Team:Pasteur Paris/Notebook
Microfluidics/Membrane
07.10.2018
Institut Curie’s lab MMBM at IPGG (Institut Pierre Gilles de Gennes) hands us the molds for the microchannel chip and grants us access to their lab. We have been taught the basic steps for the fabrication of the microfluidic microchannel chip: PDMS preparation, molding, demolding, punching, bonding.
07.11.2018
4 microchannel chips have been made. Molds for the PDMS well chip have been received. Glass microscopic slides coated with 2 nm chromium and 50 nm gold have been received for use in PDMS well chip. Glass slides have been cut into small strips with a diamond tip. Processing damaged the gold coating.
07.12.2018
First pieces of the well chip have been successfully molded. 8 microchannel chips have been made.
07.13.2018
Tested the conductivity of gold coated strips of glass. Failure. Too many scratches because of the cutting process. Second successful set of PDMS pieces of the well chip molded. 4 microchannel chips have been made. 1 microchannel successfully bonded to an imaging dish, and filled with fluorescein. Observation under a microscope revealed that it is fully functional.
Bacteriology
Cell culture
Microfluidics/Membrane
07.16.2018
We transformed pET 43.1a and pSB1C3 in DH5-α competent cells, in order to constitute a stock of empty vectors for our manipulation.
| Plasmid | C (ng/μl) | Volume (μl) | Competent cell | Medium |
| pET 43.1.a | 4.95 | 1 | DH5-α | LB/carbenicilline |
| pSB1C3 | 40 | 1 | DH5-α | LB/chloramphenicol |
See here the transformation of E. coli DH5-alpha protocol We let the transformed bacteria grow overnight (16 hours).
07.17.2018
Results: We went to see our bacterial culture:
- Bacteria transformed with pET 43.1 had not grown.
- Bacteria transformed with pSB1C3 had formed colonies.
Interpretations: Bacteria transformed with pET 43.1 did not grow. We found a non-commercial tube of pET 43.1 in the freezer from last year team, and we decided to try to amplify it because we did not have any commercial tubes of pET 43.1. Transformation did not work as expected, probably because:
- There was no DNA left in the tube.
- The concentration of DNA was too low .
We cultivated the transformed pSB1C3 bacteria in liquid medium 2 x 25ml + Chloramphenicol (25µg/ml) overnight at 37°C, 180 rpm.
Results: Bacteria successfully transformed with pSB1C3. (See here the liquid culture protocol)
07.18.2018
Extraction: We extracted the pSB1C3 plasmid from the bacterial culture. The protocol used was the Qiagen Plasmid Purification Kit (See Midiprep for plasmid extraction protocol here ) Measure of the DNA concentration in each tube thanks to the NanoDrop (Blank used : TE.1) (See the NanoDrop protocol here)
Results: We used the Nanodrop to quantify the purified DNA.
| Sample | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 |
| Volume (µl) | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 | 50 |
| C (ng/µl) | -7.8 | -8.5 | 54.8 | 5.6 | 237.4 | -7.9 | -7.2 | -7.5 | -6.9 | -6.5 |
| Abs(260 nm)/Abs(280 nm) | 1.43 | 1.42 | 1.97 | 3.04 | 1.85 | 1.32 | 1.47 | 1.56 | 1.35 | 1.44 |
Remarks: [DNA] < 0 = no DNA [DNA] > 200 good Abs(260 nm)/Abs(280 nm) [1;2]
Interpretations:
- Tube 1, 2, 6, 7, 8, 9 and 10 did not contain DNA at all. This problem can be due to the fact that we failed the precipitation with ethanol, meaning that when we removed all the supernatant, we also removed the DNA, or that we removed by mistake the DNA pellet when removing all the supernatant after precipitation (the pellet was so small that we couldn’t see it with the naked eye).
- Tube 3, 4 and 5 had DNA inside. The amount of DNA obtained is enough for us. These tubes have been placed in the freezer for later use.
Transformation: We received from Eurofins our first sequences:
- 3a_NGF construction Part1 (Seq1)
- 3a_NGF construction Part2 (Seq2)
- T7 RIP construction (Seq8)
In order to constitute a stock of this commercial vectors, we transformed DH5-α competent cells with the plasmid we received, and then we cultivated them on agar plates covered with LB medium and carbenicillin. As the bacteria transformed with pET 43.1a did not grow, we tried again to transform the bacteria with pET 43.1a in a higher quantity than previously.
| Plasmid | C (ng/μl) | Volume (μl) | Competent cell | Medium |
| pEX-A258 Seq1 | 10 | 1 | DH5-α | SOC/carbenicilline |
| pEX-A258 Seq2 | 10 | 1 | DH5-α | SOC/carbenicilline |
| pEX-A258 Seq8 | 10 | 1 | DH5-α | SOC/carbenicilline |
| pET 43.1a | 4.95 | 5 | DH5-α | SOC/carbenicilline |
See here the transformation of E. coli DH5-alpha protocol
07.19.2018
Results: We went to see our overnight bacterial culture plates:
| SEQ#1 3a_NGF_Part1 | SEQ#2 3a_NGF_Part2 | SEQ#8 T7_RIP | Pet43.1a(+) | |
| Selection | Amp | Amp | Amp | Amp |
| Growth | Yes | Yes | Yes | No |
| Liquid Culture | Yes | Yes | Yes | No |
Interpretations: Transformation of Seq#1 – 3a_NGF_Part1, Seq#2 – 3a_NGF_Part2 and Seq #8 – T7_RIP did work as expected. Transformation of Pet43.1a (+) did not work again. As mentioned before, the tube of pET43.1a (+) was a non-commercial tube that we found in the freezer from last year’s team, and we decided to try to amplify it because we did not have any commercial tubes of pET 43.1. We tried to transform our bacteria twice, with no results, so the most probable hypothesis is that the tube did not contain DNA anymore. After this experiment, we decided to buy a tube pET43.1a(+). We cultivated two different colonies from each plate (seq#1, seq#2, seq#8):
- One in an Erlenmeyer in 25 ml LB medium + Carbenicillin (100µg/ml) overnight at 37°C, 180 rpm.
- One in two Falcon tube in 15 ml LB medium + Carbenicillin (100µg/ml) overnight at 37°C, 180 rpm.
(See here the liquid culture protocol)
07.20.2018
Results of the liquid culture are good.
Extraction - MidiPrep: We extracted the 3 plasmids Seq#1 – 3a_NGF_Part1, Seq#2 – 3a_NGF_Part2 and Seq #8 – T7_RIP from the bacterial cultures. The protocol used was the Qiagen Plasmid Purification Kit (See Midiprep for plasmid extraction protocol here ) Measure of the DNA concentration in each tube thanks to the NanoDrop (Blank used : TE.1) (See the NanoDrop protocol here)
Results: We used the Nanodrop to quantify the purified DNA.
For NGF part1, Colony 1:
| ng/µL [DNA] | Abs(260 nm)/Abs(280 nm) |
| 3569.2 | 1.9 |
| 1578.7 | 1.89 |
| 848.1 | 1.90 |
| 2322.1 | 1.89 |
For NGF part1, Colony 2:
| ng/µL [DNA] | Abs(260 nm)/Abs(280 nm) |
| 488.1 | 1.89 |
| 493.7 | 1.90 |
| 445.1 | 1.89 |
| 644.6 | 1.86 |
For NGF part2, Colony 1:
| ng/µL [DNA] | Abs(260 nm)/Abs(280 nm) |
| 1555.0 | 1.88 |
| 493.7 | 1.88 |
| 666.2 | 1.87 |
| 367 | 1.90 |
For NGF part2, Colony 2:
| ng/µL [DNA] | Abs(260 nm)/Abs(280 nm) |
| 463.7 | 1.89 |
| 420.8 | 1.88 |
| 461.4 | 1.89 |
| 420.6 | 1.89 |
For RIP, Colony 1:
| ng/µL [DNA] | Abs(260 nm)/Abs(280 nm) |
| 694.4 | 1.84 |
| 1028.9 | 1.87 |
| 1408.7 | 1.88 |
| 466.8 | 1.88 |
For RIP, Colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 228.4 | 1.89 |
| 325.2 | 1.89 |
| 379.4 | 1.89 |
| 427.2 | 1.89 |
Remarks: [NA] < 0 = no DNA [NA] > 200 good Abs(260 nm)/Abs(280 nm) [1;2]
Interpretations: We have DNA in our tubes. The DNA is too concentrated so we will have to dilute them before next use. We froze the tubes at -20°C until next use.
Something was done one that day
18.07.2018
1 set of PDMS pieces for the well chip has been made. One of the pieces broke while demolding. It was discarded. 4 microchannel chips made.
