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Notebook

  • Week 25
    • Monday June 18th

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    • Tuesday June 19th

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    • Wednesday June 20th

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    • Thursday June 21st

      Who: Owen

      Aim Preparation of 200 ml YPD and 200 ml YPD with agar. Preparation of 200 ml LB medium and 200 ml LB medium with 2% agar

      For preparation of 200 ml YPD add to demi water:
      - 2 g yeast extract
      - 4 g peptone
      - 4 g glucose

      For preparation of 200 ml YPD 2% agar add to demi water:
      - 2 g yeast extract
      - 4 g peptone
      - 4 g glucose
      - 4 g agar

      For preparation of 200 ml LB add to demi water:
      - 4 g LB

      For preparation of 200 ml LB 2% agar add to demi water:
      - 4 g LB
      - 4 g agar

    • Friday June 22nd

      Who: Owen

      Aim Prepare 4 ml 1000x ampicillin stock (100mg/ml in MQ)

      - Add 400 mg ampicillin to 4 ml MQ and filter sterilize.
      - Aliquot and store at - 20 degrees C.

      Who: Owen

      Aim Pour YPD plates and LB+Amp plates

      Autoclave media at 121 degrees C for 15 minutes and cool to hand warm.

      - Add 200 ul 1000x ampicillin to 200 ml LB medium with agar.
      - Pour LB + Amp plates.
      - Pour YPD plates

      Who: Owen

      Aim Grow strain BY4741 for cloning

      Strain provided by Molecular Microbiology group RUG.
      - Plate BY4741 on YPD and grow over the weekend at 30 degrees.
      25-6-18 Colonies visible for BY4741 on YPD plate.

    • Saturday June 23rd

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    • Sunday June 24th

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  • Week 26
    • Monday June 25th

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    • Tuesday June 26th

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    • Wednesday June 27th

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    • Thursday June 28th

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    • Friday June 29th
      thing we did
    • Saturday June 30th

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    • Sunday July 1st

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  • Week 27
    • Monday July 2nd

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    • Tuesday July 3rd

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    • Wednesday July 4th

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    • Thursday July 5th

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    • Friday July 6th

      Who: Rianne & Phillip

      Aim Competent cell test

      To test the competence of our cells, we performed a competent cell test according to the IGEM Competent Cell test kit protocol.

      We dissolved the dried-down purified plasmid DNA from BBa_J04450 into 50 µl of water to obtain 100 pg/µl and 10 pg/µl concentrations. In short, 1 µl of each DNA concentration was added to 50 µl of competent cells in duplicates. We obtained plenty of colonies and the efficiency of transformation was determined sufficient. This batch of competent E. coli DH5ɑ cells was used for all of the following E. coli transformations.

    • Saturday July 7th

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    • Sunday July 8th

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  • Week 28
    • Monday July 9th

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    • Tuesday July 10th

      Who: Rianne & Phillip

      Aim Transformation of competent E. coli DH5ɑ with the devices for the iGEM Interlab study

      The next devices were provided to us by iGEM in the plates in the distribution kit. The following devices were resuspended into 10 µl sterilized deionized water.

      DeviceLocation on plate 7
      Negative control2D
      Positive control2B
      Device 12F
      Device 22H
      Device 32J
      Device 42L
      Device 52N
      Device 62P

      1 µl of this solution was transformed into 50 µl of competent DH5ɑ cells using the following protocol:

      1. LB plates with the appropriate antibiotics were prepared as described here (link to our protocol page LB agar plates)
      2. Eppendorf tubes (1.5 ml) were pre-chilled on ice and competent cells were thawed on ice
      3. 50 µl of competent cells was added to the pre-chilled eppendorf tubes, together with the DNA
      4. 30 min incubation on ice
      5. Heat shock for 45 sec in a 42℃ water bath
      6. Incubation on ice for 5 min
      7. 950 µl of LB broth was added to the cells
      8. Incubation for 1 hour, 37℃, 200 rpm
      9. Plating of the cells on the LB-agar plates. 100 µl one one plate, then the culture is centrifuged and the supernatant is partially discarded. The cell pellet is resuspended in approximately 100 µl and plated on a separate plate.
      10. Overnight incubation at 37℃ (agar side up)
    • Wednesday July 11th

      Who: Rianne

      Aim Growth of the colonies used in the iGEM Interlab study

      We obtained between 10-100 colonies per transformation. Two colonies were picked with a sterile pipette tip and transferred into 5 ml of LB with chloramphenicol. The cultures were grown in the appropriate broth overnight at 37℃ in a shaking incubator at 200 rpm.

      Who: Rianne

      Aim To purify the plasmids from Wen. et al out of E. coli for transformation into yeast

      • 1882: PYD1 - CipA1 - EGII
      • 1883: PYD1 - CipA3 - EGII
      • CB: PRS425 - CBHII - BGLI

      These three plasmids that we received from Wen. et al were kindly transformed by Vakhil Takhaveev into E. coli and plated onto LB agar plates. In order to purify the plasmids out of these cells, I grew three colonies of each strain into 10 ml of LB with the appropriate antibiotics. The next day, the plasmid was extracted from the full-grown cultures using a plasmid extraction kit. The following concentrations (ng/µl) were obtained:

      Results

      18821883CB
      1278,15572,80443,80
      2664,1098,0361,70
      3321,25652,0439,95

      The plasmids were stored at -20℃ until further use.

    • Thursday July 12th

      Who: Rianne

      Aim Production of glycerol stocks for the strains used in the iGEM Interlab study

      250 µl of culture was mixed with 250 µl of 50% glycerol and stored at -80℃. Simultaneously, a small amount of the glycerol stock was transferred into 5 ml of fresh medium supplemented with chloramphenicol and grown overnight at 37℃, 200 rpm.

