Lab Journal

• Week

  25

  Getting started

  • Jun

    20

    Our first day in the laboratory!

    
    
    Goal: Incubate the Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 on agar plates separately with antibiotics.
    
    LA- medium (1.5%) were made, and autoclaved for 20min at 121°C.
    Two different agar plates were made – one type contains ampicillin (AMP) while the other type contains chloramphenicol (CM).
    
    Incubation of bacteria
    Two Escherichia coli (E. coli) samples which carry pgRNA and pdCas9 plasmids respectively, were ordered from Addgene. E.coli which carry the pgRNA plasmid were plated on agar plates with AMP, while E.coli which carry the pdCas9 plasmid were plated on two agar plates with CM, and incubated at 37℃.
    
    Results:
    The E.coli with pgRNA and pdCas9 formed colonies on the agar plates with AMP and CM
  • Jun

    21

    Inoculation of E.coli

    Goal: Inoculate a colony from each agar plate which were prepared from the previous day, in LB- medium with antibiotics.
    
    Procedure
    One colony of pgRNA- and pdCas9- bacteria grown overnight on agar plates were picked and inoculated in LB-media (25mL) with AMP (25μL) and CM (25μL), respectively. The cell cultures were incubated at 37℃ in a shaking incubator at 204rpm.
    
  • Jun

    22

    Isolation and verification of pgRNA and pdCas9

    Goal: Isolate and verify that the E.coli carry pgRNA and pdCas9.
    
    Plasmid isolation
    pgRNA and pdCas9 were isolated from the incubated bacteria prepared yesterday (June 21) by following the protocol of ZR Plasmid Miniprep Kit:
    Determine plasmid concentration and purity
    The concentration of plasmids and the purity of each sample were determined by using Nanodrop.
    
    Restriction digest and plasmid verification
    The presence of pgRNA and pdCas9 in the cell cultures were verified after following the restriction digest protocol and separation of the DNA fragments by gel electrophoresis.
• Week

  26

  Week 26

  • Jun

    25

    Transformation of pgRNA and pdCas9 into competent cells

    Goal: Transform pgRNA and pdCas9 into competent cells (E.coli K-12 DH5α).
    
    Procedure:
    pgRNA and pdCas9 which were isolated from day 3 (22. June. 2018) were transformed into E.coli K-12 DH5α cells.
    
  • Jun

    26

    Transfer successful transformed cells to LB-medium and preparation of standard curves for the InterLab study

    Goal:
    Inoculate successful transformed competent cells to LB-medium, and prepare the standard curves for InterLab study.
    
    Procedure:
    Inoculate colony from agar plates to LB-medium:
    A colony from each agar plate were selected and inoculated to LB- medium with antibiotics. Competent cells with pgRNA were transferred to LB- medium with AMP, while competent cells with pdCas9 were inoculated into LB- medium with CM. The cell cultures were incubated at 37℃ with shaker.
    
    Preparation of 1xPBS solution for the InterLab-study.
    Preparation of agar plates with CM, LA- and LB-medium.
    Preparation of standard curves for InterLab study:
    Calibration 1: OD600 reference point – LUDOX protocol
    A conversion factor to transform absorbance data from plate reader into OD600 was obtained in spectrometer by measuring four replicates of LUDOX CL-X and ddH2O. The data were imported into Excel sheet.
    Calibration 2: Particle standard curve – Microsphere protocol
    The solution of silica beads provided in the kit from iGEM HQ, was vortexed before dilution with water (96μL Silica beads in 904μL dd H2O). A serial dilution of microspheres was obtained by adding 100μL dd H2O into 4x11 wells (E2, F2, G2, H2…E12, F12, G12, H12) on a 96 well plate. Microsphere stock solution (200μL) was pipetted into E1 and 100μL of the solution was transferred to E2 and mixed well before transferring 100μL to E3. The procedure repeated until 100μL solution was pipetted into E11, and 100μL was transferred to liquid waste. The dilution series was repeated for row F, G and H. The absorbance of the samples was measured by a plate reader with shaker at 24℃. The data were exported to Excel sheet.
    