19.07.2018
1 set of PDMS pieces for the well chip have been made. 4 microchannel chips made.
Bacteriology
Cell culture
Microfluidics/Membrane
07.24.2018
Culture of strain HB2151 transformed with pVDL 9.3 (received on 23.07.2018 from Dr. Victor de Lorenzo) Material:
- LB agar plate supplemented with chloramphenicol (25 mg/mL)
- Bacteria HB 2151 transformed with pVDL9.3
The bacteria we received was in the form of a stock: LB + agar media containing the bacteria and the plasmid in an Eppendorf tube. Sample from the solid stock was streaked on LB agar plate complemented with chloramphenicol, and secondly grown in an Erlenmeyer with 25 mL LB medium and 25 μL chloramphenicol at 25 mg/mL.
Biofilm culture on filter (0.2 μm) Material:
- Bacteria DH5α transformed with pSB1C3
- Filters - 0.2 μm Milipore (5 cm diameter)
- Petri-dishes
- Sterile Clamps
- Sterile Rakes
- Pipets
- LB media
- Falcon tubes
- Chloramphenicol (25 mg/mL)
- Make a liquid culture of DH5α transformed with pSB1C3 from colonies we had on a petri dish made on the 07.16.2017 and stored at 4°C. Let grow over night at 37°C under agitation. Made the 07.23.2017 (See here the liquid culture protocol)
- Auto-cleavage of the 0.2 μm filters
- Deposit the filters on a petri dish with a clamp. Wait until the filter is totally “wet” with LB media.
- Deposit the bacteria culture in the center of the filter with a micropipette and spread with a rake. We made 3 different petri dishes with 3 different volumes.
| DH5α-pSB1C3- biofilm culture – 1 | DH5α-pSB1C3- biofilm culture – 2 | DH5α-pSB1C3- biofilm culture – 3 | |
| Volume of culture deposit (μL) | 50 | 100 | 150 |
- Incubate at 37°C overnight.
Transformation of seq5, seq7 from Eurofins Genomics, pET 43.1 and pBR322 Material:
- LB agar plate supplemented with carbenicillin
- Sterile LB medium
- pET 43.1a: 42.36 pg/μL
- pBR322: 65.00 ng/μL
- Seq5 > AGR-RIP Part1: 1.1 μg
- Seq7 > AGR-RIP Part3: 1.9 μg
Sequences received on the 07.24.2018. Gene synthesis products are in the form of lyophilized powder, so we need to re-suspend them. Seq5 > AGR-RIP Part1: 1.1 μg Seq7 > AGR-RIP Part3: 1.9 μg
- Centrifuge in order to make sure that all the plasmids are at the bottom of the tube and not in the lid.
- Re-suspend the powder in TE 1X. Seq5: add 110 μL to have a final concentration of 10 ng/μL Seq7: add 190 μL to have a final concentration of 10 ng/μL
- Transformation of the 4 plasmids in DH5α competent cells:
- Seq5, Seq7 and pBR322: 1 μL
- pET 43.1a: 10 μL
(See here the transformation of E. coli DH5-alpha protocol) - Culture on petri dishes overnight at 37°C
07.25.2018
Transformed bacteria cultures: We went to see our overnight bacterial culture plates:
| Seq5 RIP_Part1 | Seq7 RIP_Part3 | pBR322 | Pet43.1a(+) | |
| Selection | Amp | Amp | Amp | Amp |
| Growth | Yes | Yes | Yes | No |
| CFU | 2 816 | 2 492 | 2 628 | - |
| Liquid Culture | Yes | Yes | Yes | No |
Interpretations: Transformation of Seq5 – RIP_Part1, Seq7 – RIP_Part3 and pBR322 did work as expected. Transformation of Pet43.1a (+) did not work again. The tube of pET43.1a (+) was another non-commercial tube that we found in the freezer from last year’s team, and we decided to try to amplify it because we did not have any commercial tubes of pET 43.1. We tried to transform our bacteria twice, with no results, so the most probable hypothesis is that the tube did not contain DNA anymore. We are still waiting for the commercial pET43.1a(+) (we ordered it last week).
Bacteria transformed pVDL 9.3: The culture on agar plate did work, but we were not able to isolate one colony. We stopped the liquid culture and measured the OD600 of the culture medium.
Biofilm culture:
| pSB1C3-DH5α-biofilm culture – 1 | pSB1C3-DH5α-biofilm culture – 2 | pSB1C3-DH5α-biofilm culture – 3 | |
| Volume of culture deposit (μL) | 50 | 100 | 150 |
| Biofilm formation | Yes | Yes | Yes |
We did a biofilm transfer. We took our filter with the biofilm and transferred it on another porous filter placed on a new petri dish LB + Cm. Then we removed the filter containing the biofilm and incubated the plate overnight at 37°C.
Liquid culture: We cultivated two different colonies from each plate (Seq5, Seq7 and pBR322):
- One in an Erlenmeyer in 25 mL LB medium + Carbenicillin (100 µg/ml) overnight at 37°C, 180 rpm.
- One in two Falcon tube in 15 mL LB medium + Carbenicillin (100 µg/ml) overnight at 37°C, 180 rpm.
Moreover, for each colony of each DNA part we did some streaks on a plate and incubated them at 37°C. (See here the liquid culture protocol)
Midiprep pVDL 9.3: We extracted the pVDL 9.3 plasmid from the HB2151 strain. The protocol use was the Qiagen Plasmid Purification Kit (See Midiprep for plasmid extraction protocol here ) We divided the eluted DNA into 8 tubes before centrifugation. Measure of the DNA concentration in each tube by the NanoDrop. Blank used : TE.1 (See the NanoDrop protocol here)
Results: We used the Nanodrop to quantify the purified DNA for SEQ: pVDL 9.3 1.
| Sample | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
| ng/µL [NA] | 3.7 | 111.2 | 140 | 0 | 1.9 | 47 | 108 | 8.3 |
| Abs(260 nm)/Abs(280 nm) | 1.93 | 1.87 | 1.88 | - | 1.6 | 1.9 | 1.9 | 1.91 |
07.26.2018
Results: Transfer of our biofilm growth on a filter (07.24.2018 loading of 50 µl of pSB1C3 liquid culture on a filter) on another filter on a plate and incubation overnight at 37°C:
Observations: The biofilm is able to grow again after a transfer from one filter to another as seen by the red color.
Midiprep Seq5, Seq7, pBR322: We extracted Seq5, Seq7 and pBR322 plasmid from transformed DH5α strain. The protocol used was the Qiagen Plasmid Purification Kit (See Midiprep for plasmid extraction protocol here ) We divided the eluted DNA into 4 tubes before centrifugation. Measure of the DNA concentration in each tube with NanoDrop. Blank used: TE.1 (See the NanoDrop protocol here)
Results: We used the Nanodrop to quantify the purified DNA.
For Seq, 5 Colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 245.7 | 1.87 |
| 349 | 1.87 |
| 353.2 | 1.87 |
| 306.7 | 1.87 |
For Seq 5, Colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 258 | 1.88 |
| 281 | 1.86 |
| 260 | 1.86 |
| 295 | 1.86 |
For Seq 7, Colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 293 | 1.88 |
| 299 | 1.88 |
| 305 | 1.87 |
| 288 | 1.87 |
For Seq 7, Colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 217 | 1.87 |
| 212 | 1.87 |
| 175 | 1.88 |
| 244 | 1.83 |
For pBR322, Colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 3.8 | 1.68 |
| 55.8 | 1.86 |
| 54 | 1.9 |
| 68 | 1.84 |
For RIP, Colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 32 | 1.82 |
| 28 | 1.75 |
| 41 | 1.88 |
| 30 | 1.88 |
Interpretations: There is DNA in all the tubes. For Seq5 and Seq7, we obtain high DNA concentrations, which is good. For pBR322, the DNA concentration is lower. This is probably due to the fact that pB322 is a low copy plasmid. However, the quantity of DNA is enough.
Preparing cultures for stocks: We set some pre-cultures of Seq5, Seq7 and pBR322, in order to make some stocks to store at -80°C. In a 15 mL Falcon tube, we placed 5 mL of LB media, and 10 μL of antibiotic (Carbenicillin). We added one of each colony inside each Falcon and placed the Falcon tubes inside the incubator (37°C – 180 rpm) and let grow overnight.
Something was done one that day
07.24.2018
Membrane filters from Sterlitechreceived. 8 microchannel chips and 1 set of PDMS pieces for the well chip have been made.
07.25.2018
Platinum wires received and conductivity tested. Success.
07.27.2018
4 microchannel chips have been made. 1 microchannel chip bonded for imaging test purposes.