    • Friday July 13th

      Who: Rianne & Phillip

      Aim First cell measurement for the iGEM Interlab study

      1. 500 µl of the overnight culture was transferred into 4,5 ml of LB with chloramphenicol
      2. OD600 measurement of 1:10 dilutions
      3. Colony 1Colony 2
        Negative control0.1910.192
        Positive control0.1980.204
        Device 10.1520.149
        Device 20.1890.208
        Device 30.190.191
        Device 40.150.171
        Device 50.0940.109
        Device 60.2040.195
      4. Dilution of these 1:10 cultures to target OD600 0.2 in a final volume of 12 ml
      5. 10 ml of culture was already pipetted into the 50 ml falcon tubes for all cultures, except for cultures of device 5, for which 9 ml was used. To these tubes, the following volumes (µl) were added:

        Colony 1Cell cultureLBColony 2Cell cultureLB
        Negative control1257743Negative control1249751
        Positive control1212788Positive control1176824
        Device 11579421Device 11611389
        Device 21269731Device 21154846
        Device 31263737Device 31257743
        Device 41599401Device 41404596
        Device 52553447Device 52202798
        Device 61176824Device 61231769
      6. 1000 µl of the 0 hour time point culture was pipetted into an eppendorf tube and kept on ice until further use in a box with ice at 4℃.
      7. Six hours of incubation at 37℃, 200 rpm
      8. 1000 µl of the 6 hour time point culture was pipetted into an eppendorf tube and kept on ice until further use in a box with ice at 4℃.
      9. 100 µl of these cell cultures were transferred into wells of a 96-microtiter plate.

      However, while analyzing our results, we realized that we did not set the ‘gain’ setting for fluorescence measurement in the plate reader to a fixed number across the different measurements. Therefore, we need to repeat this measurement.

      Aim Correlate OD600 measurements in our plate reader to colony forming units (CFU)

      We first diluted the overnight cultures of the negative and positive control 1:8 and measured OD600 in our plate reader. We then further diluted these cultures to target OD600 0.1, confirmed by our plate reader and plated onto plates in several dilutions.

      Aim Calibration experiments for the Interlab study

      LUDOX, silica beads and fluorescein experiments as described on our interlab page were also performed. As described above, the fluorescein calibration needs to be repeated.

      The exact protocol can be found here and the results of these experiments can be found on our Interlab page.

    • Saturday July 14th

      Who: Rianne & Phillip

      Aim Counting colony forming units

      We checked the colonies and counted them, to calculate how many cells were present in our culture of which the plate reader displayed the OD600 to be 0.1. The following numbers of colonies were found, where + and - stand for positive and negative control, respectively, and 1 and 2 stand for the two colonies that were picked at day 11-7-18. (4) and (5) stand for the dilutions plated as performed on 13-7-18.

      +1(4)+1(5)+2(4)+2(5)-1(4)-1(5)-2(4)-2(5)
      1181111922319191709
      215011208141121720219
      316619184222131120516
    • Sunday July 15th

      Who:

      Aim Growth of yeast strain YGEN 0013 and the interlab strains for second measurement

  • Week 29
    • Monday July 16th

      Who: Rianne

      Aim Growth of yeast strain YGEN 0013 and the interlab strains for second measurement

      YGEN 0013 colonies were picked and grown in Verduyn medium supplemented with the appropriate vitamins and trace elements, with addition of uracil, tryptophan and leucin. The strain was grown in 5 ml overnight at 30℃, 200 rpm.

      To repeat the Interlab fluorescence measurements, the glycerol stocks of the interlab strains 12-7-18 were taken out of the -80℃, and grown in 5 ml of LB and the appropriate antibiotic overnight at 37℃, 220 rpm.

    • Tuesday July 17th

      Who: Rianne & Phillip

      Aim Second Interlab measurement

      The same protocol as described on 13-8-18 and in the Interlab study was used. The starting OD600 of the 1:10 diluted overnight cultures were:

      Colony 1Colony 2
      Negative control0.190.182
      Positive control0.1670.168
      Device 10.2050.181
      Device 20.170.175
      Device 30.1850.19
      Device 40.1680.184
      Device 50.1780.185
      Device 60.1950.174

      Dilution of these 1:10 cultures to target OD600 0.2 in a final volume of 12 ml: 10 ml of culture was already pipetted into the 50 ml falcon tubes for all cultures. To these tubes, the following volumes (µl) were added:

      Colony 1Cell cultureLBColony 2Cell cultureLB
      Negative control1263737Negative control1319681
      Positive control1437563Positive control1429571
      Device 11171829Device 11326674
      Device 21412588Device 21371629
      Device 31297703Device 31263737
      Device 41429571Device 41304696
      Device 51348652Device 51297703
      Device 61231769Device 61379621

      The cell measurements and the fluorescein measurements were repeated, but now the gain settings were fixed between the measurements. You can find the results on our Interlab page.

    • Wednesday July 18th

      Who: Rianne & Ingeborg

      Aim Purification of PhipZ

      E. coli containing PhipZ (with both an ampicillin and zeocin marker) was grown in LB containing ampicillin and the plasmid was extracted using a plasmid extraction kit. Four parallel cultures were used to purify PhipZ and the following concentrations were obtained (ng/µl): 381.7, 319.9, 419.2 and 389.05. This will be sufficient for the rest of our project. The plasmids were stored at -20℃.

    • Thursday July 19th

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    • Friday July 20th

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    • Saturday July 21st

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    • Sunday July 22nd

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  • Week 30
    • Monday July 23rd

      Who: Rianne

      Aim PCR on EGII and CBHI gene fragments

      Primers for the gene fragments were diluted in MQ to 100 µM (a working stock of 50 µM was also prepared). Synthesized gene fragments were diluted in MQ to 5 ng/µl. For both EGII and CBHI, three PCR reactions were performed:

      ABC
      PCR buffer (5X)101010
      Primer A (50 µM)111
      Primer B (50 µM)111
      Polymerase111
      Template (5ng/µl)111
      Q buffer10
      Mg2+2
      MQ362634

      Primer melting temperatures:

      EGII:
      FW = 51,3
      Rev = 49,2

      CBHI:
      Fw = 51,3
      Rev = 48,6

      PCR programme run in a thermocycler:

      1. 95℃ - 5 min
      2. 94℃ - 15 sec
      3. 44℃ - 1 min
      4. 72℃ - 1 min
      5. 72℃ - 10 min
      6. 4℃ on hold

      Steps 2-4 were repeated 35 times

      Who: Rianne

      Aim Count colonies & pick colonies from yeast transformation

      Negative control
      -Leu, -Trp: 0 colonies
      -Trp: at least 10 colonies
      -Leu: 0 colonies

      1882+CB1883+CB18821883CB
      10%12615521
      90%3232manymanymany

      Note: -trp plates look different than others. They are white-ish and the colonies are small.