    Results:
    Sett inn bilde her.
  • Jun

    27

    Isolation of pgRNA and pdCas9 from compentent cells (DH5alpha) and preparation of stock solution for calibration 3 for InterLab study

    Goal:
    Isolate plasmids from competent cells (DH5α), and prepare the fluorecein stock solution for InterLab study.
    
    Procedure:
    Dilution of cell cultures:
    Each cell cultures (successful transformed competent cells from day 5 – 26.06.2018) (2.5mL) were transferred into fresh LB-medium (22.5mL) with CM (22.5μL). The new cultures were incubated for about 2 hours at 37℃ with shaking .
    
    Measurement of the cell density:
    The cell density of the new cultures was measured at OD600, after calibration with water (blank sample).
    
    Plasmid isolation and determination of concentration:
    The plasmids were isolated from the competent cell after the protocol of ZR plasmid miniprep kit (see lab journal from day 3 - 22. June. 2018).
    The concentration of the plasmids was determined by using Nanodrop.
    
    Restriction digest:
    The plasmids from each culture (5μL) were digested by mixing with 10xbuffer (2μL), distilled water (12.5μL) and restriction enzyme BspHI (0.5μL). The solution was centrifuged down before the samples were incubated over night at 37℃.
    
    Results:
  • Jun

    28

    Plasmid verification and storing the cell cultures

    Goal:
    Verify that the successfully transformed DH5α cells carry pgRNA or pdCas9, and store the cell cultures for future use.
    
    Procedure:
    Plasmid verification:
    The digested plasmid samples from yesterday’s incubation (lab 6 – 27. June.2018) were separated by gel electrophoresis.
    
    Bacteria glycerol stocks:
    The cell cultures made from 27. June were stored in a glycerol stock (500 uL cell culture and 500 uL 50% glycerol) in the freezer at -80℃.
    Results:
    Plasmid verification:
    L, pR1, pR2, pC1 and pC2 are the DNA-fragments from ladder solution, the two samples of pgRNA and pdCas9, respectively. From Figure 1 the two fragments with 1.5kb and 1.0kb were found from the fragments of pgRNA after digestion by BspHI. The fragment with 100bp from the digested pgRNA is not visible on the gel, probably due to masking of the dye colour at the bottom of the gel. Two bands from the digested pdCas9 with 2,7kb and 4kb were also detected. By comparing the results og gel elecrophoresis obtained from today's experiment with the results from day 3 (22. June. 2018), one can clearly see that the bands with the expected length from successful transformed competent cells, are much clearer. Hence, this also indicate the samples from the successful transformed DH5α cells are purer, which is also true by comparing the results from Nanodrop (see day 6 - 27. June. 2018, and day 3 - 22. June. 2018).
  • Jun

    29

    Insertion of anti-luxS via PCR and fluorescence standard curve for InterLab study

    Goal:
    Insert anti-luxS in pgRNA plasmid, and generate fluorescence standard curve for the InterLab study.
    Procedure:
    Insertion of anti-luxS gene and amplification of pgRNA with PCR.
    
    InterLab – Calibration 3
    A fluorescence standard curve was generated from the data obtained after measuring the fluorescence of the serial dilution of fluorescein.
    
    The fluorescence was measured with the following settings:
    
    Temperature: 24℃
    
    Gain (manual): 56
    
    

    	Wave length [nm]	Band width [nm]
    Excitation	494	4
    Emission	525	20

    
    Results:
    InterLab – Calibration 3:
    Figure 1 shows the florescence standard curve in the concentration interval [0, 2.5μM], with a R2 value of 0,9956. The model of the fluorescence standard curve is:
• Week

  27

  Week 27

  • Jul

    2

    Separation, isolation and transformation of linear DNA (pgRNA with anti-luxS)

    Goal:
    

    1. Separate the PCR product from circular DNA
    2. Isolate the linear DNA (pgRNA with anti-luxS from the gel
    3. Transform the linear DNA into competent cells
    4. InterLab study - transformation of plasmids to competent cells

    
    Procedure:
    Separation of linear DNA from circular DNA:
    The leaner DNA obtained from PCR (from day 8 – 29. June. 2018), was separated from the circular DNA (original plasmids) after running the sample (25μL) mixed with loading dye (5μl) on gel electrophoresis (gelGreen) simultaneously with a ladder (1μL gene ruler + 1μL loading dye + 4μL dH2O) for 50min at 90V. The sample and the ladder were prepared by the gel electrophoresis protocol.
    