Bacteriology
Cell culture
Microfluidics/Membrane
07.30.2018
Digestion of Seq8 and pBR322: We cut the commercial plasmid containing our Seq8 (T7-RIP) with restriction enzymes XbaI and SpeI, and pBR322 with AvaI and BsmI, in order then to insert our sequence into the plasmid pBR322. Material:
- Water baths at 37°C and 80°C
- Eppendorf tubes
- Pipets and cones
Reagents:
- pBR322 [68 ng/μL]
- commercial plasmid containing Seq8 [466,8 ng/μL]
- Restriction enzymes: AvaI, BsmI, XbaI, SpeI
- 10X Cut Smart
- Distilled water
- Mix the following volumes of reagents and incubate at 37°C for 15 minutes.
| Volume (μL) | |
| pBR322 | 22 |
| 10X Cut Smart | 5 |
| Distilled water | 20 |
| Bsml | 1.5 |
| Aval | 1.5 |
| Volume (μL) | |
| Eurofins plasmid with Seq8 | 20 |
| 10X Cut Smart | 5 |
| Distilled water | 22 |
| Xbal | 1.5 |
| Spel | 1.5 |
- Inactivate the digestion by heating the mixture in a heat block at 80 °C for 20 minutes.
Electrophoresis on agarose gel We prepared an Agarose gel. (See here the Agarose Gel Preparation protocol) We filled:
- 1 well with the digested pBR322 (n°1)
- 2 wells with the digested plasmids containing Seq8 (n°2 and 3)
- 1 well with a DNA ladder (n°4)
We let the DNA migrate for 10 minutes at 85 V and then 40 minutes at 125 V. We then revealed the gel under UV lamp. Results:
Interpretations:
- pBR322 (4361 bp) has been successfully linearized
- pEXA258 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (459 bp) and the linearized plasmid (2909 bp)
DNA Gel extraction: Here is the same gel after DNA extraction of pBR322 and of Seq8.
| Sequence name | Eppendorf weight (g) | Eppendorf + gel weights (g) | Gel weight (g) |
| Seq8 (1) | 1.08 | 1.29 | 0.21 |
| Seq8 (2) | 1.08 | 1.37 | 0.29 |
| pBR322 | 1.08 | 1.27 | 0.19 |
It is useful to know how the weight of the gel to adapt de volumes of buffer to the amount of gel we have. (See here the Gel Extraction protocol) Results: after extracting the DNA from the gel, we measured the DNA concentration using the Nanodrop.
| Sequence name | DNA concentration (ng/μL)) | Abs(260nm)/Abs(280nm) (g) | Total extracted DNA (ng) |
| Seq8 (1) | 6.4 | 1.87 | 294.4 (620.8) |
| Seq8 (2) | 6.8 | 2.07 | 326.4 (620.8) |
| Linearized pBR322 | 9.9 | 1.97 | 475.2 |
Interpretations: The initial amount of each DNA fragment before digestion was 1500 ng. We can therefore evaluate the efficiency of our digestion and extraction:
- for Seq8 insert: r = 0.414
- for pBR322 plasmid: r = 0.317
Ligation of linearized pBR322 and our insert Seq8 We used the In-Fusion cloning kit provided by Ozyme in order to clone our insert into the linearized pBR322.
- We mixed the following volumes into 1.5 mL tubes.
| Component | Cloning (μL) | Negative control (μL) | Positive control (μL) |
| Purified fragment | 4 | - | 2 (control) |
| Linearized vector | 4 | 1 | 1 (control) |
| 5X In-Fusion enzyme premix | 2 | 2 | 2 |
| Deionized water | - | 7 | 5 |
- Incubate for 15 min in a water bath at 50°C
- Ligation See here the Ligation protocol)
- Set in ice
- Transformation of the 3 plasmids into Stellar competent cells (provided with the cloning kit)
- Competent cell volume : 33 μL
- DNA volume: 2 μL
- Culture on petri dishes LB agar gel supplemented with carbenicillin overnight at 37°C
Transformation of Seq6 from Eurofins Material:
- LB agar plates supplemented with carbenicillin (25 μg/mL)
- LB medium
- Seq6 > AGR-RIP Part1: 4.6 μg
Sequences are under the form of lyophilized powder, so we need to re-suspend it.
- Centrifuge in order to make sure that all the plasmids are at the bottom of the tube and not in the lid.
- Re-suspend the powder in TE 1X. We resuspended it into 460 μL TE, to obtain a concentration of 10 ng/μL.
- Transformation of the plasmid in DH5α competent cells (See here the transformation of E. coli DH5-alpha protocol)
- Culture on petri dishes LB agar gel supplemented with carbenicillin overnight at 37°C
07.31.2018
Results: ligation cultures
Liquid culture of DH5-α with Seq6 We cultivated 2 different colonies in 250 mL Erlenmeyer containing:
- 25 mL LB medium
- 25 μL carbenicillin (25 mg/mL)
We cultivated it overnight in a shaking incubator at 37°C, 180 rpm. (See here the liquid culture protocol)
Liquid culture of Stellar transformed with pBR322-Seq8 We cultivated 20 different colonies in order to maximize our chance to get one successful ligated plasmid. Each colony was cultivated in a 15 mL Falcon tube containing:
- 5 mL LB medium
- 5 μL carbenicillin (25 mg/mL)
We cultivated it overnight in a shaking incubator at 37°C, 180 rpm. We also cultivated each colony on petri dishes LB agar plate supplemented with carbenicillin overnight at 37°C.
Transformation of Seq3 from Eurofins Genomics and commercial pET43.1a Material:
- LB agar plate supplemented with carbenicillin
- Seq3 : NGF-GFP Part1 : 4.0 μg
- pET 43.1a : 0.5 μg/μL
Sequence from Eurofins Genomics under the form of lyophilized powder so we need to re-suspend it.
- Centrifuge in order to make sure that all the plasmids are at the bottom of the tube and not in the lid.
- Re-suspend the powder in TE 1X. We resuspended it into 400 μL TE, in order to obtain a concentration of 10 ng/μL.
- Transformation of the plasmids in DH5α competent cells:
- volume of competent cells: 50 μL
- pET 43.1a: 50 pg (1 μL of commercial plasmid diluted 1/10000)
- Seq3 : 10 ng (1 μL)
- Culture on petri dishes LB agar plate supplemented with carbenicillin overnight at 37°C.
08.01.2018
We went to see our cultures:
- All the colonies of our ligation (pBR322 + Seq8) grew except one.
- DH5α transformed with Seq3 grew.
- DH5α transformed with pET 43.1a did not grow.
Hypothesis:
- We might have diluted the plasmid or the bacteria too much.
- We did not homogenize the solution enough during the dilution of the commercial solution.
- We did not pipet correctly the 1 μL of plasmid from the commercial tube.
Extraction of the ligated plasmid (pBR322 + Seq8) from Stellar (miniprep) (See here the Gel Extraction protocol) Results: (tube 8 did not grow) From NanoDrop
| Sample | DNA CONCENTRATION (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 94.8 | 2.05 |
| 2 | 105.8 | 2.06 |
| 3 | 106.3 | 2.04 |
| 4 | 84.8 | 2.02 |
| 5 | 100.1 | 2.02 |
| 6 | 79.9 | 2.00 |
| 7 | 08.9 | 2.04 |
| 8 | - | - |
| 9 | 115.1 | 2.02 |
| 10 | 116.7 | 1.96 |
| 11 | 76.6 | 2.00 |
| 12 | 69.5 | 1.99 |
| 13 | 80.7 | 1.94 |
| 14 | 63.0 | 1.98 |
| 15 | 78.4 | 2.03 |
| 16 | 153.1 | 1.94 |
| 17 | 90.7 | 2.00 |
| 18 | 119.3 | 2.02 |
| 19 | 100.8 | 1.97 |
| 20 | 85.3 | 2.03 |
We chose to verify which colony had acquired the plasmid containing the Seq8 insert. To do so, we digested the plasmid with the restriction enzymes EcoRI and PstI and ran a 1% agarose gel. The size of the plasmid pBR322 is 4361 bp. Once we cut the sequence between the sites EcoRI (bp position 4359) and PstI (bp position 3611), this leaves us with an empty backbone of 3613 bp. The size of the insert Seq8 is 461 bp. Here we made a mistake, by confusing the right restriction enzymes to use. Indeed, we should have used XbaI and SpeI instead of EcoRI and PstI. Moreover, as these two restriction sites are present in the pBR322 backbone (748 bp away), this digestion should show two DNA fragments.
