Difference between revisions of "Team:Pasteur Paris/Microbiology week8"

Aim: Based on the results of silification tests, make a larger quantity of fusion protein.

Protocol: follow in this link

What we did in the lab:
Materials:

50 ml Falcon tube

Shaking incubator (INFORS HT)

Swing bucket centrifuge (JOUAN GR41)

Cultures of C1.2

carbenicillin at 50 mg/ml

LB medium

Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)

; Ultrospec 3100

Method:

1.Put each of the C2 1.2 cultures in a 50 ml Falcon and centrifuge 8 minutes at 3500 RPM

2. Wash the pellet with 20 ml of LB after throwing away the supernatant

3. Centrifuge again 8 minutes at 3500 RPM and throw away the supernatant

4. Resuspend the pellet in 20 ml of LB

5. Pool the two Falcons

6. Put in the rotating incubator 4 Erlenmeyers of 2 L containing 1 L of LB, at 37°C and 150 RPM

7. Add in each Erlenmeyer 10 ml of C2 1.2 culture and 1 ml of carbenicillin at 50 mg/ml

8. Measure the OD_{600 nm} at several times :

Table 1
Times	OD_600nm
0	0.014
0 h 30	0.018
1 h 00	0.020
1 h 30	0.035
2 h 00	0.067
3 h 00	0.360
3 h 15	0.451
3 h 25	0.515
3 h 40	0.701

9. Pelleted the last measured sample for 3 minutes at 7000g. Then throw away the supernatant and store the pellet at &8722; 20 °C

10. Add 0.6 ml of iPTG in each Erlenmeyer and incubate overnight

Aim: DNA concentration measurement in order to find the correct ratios for ligation.

What we did in the lab:
Materials:
• Spectrophotometer
• Quartz cuvettes
• carbenicillin at 50 mg/ml
• LB medium
• B1 v2, B2 v2, C1 v2, C2 v2 DNA inserts
• Shaking incubator (INFORS HT)
• Microbiology equipment (37 °C incubator, Bunsen burner, water bath, etc… Follow this link)

Method:
All the measurements are done twice to be more accurate
The preculture of vector is prepared with 3 ml of LB, 3 µl of carbenicillin and one colony of C2 1.2

Results

Table 2
DNA	pET 43.1 dephosphorylated		B1 v2		B2 v2		C1 v2		C2 v2
A₂₆₀	0.265	0.254	0.180	0.188	0.166	0.163	0.181	0.156	0.197	Ø
A₂₈₀	2.39	0.211	0.077	0.063	0.060	0.052	0.077	0.070	0.071	Ø
A_{260 ⁄ 280}	1.11	1.20	2.35	2.97	2.76	3.16	2.35	3.04	2.79	Ø
A_260⁄230	0.31	0.34	0.01	0.01	0.01	0.01	0.01	0.01	0.01	0.01
[ DNA] (ng ⁄ μl)	13.3	12.7	9	9.4	8.3	8.2	9	7.8	9.8	Ø

Aim: Prepare the ligation before doing the transformation with the Top10 competent cell .

Protocol: follow in this link

What we did in the lab:
Materials:
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)
• 1 ml Eppendorfs
• B1 v2 , B2 v2 , C1 v2 , C2 v2 DNA inserts
• Distilled water
• Shaking incubator (INFORS HT)
• T4 ligase
• T4 buffer

Method:
1. Prepare the following samples in a 1 ml Eppendorf, finishing with the ligase :

Table 3
	B1 v2 pET 43.1(a+) from 05 ⁄ 07	B2 v2 pET 43.1(a+) from 05 ⁄ 07	C1 v2 pET 43.1(a+) from 11 ⁄ 07	C2 v2 pET 43.1(a+) from 08 ⁄ 07
100 ng dephorphorylated ( μl)	6.7	6.7	7.7	7.7
Insert (16ng) (μl)	1.6	2	2	1.6
T4 ligase (μl)	1	1	1	1
T4 buffer (μl)	1.5	1.5	1.5	1.5
H₂O (μl)	4.2	3.8	1.8	3.2
V_final (μl)	15	15	15	15

2. Let ligate 1 hour at room temperature
3.Incubate 10 minutes at 65°C to inactivate the enzymes
4.Store all the samples at −80°C until ready to transform

Aim: Increase the amount of DNA.

Protocol: follow in this link

What we did in the lab:
Materials:
• Microbiology equipement
• Mastermix 2X
• Primer S (sense direction, Forward Primer, see sequence in PCR protocol section)
• Primers AS (anti-sense, Reverse Primer, see sequence in PCR protocol section)
• Phusion DNA polymerase
• DNA template
• Distilled water
• PCR machine

Method:
1. For each insert, make 3 tubes of 0.2 ml with thin walls and prepare the following mastermix :

Table 4
Volume (μl)	Insert	Primer S	Primer AS
Mastermix 2X	75	75	75
Primer S	3	3	Ø
Primer AS	3	Ø	3
H₂O	65.4	68.4	68.4
Phusion	0.6	0.6	0.6

2. Distribute the previous mastermix in the tubes and add the template DNA to have :

Table 5
Volume (μl)	Insert	Primer S	Primer AS	Without DNA
Mastermix	25	25	25	25
Primer S	1	1	Ø	1
Primer AS	1	Ø	1	1
Template DNA diluted 1⁄10	1	1	1	Ø
H₂O	21.8	22.8	22.8	22.8
Phusion	0.2	0.2	0.2	0.2
Total	50	50	50	50

3. Launch the PCR for 24 cycles

Aim: Get back plasmid DNA with the twinned insert.