    Gel digestion and DNA isolation:
    The agarose was digested and the DNA was isolated from the sample following the gel purification protocol.
    Determine the DNA concentration and purity:
    The concentration and the purity of the isolated DNA was determined by using Nanodrop.
    
    Transformation of PCR product to competent cells: The PCR product (5μL) was transformed to competent cells after following the transformation protocol.
    InterLab – transformation of plasmids to competent cells:
    The plasmids listed on the protocol, was transformed into competent cells (DH5α) after the following protocol:
    

    1. Thaw the competent cells on ice (10min), and pre-chill the eppendorf tubes.
    2. Resuspend the DNA in the wells (provided by iGEM HQ) with d H2O (10μL).
    3. Add competent cells (50μL) to the eppendorf tubes.
    4. Add resuspended DNA (1μL) to the Eppendorf tubes.
    5. Incubate on ice for 25min
    6. Heat shock the cells for 45s at 42℃ in water bath
    7. Incubate on ice for 5min.
    8. Add LB-medium (950μL) to the tubes
    9. Incubate for 1h at 37℃ with shacker
    10. Pipette each sample (100μL) to agar plate with CM
    11. Centrifuge the samples for 3min at 6800g, discard supernatant (800μL) and resuspend the pellet with the remaining supernatant
    12. Pipette each sample (100μL) to agar plate with CM
    13. Incubate overnight at 37℃.

    
    Results:
    Separation of linear DNA from circular DNA:
    Figure 1 shows the image of the gel where the linearized DNA was separated from the circular DNA. The linearized DNA is approximately 2kb. The linearized DNA fragment was then cut out from the gel and stored in eppendorf tube.
    
    Note! Due to UV-light exposure, the DNA may mutate. In this case, this may affect the later steps of our project. The worse scenario, mutation of anti-luxS. Hence our CSRPRi system may not recognize luxS in the bacteria. Biofilm production will not be inhibited…
    
    Determine the DNA concentration and purity:
    
    Table 1 shows the results of the linear pgRNA (2) from PCR (probably with anti-luxS gene).
    
    Table 1: The concentration and the relative purity of the pgRNA (2) from PCR.

    Concentration [ng/μL]	260nm/280nm	260nm/230nm
    52.8	1.90	0.27

    
    From the 260/230 ratio, the sample has a relatively a small amount of nucleic acids. Probably, it is contaminated by the agarose from the gel electrophoresis. On the other hand, the 260/280 ratio is ok, indicating that the sample contains a relatively larger amount of RNA than DNA. InterLab – transformation of plasmids to competent cells:
    No visible colonies were detected on agar plates, except the positive and negative control cells.
  • Jul

    3

    Inoculation of successful transformed competent cells and InterLab study

    Goal:
    

    1. Inoculate colonies of successful transformed competent cells
    2. InterLab study - transformation of plasmids to competent cells

    
    Procedure:
    InterLab – transformation of plasmids to competent cells:
    No visible cell colonies were formed on the agar plates that were incubated on day 9 - 02. Junly. 2018. Only the positive and negative control cells formed colonies.
    
    Therefore, the remaining plasmids (6μL) were transformed to the competent cells and plated on agar based on the same protocol from day 2. Jul. 2018. During the incubation at 37℃ with shaker, the incubation time was extended to 2h. The cell cultures were centrifuged, and 700μL supernatant was discarded, and the pellets were resuspended with the remaining supernatant. The cell cultures were then plated on agar plated with CM, and incubated overnight at 37℃.
    
    Inoculation of successful transformed competent cells:
    Colonies of successful transformed competent cells with pgRNA (probably containing anti-luxS) were inoculated from the agar plates (from day 9 – 02. July. 2018) to LB-medium with AMP. The cell cultures were incubated with shaker overnight at 37℃.
    