1% Agarose gel of the miniprep of the ligated plasmid (pBR322 + Seq8) from Stellar Only the first half of the samples (1 to 11) were deposed today. The preparation of the gel was done according to the Agarose Gel Preparation protocol. The samples were made according to the following proportions:
- 5 µL DNA
- 3 µL 10X Cutsmart Buffer
- 1 µL EcoRI
- 1 µL PstI
- 20 µL H2O
These samples were then incubated for 10 min at 37°C to allow digestion by the enzymes. The reaction was stopped by the addition of 6 µL of 6X Loading Dye. Results:
This resulting gel shows the two DNA fragments we expected. Moreover, the column 3 shows a lower molecular weight (MW) than others for the plasmid part. As this part is supposed to contain our insert, it might suggest that colony 3 doesn’t possess the insert, but all others do. However, we will need to make the right experiment using restriction enzymes XbaI and SpeI (see date 08.02.2018) to verify that our insert was correctly put into the plasmid.
Extraction of Seq6 plasmid from DH5α (midiprep) We extracted the plasmids containing Seq6 from the DH5-α cells. (See Midiprep for plasmid extraction protocol here ) Results from NanoDrop: (Blank: TE.1)
For the colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) | |
| 1 | 1572.9 | 1.88 |
| 2 | 2800.1 | 1.88 |
| 3 | 2598.7 | 1.88 |
| 4 | 2285.1 | 1.89 |
For the colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) | |
| 1 | 4996.8 | 1.87 |
| 2 | 3263.2 | 1.89 |
| 3 | 3625.0 | 1.90 |
| 4 | 2339.7 | 1.90 |
The DNA concentrations were too high and so did not answer to the Beer-Lambert’s law. We needed to dilute the samples before using the nanodrop again. We did 1/10 dilutions and obtained average concentrations of 34 ng/µL, with Abs(260 nm)/Abs(280 nm) ratios of 1.92.
Digestion of pET 43.1a, NGF_Part1 (Seq1) and NGF_Part2 (Seq2) Digestion of the following plasmids:
- pET43.1a (500 ng/µl)
- Commercial plasmid containing Seq1 (445.1 ng/μL)
- Commercial plasmid containing Seq2 (420.6 ng/μL)
- Restriction enzymes: NdeI, PacI, NheI, BamHI, MscI, HindIII
- Mix the following volumes of reagents and incubate at 37°C for 15 min.
| Volume (μL) | |
| pET43.1a | 1.6 |
| 10X Cut Smart | 5 |
| Distilled water | 40.4 |
| Ndell | 1.5 |
| Pacl | 1.5 |
| Volume (μL) | |
| Eurofins plasmid with Seq1 | 4.3 |
| 10X Cut Smart | 5 |
| Distilled water | 37.7 |
| Nhel | 1.5 |
| BamHI | 1.5 |
| Volume (μL) | |
| Eurofins plasmid with Seq2 | 4.4 |
| 10X Cut Smart | 5 |
| Distilled water | 37.6 |
| Mscl | 1.5 |
| MindIII | 1.5 |
- Inactivate the digestion by heating the mixture in a heat block at 80 °C for 20 min.
Electrophoresis on agarose gel We prepared an 0.8 % agarose gel to separate the different fragments of the cut plasmids. (See here the Agarose Gel Preparation protocol) We filled:
- 2 wells with digested pET43.1a (n°1 and n°2)
- 2 wells with insert Seq1 (n°3 and n°4)
- 2 wells with insert Seq2 (n°5 and n°6)
- 1 well with the DNA ladder
We let the DNA migrate for 10 minutes at 85 V on order to let the DNA penetrate the gel, and then 40 min at 125 V to efficiently separate the fragments. We then revealed the gel under UV lamp.
Interpretations:
- pET43.1a (7275 bp) has been successfully linearized into two fragments (5 kb and 2 kb)
- pEXA258 – Seq1 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (1105 bp) and the linearized plasmid (2446 bp)
- pEXA258 – Seq2 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (1159 bp) and the linearized plasmid (2446 bp)
DNA Gel extraction: We cut the gel to extract our inserts and linearized plasmid:
| Eppendorf weight (g) | Eppendorf + gel weights (g) | Gel weight (g) | |
| pET43.1a (1) | 1.13 | 1.365 | 0.23 |
| pET43.1a (2) | 1.08 | 1.286 | 0.21 |
| Seq1 (1) | 1.07 | 1.265 | 0.20 |
| Seq1 (2) | 1.08 | 1.306 | 0.23 |
| Seq2 (1) | 1.07 | 1.303 | 0.23 |
| Seq2 (2) | 1.07 | 1.284 | 0.21 |
It is useful to know how the weight of the gel to adapt de volumes of buffer to the amount of gel we have. (See here the Gel Extraction protocol) Results: After extracting the DNA from the gel, we measured the DNA concentration using the Nanodrop.
| C (ng/μL) | Abs(260 nm)/Abs(280 nm) | |
| pET43.1a (+) (1) | 5.5 | 3.14 |
| pET43.1a (+) (2)) | 7.1 | 2.50 |
| Seq1 (1) | 5.1 | 2.71 |
| Seq1 (2) | 7.8 | 1.90 |
| Seq2 (1) | 6.9 | 2.92 |
| Seq2 (2) | 6.0 | 3.11 |
Ligation of linearized pET43.1a and our inserts Seq1,2 /br> We used the In-Fusion cloning kit provided by Ozyme to clone our two inserts together in linearized pET43.1a.
- We mixed the following volumes into 1.5 mL tubes.
| Component | Cloning (μL) | Negative control (μL) | Positive control (μL) |
| Purified Seq1 | 6 | - | 2 (control) |
| Purified Seq2 | 6 | - | 2 (control) |
| Linearized vector | 3 | 1 | 1 (control) |
| 5X In-Fusion enzyme premix | 4 | 2 | 2 |
| Deionized water | 1 | 7 | 5 |
- Incubate for 15 min in a water bath at 50°C
- Ligation (See Ligation protocol)
- Set on ice
- Transformation of the 3 plasmids into Stellar competent cells (provided with the cloning kit):
- Competent cell volume: 50 μL
- DNA volume: 2 μL
- Culture on petri dishes LB agar plate supplemented with carbenicillin overnight at 37°C
08.02.2018
2nd Agarose gel of the miniprep of the ligated plasmid (pBR322 + Seq8) from Stellar, using the correct enzymes Yesterday we made a mistake, so today we carried out exactly the same protocol but with restriction enzymes SpeI and XbaI. As a negative control, we also deposited a sample we called 1x, without digesting it with restriction enzymes.
Liquid culture of pET43 1.a We cultivated 2 different colonies in 250 mL Erlenmeyer containing:
- 25 mL LB medium
- 25 μL carbenicillin (25 mg/mL)
We cultivated it overnight in a shaking incubator at 37°C, 180 rpm. (See here Liquid Culture protocol)
Liquid culture of Stellar transformed with pET43 1.a-Seq1-Seq2 We cultivated 20 different colonies in order to maximize our chance to get one successful ligated plasmid. Each colony was cultivated in a 15 mL Falcon tube containing:
- 5 mL LB medium
- 5 μL carbenicillin (25 mg/mL)
We cultivated it overnight in a shaking incubator at 37°C, 180 rpm.< We also cultivated each colony in an LB agar plate supplemented with carbenicillin.
Extraction of Seq3 plasmid from Stellar (midiprep) We extracted the plasmids containing Seq3 from the stellar cells (See here the Midiprep for plasmid extraction protocol) Results from NanoDrop (with Blank: TE.1) For the colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 153.3 | 1.90 |
| 155.2 | 1.90 |
| 164.6 | 1.89 |
| 179.1 | 1.91 |
For the colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 166.4 | 1.91 |
| 150.4 | 1.90 |
| 177.1 | 1.91 |
| 188.6 | 1.89 |
Interpretations: There is DNA in all the tubes
Digestion of pBR322, Agr-RIP-Part1 (Seq5), Agr-RIP-Part2 (Seq6) and Agr-RIP-Part3 (Seq7) Material:
- Water baths at 37°C and heating block of 80°C
- Eppendorf tubes
- Pipets and cones
Reagents:
- PBR322 (conc. 68 ng/μL)
- Eurofins Genomics plasmid containing Seq5 (conc. 353 ng/ μL)
- Eurofins Genomics plasmid containing Seq6 (conc. 350 ng/ μL)
- Eurofins Genomics plasmid containing Seq7 (conc. 305 ng/ μL)
- Restriction enzymes: BsmI, AvaI, XbaI, BamHI, MscI, SphI, HindIII, SpeI
- 10X Cut Smart
- Distilled water
- Mix the following volumes of reagents and incubate at 37°C for 15 min
| Volume (μL) | |
| pBR322 | 122 |
| 10X Cut Smart | 5 |
| Distilled water | 20 |
| BsmI | 1.5 |
| Aval | 1.5 |
| Volume (μL) | |
| Plasmid containing Seq5 | 12 |
| 10X Cut Smart | 5 |
| Distilled water | 30 |
| Xbal | 1.5 |
| BamHI | 1.5 |
| Volume (μL) | |
| Plasmid containing Seq7 | 21 |
| 10X Cut Smart | 5 |
| Distilled water | 21 |
| HindIIIl | 1.5 |
| Spel | 1.5 |
| Volume (μL) | |
| Plasmid | 16 |
| 10X Cut Smart | 5 |
| Distilled water | 26 |
| Mscl | 1.5 |
| Sphl | 1.5 |
- Inactivate the digestion by heating the mixture in a heat block at 80 °C for 20 min.
