Difference between revisions of "Team:Pasteur Paris/Microbiology week13"

Aim: Measure the quantity of plasmid using a Nanodrop (Thermofisher) before sending for sequencing (inserts B1 and C2)

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(1)	0.202	0.124	1.62	10.1
A1(2)	0.259	0.169	1.53	13.0
A2(1)	0.179	0.105	1.70	8.9
A2(2)	0.179	0.103	1.73	8.9
A2(3)	0.098	0.052	1.86	4.9
A2(4)	0.152	0.099	1.53	7.6

Absorbance

Aim: To start a culture for Miniprep of insert C2 in pET43.1a in BL21(DE3) from 22/08 and A1/C2 in pET43.1a in TOP1O.
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
• 50mL erlenmeyers
• Carbenicillin 50 mg/ml
• LB medium

Method:
One colony is picked from the plates and shaken in 25.0 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: 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)
9:36AM	0.024	0.023
10:06AM	0.049	0.046
11:02AM	0.175	0.165
11:36AM	0.395	0.402
12:05AM	0.568	0.540
12:27AM	0.658	0.638
12:38AM	0.694	0.680
14:31PM	0.872	0.859

Optical Density

5. Add IPTG to reach a concentration of 0.1mM. (12:57AM)
6. The last measure before induction is pelleted 3min at 8000g and stored at -20°C.
 7. Let induce overnight in the shaking incubator
8. After 7 hours of induction, 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: To perform a Midiprep to isolate plasmid DNA of pET43.1a with the inserts A1/C2 from cultures made on the 1/09.
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

@@ Line 249: / Line 249: @@
                 <p>
                 <U> Aim:</U> Measure the quantity of plasmid using a Nanodrop (Thermofisher) before sending for sequencing (inserts B1 and C2)</br></br>
-               <U> Protocol:</U> follow in this link</br></br>
                 <U>What we did in the lab:</U></br>
                 <U>Materials:</U></br>
@@ Line 336: / Line 335: @@
                    In order to obtain a large amount of plasmid, we need to grow the bacteria overnight.
                  </br></br>
+<U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/4/4b/T--Pasteur_Paris--Bacterial_culture_protocol.pdf">link</a><br/><br/>
-                  <U> Protocol:</U> follow in this link</br></br>
                    <U>What we did in the lab:</U></br>
                    <U>Materials:</U></br>
@@ Line 360: / Line 358: @@
                 <figcaption>
                    <p><U> Aim:</U> Produce our protein in BL21(DE3) competent cells, the production is induced with IPTG once it reaches an optical density of 0.7.</br></br>
+<U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/a/a4/T--Pasteur_Paris--Protein_induction_protocol.pdf">link</a><br/><br/>
-                  <U> Protocol:</U> follow in this link</br></br>
                    <U>What we did in the lab:</U></br>
                    <U>Materials:</U></br>
@@ Line 449: / Line 446: @@
                 <p>
                 <U> Aim:</U> To perform a Midiprep to isolate plasmid DNA of pET43.1a with the inserts A1/C2 from cultures made on the 1/09. </br>The amplification method to increase the amount of plasmid is called Midiprep.</br></br>
+ <U> Protocol:</U> follow in this <a href="https://static.igem.org/mediawiki/2016/d/d5/T--Pasteur_Paris--Miniprep_protocol.pdf">link</a><br/><br/>
-               <U> Protocol:</U> follow in this link</br></br>
                 <U>What we did in the lab:</U></br>
                 <U>Materials:</U></br>

Difference between revisions of "Team:Pasteur Paris/Microbiology week13"

Revision as of 13:18, 18 October 2016

click on the weeks

Microbiology Notebook

Week 13

August 29, 2016:

232. Measure the amount of DNA extracted from the miniprep

September 1, 2016:

233. Harvest the culture with Midiprep

September 2, 2016:

234. Growth of bacteria

235. Extraction of plasmid DNA