Protocol: follow in this link

What we did in the lab:
Materials:
• QIAGEN plasmid Midi Kit
• 2 ml Eppendorfs
• Spectrophotometer
• Ethanol 70%
• Cultures of BL21DE3 from the 25⁄07

Method:
1. When isopropanol is added, spread the volume in 5 x 2 (2 ml Eppendorfs) and centrifuge 10 minutes at 13000g
2. Add 1 ml of ethanol in each pellet and centrifuge 10 minutes at 13000g

Results:
Make 3 measurements of the concentration (1⁄200 dilution)

Table 6
	Measurement 1	Measurement 2	Measurement 3
OD₂₆₀	0.046	0.44	0.073
[DNA] (μg⁄ml)	460	4.40	730

Aim: Prepare our bacteria before the protein purification.

What we did in the lab:
Materials:
• Microbiological equipment
• PMSF at 100 mM
• Cultures of BL21DE3
• Buffer A
• 50 ml Falcons

Method:
1.Centrifuge 4x 1 l of cultures 20 minutes at 4500g, in a Beckman JLA 8.1000 rotor in a Avanti x26-J centrifuge
2.Throw away the supernatant
3.Add 40 μl of PMSF in 40 ml of buffer A and add 5 ml of this solution in each pellet
4.Scratch the pellet to resuspend it
5.Add again 5 ml of the buffer A solution and mix the slurry until it becomes smooth, and to recover all the pellet
6.Put each product in a clean 50 ml Falcon : store at −80°C.

Table 7
Tubes	1	2	3	4
Weight (g)	15	15	15.3	16.1

Aim: Extract the bands C1 and C2 amplified with 900 bp inserts, and separate non-specific bands (700 bp).

Protocol: follow in this link

What we did in the lab:
Materials:
• QIAGEN Gel extraction Kit
• Buffer QG
• Gel bands C1 and C2
• Isopropanol
• 2 ml Eppendorfs

Method:
1. Calculate the amount of buffer QG for the extraction :

Table 8
	Weight of our tubes (mg)	Weight of our extraction (mg)	Buffer QG (μl)
C1	1.0360	40.2	121
C2	1.0154	32.8	97

2. Add 1 volume of isopropanol for C2 (32.3 μl) and 3 volumes of isopropanol for C1 (121 μl) 3. Recovery of DNA in 40 μl extraction buffer (20 x 2 μl)

Results:
Measurement of concentration with a dilution of 1⁄250 :

Table 9
	C1	C2
OD_{260 nm}	0.003	0.003
OD_{280 nm}	0.003	0.003
[DNA] (μg⁄ml)	30	120

Aim: To link vectors with the inserts.

Protocol: follow in this link

What we did in the lab:
Materials:
• Colonies C1 v2 and C2 v2 Insert bands
• Salt solution
• Distilled water
• TOPO vector

Method:

Table 10
	C1 v2	C2 v2
DNA from colonies (inserts) (μl)	4	4
Salt solution (μl)	1	1
Distilled water (μl)	5	5
TOPO vector (μl)	1	1
V_final (μl)	6	6

Aim: Save the bacteria with the recombinant vector for storage.

Protocol: follow in this link

What we did in the lab:
Materials:
• Microbiological equipment
• Carbenicillin 50 mg⁄ml
• LB medium
• 50 ml Falcons
• 2 ml Eppendorfs
• Recombinant vector
• BL21DE3 colonies

Method:
1. Prepare in a falcon of 50 ml a preculture of the recombinant vector with one colony, 5 ml of LB and 5 μl of carbenicillin 50 mg⁄ml
2. Add 5 ml of LB and centrifuge 7 minutes at 3500 RPM
3. Discard the supernatant and add 5 ml of LB. Then, centrifuge again 7 minutes at 3500RPM
4. Discard the supernatant and add 5 ml of LB
5. Put 200 μl of this preparation into another Falcon of 50 ml, add 25 ml of LB and 25 μl of carbenicillin
6. Let the culture shake at 37°C for 4 hours (until the culture growth is sufficient, OD_{600 nm} of approx. 0.7) and check the concentration at several times during it :

Table 11
Time	OD_{600 nm}
0	0.007
1h19	0.059
2h39	0.458
3h54	0.827

7. In 9 Eppendorfs of 2 ml, put 1 ml of LB with AGAR and 1 μl of carbenicillin. Then mix it
8. Dip a toothpick in the culture, and stab in the agar in each Eppendorf, and let it incubate at 37°C overnight. Afterwards store at 4°C.
9. On the July 28, 2016 : restreaking of cultures in a Petri dish (verification of STABs)

Aim: Separate the amplification bands of specific DNA (900 bp) from non-specific bands (700 bp).

Protocol: follow in this link

What we did in the lab:
Method:
We skipped this part to concentrate on the new versions of C1 and C2 inserts.

Aim: To determine if the two primers For (Forward direction) and Rev (Reverse direction) that were previously prepared are specific or not.

Protocol: follow in this link

What we did in the lab:
Materials:
• Mastermix 2X
• Primer S
• Primer AS
• Distilled water
• C1 and C2 inserts
• Phusion DNA polymerase
• Tubes for PCR
• PCR machine

Method:
1. For each inserts prepare the following Globalmix :

Table 12
Volume (μl)	Insert	Primer S	Primer AS
Mastermix 2X	75	75	75
Primer S	3	3	Ø
Primer AS	3	Ø	3
H₂O	65.4	68.4	68.4

2. Distribute the samples and add DNA to have :

Table 13
Volume (μl)	Insert	Primer S	Primer AS	Without DNA
Globalmix	48.4	48.4	48.4	48.4
C1 or C2	1	1	1	1
Phusion	0.2	0.2	0.2	0.2
Total	50	50	50	50

3. Dispense these samples in 10 tubes and launch the PCR for 24 cycles; T_annealing=63 ºC

Aim: Check the results of the previous PCR of the new versions of C1 and C2

Protocol: follow in this link

What we did in the lab:
Materials:
• Ladder
• Inserts (old)
• C1 and C2
• Primer S
• Buffer EX
• Electrophoresis machine

Method:
Add 5 μl of DNA and 1 μl of lead buffer EX:

Table 14

Samples L1 L2 L3 L4 L5 L6 L7 L8

**Contain**
Ladder C1 + insert C1 + S C1 + AS C2 + insert C2 + S C2 + AS C without DNA

Results:
None of the bands of our samples can be seen because the temperature is not suitable (too hot). This experiment has to be redone another time at lower temperature.