Electrophoresis on agarose gel We prepared an 0.8 % agarose gel to separate the different fragments of the cut plasmids. (See here the Agarose Gel Preparation protocol) We filled:
- 2 wells with digested pBR322 (n°1 and n°2)
- 2 wells with insert Seq5 (n°3 and n°4)
- 2 wells with insert Seq6 (n°5 and n°6)
- 2 wells with insert Seq7 (n°7 and n°8)
- 1 well with the DNA ladder
We let the DNA migrate for 10 minutes at 85 V on order to let the DNA penetrate the gel, and then 40 min at 125 V to efficiently separate the fragments. We then revealed the gel under UV lamp.
- 1. 2. : pBR322
- 3. 4. : Seq5
- 5. 6. : Seq6
- 7. 8. : Seq7
- pET43.1a (7275 bp) has been successfully linearized into two fragments
- pEXA258 – Seq5 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (1422 bp) and the linearized plasmid (2.5 kb)
- pEXA258 – Seq6 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (960 bp) and the linearized plasmid (2.5 kb)
- pEXA258 – Seq7 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (762 bp) and the linearized plasmid (2.5 kb)
- We mixed the following volumes into 1.5 mL tubes.
- Incubate for 15 min in a water bath at 50°C
- Ligation See here the Ligation protocol)
- Set in ice
- Transformation of the 3 plasmids into Stellar competent cells (provided with the cloning kit)
- Competent cell volume : 33 μL
- DNA volume: 2 μL
- Culture on petri dishes LB agar gel supplemented with carbenicillin overnight at 37°C
- 5 mL of LB
- 10 µL of Carbenicillin (25 mg/mL)
Interpretations:
DNA Gel extraction We cut the gel to extract our inserts and linearized plasmid:
We extract the DNA (our linearized vector and our plasmid) from the agarose gel. (See here the Gel Extraction protocol)
Results: After extracting the DNA from the gel, we measured the DNA concentration using the Nanodrop
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) | |
| pBR322 | 10.3 | 2.07 |
| Seq5 | 8.3 | 3.07 |
| Seq6 | 14.0 | 2.06 |
| Seq7 | 7.6 | 1.97 |
Ligation of linearized pBR322 and our insert Seq5,6,7 We used the In-Fusion cloning kit provided by Ozyme (See here theLigation protocol) in order to clone our insert into the linearized pBR322.
| Component | Cloning (μL) | Negative control (μL) | Positive control (μL) |
| Purified Seq 5 | 5 | - | 2 (control) |
| Purified Seq 6 | 3 | - | 2 (control) |
| Purified Seq 7 | 5 | - | 2 (control) |
| Linearized vector | 3 | 1 | 1 (control) |
| 5X In-Fusion enzyme premix | 4 | 2 | 2 |
| Deionized water | - | 7 | 5 |
08.03.2018
Midiprep pET43.1a: (See here the Midiprep for plasmid extraction protocol) 2 colonies from pET43.1a petri dish (08.01.2018 – pET43.1a) were placed in liquid culture the day before Results from NanoDrop (with Blank: TE.1) For the colony 1:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 71.7 | 1.88 |
| 75.2 | 1.88 |
| 73.6 | 1.84 |
| 70.2 | 1.87 |
For the colony 2:
| ng/µL [NA] | Abs(260 nm)/Abs(280 nm) |
| 65.0 | 1.85 |
| 34.7 | 1.80 |
| 64.9 | 1.86 |
| 55.5 | 1.82 |
Observations: Enough concentrations for further uses
Miniprep pET 43.1a + Seq1 + Seq2
(See here the Miniprep for plasmid extraction protocol)
20 colonies from pET43.1a + Seq1 + Seq2 from petri dish (08.01.2018) were placed in liquid culture the day before (5 mL of LB + 10 µL of Carbenicillin).
Results from NanoDrop (Blank used is Buffer EB):
| Sample | DNA CONCENTRATION (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 170.9 | 1.86 |
| 2 | 120.8 | 1.88 |
| 3 | 73.1 | 1.87 |
| 4 | 89.8 | 1.84 |
| 5 | 75.4 | 1.97 |
| 6 | 136.6 | 1.87 |
| 7 | 101.4 | 1.88 |
| 8 | 99.0 | 1.91 |
| 9 | 72.7 | 1.88 |
| 10 | 172.8 | 1.87 |
| 11 | 107.8 | 1.86 |
| 12 | 151.1 | 1.86 |
| 13 | 92.6 | 1.92 |
| 14 | 78.7 | 1.93 |
| 15 | 101.2 | 1.87 |
| 16 | 223.9 | 1.97 |
| 17 | 145.5 | 1.85 |
| 18 | 149.8 | 1.86 |
| 19 | 68.1 | 1.89 |
| 20 | 87.8 | 1.93 |
Observations: Samples were not transferred to the micro tubes at the right moment, so it is very probable that the samples are contaminated with genomic DNA.
08.05.2018
Liquid culture of pBR322 + Seq5 + Seq6 + Seq7 (See here the Liquid Culture protocol) 6 colonies from the petri dish (pBR322 + Seq5,6,7 – 08.02.2018) were placed in a liquid culture containing:
Cultures were incubated at 37°C, 180 rpm overnight. Observations: All the colonies grew.
Something was done one that day
07.30.2018
First PDMS well chip entirely assembled and bonded, with platinum wire and gold membrane filter. Leaking problems required us to seal the leaks with additional PDMS.4 microchannel chips and 1 set of PDMS pieces for the well chip have been made.
07.31.2018
2 additional PDMS wells assembled. First PDMS vertical chip PDMS pieces prepared (cut and punched, silver paste applied and membrane filter glued). 4 microchannel chips and 1 set of PDMS pieces for the well chip have been made.
08.01.2018
Conductivity tests on membranes assembled on chips. Well chips not functional. It was decided for the well chips to stop using silver paste for connecting the platinum wire to the membrane and instead mount the wire on top of the membrane. Bonding of the vertical chip PDMS pieces failed
Bacteriology
Cell culture
Microfluidics/Membrane
08.06.2018
Miniprep pBR322 + Seq5 + Seq6 + Seq7 (See here the Miniprep for plasmid extraction protocol) Results from NanoDrop (Blank used is buffer EB):
| Sample | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 61.2 | 2.00 |
| 2 | 86.3 | 2.03 |
| 3 | 58.8 | 1.98 |
| 4 | 65.9 | 2.00 |
| 5 | 74.5 | 2.03 |
| 6 | 84.4 | 2.07 |
Observations: Enough concentrations for further use.
Digestion of pET43.1a + Seq1 + Seq2 Aim: Check that the ligation has successfully worked. Restriction enzymes used: NdeI and XbaI Expected results:
| pET43.1a | linearized | 7.3 kB |
| pET43.1a + Seq1 | 1 fragment | 6.63 kB |
| pET43.1a + Seq2 | 2 fragments | 6.63 kB + 0.1 kB |
| pET43.1a + Seq1+ Seq2 | 2 fragments | 6.63 kB + 1 kB |
We digested 10 samples of our cloning products, and we also did some controls:
- Colony 10 with no enzyme (well 11)
- Plasmid pET43.1a + enzyme (well 12)
- Plasmid pET43.1a + no enzyme (well 13)
Well 1 to 10: samples from colony 1 to 10 Well 14: ladder Procedure:
| Volume (μL) | |
| DNA | 5 |
| Cut Smart | 3 |
| Ndel | 1 |
| Xbal | 1 |
| H2O | 20 |
- Digestion at 37°C for 15 min
- Addition of 6 µL of loading dye
We deposited all the samples in an agarose gel previously made. We let the gel run for 10 min at 85 V + 80 min at 125 V. Results:
Observations: For samples 1 to 11, we can only see DNA streaks. In wells 12 and 13, we can clearly see the plasmid pET43.1a linearized (well 12) and circular (well 13). In the well 14 we can clearly see the ladder. Interpretations: The streaks observed on the gel are probably due to the genomic DNA contamination. As mentioned the 08.03.2018, there was an error in the Miniprep of pET43.1a + Seq1 + Seq2.
