait until you don't see the droplet anymore (2min)
put a coverslip and attach it with nailpolish
optionally : you can put wax around

Turning on the microscope

turn on : the light, the microscope, the shutter, the joystick
launch Metamorph
turn up the condenser and the objectives in load position
!! take care : not keeping the light on if we doesn't use it
!! do not switch on short after
wait 5 min (the microscope is checking the ranges of movement

Visualisation

put a droplet of immersion oil on your slide, and attach it on the slide
Journal >> Show task bar
Task bar

>> Trans ON/OFF: turn on the halogen lamp

>> Binocular/Camera: turn on the binocular or the camera

>> Choose the fiter

Move up the objective until oil touches the slides
Turn on the binocular with trans filter
Move up the stage with micrometric "screw" until you see your cells, or something moving
Acquire:

- Digitizer (10MHz!!)

- Image >> New !!! ( without this, each image you take will overwrite)

- Settings >> (trans ou fluo; choice of exposure time)

Turn on the camera (Task bar >> Camera)
- Trans Image:

Turn trans light on (Task bar >> Trans ON) and trans filter

Acquire >> 100ms trans

Acquire >> Show Live

Acquire >> Acquire: acquire the trans image

Fluo image:

Task bar >> fluo filter; trans OFFOFF)

Acquire your images, etc, have fun
save your images in E:\iGEM\YYYY-MM-DD\a_proper_name

NB : Nile Red, choose mRFP1/TexasRed filter <<home

@@ Line 145: / Line 145: @@
 * put a droplet of immersion oil on your slide, and attach it on the slide
 * Journal >> Show task bar
-* Task bar >> Trans ON/OFF : turn on the halogen lamp
+* Task bar
-* Move the stage with the joystick to put the objective face to your sample
+: >> Trans ON/OFF: turn on the halogen lamp
+: >> Binocular/Camera: turn on the binocular or the camera
+: >> Choose the fiter
 * Move up the objective until oil touches the slides
+* Turn on the binocular with trans filter
 * Move up the stage with micrometric "screw" until you see your cells, or something moving
-* Acquire >> Acquire
+* Acquire:
-* Image >> New !!! ( without this, each image you take will overwrite
+:- Digitizer (10MHz!!)
-* Settings >> (trans ou fluo), and here you have the choice of exposure time
+:- Image >> New !!! ( without this, each image you take will overwrite)
-* Digitizer (10MHz!!) take care
+:- Settings >> (trans ou fluo; choice of exposure time)
-* Task bar >> Camera
+* Turn on the camera (Task bar >> Camera)
-* Acquire >> Show live
+** Trans Image:
-* Remember trans on off : turn trans light on
+: Turn trans light on (Task bar >> Trans ON) and trans filter
-* Then choose your filter (task bar)
+: Acquire >> 100ms trans
+: Acquire >> Show Live
+: Acquire >> Acquire: acquire the trans image
+* Fluo image:
+: Task bar >> fluo filter; trans OFFOFF)
+:
 * Acquire your images, etc, have fun
 * save your images in E:\iGEM\YYYY-MM-DD\a_proper_name

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