    Results:
    
  • Jul

    4

    Verification of successful inserted anti-luxS in pgRNA

    Goal:
    

    1. InterLab - transformation of plasmids into competent cells
    2. Verification of succsesful insertion of anti-luxS in pgRNA(2)

    
    Procedure:
    InterLab – Transformation of plasmids to competent cells
    There has been a mistake of numbering the plates with plasmids provided by iGEM HQ. Therefore, we did not get any cell colonies from the previous two transformations…
    
    The plasmids (1.5μL) from the right wells were transformed to competent cells by following the transformation protocol from day – 02. July. 2018, after resuspension of the plasmids in the wells.
    
    Cell density:
    The cell cultures with pgRNA(2) (probably with anti-luxS), inoculated from day 10 – 04. July. 2018, were diluted 10 times by following the same dilution procedure from day 6 – 27. June. 2018. The cells were incubated with shaker for 1h before measuring the OD600.
    
    Plasmid isolation:
    The plasmids from the two cell cultures were isolated after the same mini-prep protocol from day 3 – 22. June. 2018. The concentration and the purity of the isolated plasmids were measured by Nanodrop.
    
    Restriction digest and gel elecrophoresis:
    Insertion of anti-luxS gene was verified after the protocol of restriction digest and gel electrophoresis (see the protocols from day 3 – 22. June. 2018). The restriction enzyme PstI was chosen, and the expected length of the plasmid fragments are 490bp and 2094bp.
    
    Note! PstI has a cut site at the anti-luxS gene in the plasmid.
    
    Bacteria glycerol stock:
    Two samples of the diluted cell cultures (made at this morning), were stored in 50% glycerol solution at -80℃ (the same green box with the other successful transformed cells with pgRNA (without anti-luxS) or cells with pdCas9 plasmids).
    
    Results:
    InterLab - Transformation:
    Colonies were formed on agar plates with CM.
    
    Cell density:
    
    Table 1: Absorbance of the cell cultures with pgRNA(2) after 1h incubation at 37℃ with shaker.

    Culture	OD600
    pR2 (1)	0.954
    pR2 (2)	0.998

    Plasmid isolation: Table 2: Concentration and the relative purity of isolated pgRNA(2) from the two cell cultures.

    	Concentration (ng/μL)	260nm/280nm	260nm/230nm
    pR2(1)	37.2	2.06	4.29
    pR2(2)	123.3	1.77	1.01

  • Jul

    5

    Double transformation and InterLab study - Inoculation

    Goal:
    

    1. Transform both pdCas9 and pgRNA with anti-luxS into competent cells
    2. InterLab study - inoculate colonies in LB-medium

    
    Procedure:
    Double transformation of pdCas9 and pgRNA with anti-luxS:
    Both pdCas9(2) and pgRNA(2) with anti-luxS (isolated from day 11 – 05. July. 2018) were simultaneously transformed into competent cells (DH5α). The amount of added pdCas9(2) (5μL) and pgRNA(2) with anti-luxS was 5 uL per/plasmid, and it was added to the same tube containing competent cells. The cells were plated on agar with both AMP and CM. A couple of steps were added at the end, and the purpose was to increase the cell concentration plated on agar, and probably increase the possibility of colony formation. The cell culture was therefore centrifuged for 3 minutes at 6800g, and the supernatant discarded. The pellet was then resuspended and cells were plated.
    
    InterLab – Inoculation of colonies
    A colony from each agar plate was inoculated in LB-medium (5mL) with CM (5μL). The cell cultures were incubated overnight at 37℃ with shaker.
    
    Results:
    
  • Jul

    6

    Inoculation of successful double transformed cells, interLab study - Cell measurement

    Goal:
    

    1. Inoculate successful double transformed cells (probably carrying pdCas9 and pgRNA with anti-luxS)
    2. InterLab study - measure absorbance and the fluorescence of each cell cultures

    
    Procedure:
    Inoculation of successful double transformed cells
    

    1. A colony from each agar plates with AMP and CM (made from day 13 – 05. July 2018) was picked and inoculated in LB medium (20mL) with AMP (25μL) and CM (25μL).
    2. The cell cultures were incubated at 37℃ with shaker.

    
    InterLab – Cell measurement
    We were not able to measure the cell cultures today, since the TECAN device was under reparation.
    Each cell cultures were stored with 50% glycerol (see day 7 – 28. June. 2018) at -80℃.
    