Digestion of pBR322+ Seq5 + Seq6 + Seq7 Aim: Check that the ligation has successfully worked. Restriction enzyme used: EcoRI Expected results:
| pBR322 | linearized | 4 kB |
| pBR322 + Seq5 | 1 fragment | 5.4 kB |
| pBR322 + Seq5 + Seq6 | 2 fragments | 6.3 kB |
| pBR322 + Seq5 + Seq6 + Seq7 | 2 fragments | 7 kB |
Procedure:
| Volume (μL) | |
| DNA | 5 |
| Cut Smart | 3 |
| EcoRI | 1 |
| H2O | 20 |
- Digestion at 37°C for 15 min
- Addition of 6 µL of loading dye
We digested 6 samples of our cloning products, and we also did some controls.
- Colony 6 with no enzyme (well 7)
- Plasmid pBR322 + enzyme (well 8)
- Plasmid pBR322 + no enzyme (well 9)
Wells 1 to 6: samples from colony 1 to 6 Well 10: ladder We deposited all the samples in an agarose gel previously made. We let the gel run for 10 min at 85 V + 90 min at 125 V. Results:
Observations: The 6 samples are linearized and migrated exactly like the plasmid pBR322 + Enzyme. Moreover, sample 6 without enzyme migrated like pBR322 without enzyme. Interpretations: This leads to the conclusion that none of the colonies were transformed with the plasmid AND the insert.
Liquid culture of pET43.1a + Seq1 + Seq2 (See here the liquid culture protocol) 8 colonies from the petri dish (pET43.1a + Seq1,2 from 08.01.2018) were placed in a liquid culture containing:
- 5 mL of LB
- 5 µL of Carbenicillin (25 mg/mL)
Cultures were incubated at 37°C, 180 rpm overnight.
Cloning pBR322 + Seq8 We used the In-Fusion cloning kit provided by Ozyme in order to clone our insert in the linearized pET 43.1a.
- We mixed the following volumes into 1.5mL tubes.
| Component | Cloning (μL) | Negative control (μL) | Positive control (μL) |
| Purified Seq8 | 4 | - | 2 (control) |
| Linearized vector | 15 | 1 | 1 (control) |
| 5X In-Fusion enzyme premix | 4 | 2 | 2 |
| Deionized water | - | 7 | 5 |
- Incubate for 15 minutes in a water bath at 50°C
- Ligation (See Ligation protocol)
- Set in ice
- Transformation of the 3 plasmids into Stellar competent cells (provided with the clonage kit):
- Competent cell volume: 50 μL
- DNA volume: 2 μL
- Culture on petri dishes LB agar plate supplemented with carbenicillin overnight at 37°C
08.07.2018
<+br>Miniprep pET43.1a + Seq 1 + Seq 2 (See here the Miniprep for plasmid extraction protocol) Results from NanoDrop (Blank used is buffer EB):
| Sample | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 141.2 | 1.84 |
| 2 | 173.3 | 1.86 |
| 3 | 155.2 | 1.83 |
| 4 | 151.9 | 1.85 |
| 5 | 106.9 | 1.85 |
| 6 | 143.0 | 1.88 |
| 7 | 151.1 | 1.89 |
Observations: Enough concentrations for further use.
Digestion of pET43.1a + Seq1 + Seq2 Aim: Check that the ligation has successfully worked. Restriction enzymes used: NdeI and XbaI Expected results:
| pET43.1a | linearized | 7.3 kB |
| pET43.1a + Seq1 | 1 fragment | 6.63 kB |
| pET43.1a + Seq2 | 2 fragments | 6.63 kB + 0.1 kB |
| pET43.1a + Seq1+ Seq2 | 2 fragments | 6.63 kB + 1 kB |
We digested 10 samples of our cloning products, and we also did some controls:
- Colony 8 with no enzyme (well 8)
- Plasmid pET43.1a + enzyme (well 9)
- Plasmid pET43.1a + no enzyme (well 10)
Well 1 to 7: samples from colony 1 to 8 Well 11: ladder Procedure:
| Volume (μL) | |
| DNA | 5 |
| Cut Smart | 3 |
| Ndel | 1 |
| Xbal | 1 |
| H2O | 20 |
- Digestion at 37°C for 15 min
- Addition of 6 µL of loading dye
We deposited all the samples in an agarose gel previously made. We let the gel run for 10 min at 85 V + 80 min at 125 V.
Liquid culture of pBR322 + Seq8 (See here the liquid culture protocol) We cultivated:
- 8 colonies of Stellar bacteria transformed with the result of our cloning
- 2 colonies from the negative control
Each colony is cultivated in a 15 mL Falcon tube with 5 mL LB medium and 5 μL carbenicillin. In parallel, we set each colony to grow on a LB agar plate supplemented with carbenicillin overnight at 37°C.
08.08.2018
Miniprep pBR322 + Seq8 (See here the Miniprep for plasmid extraction protocol) Results from NanoDrop (Blank used is buffer EB):
| Sample | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 93.0 | 1.97 |
| 2 | 101.8 | 1.83 |
| 3 | 121.7 | 1.98 |
| 4 | 112.1 | 2.00 |
| 5 | 101.9 | 1.98 |
| 6 | 97.5 | 1.98 |
| 7 | 113.4 | 1.98 |
| 8 | 97.0 | 2.02 |
| Control (-) 1 | 91.9 | 2.01 |
| Control (-) 2 | 73.5 | 1.90 |
Observations: Concentrations are good for further use.
Digestion of BR322 + Seq8 Aim: Check that the ligation has successfully worked. Restriction enzymes used: NdeI Expected results:
| pET43.1a | linearized | 4 kB |
| pET43.1a + Seq8 | 2 fragments | 4 kB + 0.9 kB |
We digested 8 samples of our cloning products, and we also did some controls:
- Colony 8 with no enzyme (well 8)
- Two colonies from the negative control of the cloning with enzyme
We filled the wells with:
- Plasmid extracted from colonies 1 to 8 and digested with NdeI (n°1 to n°8)
- Plasmid extracted from the negative control digested with NdeI (n°9 and n°10)
- Plasmid extracted from colony 8 without enzyme (n°11)
Results:
- A too low initial amount of linearized vector before cloning, resulting in all the Stellar bacteria being transformed with an empty and uncut vector.
- Too long overlaps, or too GC rich overlaps.
Digestion of pBR322, PET 43.1, AND PLASMIDS CONTAINING Seq1, Seq2 and Seq8 We plan to try cloning again with longer digestion and longer electrophoresis migration, in order to digest all the vector and to increase the efficiency of our separation. Reagents:
- pBR322 (conc. 54 ng/μl)
- pET 43.1a (conc. 65 ng/μl)
- Seq1 (conc. 445 ng/μl)
- Seq2 (conc. 460 ng/μl)
- Seq8 (conc. 379 ng/μl)
We digest the 5 plasmids by mixing the following amounts:
| Volume (μL) | |
| DNA | 22 |
| Cut Smart | 3.2 |
| Enzyme 1 | 1 |
| Enzyme 2 | 1 |
| DNA | Enzyme 1 | Enzyme 2 |
| pET 43.1a | Ndel | Pacl |
| pBR322 | Aval | Bsml |
| Seq 1 | Nhal | BamHI |
| Seq 2 | Mscl | HindIII |
| Seq 8 | Xbal | Spel |
Incubation time at 37°C : 1 hour Inactivation time at 80°C : 20 min After digestion, we added 8 μL 6X Loading dye to each tube.
Electrophoresis on agarose gel< We prepared a 0.8% agarose gel in order to separate the different fragments of the cut plasmids. (See here the Agarose Gel Preparation protocol) We filled:
- 2 wells with digested pBR322 (n°1 and n°2)
- 2 wells with digested pET 43.1a (n°3 and n°4)
- 2 wells with insert Seq1 (n°5 and n°6)
- 2 wells with insert Seq2 (n°7 and n°8)
- 2 wells with insert Seq8 (n°9 and n°10)
We let the DNA migrate for 10 min at 85 V on order to let the DNA penetrate the gel, and then 80 min at 125 V to efficiently separate the fragments. We then revealed the gel under UV lamp. Results: DNA Gel extraction We cut the gel to extract our inserts and linearized plasmid: (See here the Gel Extraction protocol) Results: After extracting the DNA from the gel, we measured the DNA concentration using the Nanodrop.
| Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) | |
| pBR322 | 7.0 | 3.85 |
| pET43.1a | 5.1 | 3.40 |
| Seq1 | 5.7 | 3.40 |
| Seq2 | 6.3 | 10.55 |
| Seq8 | 5.0 | 4.48 |
Interpretations: Values of the ratio Abs(260 nm)/Abs(280 nm) are very high, indicating that our DNA is highly contaminated. Moreover, the concentrations obtained are too low for further use for cloning. We have several hypotheses to explain why our experiment did not work:
- The Gel extraction kit we used might be expired (particularly the final buffer with which we elute DNA might have turned unusable)
- We need to check the wavelength of the nanodrop
We are going to try the digestion and extraction again tomorrow in order to try having better concentrations before proceeding to cloning.