      Two colonies of each plate were used to inoculate 5 ml of Verduyn medium with the appropriate uracil, leucin or tryptophan supplementation. The cultures were grown overnight at 30℃ and 200 rpm

    • Tuesday July 24th

      Who: Rianne

      Aim Agarose gel of 23-07-18 PCR products

      3 µl of the ladder was loaded, 12 µl of the PCR products were mixed with 3 µl of sample buffer. NC = negative control (no template added). L = ladder.

      • Upper lane: L - EGII(A)-NC(A)-EGII(B)-NC(B)-EGII(C)-EGII(C)-NC(C)-CBHII(A)-NC(A)
      • Lower lane: L- CBHII(B)-NC(B)-CBHII(C)-NC(C)-ctrl EGII-ctrl CBHII
    • Wednesday July 25th

      Who: Rianne

      Aim Sending plasmids pNZ8048 and pPMK4 to Leiden for collaboration

      A small volume of purified plasmid pNZ8048 (obtained from Alisa Garaeva) and PMK4 (obtained from Buu Minh Tran) were transferred to screw-capped microtubes, and, accompanied by a dried drop on Whatman filter paper, sent to Leiden by mail.

      The plasmids arrived in Leiden soon!

      The Leiden Igem team with the eppendorf tubes containing the plasmids.
    • Thursday July 26th

      Who: Rianne & Bram

      Aim PCR of EGII

      Because two bands appeared in the previous PCR reaction, we want to change the reaction conditions to see if we can obtain a single product with the right length. Two conditions were tested. The temperature was increased to prevent non-specific binding and DMSO was added.

      AB
      PCR buffer (5X)1010
      Primer A (50 µM)11
      Primer B (50 µM)11
      Polymerase11
      Template (5ng/µl)22
      DMSO3
      MQ3532

      Primer melting temperatures:

      EGII:
      FW = 51,3
      Rev = 49,2

      PCR programme run in a thermocycler:

      1. 95℃ - 5 min
      2. 94℃ - 15 sec
      3. 46℃ - 1 min
      4. 72℃ - 1 min
      5. 72℃ - 10 min
      6. 4℃ on hold

      Steps 2-4 were repeated 35 times

      Ladder - EGII A - EGII B

      Gel was kept in the fridge overnight before use, which is probably the reason why the bands are not as clear as desired

    • Friday July 27th

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    • Saturday July 28th

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    • Sunday July 29th

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  • Week 31
    • Monday July 30th

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    • Tuesday July 31st

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    • Wednesday August 1st

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    • Thursday August 2nd

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    • Friday August 3rd

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    • Saturday August 4th

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    • Sunday August 5th

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  • Week 32
    • Monday August 6th

      Who: Rianne

      Aim Restrictions of cellulosome PCR products or gene fragments

      Restriction reactions were performed in a 50 µl total reaction volume. (1µl of each restriction enzyme, 5 µl of 10X restriction buffer, 1 µg of DNA). For all reactions, NEB buffer 3.1 was used with enzymes BamH1 and Xho1.

      Concentration stock (ng/µl)For ~1 µg (µl)MQ
      CBHI225,5538
      EGII (PCR with DMSO, 26-7)1457,535,5
      EGII (no DMSO, 26-7)1507,535,5
      PhipZ300439

      Reactions were incubated at 37℃ for 1,5 hours.

      • PCR clean-up gave the following concentrations of restricted fragments:
      • -CBHI31,35
      • -EGII (DMSO)27,05
      • -EGII 28,35
      • -PhipZ32,55

      The restricted clean fragments were stored at -20℃ until further use. The genes Scaffold part 1 and Scaffold part 2 were diluted to 5 ng/µl by addition of 200 µl MQ to the delivered dried genes. One third (~300 ng in 65,5 µl) was used for a 75 µl restriction reaction with the following additions:

      Enzyme 1 (1 µl)Enzyme 2 (1 µl)Buffer (7,5 µl)
      Scaffold part 1BamH1Cla1NEB 3
      Scaffold part 2Xho1Cla1Cutsmart

      The mixtures were incubated for 2,5 hrs at 37℃ and then kept at 4℃ overnight. The genes BGL part 1 and BGL part 2 were diluted to 10 ng/µl by addition of 100 µl MQ to the delivered dried genes. One third (~300 ng in 30 µl) was used for a 50 µl restriction reaction with the following additions:

      Enzyme 1 (1 µl)Enzyme 2 (1 µl)Buffer (5 µl)
      BGL part 1BamH1Nru1NEB 3
      BGL part 2Xho1Nru1NEB 3

      The mixtures were filled up to 50 µl by addition of 13 µl MQ and incubated for 1,5 hrs at 37℃ and then kept at 4℃ overnight.

    • Tuesday August 7th

      Who: Rianne

      Aim Restriction cleanup and ligation

      PCR cleanup of the previous restriction reactions gave the following concentrations:

      • -Scaffold part 13,2 ng/µl
      • -Scaffold part 24,8 ng/µl
      • -BGL part 12,55 ng/µl
      • -BGL part 22,9 ng/µl

      For a vector:insert(:insert) equimolar ratio of around 1:3(:3), the following ligation mixtures were prepared:

      A, B: 100 ng plasmid. C, D: 50 ng plasmid reactions.

      A (µl)B (µl)C (µl)D (µl)Control
      PhipZ3.13.11,541,543,1
      CBH3
      EGII3.12
      BGLI part 113.2
      BGLI part 216.1
      Scaffold part 111
      Scaffold part 27
      T4 ligase11221
      Ligase buffer113.52.51
      MQ1.91.7814.9
      Total volume1010352510

      The ligation mixtures were incubated for 2 hours at 37℃, following 20 minutes at 80℃ to heat-kill the enzymes.

      Who: Rianne

      Aim Transformation

      Ligated amountInto X competent cells (µl)
      Aall75
      Ball75
      C35200
      D25150
      Vall75

      Following the same protocol as previously used. Cells were plated on LB-ampicillin plates (100µl, 250µl and rest) and incubated at 37℃ overnight.

    • Wednesday August 8th

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    • Thursday August 9th

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    • Friday August 10th

      Who: Rianne

      Aim Grow the cellulosome-strains on cotton

      Common cotton pads were purchased from a local supermarket and 20 mg cotton was weighed and transferred into glass tubes. The tubes were subsequently autoclaved.