*Figure 1 : PCR gel of C1/C2*

Table 14
Samples	L1	L2	L3	L4	L5	L6	L7	L8
Contain	Ladder	C1 + insert	C1 + S	C1 + AS	C2 + insert	C2 + S	C2 + AS	C without DNA

Aim: PCR of the new versions of C1 and C2 at lower annealing temperature 55 ºC
Re-amplify some of the previous PCR reaction solution with fresh dNTPs, buffer and polymerase..

Protocol: follow this link

What we did in the lab:
Materials:
• Samples from the previous PCR of the 26⁄07
• Tubes for PCR
• PCR machine
• dNTPs
• MgCl₂ solution
• Phusion

Method:
1. Take 7 of the samples from the previous PCR (which contains only 45 μl after the electrophoresis)
2. With these samples, prepare the following samples by adding in order: dNTPs, MgCl₂ and Phusion enzyme :

Table 15
Volume (μl)	Insert	Primer S	Primer AS	Without DNA
Samples	45	45	45	45
dNTPs	6	6	6	6
MgCl₂	8.4	8.4	8.4	8.4
Phusion	0.5	0.5	0.5	0.5
V_final	60	60	60	60

3. Vortex all the samples mix and centrifuge them at room temperature at 3500 RPM
4. Run PCR following previous protocol, except for the T_annealing.

Aim: Recovering the product of our previous PCR.

What we did in the lab:
Materials:
• QIAGEN Gel extraction Kit
• Products of the PCR of the 27/07
• 6X loading buffer
• Molecular weight DNA Ladder
• 10 µl pipette
• 200 µl pipette
• PCR tubes

Method:
1. Recovery from the agarose gel of 8 wells
2. Take 50 µl in PCR tubes and prepare several samples by adding in each tubes:
2.a 10 µl of 6X loading buffer and mix with one pipette
2.b 6 µl of ladder
3.Determination of the weight of the gel for extraction bands of C1 with For and Rev primers :
m(tube) = 1.1258g
m(tube+gel) = 1.2919
→ m(gel) = 165 mg which correspond to 496.5 µl of buffer
4. Follow the QIAGEN gel extraction Kit protocol
Results :

*Figure 2 : PCR gel of C1/C2*
1: Ladder
2: Without DNA
3: C1 insert For and Rev
4: C1 For
5: C1 Rev
6: C2 insert
7: C2 For
8: C2 Rev

Aim: Transform our new plasmid (vector TOPO + C1 v2 and C2 v2).

Protocol: follow in this link

What we did in the lab:
Materials:
• Microbiological equipment
• Carbenicillin at 50 mg⁄ml
• LB medium
• Petri dish
• TOP 10 competent cells
• Dimethylformamide (DMF)
• Xgal 20 mg/ml in DMF

Method:
1. Prepare the solution of Xgal for the Petri dish with :
1.a 10 ml of DMF
1.b 200 mg of Xgal
2. Put 100 µl of this solution on 6 Petri dishes which already contain LB and carbenicillin. Then spread the solution in an additional volume of LB (100 &181#l). Let the Petri dishes dry at 37°C for approx. 1 hr. 3. Recovery C2 v2 and C1 v2 prepared on the 26⁄07 (to perform the TOP 10 cloning reaction)
4. Put 50 µl of bacteria TOP 10 in ice and add 6 µl of C1 v2 or C2 v1
5. Follow the protocol to transform thermally competent bacteria

Aim: Know the concentration of the inserts.

What we did in the lab:
Materials:
See protocol

Result

Table 16
	C1 v2	C2 v2
V_TE (µl)	498	498
V_DNA (µl)	2	2
A_{260 nm}	0.002	0.001
A_{280 nm}	0.001	0.001
Ratio 260/280	2	1
[Insert] (µg⁄ml)	20	25

Aim: Send the recombinant vector C2.1 (from the Midiprep of the 26⁄07) for sequencing to Eurofins-MWG.

Results:

Table 17
[DNA_C2.1] (ng⁄ml)	450
V_DNA (µl)	3.3
V_H₂O (µl)	11.7
V_{primer d1⁄50} (µl)	2
V_total (µl)	17

Aim: Check if the transformation worked.

What we did in the lab :
Materials :
• Microbiological equipment
• 50 ml Erlenmeyer
• Incubator
• LB medium
• Carbenicillin at 50 mg⁄ml

Method
1. Only one colony had grown so we put it into a 50 ml Erlenmeyer with 25 ml of LB and 25 µl of carbenicillin
2. Put the Erlenmeyer into the incubator at 37°C with agitation overnight

Aim: Have Petri dishes ready for future transformations with TOP 10 cells.

What we did in the lab :
Materials :
• Solution from TOP 10 transformation with the ligation TOPO10 cloning product (experiment from the 27⁄07)
•DMF
• Xgal at 10 mg⁄ml
• 200 µl micropipette
• 10 ml pipette
• Petri dishes

Method
1. In a Petri dish, put 100 μl of the solution from TOPO10 transformation with the ligation TOPO cloning product
2. Add 10 ml of DMF and 10 mg of Xgal
3. Spread 200 µl of Xgal on the Petri dishes, and allow drying at 37°C for approximately 1 hour.
4. Carry out the transformation according to the thermal protocol

Aim: Know the concentration of purified C1 (For + Rev).