08.09.2018
The digestion and extraction of yesterday did not work well (the obtained concentrations of plasmid and insert were still too low to proceed to the cloning step with a suitable volume). Today, we will proceed again with the digestion, extraction and then try the cloning again, using this time the right amount of insert and vector (as recommended by Clontech molar ratio tool) and following the pieces of advice given to us by Takara Clontech technician we called.Digestion of pET 43.1a, pBR322, Seq1, Seq2 and Seq8 Material:
- Water baths at 37°C and heating block of 80°C
- Eppendorf tubes
- Pipets and cones
Reagents:
- pET 43.1a (conc. 74.1 ng/μL)
- pBR322 (conc. 29.6 ng/μL)
- Eurofins Genomics plasmid containing Seq1 (conc. 1430.1 ng/ μL)
- Eurofins Genomics plasmid containing Seq2 (conc. 780.6 ng/ μL)
- Eurofins Genomics plasmid containing Seq8 (conc. 714.6 ng/ μL)
- Restriction enzymes : NdeI, PacI, NheI, BamHI, MscI, HindIII, BsmI, AvaI, SpeI, XbaI
- 10X Cut Smart
- Distilled water
- Mix the following volumes of reagents and incubate at 37°C for 20 min
| Volume (μL) | |
| pET 43.1a | 42 |
| 10X Cut Smart | 5 |
| Distilled water | - |
| Nhel | 1.5 |
| Pacl | 1.5 |
| Volume (μL) | |
| pBR322 | 42 |
| 10X Cut Smart | 5 |
| Distilled water | - |
| Bsml | 1.5 |
| Aval | 1.5 |
| Volume (μL) | |
| Seq1 | 8 |
| 10X Cut Smart | 5 |
| Distilled water | 31.5 |
| Hhel | 1.5 |
| BamHI | 1.5 |
| Volume (μL) | |
| Seq1 | 8 |
| 10X Cut Smart | 5 |
| Distilled water | 32 |
| Hhel | 1.5 |
| BamHI | 1.5 |
| Volume (μL) | |
| Seq8 | 4.5 |
| 10X Cut Smart | 5 |
| Distilled water | 31.5 |
| Hhel | 1.5 |
| BamHI | 1.5 |
| Volume (μL) | |
| Seq8 | 17.8 |
| 10X Cut Smart | 5 |
| Distilled water | 24.2 |
| Hhel | 1.5 |
| BamHI | 1.5 |
- Inactivate the digestion by heating the mixture in a water bath at 80 °C for 20 min
Electrophoresis on agarose gel We prepared a 0.8 % agar gel in order to separate the different fragments of the cut plasmids. (See here the Agarose Gel Preparation protocol) We filled:
- 2 wells with digested pBR322 (n°1 and n°2)
- 2 wells with digested pET 43.1a (n°3 and n°4)
- 2 wells with insert Seq1 (n°5 and n°6)
- 2 wells with insert Seq2 (n°7 and n°8)
- 2 wells with insert Seq8 (n°9 and n°10)
We let the DNA migrate for 10 min at 85 V on order to let the DNA penetrate the gel, and then 80 min at 125 V to efficiently separate the fragments. We then revealed the gel under UV lamp. Results of the agarose gel after migration:
Interpretations:
- pBR322 has been linearized, and we observe one fragment corresponding to the linearized plasmid
- pET 43.1a (7275 bp) has been successfully linearized into two fragments (5 kb and 2 kb)
- pEX A258 – Seq1 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (1105 bp) and the linearized plasmid (2446 bp)
- pEX A258 – Seq2 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (1159 bp) and the linearized plasmid (2446 bp)
- pEX A258 – Seq8 from Eurofins Genomics has also been successfully digested. We obtained two fragments corresponding to our insert (459 bp) and the linearized plasmid (2446 bp)
| Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) | |
| pBR322 | 11.1 | 2.19 |
| pET43.1a | 17.0 | 2.00 |
| Seq1 | 16.9 | 2.19 |
| Seq2 | 14.8 | 2.61 |
| Seq8 | 15.7 | 2.17 |
Cloning : We used the In-Fusion cloning kit provided by Ozyme in order to clone:
- Our two inserts Seq1 and Seq2 together in linearized pET 43.1a.
- Our insert Seq8 into linearized pBR322
- Following the advice of the Takara Clontech technician we contacted, we first incubated the linearized vectors and inserts at 50°C for 5 min
- We then placed it on ice for 3 min
- We mixed the following volumes into 1.5 mL tubes.
| Component | Cloning (μL) | Negative control (μL) | Positive control (μL) |
| Purified Seq1 | 5 | - | 2 (control) |
| Purified Seq2 | 6 | - | 2 (control) |
| Linearized vector | 9 | 9 | 1 (control) |
| 5X In-Fusion enzyme premix | 4 | 2 | 2 |
| Deionized water | - | 9 | 5 |
| Component | Cloning (μL) | Negative control (μL) |
| Purified Seq8 | 4.5 | - |
| Linearized vector | 13.5 | 13.5 |
| 5X In-Fusion enzyme premix | 4 | 2 |
| Deionized water | - | 4.5 |
- Incubate for 15 minutes in a water bath at 50°C.
- Set in ice.
- Ligation (See here the Ligation protocol)
- Transformation of the 5 plasmids into Stellar competent cells (provided with the cloning kit):
- Competent cell volume: 40 μL
- DNA volume: 2 μL
- Culture on LB agar plate supplemented with carbenicillin overnight at 37°C (with 1/5 dilution)
08.10.2018
Observation overnight plate culture of pBR322 + Seq8 and pET43.1a + Seq1 + Seq2 after InFusion
| pBR322 Neg Control | pBR322 + Seq8 | pET43.1 Neg Control | pET43.1 + Seq1 + Seq2 | |
| CFU | 46 | 136 | 27 | 59 |
Liquid culture of pBR322 + Seq8 and pET43.1a + Seq1 + Seq2 We did 12 liquid cultures of 5 mL (6 of each).
08.11.2018
Miniprep pET43.1a + Seq1 + Seq2 and pBR322 + Seq8 We extracted our plasmids from the colonies set in liquid culture yesterday. We had:
- 5 colonies of pET43.1a + Seq1+ Seq2
- 6 colonies of pBR322 + Seq8
- 1 colony from negative control of pET43.1
- 1 colony from negative control of pBR322
| Colony | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 116.5 | 1.99 |
| 2 | 124.8 | 1.95 |
| 3 | 98.1 | 2.01 |
| 4 | 114.3 | 1.95 |
| 5 | 96.8 | 1.96 |
For pBR322 + Seq8
| Colony | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| 1 | 88.7 | 2.03 |
| 2 | 105.6 | 1.95 |
| 3 | 84.0 | 2.12 |
| 4 | 104.0 | 1.97 |
| 5 | 95.6 | 2.08 |
| 6 | 90.1 | 2.01 |
| Colony | DNA Concentration (ng/µL) | Abs(260 nm)/Abs(280 nm) |
| pET 43.1 negative control | 110.6 | 1.98 |
| pBR322 negative control | 106.2 | 2.02 |
Observations: Concentrations are good enough for further use.
Digestion of pET43.1a + Seq1 + Seq2 Aim: Check that the ligation has successfully worked. Restriction enzymes used: NdeI Expected results:
| pET43.1a | linearized | 7.3 kB |
| pET43.1a + Seq1 | 1 fragment | 6.63 kB |
| pET43.1a + Seq2 | 2 fragments | 6.63 kB + 0.1 kB |
| pET43.1a + Seq1+ Seq2 | 2 fragments | 6.63 kB + 1 kB |
We digested 5 samples of our cloning products, and we also did some controls. Procedure:
| Volume (μL) | |
| DNA | 5 |
| Cut Smart | 3 |
| Ndel | 1 |
| H2O | 21 |
Digestion of pBR322 + Seq8 Aim: Check that the ligation has successfully worked. Restriction enzymes used: NdeI Expected results:
| pBR322 | linearized | 4 kB |
| pBR322 + Seq8 | 2 fragments | 4 kB + 0.9 kB |
We digested 6 samples of our cloning products, and 1 negative control. Procedure:
| Volume (μL) | |
| DNA | 5 |
| Cut Smart | 3 |
| Ndel | 1 |
| H2O | 21 |
- Digestion at 37°C for 15 min
- Addition of 6 µL of 6X loading dye in each tube
Electrophoresis on agarose gel We prepared an Agarose gel. (See here the Agarose Gel Preparation protocol) We filled:
- Wells 1 to 6: pBR322 + Seq8 (colonies 1 to 6)
- Well 7: pBR322 negative control
- Wells 8 to 12: pET43.1a + Seq1 + Seq2 (colonies 1 to 5)
- Well 13: pET 43.1 negative control
We let the DNA migrate for 10 minutes at 85 V and then 40 minutes at 125 V. Results:
Remark: Date shift -2 days on photograph Interpretations:
- For pBR322 + Seq8: On lanes corresponding to Col 1,3,4,5,6 two bands are clearly visible. One at 4 kb and another one at 1 kb, meaning that the plasmid digested by NdeI contained the insert Seq8. One band is visible on lane 2, Col 2 did not contain the insert. The control on lane 7 shows the plasmid digested without the insert at a higher molecular weight. The cloning worked for this construction, because bands observed between 700 bp and 1000 bp.