      Glass tubes with 2%, 0,2%, 0,02%, 0,002% and 0,0002% galactose were prepared. Both with and without the cotton. 10 ml of Verduyn medium (supplemented with the appropriate vitamins, trace elements and with uracil) was added to each tube. As a positive control, LB and E. coli bacteria were added to a glass tube containing cotton, to exclude non-growth because of chemicals in the cotton pads. Also, Verduyn medium containing 2% glucose was added to one of the glass tubes with cotton, to ensure viability of the yeast strains.

      Colonies of CB1883 and CB1882 were taken from the plate and inoculated into the tubes. The cultures were incubated at 30℃, 150 rpm.

      Results Growth in both positive controls, no growth in the remaining tubes.

    • Saturday August 11th

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    • Sunday August 12th

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  • Week 33
    • Monday August 13th

      Who: Jan Marten

      Aim Negative controls for 10-08-2018

      Colony PCR on e.coli pHIPZ7 as negative controls. Same primers and PCR settings as on 10-08-2018. A sample without primers is also made.

      Gel was imaged on a UV lightbox, as the imaging PC was acting strange. No bands were visible on the negative controls.

    • Tuesday August 14th

      Who: Rianne

      Aim Pick and grow colonies

      Colonies 9 and 10 of both EGII and CBHI (of 10-08-18) were cultured, as well as 10 colonies from the plated with the transformed scaffold. The colonies were grown overnight in 5 ml LB supplemented with ampicillin.

      Who: Matthijs

      Aim Restriction digest of gBlock genes + restriction analysis on scaffold

      Restriction digest of gBlock genes

      Since the genes PAL2, CipA3 and BGLI were synthesized in two parts, they had to be ligated to use for further experiments.

      • The CipA3 fragment contained a ClaI site
      • BGLI contained ApaI and NruE, but since NruE cuts blunt ends, ApaI was used
      • PAL2 contained NcoI

      The fragments were hydrated to arrive at a final concentration of 10 ng/µl, the CipA3 fragments were already hydrated to a concentration of 5 ng/µl. The final reaction mixture contained the following ingredients:

      Sampleµl DNAµl Enzymeµl Bufferµl MQµl Final
      PAL230151450
      BGLI30151450
      CipA3651.17.50~75

      Where the enzyme used was corresponds to the enzyme as described above, and the buffer corresponds to the appropriate buffer for the enzyme. Both fragments for each gene are here already mixed.

      Restriction digest was incubated at 37℃ for 2 hours and inactivated by heating to 80℃ for 20 minutes. The mixture was finally held at 4℃

      Restriction analysis on scaffold

      Colonies were picked previously by Rianne. 10 of these were selected for restriction analysis to verify the transformation. For the plasmid containing CipA3, the enzyme SmaI was used. SmaI has two recognition sites on the empty plasmid, pHIPZ7, producing one fragment of 4.6kb and one of 900b. When the gene is successfully inserted it will remove one of the recognition sites, producing only one large fragment of roughly 8.2kb.

      The following scheme was used to prepare the reaction mixtures for all restriction digests of the CipA3 containing plasmids.

      Sampleµl DNAµl Enzymeµl Bufferµl MQµl Final
      CipA3 11.30.52.515.720
      CipA3 21.70.52.515.320
      CipA3 31.430.52.515.620
      CipA3 42.930.52.51420
      CipA3 52.960.52.51420

      The amount of DNA to add was calculated such that a final content of 250 ng of DNA would be reached. The restriction digest was incubated at 37℃ for 2 hours, after which the enzymes were inactivated by heating at 80℃ for 20 minutes.

      Who: Matthijs

      Aim Ligation of gBlock fragments + Restriction analysis on gel

      Ligation of gBlock fragments

      After the restriction digest, the fragments had to be ligated together. For this we use T4 ligase. The reaction was mixed as follows:

      Sampleµl DNAµl T4µl Bufferµl MQµl Final
      PAL260.512.510
      BGLI60.512.510
      CipA38.50.51110

      The amount of DNA to add was calculated such that a total of 25 ng for each fragment was present. The ligation reaction was incubated at 16℃ for 16 hours overnight, after which the enzyme was heat inactivated by heating to 80℃ for 20 minutes.

      Restriction analysis on gel

      The restriction analysis of the CipA3 containing plasmids was run on an agarose gel. 1% of agarose was used in TAE buffer. 5 µl of SYBR green was added to 50 ml of agarose in TAE as prescribed by the manual. The gel was run at 100V for about 30 minutes after which it was imaged using a UV light source. As a standard DNA ladder, 1 kb generuler was added to the well in the middle.

      CipA3 1-CipA3 2-CipA3 3-CipA3 4-CipA3 5-Ladder-CipA3 6-CipA3 7-CipA3 8-CipA3 9-CipA3 10

      Who:

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    • Wednesday August 15th

      Who: Rianne

      Aim Glycerol stocks and plasmid minipreps

      The cultures of the transformed EGII, CBHI and the scaffold were taken out of the incubator and glycerol stocks were prepared and stored. A plasmid miniprep of the cultures resulted in the following concentrations (ng/µl) of plasmid for restriction analysis and stored at -20℃:

      • EGII 9 - 144,50
      • EGII 10 - 160,05
      • CBHI 9 - 115,20
      • CBHI 10 - 207,40
      • Scaffold 1 - 193,59
      • Scaffold 2 - 146,95
      • Scaffold 3 - 175,05
      • Scaffold 4 - 85,35
      • Scaffold 5 - 84,50
      • Scaffold 6 - 96,75
      • Scaffold 7 - 103,95
      • Scaffold 8 - 95,65
      • Scaffold 9 - 105,05
      • Scaffold 10 - 108,0
    • Thursday August 16th

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    • Friday August 17th

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    • Saturday August 18th

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    • Sunday August 19th

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  • Week 34
    • Monday August 20th

      Who: Matthijs

      Aim HF PCR on gblocks fragments

      High fidelity PCR was used to amplify the ligated gblock fragments. The following primers were used:

      SampleFWRV
      PAL2PAL2.1-FWPAL2.2-REV
      BGLIBGLI-FWBGLI-RV
      CIPA3CIP3A-FWCIP3F-REV

      Primers were diluted to 30 pmol/μl. The pipetting scheme was as follows:

      SampleDNA µlFW µlRV µlBuffer µlHF µlH2O µl
      PAL221,71,710232,6
      BGLI21,71,710232,6
      CIPA321,71,710232,6
      Control01,71,710234,6

      The PCR protocol was as follows:

      • activation - 95C - 5m
      • denaturing - 94C - 15s,30x
      • annealing - 50C - 1m, 30x
      • extension - 68C - 2m, 30x
      • Final extension - 72C - 10m
      HF PCR on PAL2, BGLI and CIPA3

      The BGLI fragment seems to have a size of about 3kb which is as expected. The size of PAL2 is too small and is most likely not correct. CIPA3 did not give any signal. BGLI concentration after PCR: 69.2 ng/µl

    • Tuesday August 21st

      Who: Matthijs

      Aim Ligation of BGLI into pHIPZ7

      Since BGLI was the only sample with a proper PCR signal, it was attempted to ligate into pHIPZ7, our standard yeast expression plasmid.
      First, double restriction with BamHI and XhoI was done using the following scheme:

      sampleDNABufferBamHIXhoIH2O
      BGLI3.6 µl2.5 µl0.5 µl0.5 µl12.9 µl

      The reaction was performed at 37℃ for two hours after which the enzymes were inactivated by heating the sample at 80℃ for 20 minutes.
      This product was purified by using a PCR purification column to remove the enzymes and buffer components.
      Next the product was mixed with linearized plasmid at a 1:3 weight ratio and T4 ligase was added to ligate the product into the plasmid.

      SampleInsert DNApHIPZ7T4 bufferT4H2O
      BGLI6 µl5 µl1.5 µl1 µl1.75 µl

      The reaction was performed overnight at 16℃ after which the enzyme was inactivated by heat treatment at 80℃ for 20 minutes.

      The product was again cleaned up and Taq polymerase was performed to verify insertion. The general sequence primers were used as these should give a large product when a sequence has inserted at the restriction site and a small product otherwise.

      PCR conditions were standard Taq conditions with an annealing temperature of 50℃ as the melting temperature of the primers was quite low.

      Who: Ingeborg

      Aim Restriction digest of EGII and CBHII

      Restriction digest
      For the plasmids containing EGII and CBHII, the enzyme NCOI was used.
      NCOI has one recognition site on the empty plasmid, pHIPZ7, producing one fragment of 5.8kb. When the EGII gene is successfully inserted it will add one recognition site, producing one large fragment of roughly 6.4kb and a smaller fragment of 967b.
      When the CBHII gene is successfully inserted it will add two recognition sites, producing one large fragment of roughly 5.5kb and two smaller fragments, a fragment of 1186b and one of 766b.

      The following scheme was used to prepare the reaction mixtures for all restriction digests of the EGII and CBHII containing plasmids.

      Sampleµl DNAµl Enzymeµl Bufferµl MQµl Final
      EGII - E92.180.52.514.8220
      EGII - E101.560.52.515.4420
      CBHII - C92.170.52.514.8320
      CBHII - C101.20.52.515.820

      The amount of DNA to add was calculated such that a final content of 250 ng of DNA would be reached.

      The restriction digest was incubated at 37℃ for 2 hours, after which the enzymes were inactivated by heating at 80C for 20 minutes.

      Restriction analysis on gel
      The restriction analysis of the EGII and CBHII containing plasmids was run on an agarose gel. 1% of agarose was used in TAE buffer. 5 µl of SYBR green was added to 50 ml of agarose in TAE as prescribed by the manual. The gel was run at 100V for about 55 minutes after which it was imaged using a UV light source. As a standard DNA ladder, 1 kb generuler was added to the well in the middle.

      E9-E10-C9-C10-Ladder
    • Wednesday August 22nd

      Who:

      Aim

    • Thursday August 23rd

      Who: Ingeborg

      Aim Transformation of BGL1 and PAL2

      Cells were plated on LB-ampicillin plates (250µl and 100µl concentrated) and incubated at 37℃ overnight.

    • Friday August 24th

      Who:

      Aim

    • Saturday August 25th

      Who: Jan Marten

      Aim Restriction analysis on BGL1 and PAL2

      5 colonies of BGL1 and 5 colonies of the PAL2 transformations are inoculated into LB ampicillin medium, and incubated overnight with agitation at 37℃.

    • Sunday August 26th

      Who: Jan Marten

      Aim Restriction analysis of BGL1 and PAL2

      The colonies have grown overnight and are miniprepped to isolate the plasmids. The BGL1 plasmids, along with a pHIPZ7 control plasmid are restricted with XbaI. The PAL2 plasmids are not processed, as it turns out the PCR reaction didn’t add the needed restriction sites. Therefore these plasmids cannot be correct.
      The restriction tubes are placed in a PCR machine. 2 hours at 37℃, then infinite time at 4℃.

  • Week 35
    • Monday August 27th

      Who:

      Aim

    • Tuesday August 28th

      Who: Ingeborg

      Aim Transformation of BGL1 (ligation product made by Matthijs)

      Cells were plated on LB-ampicillin plates (250µl and 100µl concentrated) and incubated at 37℃ overnight.

      Who: Rianne

      Aim Agarose gel of Matthijs’ ligation products of BGLI fragments

      4µl ladder, 8µl of the samples

      Ladder-B1-B2-Control

      Who: Rianne

      Aim Grow colonies EGII and BGLI 9

      EGII and BGLI colonies 9 were take from the glycerol stocks and inoculated into 5 ml LB with ampicillin and grown overnight in a 37℃ incubator, whilst shaking at 220 rpm.

    • Wednesday August 29th

      Who: Rianne

      Aim Taq colony PCR of EGII, BGLI and CBHI colonies/cultures

      20µl reaction volume, taq polymerase (according to manual manufacturer)

      Different sets of repair fragment primers:
      A) CasR2 Fw & Rv
      B) CasR3 Fw & Rv
      C) CasR5 Fw & Rv
      D) CasR4 Fw & CasR1 Rv

      Expected sizes:
      Insert + promotor, terminator, docking module (2150 bp)
      BGLI = 3150 bp + 2150 = 5300
      EGII = 1640 bp + 2150 = 3790
      CBHI = 1820 bp + 2150 = 3970

      All primer sets are tested on the empty PhipZ plasmid as a control reaction.
      For the CBHI colony 9 primer set B was used and EGII was tested with primer set A. A small amount of culture was added to the reaction mix to provide the template DNA. 30 colonies of the BGLI plates were tested with primer set A.

