Difference between revisions of "Team:Pasteur Paris/Microbiology week14"

Aim: Produce our protein in BL21(DE3) competent cells, the production is induced with IPTG once it reaches an optical density of 0.7.

Protocol: follow in this link

What we did in the lab:
Materials:
• 2 2L erlenmeyers
• LB (lysogeny Luria broth)
• IPTG (0.1M)
• Precultures in 25ml erlenmeyers
• UV spectrophotometer (Ultrospec 3100)
• Shaking incubator (INFORS HT)
• Centrifuge
• Buffer A (50mM Tris, 150mM of NaCl)

Method:
Put 1L of LB in each erlenmeyer and make them warm with the shaking incubator at 37°C and 150RPM
Once warmed, add 12.5ml of preculture in each erlenmeyer
Let grow in the shaking incubator.
Measure the absorbance with the UV spectrophotometer every 30min

Time	C2(1)	C2(2)
10:30AM	0	0
01:55PM	0.438	/
2:25PM	0.602	0.429
2:45PM	0.679	0.600

Optical Density

5. Add IPTG to reach a concentration of 0.1mM. (3:00PM)
6. The last measure before induction is pelleted 3min at 8000g and stored at -20°C.
 7. Let induce overnight in the shaking incubator at 15°C at 150RPM
8. The day after, measure the OD and store the measure pelleted at -20°C.
9. Centrifuge at 4500RPM the culture and throw out the supernatant, the pellet resuspended in 5ml of buffer A are stored at -80°C before protein extraction.

Aim: Purifying the protein C2 produced by BL21(DE3) using a Fast Purification Liquid Chromatography. We use the culture induced the previous day.

Protocol: follow in this link

What we did in the lab:
Materials:
• Fast Purification Liquid Chromatography
• Chaotropic reagent (Guanidinium 6M)
• EDTA 0,1M
• PMSF (100mM)
• Ni 2+ solution (100mM)
• Centrifuge (labo deshmukh)
• Buffer A (50mM Tris, 150mM of NaCl)
• Buffer B (50mM Tris, 150mM of NaCl, 250mM Imidazole, pH=7.4)

Method:
Melt the pellet of bacteria C2 (from 1L culture) and resuspend it with 10ml of buffer A. We had 25ml of pellet we complete until 40ml with buffer A.
Add 40 µL of PMSF to avoid protein denaturation.
Put the column on the FPLC, clean the FPLC with water and then fill it with buffer A.
Sonicate the sample three times one minute at 60%, wait 90 seconds between each sonication.
Centrifuge 25 min at 16000g (rotor JA 25.50)
Inject your sample in the FPLC
Get back several samples:
• C: Crude extract : before centrigugation
• P: Pellet
• SN: Supernatant
• F: Flow through (unfixed proteins)
• W: Wash 5% of buffer B
• Fractions (depending on the gradient)

Aim: Get the size of the protein purified thanks to FPLC in order to know if it is our protein

Material: • SDS-Page cuve
• SDS-Page gel (BIORAD)
• Protein migration buffer
• Protein ladder
• Laemmli 2X
• Coomassie Blue
• Microbiology equipment (Follow this link)

Method: In 9 1.5ml eppendorf, put 20 µL of a sample and 20 µL of Laemmli 2X.
Let denaturate the proteins 5min at 95°C
Place the gel into the cuve and fill it with migration buffer
Follow the next deposit table:
• Fraction 13
• Fraction 15
• Fraction 17
• Fraction 19
• Fraction 21
• Fraction 23
• Fraction 25
• Fraction 27
• Protein gene ruler (8 µL)
4. Launch the migration at 130V.
5. Wash the gel three times with distilled water during 5min.
6. Color the gel with Coomassie Blue diluted 1/5 during 30min.
7. Wash with distilled water for 5min then let wash 15min.

Aim: To start a culture for Miniprep of insert A1 / A2 / B1 / B2 / C1 / C2 / D1 / D2 / E1 / E2
In order to obtain a large amount of plasmid, we need to grow the bacteria overnight.

Protocol: follow in this link

What we did in the lab:
Materials:
• Microbiology equipement
• 15 mL Falcons
• Carbenicillin 50 mg/ml
• LB medium

Method:
One colony is picked from the plates and shaken in 5.0 mL of LB supplemented with Carbenicillin at 50 µg/ml.
The flask is placed in a shaking incubator at 37°C, 150 rpm overnight.