What we did in the lab :
Materials :
• Ultrospec 3100
• Quartz cuvette
• TE buffer
• C1 DNA from the PCR purification (27⁄07)
• Petri dishes

Method
1. Do the blank with 500 µl of TE buffer
2. For the sample, use 498 µl of TE buffer and 2 µl of C1 DNA from the PCR purification

Results

Table 18
OD₂₆₀	OD₂₈₀	[DNA_C1] (µg⁄ml)
0.002	0.001	50

Aim: Protein purification.

Protocol: follow in this link

What we did in the lab :
Materials :
• FPLC machine (Fast Protein Liquid Chromatography)(Akta Prime Plus, GE Lifesciences)
• 5 ml Ni-NTA His-trap column (GE lifesciences)
• Buffer A (Tris 50 mM pH 7.4 ; NaCl 150 mM), Buffer B=Buffer A + Imidazole 250 mM
• PMSF at 100 mM in ethanol
• Branson 450 (sonicator)
• JA 25.5 rotor for Beckman Avanti X26-J centrifuge

Method
On ice :
1. Defrost one aliquot of C1 bacteria culture under cold running water
2. Equilibrate the column on the FPLC machine with buffer A
3. Once the bacteria are thawed out, add 22 ml of buffer A and 37µl of PMSF
4. Lyse the bacteria with a sonicator
5. Use a medium size tip, put the duty cycle at 60% and power under the limit of the micro tip setting
6. With the sonicator machine, do 3 times 30 seconds of sonication followed-up with 1 minute of rest on ice
7. Balance polycarbonate 50 ml tubes containing the lysate on a microbalance
8. Centrifuge the lysate at 16000 RPM in a JA 25.5 rotor in a Beckman Avanti X26-J at 4°C during 30 minutes
9. Transfer the supernatant to a 50 ml Falcon and add 37µl of PMSF
10. Inject 10 ml of this sample with a syringe equipped with a 0.45 µm filter in the injection port and load it on the column (Ni-NTA His Trap, 5 ml, GE Lifesciences)
12. Wash the injection loop and column with buffer A until the UV detector output at 280 nm is close to the baseline and repeat the injection 3 times
13. Wash the column with 5% buffer B
14. Run a gradient from 5&#37 to 100&#37 buffer B over 12 column volumes and collect fractions of 1 ml
15. Wash the column with buffer A

Aim: Detection of the proteins present in each fraction/peak.

What we did in the lab :
Materials :
• 10X TGS buffer (Biorad)
• Distilled water
• PAGE Ruler Protein Molecular weight ladder (Thermofisher)
• 1 SDS PAGE gel, BioRad (TGS: Tris Glycine SDS)
• Electrophoresis chamber , Power supply and electrodes (Biorad)
• 2X SDS (Laemli buffer with β-mercapto ethanol)
• 95°C Heater block
• Gel Code blue stain (Pierce) with G250 Coomassie blue

Method
1. At the beginning, prepare 1X from 10X TGS buffer with 25 ml of buffer and 225 ml of distilled water
2. Heat samples at 95°C for 5 minutes, cool at RT, and load 20 µl in each well; 6 µl of ladder.
3. Run at 130 V

Results :
1 : PAGE ruler Ladder
2 : Well 19
3 : Well 21
4 : Well 25
5 : Well 30
6 : Well 34
7 : Well 36
8 : Well 37
9 : Well 38
10 : Well 39
The concentration of proteins is too high so this experiment has to be redone

*Figure 3 : SDS PAGE gel of our protein*

Aim :
Revelation of proteins in each well.

What we did in the lab :

Materials :
• TGS 10X
• PAGE ruler molecular weight marker (Thermofisher)
• Distilled water
• Protein fraction solutions from FPLC
• Buffer A
• Laemli 2X
• SDS PAGE gel, electrophoresis chamber, 3000 V power supply (Biorad)

Method :
1. Prepare 400 ml of TGS 1X with 40 ml of TGS 10X and 360 ml of distilled water
2. Dilute protein solutions :

*Table 19 : Volumes*

Fractions from FPLC Dilution Contain

19, 21, 25 Ø Ø

30, 34, 36 (1/100) in buffer A 1 µl of protein with 99 µl of buffer A

37, 38, 39 (1/10) in buffer A 1 µl of protein with 9 µl of buffer A

3. In each gel well, add 10 µl of diluted protein solution and 10 µl of laemli 2X.
4. Put all samples at 95°C during 5 minutes and follow the protocol for SDS PAGE gel.

Results :
The distribution of samples in lanes is the same as the previous experiment :
*Figure 4 : SDS PAGE gel of diluted proteins*
1 : Ladder
2 : Well 19
3 : Well 21
4 : Well 25
5 : Well 30
6 : Well 34
7 : Well 36
8 : Well 37
9 : Well 38
10 :Well 39

*Table 19 : Volumes*
Fractions from FPLC	Dilution	Contain
19, 21, 25	Ø	Ø
30, 34, 36	(1/100) in buffer A	1 µl of protein with 99 µl of buffer A
37, 38, 39	(1/10) in buffer A	1 µl of protein with 9 µl of buffer A

Aim:

Test the specificity of our two primers : For and Rev. Use a different DNA polymerase

Protocol:

follow in this link

What we did in the lab :

Materials :

• dNTPs
• Solution of MgCl₂
• RNA free
• Buffer 10X pfu DNA polymerase
• Inserts C1 v2 and C2 v2
• For primer (see PCR protocol for sequence)
• Rev primer (see PCR protocol for sequence)
• 2 ml Eppendorfs
• Distilled water

Method

1. Make a global mix for the 7 samples :

*Table 20 : Volumes*
	Volumes (µl)
dNTPs	22.5
MgCl₂	22.5
RNA free	327.6
Buffer 10X pfu	22.5
Total	417.6