      Cycling programme:
      94℃ 5 min

      15 cycles:
      94℃ 45 sec
      64-57℃ 45 sec
      72℃ 5:30 min

      15 cycles:
      94℃ 45 sec
      57℃ 45 sec
      72℃ 5:30 min

      72℃ 10 min
      12℃ indefinite

    • Thursday August 30th

      Who: Rianne

      Aim Agarose gel of 29-8 pcr products

      APhipZ - BPhipZ - CPhipZ - DPhipZ - Ladder - CBHI - EGII
      BGLI: Ladder - 1 - 2 - 3 - 4 - 5 - 6/10 - 11/15 - 16/20 - 21/25 - 26-30

      Who: Jan Marten

      Aim PCR on the PAL2 and CIPA3 fragments

      PCR is performed on the PAL2 and CIPA3 gene fragments.
      Primers: For PAL2, PAL2f-fw and pal2f-rv are used to attach a C-terminal His-tag, and pal2g-fw and pal2g-rv are used to attach a N-terminal His-tag.
      For CIPA3, primers cipa3a-fw and cipa3c-rv are used.
      Master mix: 5 ul buffer, 1 ul dntp’s, 0.2 ul of each primer, 1 ul template, 0,5 ul Qiagen high fidelity polymerase, 42 ul MQ water.
      9 mixes are made:

      1. CIPA3
      2. CIPA3
      3. CIPA3
      4. PAL2 primer set F
      5. PAL2 primer set F
      6. PAL2 primer set F
      7. PAL2 primer set G
      8. PAL2 primer set G
      9. PAL2 primer set G

      Machine settings:
      94 degrees, 3 minutes initial denaturation
      94 degrees, 45 seconds denaturation
      52 degrees, 45 seconds, annealing
      72 degrees, 2 minutes, extension
      Repeat denaturation, annealing, extension 35 times
      72 degrees, 10 minutes, final extension

    • Friday August 31st

      Who:

      Aim

    • Saturday September 1st

      Who:

      Aim

    • Sunday September 2nd

      Who:

      Aim

  • Week 36
    • Monday September 3rd

      Who: Jan Marten

      Aim measuring OD of cultures, and galactose induction

      The OD of the cultures are measured:

      Strainfructoseraffinose
      1882 10.050.02
      1882 20.160.09
      1882 30.520.22
      1883 10.020.02
      1883 20.20.07
      1883 20.550.25

      At 13.10, 0.5% final concentration galactose is added to 1882.3 and 1883.3 cultured on fructose.
      At 15.10, 0.5% final concentration galactose is added to 1882.3 and 1883.3 cultured on raffinose.
      After 2 hours of incubation, the cells are spun down at 6000 rcf, 5 minutes, and resuspended in 10 ml of Verduyn medium. Spun down again, and resuspended in 20 ml Verduyn medium.
      10 ml of this is transferred to a culture flask, more Verduyn medium is added, to a final volume of 20 ml. 2% cellobiose final concentration is added, along with uracil.

      At 17.10, the OD of the cultures is measured:

      fructoseraffinose
      1882.30.440.108
      1883.30.4560.134

      The positive control had an OD of 0.432, the negative control was 0.514

    • Tuesday September 4th

      Who: Ingeborg

      Aim Transformation of the PAL2 plasmid (obtained from Shreyans)

      Cells were plated on LB-kanamycin plates (250µl and 250µl concentrated) and incubated at 37℃ overnight.

      Who: Rianne

      Aim PCR PAL2 on pAL2 syn gene in pUC57-kan obtained from Shreyans (Roelfes group)

      Phusion polymerase with primer sets:
      PAL2C Fw & PAL2B Rv
      PAL2B Fw & PAL2A Rv

      Mix (50 µl):
      PCR buffer 10 µl
      Primer A 5 µl (final concentration 1µM)
      Primer B 5 µl
      Polymerase 1,5 µl
      Template 1 µl (from 51,3 ng/µl stock)
      MQ 27,5 µl

      1. 95℃ - 5 min
      2. 94℃ - 15 sec
      3. 65℃ - 1 min
      4. 72℃ - 4.5 min
      5. 2-4 - 35X
      6. 72℃ - 10 min
      7. 4℃ - indefinite

      Who: Rianne

      Aim Culture BGLI colony number 2

      Colony number 2 (see 30-8-18) was grown overnight in 5 ml LB with ampicillin, at 37℃, 200 rpm.

      Who: Rianne

      Aim Prepare yeast extract samples for SDS-PAGE

      Samples prepared by Jan Marten were taken from the -20℃ storage and thawed. The samples include the 1883 pellet and 1883 supernatant, and 1882 pellet and 1882 supernatant.

      1ml of the supernatant was added to 667 µl of 12,5% TCA. After washing, the pellet was resuspended into 400 µl of 12,5% TCA. The samples were stored at -20℃ overnight.

      Who: Jan Marten

      Aim Measure OD of yesterday’s cultures, and to start new cultures of the 1882 and 1883 strains on Verduyn medium with fructose

      At 14.00 hrs the OD of yesterday’s cultures are measured.

      fructoseraffinose
      1882.33.93.6
      1883.33.54.3

      The positive control had an OD of 4.5, the negative control was 4.4. Since the negative control is not supposed to grow, the experiment is performed again.
      20 ml of Verduyn medium with uracil and 1% fructose is used as a growth medium. Inoculate 2 cultures of 1882 and 1883 each. (1882.1, 1882.2, 1883.1, 1883.2)

    • Wednesday September 5th

      Who:

      Aim

    • Thursday September 6th

      Who: Jan Marten

      Aim Transfer cultures to fresh medium

      100 ul of each culture started on 04-09-2018 is transferred to 20 ml of fresh Verduyn medium with uracil and fructose. Incubate the cultures at 30 degrees celsius.