    Results:
    
  • Jul

    7

    Verification of pdCas9 and pgRNA with anti-luxS after double tranformation

    Goal:

    Verify that both pdCas9 and pgRNA with anti-luxS are tranformed into DH5α cells
    
    

    Procedure:

    Dilution of cell culture:
    Each cell cultures, inoculated and incubated from day 13 – 07. July. 2018, were diluted (1mL) with LB medium with antibiotics until the OD600 reached 1.9.
    
    Plasmid verification:
    Plasmid isolation:
    The plasmids were isolated from each cell cultures after following the mini-prep plasmid protocol from day 3 – 22. June. 2018. The concentration and the purity of the samples were determined by Nanodrop.
    
    Restriction digest and gel electrophoresis:
    The plasmids in each sample were digested with restriction enzymes BamHI-HF and PstI, after the following protocol:
    
    The other protocol:

    • 7.1μL Plasmids
    • 0.5μL PstI
    • 0.5μL BamHI-HF
    • 2μL NEBuffer 1.1
    • 10.4μL ddH2O

    The samples were incubated for 1.5h at 37℃.
    Note! NEBbuffer 1.1 was chosen instead of Cut smart since the activity of PstI in Cut smart was 50%.
    The activity of the enzymes in NEBbuffer 1.1:
    BamHI-HF: 100%
    PstI:75%
    After the plasmids have been degraded by restriction enzymes, the fragments were separated by gel electrophoresis after the protocol from day 3 – 22. June. 2018.
    
    

    Results:

    Plasmid verification:
    Plasmid isolation:
    

    Sample	Concentration [ng/μL]	260nm/280nm	260nm/230nm
    1	219.9	2.01	1.82
    2	35.3	2.03	3.86

    Restriction digest and gel electrophoresis:
    The bands on the gel, corresponded with the expected fragments (6705bp, 2094bp, 465bp, 25bp) from digestion of the plasmids by PstI and BamHI-HF. Therefore, we concluded that both of pdCas9 and pgRNA with anti-luxS have successfully been transformed into DH5α cells.
• Week

  28

  Week 28

  • Jul

    9

    Monday

    Lorem ipsum dolor sit amet.
  • Jul

    10

    Tuesday

    Lorem ipsum dolor sit amet.
  • Jul

    11

    Wednesday

    Lorem ipsum dolor sit amet.
  • Jul

    12

    InterLab Study: Revive bacteria glycerol stock

    Goal : InterLab Study: Revive bacteria glycerol stock

    Procedure: The frozen bacteria glycerol stock made from day 13- 06. July. 2018, were thawed on ice. Each culture were inoculated in LB medium with CM (5mL), and incubated over night at 37C.
  • Jul

    13

    InterLab Study: CFU/mL/OD calculations

    Goal:
    Count colony forming units on plates spread the day before.
    
    Procedure:
    Counted CFU on all 36 plates incubated 13. July.
    
    Results:
    The colonies on agar plates, from yesterday’s incubation, were counted and registered:

    CFU	Dilution 3	Dilution 4	Dilution 5
    1.1	195	6	1
    1.2	185	2	0
    1.3	203	15	3
    2.1	222	19	2
    2.2	38	22	1
    2.4?	52	15	1
    3.1	113	56	3
    3.2	112	12	2
    3.3	127	25	2
    4.1	79	4	0
    4.2	75	10	1
    4.3	107	3	1

    where 1 and 2 are positive controls, 3 and 4 are negative controls. (= 2.1 means the second dilution of the second positive control culture)
  • Jul

    14

    InterLab – CFU/mL/OD calculation

    Goal:
    Counting colonies on each agar plate, and calculate CFU/mL in starting samples with an OD600 = 0,1.
    
    Procedure:
    The colonies on the agar plates, prepared from yesterday’s incubation, were counted and registered.
    
    Results:
    
    Table 1: The average values of counted colonies from two cultures of positive and negative controls with different final dilution factor (dilution 1 = 8x104, dilution 2 = 8x105, dilution 3 = 8x106).