2. Distribute the global mix in each tubes and add DNA :

*Table 21 : Volumes*
Tubes	Name	V(premix) (µl)	V(C1 v2) (µl)	V(C2 v2) (µl)	V(primer For) (µl)	V(primer Rev) (µl)	V(H₂O) (µl)
1	C1 v2 insert For and Rev	46.4	1	0	1	1	0
2	C1 v2 insert For	46.4	1	0	1	0	1
3	C1 v2 insert Rev	46.4	1	0	0	1	1
4	C2 v2 insert For and Rev	46.4	0	1	1	1	0
1	C2 v2 insert For	46.4	0	1	1	0	1
1	C1 v2 insert Rev	46.4	0	1	0	1	1
1	Without DNA	0	0	0	0	0	0

3. Put the tubes in a PCR machine heat to 94°C during 1 minute and then add the enzyme.

Aim :
Test the specificity of our two primers : For and Rev.

Protocol :
follow in this link

What we did in the lab :

Materials :
• 100 ml Erlenmeyer
• TAE 1X
• Agarose gel
• Ethidium bromide drops (EB)
• Gel electrophoresis apparatus
• Gene ruler ladder
• Loading buffer 6X
• DNA (C1 and C2, For and Rev)

Method :
1. Prepare a 0.7% agarose gel :
1.a In an Erlenmeyer of 100 ml, put 50 ml of TAE 1X and add 0.35 g of agarose
1.b Warm it in a microwave 2 minutes and let it cool down a little
1.c Add 2 drops of EB and mix it
1.d Transfer it on combs in a gel caster and let it solidify
2. Put samples in the wells:

Table 22

Wells Samples

1
7 µl of gene ruler

2
2 µl of 6X + 10 µl of DNA (C1 For and Rev)

3
2 µl of load 6X + 10 µl of DNA (C1 For)

4
2 µl of load 6X + 10 µl of DNA (C1 Rev)

5
2 µl of load 6X + 10 µl of DNA (C2 For and Rev)

6
2 µl of load 6X + 10 µl of DNA (C2 For)

7
2 µl of load 6X + 10 µl of DNA (C2 Rev)

8
2 µl of load 6X + 10 µl of distilled water

Results :

*Figure 5 : PCR gel of C1 v2 / C2 v2*
1 : Gene ruler 7 μl
2 : C1 For + Rev
3 : C1 For
4 : C1 Rev
5 : C2 For + Rev
6 : C2 For
7 : C2 Rev
8 : Without DNA
The experiments did not work.

Table 22
Wells	Samples
1	7 µl of gene ruler
2	2 µl of 6X + 10 µl of DNA (C1 For and Rev)
3	2 µl of load 6X + 10 µl of DNA (C1 For)
4	2 µl of load 6X + 10 µl of DNA (C1 Rev)
5	2 µl of load 6X + 10 µl of DNA (C2 For and Rev)
6	2 µl of load 6X + 10 µl of DNA (C2 For)
7	2 µl of load 6X + 10 µl of DNA (C2 Rev)
8	2 µl of load 6X + 10 µl of distilled water

Aim: Extracting DNA from the colony obtained after transformation.
Protocol: follow in this link

Materials :
• Miniprep QIAGEN Kit
• TOPO cloning colony
• Buffer EB
• Spectrophotometer

Method
1. For the Miniprep prepare 6x 2 ml of cultures and recover it in 50 μl of buffer EB
2. Do the prep with the QIAGEN Miniprep Kit
3. Measure the absorbance of the products to determine the amount of DNA obtained after extraction

Results :

Table 23
Samples	A_{260 nm}	A_{280 nm}	[DNA] (μg⁄ml)
1	0.009	0.001	120 → wrong
2	0.001	0.003	10
3	0.001	0.003	11

Aim:Check if the insert is in the TOPO vector.
Protocol: follow in this link

Materials :
• Biochemical equipment
• TOPO vector
• Xba I (NEB)
• Hind III (NEB)
• Buffer Cutsmart 10X (NEB)
• Distilled water

Method

Table 24
	Volumes (μl)
DNA (10 μg⁄ml)	5
Xba I	1
Hind III	1
Buffer Cutsmart 10X	4
H₂O	29
Total	40

Aim:Protein conservation.
Materials :
• Biochemical equipment
• Glycerol 80 %

Method
To prepare glycerol 80% with a final volume of 40 ml, use 32 ml of glycerol with 8 ml of H₂O (40×80)⁄100 = 32 ml

Difference between revisions of "Team:Pasteur Paris/Microbiology week8"

Revision as of 18:44, 19 October 2016

click on the weeks

Microbiology Notebook

Week 8

July 25, 2016:

92. Next step for the growth curve

93. Measurements of insert quantity with Nanodrop

94. Ligation of the new version of the inserts

95. PCR of C1 and C2 (v2)

July 26, 2016:

96. Midiprep of the culture made on the 25^th of July

97. Extraction and resuspension of culture made on the 25^th of July

98. Extraction gel bands C1 and C2

99. Set up the TOPO cloning ratios, ligation of C2 and C1 (v2)

July 27, 2016:

100. STAB culture

101. Electrophoresis of PCR amplifications with the two inserts

102. PCR of the new versions of C1 and C2 at 63 °C

103. Electrophoresis of PCR products from C1 and C2

104. PCR of the new versions of C1 and C2

105. PCR purification

106. TOP 10 cells transformation with the TOPO cloning ligation product

107. Dosage of C1 v2 and C2 v2 after PCR and purification

July 28, 2016:

108. Send the recombinant vector C2.1 (from the Midiprep of the 26^th of July) for sequencing to Eurofins-MWG

109. Observation of the transformation of C1 v2 and C2 v2 and culture of one colony

110. Preparation of Petri dishes with Xgal

111. Dosage of C1 after PCR product purification

112. Fast Protein Liquid Chromatography (FPLC)

July 29, 2016:

113. SDS PAGE gel of purified protein fractions from FPLC

114. SDS PAGE gel of purified protein fractions from FPLC

115. PCR of C1 v2 and C2 v2

116. Agarose gel Electrophoresis

117. DNA extraction with TOPO cloning colony obtained on the 27^th of July

118. DNA digestion with Xba I and Hind III

July 30, 2016:

119. Protein cryoconservation

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@@ Line 217: / Line 225: @@
 <body>
+<div>
+  <a href="https://2016.igem.org/Team:Pasteur_Paris/Microbiology"><h2><B>Microbiology Notebook</B></h2><a/>
+</div>
+<div id="home">
+<center></a><a href="https://2016.igem.org/Team:Pasteur_Paris/Microbiology"><img src="https://static.igem.org/mediawiki/2016/5/5a/Labwork_pasteur.png" width="40%" alt=""/></img></a></center>
+</div>
 <div id="week8">
@@ Line 1,163: / Line 1,178: @@
 <U>Results: </U><br/>
 None of the bands of our samples can be seen because the temperature is not suitable (too hot). This experiment has to be redone another time at lower temperature. <br/>
-<img src = “picture of the gel”; alt “”/><br/>
+<center><img src = “https://static.igem.org/mediawiki/2016/0/07/Week_8_Figure_1_Electrophoresis_PCR_C1-C2.jpg”; alt “PCR gel of C1/C2”/><br/>
-<center> Figure 1</center>
+<i><p><U>Figure 1 :</U> PCR gel of C1/C2 </p></i></center>
 </br></br></br>
          </p>
@@ Line 1,280: / Line 1,295: @@
 . Follow the QIAGEN gel extraction Kit protocol <br/>
 <U>Results :</U><br/>
-<img scr = “picture of the gel”; alt “”/><br/>
+<center><img scr = “https://static.igem.org/mediawiki/2016/3/3c/Week_8_Figure_2_PCR_C1-C2.jpg”; alt “PCR gel of C1/C2”/>
-<center> Figure 2 </center>
+<i><p>Figure 2 :</U> PCR gel of C1/C2 </p></i></center>
 : Ladder<br/>
 : Without DNA<br/>
@@ Line 1,608: / Line 1,623: @@
 The concentration of proteins is too high so this experiment has to be redone<br/>
-<img src = “”; alt = “”/>
+<center><img src = "https://static.igem.org/mediawiki/2016/4/43/Week_8_Figure_3_SDS_PAGE_gel_proteins.jpg"; alt = "SDS PAGE gel of our protein"/>
-<center> Figure 3 </center>
+<i><p><U>Figure 3 :</U> SDS PAGE gel of our protein </p></i></center>
 </br></br></br>
          </p>
@@ Line 1,624: / Line 1,639: @@
      <figcaption>
-<p><U> Aim:</U> Revelation of proteins in each well. <br/> <br/>
+<p>
-<U>What we did in the lab :</U><br/>
+<h6><U> Aim :</U></h6> Revelation of proteins in each well. <br/><br/>
-<U>Materials :</U><br/>
+<h6><U>What we did in the lab :</U></h6><br />
-&bull; TGS 10X<br/>
+<h6><U>Materials :</U></h6>
-&bull; PAGE ruler molecular weight marker (Thermofisher) <br/>
+&bull; TGS 10X<br />
-&bull; Distilled water<br/>
+&bull; PAGE ruler molecular weight marker (Thermofisher) <br />
-&bull; Protein fraction solutions from FPLC<br/>
+&bull; Distilled water<br />
-&bull; Buffer A<br/>
+&bull; Protein fraction solutions from FPLC<br />
-&bull; Laemli 2X<br/>
+&bull; Buffer A<br />
+&bull; Laemli 2X<br />
 &bull; SDS PAGE gel, electrophoresis chamber, 3000 V power supply (Biorad)
-<br/><br/>
+<br /><br />
-<U> Method </U><br/>
+<h6><U> Method :</U></h6>
-. Prepare 400 ml of TGS 1X with 40 ml of TGS 10X and 360 ml of distilled water <br/>
+. Prepare 400 ml of TGS 1X with 40 ml of TGS 10X and 360 ml of distilled water <br />
-. Dilute protein solutions : <br/>
+. Dilute protein solutions : <br />
 <table>
-<caption align="bottom" align="center">Table 19</caption>
+<caption align="bottom" align="center"><i>Table 19 : Volumes<i></caption>
     <thead>
        <tr>
@@ Line 1,655: / Line 1,671: @@
              <tr>
        <td align="center" ; valign = “center”> 30, 34, 36 </td>
-       <td align="center" ; valign = “center”> (1&#8260;100) in buffer A </td>
+       <td align="center" ; valign = “center”> (1/100) in buffer A </td>
        <td align="center" ; valign = “center”> 1 &#181;l of protein with 99 &#181;l of buffer A </td>
 </tr>
              <tr>
        <td align="center" ; valign = “center”> 37, 38, 39 </td>
-       <td align="center" ; valign = “center”>(1&#8260;10) in buffer A </td>
+       <td align="center" ; valign = “center”>(1/10) in buffer A </td>
        <td align="center" ; valign = “center”> 1 &#181;l of protein with 9 &#181;l of buffer A </td>
 </tr>
 </tbody>
-</table><br>
+</table><br />
-. In each gel well, add 10 &#181;l of diluted protein solution and 10 &#181;l of laemli 2X <br/>
+. In each gel well, add 10 &#181;l of diluted protein solution and 10 &#181;l of laemli 2X. <br />
-. Put all samples at 95&#176;C during 5 minutes and follow the protocol for SDS PAGE gel
+. Put all samples at 95°C during 5 minutes and follow the protocol for SDS PAGE gel.
-<br/><br/>
+<br /><br />
-<U>Results :</U><br/>
+<h6><U>Results :</U></h6>
-The distribution of samples in lanes is the same as the previous experiment:<br/>
+The distribution of samples in lanes is the same as the previous experiment :<br />
-<img src = “”; alt = “”/>
+<center><img src = "https://static.igem.org/mediawiki/2016/0/0e/Week_8_Figure_4_SDS_PAGE_gel_of_diluted_proteins.jpg"; alt = "SDS PAGE gel of diluted proteins"/>
-<center> Figure 4 </center>
+<i><p> <U>Figure 4 :</U> SDS PAGE gel of diluted proteins </p></i></center>
- : Ladder <br/>
+ : Ladder <br />
- : Well 19<br/>
+ : Well 19<br />
- : Well 21<br/>
+ : Well 21<br />
- : Well 25<br/>
+ : Well 25<br />
- : Well 30<br/>
+ : Well 30<br />
- : Well 34<br/>
+ : Well 34<br />
- : Well 36 <br/>
+ : Well 36 <br />
- : Well 37<br/>
+ : Well 37<br />
- : Well 38<br/>
+ : Well 38<br />
- :Well 39
+ :Well 39<br />
 </br></br></br>
          </p>
@@ Line 1,696: / Line 1,712: @@
      <figcaption>
-<p><U> Aim:</U> Test the specificity of our two primers : For and Rev. Use a different DNA polymerase<br/> <br/>
+<p>
-<U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/b/be/T--Pasteur_Paris--PCR_protocol.pdf">link</a><br/><br/>
+<h6><U> Aim:</U></h6> Test the specificity of our two primers : For and Rev. Use a different DNA polymerase<br /><br />
-<U>What we did in the lab :</U><br/>
+<h6><U> Protocol:</U></h6> follow in this <a href="https://static.igem.org/mediawiki/2016/b/be/T--Pasteur_Paris--PCR_protocol.pdf">link</a><br /><br />
-<U>Materials :</U><br/>
+<h6><U>What we did in the lab :</U></h6><br />
-&bull; dNTPs <br/>
+<h6><U>Materials :</U></h6>
-&bull; Solution of MgCl<sub>2</sub> <br/>
+&bull; dNTPs <br />