Aim: To perform a Midiprep to isolate plasmid DNA of pET43.1a with the inserts A1 / A2 / B1 / B2 / C1 / C2 / D1 / D2 / E1 / E2 from cultures made on the 8/09.
The amplification method to increase the amount of plasmid is called Midiprep.
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)
• QIAGEN Miniprep kit
• Microbiology equipment (type of incubator, Bunsen burner, water bath, etc… Follow this link)

Method:
The protocol in step 1 ask for spinning at 6000g but we can only achieve 3500 g so we used 3500 g for 8 minutes. We will follow most of the protocol of QIAGEN Miniprep 2016 except for a few modifications, which we describe, therefore, below.

Follow QIAGEN kit steps. Final volume: 100 µL

Aim: Measure the quantity of plasmid using a Nanodrop (Thermofisher)

What we did in the lab:
Materials:
• Nanodrop (Thermofisher)
• Elution buffer from QIAGEN kit
• Microbiology equipment (Follow this link)

Method:
Analyze absorbance at 260nm
Clean the Nanodrop with water
Make the blank with 1ul of elution buffer
Put 1ul of your sample on the Nanodrop
Make the measure and clean the Nanodrop between each measure

Results:

Absorbance at 260nm	A260	A280	A260/280	Concentration (ng/µL )
A1	0.645	0.345	1.87	32.3
A1’ _{(diluted 1/2)}	1.314	0.704	1.86	65.7
A2_{(diluted 1/4)}	1.404	0.752	1.87	70.2
A2’_{(diluted 1/4)}	0.494	0.269	1.87	24.7
C1_{(diluted 1/4)}	0.305	0.165	1.85	15.2
C1’_{(diluted 1/4)}	0.812	0.445	1.83	40.6
C2_{(diluted 1/4)}	0.499	0.272	1.83	24.9
C2’_{(diluted 1/4)}	0.757	0.402	1.88	37.8
D1_{(diluted 1/4)}	0.441	0.233	1.89	22.1
D1’_{(diluted 1/4)})	0.725	0.396	1.83	36.3
D2_{(diluted 1/4)})	0.264	0.141	1.87	13.2
D2’_{(diluted 1/4)})	0.418	0.216	1.94	20.9
E1_{(diluted 1/4)})	0.487	0.266	1.83	24.3
E1’_{(diluted 1/4)})	0.478	0.247	1.94	24.0
E2_{(diluted 1/4)})	1.364	0.742	1.84	68.2
E2’_{(diluted 1/4)})	1.041	0.562	1.85	52.1

Absorbance

@@ Line 231: / Line 231: @@
      <p><h3><B>September 6, 2016:</B></h3></p>
      <p>
-         <a href="#exp1"> <h4>Growth of bacteria </h4></a></br>
+         <a href="#exp1"> <h4> 236. Growth of bacteria </h4></a></br>
     </p>
      <p><h3><B>September 7, 2016:</B></h3></p>
      <p>
-         <a href="#exp2"><h4> Purification of the protein </h4></a></br>
+         <a href="#exp2"><h4> 237. Purification of the protein </h4></a></br>
      </p>
      <p><h3><B>September 8, 2016:</B></h3></p>
      <p>
-           <a href="#exp3"><h4> Protein gel on SDS-Page </h4></a></br>
+           <a href="#exp3"><h4> 238. Protein gel on SDS-Page </h4></a></br>
-           <a href="#exp4"><h4> Harvest the culture with Miniprep </h4></a></br>
+           <a href="#exp4"><h4> 239. Harvest the culture with Miniprep </h4></a></br>
      </p>
 <p><h3><B>September 9, 2016:</B></h3></p>
      <p>
-           <a href="#exp5"><h4> Extraction of plasmid DNA </h4></a></br>
+           <a href="#exp5"><h4> 240. Extraction of plasmid DNA </h4></a></br>
-           <a href="#exp6"><h4> Measure the amount of DNA extracted from the miniprep </h4></a></br>
+           <a href="#exp6"><h4> 241. Measure the amount of DNA extracted from the miniprep </h4></a></br>
      </p>

Difference between revisions of "Team:Pasteur Paris/Microbiology week14"

Revision as of 06:50, 18 October 2016

click on the weeks

Microbiology Notebook

Week 14

September 6, 2016:

236. Growth of bacteria

September 7, 2016:

237. Purification of the protein

September 8, 2016:

238. Protein gel on SDS-Page

239. Harvest the culture with Miniprep

September 9, 2016:

240. Extraction of plasmid DNA

241. Measure the amount of DNA extracted from the miniprep