    	Positive control	Negative control
    Culture 1, dilution 1	194,3	117,3
    Culture 1, dilution 2	7,7	31,0
    Culture 1, dilution 3	1,3	2,3
    Culture 2, dilution 1	104,0	87,0
    Culture 2, dilution 2	18,7	5,7
    Culture 2, dilution 3	1,3	0,7

• Week

  29

  Week 29

  • Jul

    16

    Transformation of the RFP-biobrick (test)

    Goal:
    1. Transform the RFP-biobrick (BBa_J04450) into competent DH5α-cells
    
    Procedure :
    1. Thaw competent cells on ice for approximately 10 minutes
    2. Take 10 µL distilled water and resuspend the biobrick in the plate (position 23O, plate 7)
    3. Add 2µL of the biobrick-solution to the tube containing competent cells. Pipette up and down while stirring carefully with the tip.
    4. Incubate the cells on ice for 20min.
    5. Heat shock the cells for 45s at 42℃.
    6. Incubate the cells on ice for 3 min.
    7. Add LB- medium (900μL).
    8. Incubate the cells for 1 h at 37℃ with shaker.
    9. Plate the cells (100μL) on agar with CM (1 plate)
    10. Centrifuge the cell culture for 3 min at 6800g.
    11. Discard the supernatant (200μL)
    12. Resuspend the pellet with the remining supernatant in the tube
    13. Plate the cells (100μL) on agar with CM (1 plate).
    14. Add LB-medium to the DH5α-cells that doesn´t contain CM resistance, and plate the negative control on agar (1 plate)
    15. Repeat 10, 11 and 12 for the negative control and plate the cells on agar (1 plate)
    
    Steps 10–12 are optional. The purpose of the last four steps are to increase the cell concentration plated on agar, and probably increase the possibility of colony formation. The total amount of plates are 4
    
    Results:
    There was only 1 colony on each plate
  • Jul

    17

    Colony picking biobrick (test) and transformation

    Goal :
    1. Get colonies of the transformed DH5α (biobrick) 2. Get colonies on the negative control plate
    
    Procedure:
    1. Due to the lack of colonies on the negative control plates, crossing lines was made with the bacteria on new plates.
    2. New LA-plates without antibiotics were made.
    3. Colonypicking the two colonies from the plates with the transformed bacteria in to liquid medium.
    4. The transformation of bacteria with the biobrick plasmid was redone on 4 plates because of the lack of growth on the plates (see 16.07.18).
    
    Results:
    There were more colonies on the 4 new plates, and they were light red as well (About 20 colonies). The new negative control plates had colonies as well.
    
    
  • Jul

    18

    RFP biobrick fluorescens measurement (test)

    Goal:
    1. To get a descriptive curve for the rise in fluorescens (transformed DH5α)
    2. Find out how often the measurements need to be done.
    
    Procedure:
    The second batch of plates from transformation and the negative control:
    1. Colonypicking and exchange to liquid medium
    
    Measurements of the first batch (Tecan):
    1. Measured the OD of the blank (LB and CM), and measured the OD of the two cultures.
    2. For the next measurements we diluted the cultures by 1:100 in separate tubes.
    3. Incubation of the tubes
    4. The first measurement was done in the Tecan, and repeated for every 30 minutes and then 1 hour (because of minor changes in values)
    5. The measurements was set overnight as well using the following script: FluorescenceLong. The data was set to 588 nm absorbance, 584 nm excitation, 607 nm emission, 37°C, 40 gain, 150 kinetic cycles, 300s shaking (orbital 3 mm amplitude)
    
    Results:
    The second batch from transformation has turned red. From the measurements of the test batch we have an idea of the increase in fluorescence intensity and the change in absorbance over time. This can be used to determine the timing of the second batch with the negative control as well.
    
  • Jul

    19

    Biobrick: Preparations, Fluoresence microscopy

    Goal:
    Prepare for measurements tomorrow.
    Learn about fluorescence microscopy
    
    Procedure:
    Preparations:
    Made agar-plates from one litre LA+CM solution in sterile cabinets. Diluted cultures of the biobrick J04450 and negative control and incubated them at 37*C overnight.
    
    Demonstration and training in fluorescence microscopy:
    Astrid Bjørkøy showed us how to use the fluorescence microscope, and we tried it out by taking photos of cultures of the J04450 biobrick. She also told us how to count cells by adjusting a photo's threshold and calculate based on image size.
    