-&bull; RNA free <br/>
+&bull; Solution of MgCl<sub>2</sub> <br />
-&bull; Buffer 10X pfu DNA polymerase  <br/>
+&bull; RNA free <br />
-&bull; Inserts C1 v2 and C2 v2  <br/>
+&bull; Buffer 10X pfu DNA polymerase  <br />
-&bull; For primer (see PCR protocol for sequence) <br/>
+&bull; Inserts C1 v2 and C2 v2  <br />
-&bull; Rev primer  (see PCR protocol for sequence) <br/>
+&bull; For primer (see PCR protocol for sequence) <br />
-&bull; 2 ml Eppendorfs  <br/>
+&bull; Rev primer  (see PCR protocol for sequence) <br />
+&bull; 2 ml Eppendorfs  <br />
 &bull; Distilled water
-<br/><br/>
+<br /><br />
-<U> Method </U><br/>
+<h6><U> Method </U></h6>
-. Make a global mix for the 7 samples : <br/>
+. Make a global mix for the 7 samples : <br />
 <table>
-<caption align="bottom" align="center">Table 20</caption>
+<caption align="bottom" align="center"><i>Table 20 : Volumes</i></caption>
     <thead>
        <tr>
           <th>  </th>
-          <th> Volumes (&#956;l) </th>
+          <th> Volumes (&#181;l) </th>
 </tr>
     </thead>
@@ Line 1,742: / Line 1,759: @@
 </tr>
 </tbody>
-</table><br/>
+</table><br />
-. Distribute the global mix in each tubes and add DNA : <br/>
+. Distribute the global mix in each tubes and add DNA : <br />
 <table>
-<caption align="bottom" align="center">Table 21</caption>
+<caption align="bottom" align="center"><i>Table 21 : Volumes</i></caption>
     <thead>
        <tr>
           <th> Tubes </th>
           <th> Name </th>
-          <th> V(premix) (&#956;l) </th>
+          <th> V(premix) (&#181;l) </th>
           <th> V(C1 v2) (&#181;l) </th>
           <th> V(C2 v2) (&#181;l) </th>
@@ Line 1,830: / Line 1,847: @@
 </tr>
 </tbody>
-</table><br/>
+</table><br />
-. Put the tubes in a PCR machine heat to 94&#176;C during 1 minute and then add the enzyme.
+. Put the tubes in a PCR machine heat to 94°C during 1 minute and then add the enzyme. <br />
-</br></br></br>
+<br /><br /><br />
          </p>
        </figcaption>
@@ Line 1,845: / Line 1,862: @@
      <figcaption>
-<p><U> Aim:</U> Test the specificity of our two primers : For and Rev. <br/><br/>
+<p>
-<U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/6/60/T--Pasteur_Paris--Gel_electrophoresis_protocol.pdf">link</a><br/><br/>
+<h6><U> Aim :</U></h6> Test the specificity of our two primers : For and Rev. <br /><br />
-<U>What we did in the lab :</U><br/>
+<h6><U> Protocol :</U></h6> follow in this <a href="https://static.igem.org/mediawiki/2016/6/60/T--Pasteur_Paris--Gel_electrophoresis_protocol.pdf">link</a><br /><br />
-<U>Materials :</U><br/>
+<h6><U>What we did in the lab :</U></h6><br />
-&bull; 100 ml Erlenmeyer<br/>
+<h6><U>Materials :</U></h6>
-&bull; TAE 1X <br/>
+&bull; 100 ml Erlenmeyer<br />
-&bull; Agarose gel <br/>
+&bull; TAE 1X <br />
-&bull; Ethidium bromide drops (EB) <br/>
+&bull; Agarose gel <br />
-&bull; Gel electrophoresis apparatus <br/>
+&bull; Ethidium bromide drops (EB) <br />
-&bull; Gene ruler ladder <br/>
+&bull; Gel electrophoresis apparatus <br />
-&bull; Loading buffer 6X <br/>
+&bull; Gene ruler ladder <br />
+&bull; Loading buffer 6X <br />
 &bull; DNA (C1 and C2, For and Rev)
-<br/><br/>
+<br /><br />
-<U> Method </U><br/>
+<h6><U> Method :</U></h6>
-. Prepare a 0.71&#37; agarose gel :<br/>
+. Prepare a 0.7% agarose gel :<br />
-&emsp; 1.a In an Erlenmeyer of 100 ml, put 50 ml of TAE 1X and add 0.35 g of agarose <br/>
+&emsp; 1.a In an Erlenmeyer of 100 ml, put 50 ml of TAE 1X and add 0.35 g of agarose <br />
-&emsp; 1.b Warm it in a microwave 2 minutes and let it cool down a little <br/>
+&emsp; 1.b Warm it in a microwave 2 minutes and let it cool down a little <br />
-&emsp; 1.c Add 2 drops of EB and mix it <br/>
+&emsp; 1.c Add 2 drops of EB and mix it <br />
-&emsp; 1.d Transfer it on combs in a gel caster and let it solidify <br/>
+&emsp; 1.d Transfer it on combs in a gel caster and let it solidify <br />
-. Put samples in the wells:<br/>
+. Put samples in the wells:<br />
 <table>
 <caption align="bottom" align="center">Table 22</caption>
@@ Line 1,876: / Line 1,894: @@
        <tr>
        <td align="center" ; valign = “center”><strong><p> 1 </p></strong></td>
-       <td align="center" ; valign = “center”> 7 &#956;l of gene ruler  </td>
+       <td align="center" ; valign = “center”> 7 &#181;l of gene ruler </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 2 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of 6X + 10 &#956;l of DNA (C1 For and Rev) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of 6X + 10 &#181;l of DNA (C1 For and Rev) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 3 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of DNA (C1 For) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of DNA (C1 For) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 4 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of DNA (C1 Rev) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of DNA (C1 Rev) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 5 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of DNA (C2 For and Rev) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of DNA (C2 For and Rev) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 6 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of DNA (C2 For) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of DNA (C2 For) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 7 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of DNA (C2 Rev) </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of DNA (C2 Rev) </td>
 </tr>
        <tr>
        <td align="center" ; valign = “center”><strong><p> 8 </p></strong></td>
-       <td align="center" ; valign = “center”> 2 &#956;l of load 6X + 10 &#956;l of distilled water </td>
+       <td align="center" ; valign = “center”> 2 &#181;l of load 6X + 10 &#181;l of distilled water </td>
 </tr>
 </tbody>
-</table><br/><br/>
+</table><br /><br />
-<U>Results :</U><br/>
+<h6><U>Results :</U></h6>
-<img src = “”; alt “”><br/>
+<center><img src = "https://static.igem.org/mediawiki/2016/0/02/Week_8_Figure_5_Agarose_gel_Electrophoresis_C1-C2.jpg"; alt "PCR gel of C1 v2 / C2 v2"/><br/>
-<center> Figure 5 </center>
+<i><p>Figure 5 :</U> PCR gel of C1 v2 / C2 v2 </p></i></center>
  : Gene ruler 7 &#956;l <br/>
  : C1 For + Rev <br/>