    • Friday September 7th

      Who: Rianne

      Aim PCR purification of the restricted product and ligation into PhipZ

      Vector (5800 bp) 25 ng: insert (2200 bp) 28,5 ng

      • 2 µl T4 ligation buffer
      • 2 µl T4 ligase
      • 2.4 µl restricted PhipZ (21.2 ng/µl)
      • 6.1 µl restricted PAL2 (9.4 ng/µl)
      • 7.5 µl MQ

      Incubation for 3 hours at 37℃

      Transformation: 5 µl of the ligation product into 50 µl of competent E. coli cells.
      As a control, 1.5 µl of the restricted PhipZ plasmid was transformed in parallel.
      The transformed cells were plated 100 µl, 200 µl, 350 µl and Rest. Of the control 200 µl was plated only. The plates were incubated at 37℃ overnight.

      Who: Jan Marten

      Aim Measure OD and galactose induction

      At 12.00 hrs, the OD of the cultures is measured.
      1882.1: OD 1.35
      1882.2: OD 1,26
      1883.1: OD 1,53
      1883.2: OD 1,29

      Induce with 0.25 ml 40% galactose solution. This leads to a concentration of 0.5% in the medium.
      Dilute: 10 ml culture + 10 ml fresh medium. Incubate the cultures at 30 degrees celsius.

      At 18.00 hrs, 1 sample of each strain is spinned down, washed 2x with Verduyn medium without carbon source, and inoculated in Verduyn medium with uracil and cellobiose (0.5% final concentration).

      OD at T=0:
      1882.1: 0,59
      1882.2: 0,63
      1883.1: 0,54
      1883.2: 0,36

    • Saturday September 8th

      Who: Rianne

      Aim Taq colony PCR on PAL2-PhipZ colonies

      Primer set A was used (see 29-08-18). Taq reaction mixture following manufacturers manual. 50 colonies were screened. The first 5 were transferred to a single reaction tube (A-E), subsequently 5 colonies per reaction tube (F-N), resulting in 14 reactions, 20 µl each.

      Expected size: approximately 4400 bp

      Cycling programme:
      94℃ 5 min

      15 cycles:
      94℃ 45 sec
      64-57℃ 45 sec
      72℃ 5 min

      15 cycles:
      94℃ 45 sec
      57℃ 45 sec
      72℃ 5 min

      72℃ 10 min
      12℃ indefinite

      Who: Jan Marten

      Aim measure OD and inoculate cellobiose cultures

      At 12.00 hrs the 24 hrs galactose induction cultures are washed with Verduyn medium without carbon source, and inoculated into Verduyn medium with 0.5% cellobiose. As described yesterday.
      Some of the leftover cultures is pelleted and plated onto ReCell plates.

      At 13.00 hrs the OD of all cultures is measured

      StrainEvening culture (T=18 hrs)Morning culture (T=0 hrs)
      1882.11.640.85
      1882.21.471.04
      1883.11.650.81
      1883.21.220.81
    • Sunday September 9th

      Who: Rianne

      Aim Gel of the PCR samples of 8-9-18 PAL2

      Ladder: 4µl, samples: 10µl

      Gel 1: Ladder - A - B - C - D - E - F - G
      Gel 2: Ladder - H - I - J - K - L - M - N

      All colonies are negative.

      Who: Rianne

      Aim BGL1 another colony PCR and agarose gel

      Another colony PCR on the BGL1 colonies was performed similar to the PCR on 29-8-18. Samples A-E contain 1 colony (31-35), samples F-N contain 5 each (36-80). Primer set A was used.

      Gel 1: Ladder - A - B - C - D - E - F- G
      Gel 2: Ladder - H - I - J - K - L - M - N

      Who: Jan Marten

      Aim Measure OD of cellobiose grown cultures

      At 13.00 hrs the OD of the cultures is measured.

      StrainEvening (T=40 hrs)Morning (T=24 hrs)
      1882.122.04
      1882.21.842.12
      1883.121.85
      1883.21.621.94
  • Week 37
    • Monday September 10th

      Who: Rianne

      Aim Prepare yeast extract samples for SDS-PAGE

      Jan Marten prepared samples and stored them at -20℃. The samples included 1882 1 and 2, 1883 1 and 2, both 0 hours and 24 hours induction. For each sample, pellet and supernatant were stored. The pellets were transferred into 400 µl 12.5% TCA. 1 ml of the supernatant was added to 667 µl 12.5% TCA. Except for the 24 hours samples, where only approximately 800 µl of supernatant was available but added to the same amount of TCA. The samples were stored at -20℃ overnight.

    • Tuesday September 11th

      Who: Rianne

      Aim SDS-PAGE and Western blot of protein samples 10-09-18

      The samples were taken from the -20℃ storage and processed further according to the protocol. The samples were loaded onto two SDS-PAGE gels. One of the gels was stained, the other was used for Western blotting. The samples were loaded in the following order: Ladder - 1882(1)(Pellet)(0 hours), 1882(2)(P)(0), 1883(1)(P)(0), 1883(2)(P)(0), 1882(1)(P)(24), 1882(2)(P)(24), 1883(1)(P)(24), 1883(2)(P)(24) - empty well - 1µM OsmY positive control (obtained from A. Iyer).

    • Wednesday September 12th

      Who:

      Aim

    • Thursday September 13th

      Who: Rianne

      Aim Colony PCR BGLI

      The same protocol as described on 29-8-18 was used. Reactions A-J contained 1 single colony, reactions K-N five.

    • Friday September 14th

      Who: Rianne

      Aim Colony PCR BGLI agarose gel

      4 µl ladder, 10 µl sample loaded

      Gel 1: Ladder - A - B - C - D - E - F - G
      Gel 2: Ladder - H - I - J - K - L - M - N
    • Saturday September 15th

      Who:

      Aim

    • Sunday September 16th

      Who:

      Aim

  • Week 38
    • Monday September 17th

      Who: Jan Marten

      Aim Start cultures to make a growth curve for strains 1882 and 1883 in a plate reader

      11 cultures are started, including induced and uninduced cultures, positive and negative controls.
      1883.1 2 hrs galactose induction, to be cultured on cellobiose
      1883.2 2 hrs galactose induction, to be cultured on cellobiose
      1883.1 6 hrs galactose induction, to be cultured on cellobiose
      1883.2 6 hrs galactose induction, to be cultured on cellobiose
      1883.1 not induced, to be cultured on cellobiose
      1883.2 not induced, to be cultured on cellobiose
      1883.1 6 hrs galactose induction, to be cultured without carbon source
      1883.2 6 hrs galactose induction, to be cultured without carbon source
      1883.1 positive control, 6 hrs galactose induction, to be cultured with 1.25% glucose
      1883.2 positive control, 6 hrs galactose induction, to be cultured with 1.25% glucose
      negative control (wildtype s. cerevisiae, 6 hrs galactose induction, cultured on cellobiose)

      All cultures are grown on 20 ml Verduyn medium with 0.5% fructose and uracil, and leucine and tryptophan added for the negative control. Culture at 30 degrees Celsius with agitation.