- For pET43.1a + Seq1 + Seq2: From lanes 8 to 11, only one band is visible, and bands are visible at the same molecular weight as the control one (pET43.1a w/o insert and digested with NdeI). On lane 12, the band is lightly lower than the others but no other band corresponding to an insert is visible on lane 12. The cloning did not work for this construction.
Liquid culture pET43.1a + Seq1 + Seq2 and pBR322 + Seq8 Colonies transformed with pET43.1a+Seq1+Seq2 (Colonies 7 to 25) were cultured in 5 mL LB media + 5 µL carbenicillin each (50 mg/mL) Two culture of pBR322+ Seq8 (Col 3 and Col 4) were cultured in 25 mL LB media + 25 µl carbenicillin each (50 mg/mL) (See here the Liquid Culture protocol)
Something was done one that day
08.06.2018
20 microchannel chips bonded to imaging dishes. 8 microchannel chips and 1 set of PDMS pieces for the well chip have been made.
08.07.2018
20 bonded microchannel chips sterilized by UV exposure. 8 microchannel chips and 1 set of PDMS pieces for the well chip have been made. Preparation of vertical chip PDMS pieces.
08.09.2018
10 membrane microchannel chips have been made. Leaks made this a difficult operation. 8 microchannel chips and 1 set of PDMS pieces for the well chip have been made. Preparation of vertical chip PDMS pieces.
08.10.2018
Membrane microchannel chips sterilized by UV exposure. Vertical chips bonded. 8 microchannel chips and 1 set of PDMS pieces for the well chip have been made. First successful vertical chip bonding, by modifying silver paste path.
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
08.13.2018
4 vertical chips bonded. Gold membrane PDMS well chips modification to enable current transmission.
08.16.2018
Conductivity measurements of the 3 gold-membrane PDMS well chips. Success.
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
08.22.2018
8 microchannel chips and 1 set of PDMS pieces for the well chip have been made.
08.23.2018
PEDOT:PSS coated on alumina oxide membranes. Success.
08.24.2018
PEDOT:Ts and PEDOT:Cl coated on alumina oxide membranes. Success.
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
08.27.2018
4 well chips have been made, each with a different type of membrane alumina oxide membrane filter (bare, PEDOT:PSS, PEDOT:Cl, PEDOT:Ts). 4 vertical chips bonded to tissue culture dishes.
08.28.2018
8 double membrane microchannel chips have been bonded to imaging dishes and sterilized by exposure to UV rays. Leaks made this a difficult and time-consuming operation. 8 microchannel chips have been made.
Bacteriology
Cell culture
Something was done one that day
Something was done one that day
Something was done one that day
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
09.11.2018
Bonding to imaging dishes and UV sterilization of 20 microchannel chips.
Bacteriology
Cell culture
Something was done one that day
Something was done one that day
Bacteriology
Cell culture
Something was done one that day
Something was done one that day
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
10.04.2018
Liquid culture of BL21. Biofilm culture on 6 PDMS well chips (membranes: 2 gold, 1 alumina oxide, 1 PEDOT:PSS, 1 PEDOT:Cl and 1 PEDOT:Ts).
10.05.2018
Biofilm growth measurement. Liquid culture of BL21 and biofilm culture on 6 PDMS well chips.
Membrane microchannel chip bacteria confinement experiment. Optical density measure of a sample of liquid culture. Liquid culture was poured in a microchannel chip on one side, and optical density of the liquid that flowed to the other side of the microchannnels was measured.
Results
Liquid culture OD: 0.44
OD of liquid after flowing through the chip: 0.41.
Interpretation
We expected a much lower OD after liquid flow through the chip, so this suggests the presence of a leak in the chip, that allows the liquid culture to flow without retaining the bacteria. The decision was taken to investigate further and to observe the flow under a microscope.
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
10.08.2018
Liquid culture of BL21. Biofilm culture on 6 PDMS well chips
Biofilm growth measurement.
10.11.2018
Liquid culture of BL21. Biofilm culture on 6 PDMS well chips
Biofilm growth measurement.
10.12.2018
Liquid culture of BL21. Biofilm culture on 6 PDMS well chips
Biofilm growth measurement.
Measurement of the electrical resistance of the membranes with the biofilm.
Bacteriology
Cell culture
Microfluidics/Membrane
Something was done one that day
Something was done one that day
10.15.2018
Liquid culture of BL21. Biofilm culture on 6 PDMS well chips
Biofilm growth measurement.
Measurement of the electrical resistance of the membranes with the biofilm.
Measurement of the membrane's electrical resistance without biofilm.
Results: membrane conductivity
Function generator was set on square at 200 Hz. The physical quantities measured are Eg, the generator tension amplitude, and Ep, the amplitude of the voltage difference between a point on the membrane inside the well and the extremity of the platinium strip outside the well. Tension amplitude of the resistor is given by Er = Eg - Ep. Current flowing through the electric circuit is calculated with I = Er/R. Conductivity of the membrane is given by I/Ep. Conductivity of each membrane was measured 3 times. Figure 1 shows the mean value for each membrane and the standard deviation.
Interpretation
Bare alumina oxide and PEDOT:PSS-coated membranes show similar conductivies, indicating the incomplete coating of PEDOT:PSS on alumina oxide membranes. On the opposite, PEDOT:Cl and PEDOT:Ts seem to exhibit on average better conductivities, but in the same time, the coating of these membranes revealed by electron microscopy seemed to have covered the alumina oxide membranes in a more uniform way, assuring enhanced conductive capabilities. These results can be criticized because of the high deviation and because the membranes conductivity was measured after several biofilms were grown on them, which may have affected the measurements.
10.16.2018
Measurement of the electrical resistance of the membranes with the biofilm. Measurement of the biofilm's growth.
Results: biofilm growth
Biofilm growth was measured 4 times in total. For each series of measure, the measured optical densities were divided by the optical density of the base liquid culture, to normalize the measures. Figure 2 shows the mean value for each type of membrane and the standard deviation.
Results: biofilm conductivity
For conductivity measurements, function generator was set on square at 200 Hz. The physical quantities measured are Eg, the generator tension amplitude, and Ep, the amplitude of the voltage difference between a point on the biofilm inside the well and the extremity of the platinium strip outside the well. Tension amplitude of the resistor is given by Er = Eg - Ep. Current flowing through the electric circuit is calculated with I = Er/R. Conductivity of the membrane is given by I/Ep. Conductivity of each membrane with a biofilm was repeated 3 times. Figure 4 shows the average conductivity of the membrane with the biofilm, and the standard deviation.
To approximate very roughly the conductivity of the biofilm, the average conductivity values of the membranes with a biofilm were divided by the corresponding average biofilm growth values, and the conductivity of the membrane was then substracted. Figure 4 shows the estimated biofilm conductivity.
Interpretation
As told by the membrane manufacturer, biofilm formation on gold membranes seems indeed to be more difficult than on other membranes. However we expected PEDOT:PSS-coated membranes to stimulate more the growth of biofilm, but perhaps that may be just another indicator of the imcomplete coating. Surprisingly, PEDOT:Cl tends to allow better formation of biofilms. We realized only after the experiments the need for a control biofilm culture without membrane.
Conductivity with a biofilm is better with gold membranes, although the conductivity of gold membranes themselves isn't the best. This may be explained by the fact, that because of the thinner biofilm formation on gold membranes, the electrical wires touched not only the biofilm, but also the membrane, bypassing the biofilm and leading to imprecise measurements.
Approximate biofilm conductivity is therefore probably wrong for the gold membrane. However, it is interesting to notice that the biofilm conductivity measured for the bare alumina oxyde, PEDOT:Ts-coated one and PEDOT:PSS-coated give more or less the same value, suggesting that with more measurements, adapted equipement and better methods it would be indeed possible to measure the biofilm's conductivity with our PDMS well chips.