Difference between revisions of "Team:Pasteur Paris/Microbiology week8"

Revision as of 18:44, 19 October 2016

click on the weeks

Microbiology Notebook

Week 8

July 25, 2016:

92. Next step for the growth curve

93. Measurements of insert quantity with Nanodrop

94. Ligation of the new version of the inserts

95. PCR of C1 and C2 (v2)

July 26, 2016:

96. Midiprep of the culture made on the 25th of July

97. Extraction and resuspension of culture made on the 25th of July

98. Extraction gel bands C1 and C2

99. Set up the TOPO cloning ratios, ligation of C2 and C1 (v2)

July 27, 2016:

100. STAB culture

101. Electrophoresis of PCR amplifications with the two inserts

102. PCR of the new versions of C1 and C2 at 63 °C

103. Electrophoresis of PCR products from C1 and C2

104. PCR of the new versions of C1 and C2

105. PCR purification

106. TOP 10 cells transformation with the TOPO cloning ligation product

107. Dosage of C1 v2 and C2 v2 after PCR and purification

July 28, 2016:

108. Send the recombinant vector C2.1 (from the Midiprep of the 26th of July) for sequencing to Eurofins-MWG

109. Observation of the transformation of C1 v2 and C2 v2 and culture of one colony

110. Preparation of Petri dishes with Xgal

111. Dosage of C1 after PCR product purification

112. Fast Protein Liquid Chromatography (FPLC)

July 29, 2016:

113. SDS PAGE gel of purified protein fractions from FPLC

114. SDS PAGE gel of purified protein fractions from FPLC

115. PCR of C1 v2 and C2 v2

116. Agarose gel Electrophoresis

117. DNA extraction with TOPO cloning colony obtained on the 27th of July

118. DNA digestion with Xba I and Hind III

July 30, 2016:

119. Protein cryoconservation

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What we did in the lab :

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96. Midiprep of the culture made on the 25^th of July

97. Extraction and resuspension of culture made on the 25^th of July

108. Send the recombinant vector C2.1 (from the Midiprep of the 26^th of July) for sequencing to Eurofins-MWG

117. DNA extraction with TOPO cloning colony obtained on the 27^th of July