    • Tuesday September 18th

      Who:

      Aim

    • Wednesday September 19th

      Who: Jan Marten

      Aim to induce, wash, and distribute the cultures from 17-09-2018

      At 10.30 hrs the cultures to be induced for 6 hrs are induced by adding 2.0% final concentration of galactose.
      At 14.30 hrs the cultures to be induced for 2 hrs are induced by adding 2.0% final concentration of galactose.
      At 16.30 hrs the cultures are spinned down in falcon tubes at 4000 rpm in a large centrifuge. Samples are washed 2x with Verduyn medium without a carbon source.
      The cultures are mixed with supplements as described on 17-09-2018 and 200 ul of each culture are loaded into a 96 well plate, in duplo, with starting OD’s of 0.2, 0.1, and 0.05. 3 Verduyn cellobiose blanks and 2 Verduyn cellobiose glucose blanks are loaded as well.

      The plate reader is set to measure, for 48 hrs, once every 20 minutes. The plate is agitated for 30 seconds before every measurement, and the interior is kept at 30 degrees Celsius over the duration of the experiment.
      The plate reader is a Tecan Geneos.

    • Thursday September 20th

      Who: Rianne

      Aim Colony PCR BGLI

      The same protocol as described on 29-8-18 was used. Reactions A-O contained 1 single colony, reactions P-Y 2. The reaction volume was 15 µl. The colonies were taken from the plates of 28.08.18. Gels were run by Owen.

      Samples A-R
      Samples S-Y
    • Friday September 21st

      Who: Rianne

      Aim Colony PCR BGLI

      PCR was performed on the plates of 11-9-18. 50 colonies were picked in 15 µl reactions. The agarose gels were run by Owen.

      Samples 1-36
      Samples 37-50
    • Saturday September 22nd

      Who: Jan Marten

      Aim To miniprep and restrict Puc57kan Pal2

      1.5 ml of e.coli containing Puc57kan Pal2 (induced yesterday) is miniprepped. Eluate in 50 ul.
      1) 25 ul is mixed with 10 ul Jena 10x universal buffer, 1 ul BamHI and 1 ul PstI, and 63 ul MQ
      2) 12.5 ul is mixed with 5 ul Jena 10x universal buffer, 1 ul BamHI, and 31.5 ul MQ
      3) 12.5 ul is mixed with 5 ul Jena 10x universal buffer, 1 ul PstI, and 31.5 ul MQ
      Incubate 2 hrs at 37 degrees, and store overnight at 4 degrees.

      E.coli pHIPZ7 is inoculated into LB ampicillin and grown overnight at 37 degrees.

    • Sunday September 23rd

      Who: Jan Marten

      Aim To miniprep e.coli pHIPZ7, restrict, and load and run an agarose gel

      E. coli pHIPZ7 is miniprepped.
      A gel is loaded:
      Slot 1: Ladder (Jena 1kb ladder). Load 3 ul.
      Slot 2: Unrestricted pHIPZ7 plasmid
      Slot 3: Sample 1 from yesterday, 5 ul, mixed with 1 ul 5x loading dye
      Slot 4: Sample 2 from yesterday, 5 ul, mixed with 1 ul 5x loading dye
      Slot 5: Sample 3 from yesterday, 5 ul, mixed with 1 ul 5x loading dye
      Run for 30 minutes at 90 mA.

      It appears that 1) from yesterday has cut only once, the same goes for 2) and 3).
      Add 2 ul of PstI to 1) and 2), and add 1 ul BamHI to 3).
      Incubate 2 hrs at 37 degrees Celsius.

      Mix 5 ul of each sample with 1 ul 5x loading dye, load in the same order as above, and run for 30 minutes at 90 mA.

  • Week 39
    • Monday September 24th

      Who:

      Aim

    • Tuesday September 25th

      Who:

      Aim

    • Wednesday September 26th

      Who:

      Aim

    • Thursday September 27th

      Who:

      Aim

    • Friday September 28th

      Who:

      Aim

    • Saturday September 29th

      Who:

      Aim

    • Sunday September 30th

      Who:

      Aim

  • Week 40
    • Monday Oktober 1st

      Who:

      Aim

    • Tuesday Oktober 2nd

      Who:

      Aim

    • Wednesday Oktober 3rd

      Who: Jan Marten

      Aim Transform E. coli BL21 DE3 Star with Pal2 and His-EGII

      E. coli BL21 DE3 Star is transformed with pSB1C3 T7 promotor + Pal2 colonies 1 and 7, pSB1C3 T7 promotor + His-EGII colonies 1 and 2, and Bba_K1692003 (pSB1C3 T7 promotor + Pal2).
      Thaw cells on ice, make 100 ul aliquots, add 100 ng of DNA to each aliquot, incubate for 30 minutes. Heat shock 1 minute at 42 degrees celsius, and incubate on ice for 2 minutes. Add 900 ul LB medium, and incubate at 37 degrees celsius for 1 hour. Plate on LB chloramphenicol plates, in 10% and 90% fractions. Incubate overnight at 37 degrees celsius.

    • Thursday Oktober 4th

      Who:

      Aim

    • Friday Oktober 5th

      Who:

      Aim

    • Saturday Oktober 6th

      Who:

      Aim

    • Sunday Oktober 7th

      Who:

      Aim

  • Week 41
    • Monday Oktober 8th

      Who:

      Aim

    • Tuesday Oktober 9th

      Who:

      Aim

    • Wednesday Oktober 10th

      Who:

      Aim

    • Thursday Oktober 11th

      Who:

      Aim

    • Friday Oktober 12th

      Who:

      Aim

    • Saturday Oktober 13th

      Who:

      Aim

    • Sunday Oktober 15th

      Who:

      Aim