    Results:
    The biobrick J004450 was very bright. We used excitation 561 nm and emission ca 625-680 as the biobrick was too bright at emission 607. Consider using another laser further away from excitation point (584nm) for the real photos of the biobrick, and the improved biobrick.
    
  • Jul

    20

    Biobrick: Red Fluorescent Protein measurement (FAILED)

    Goal:
    Measure the expression of the J04450 biobrick in transformed dH5α cells. This is done by measuring fluorescence.
    
    Procedure:
    1. Incubated dH5α, J04450 transformed cells were dilluted 1:100 with LB
    2. 200 µL, 5 replicates of LB, LB with Chloramphenicol and 5 dH5α dillutions made from different batches were applied to a 96 well plate
    3. Tecan plate reader was used to measure absorbance at 588 nm and fluorescence at excitation 584 nm and emission 607 nm with the following parameters:
    4. Temperature: 37,0°C, varying from 36,5 °C to 37,5 °C
    5. Kinetic cycles: 750
    6. Gain: 40
    7. Z position: 18055 µM
    8. Shaking: 300 s
    9. Orbital shaking amplitude: 3 mm
    
    Results:
    The wells dried out, presumably due to us choosing not to use a lid on the plate, and the measurements were therefore aborted by the machine.
    
• Week

  30

  Week 30

  • Jul

    23

    Make super competent cells of the TG1

    Goal:
    Make supercompetent cells of the e.coli - TG1 strain
    
    Procedure:
    
    DAY 1:
    
    - Made Psi media, transformation buffer 1 and transformation buffer 2.
    - Made an E.coli TG1 culture in a small flask with 10mL Psi- medium. Inoculated culture at the end of the day and left the flask for incubating while shaking and at 37degrees overnight.
    
    Psi media:
    - Tryptone 20 g
    - Yeast extract: 5g
    - MgCl₂ : 5g
    Adjust to pH=7.6 with KOH. Add water to 1L and autoclave.
    
    TFB1:
    Add the following to a 250mL flask:
    - Potassium acetat : 0.588g
    - Rubidium chloride: 2.42g
    - Manganese chloride: 2.00g
    - Glycerol: 30mL
    Fill up with MiliQ to a volume of 180mL Adjust pH to 5.8 with a pH-meter by adding diluted acetic acid (0.2M) Fill up with MiliQ to a total volume of 200mL
    
    TFB2:
    Add the following to a 250mL flask:
    - MOPS: 0.21g
    - Rubidium chloride: 0.121g
    - Calcium chloride: 1.1g
    - Glycerol: 15mL
    Fill up with MiliQ to a total volume of 90mL Adjust pH to 6.5 with a pH-meter by adding diluted NaOH (0.2M) Fill up with MiliQ to a total volume of 100mL
    
    
    
    Results:
    
  • Jul

    24

    Make supercompetent cells of the TG1, day 2

    DAY 2:
    1. Transferred 1mL culture to a new shaking flask with 100mL Psi-medium. Grew in shaking incubator until OD(600) reached 0.4
    2. Placed the culture on ice for 15 minutes, along with TFB1 and TFB2
    3. Centrifuged the culture for 5 minutes at 4000 rpm at 4 degree Celcius. Poured of the supernatant.
    4. Resuspended the pellet carefully in 40mL TFB1. Let sit on ice for 5 min.
    5. Centrifuged for 5 minutes at 4000rpm at 4degree celcius. Poured of supernatant and resuspended pellet carefully in 3 mL TFB2.
    6. Marked ca 20 2 mL cryotubes at aliquoted 100 mL of resuspended cells in each tube. Left all on ice until finished aliquoting.
    7. Flash freeze for 5-10 secs in liquid nitrogen. Then stored at -80 degree celcius.
    
  • Jul

    25

    Miniprep and transformation of TG1-cells

    Goal:
    1. Transformation of TG1-cells with DNA that includes pdCas9 and pgRNA with antiluxS-gene.
    2. Make LA-plates with both CM and AMP antibiotics
    
    Procedure:
    pgRNA with antiluxS and pdCas9 has already been transformed into E.coli DH5α. The plasmid was isolated and extracted during the following miniprep protocol:
    ZR plasmid miniprep kit:
    1.1mL of each cell culture (which carry both pgRNA and pdCas9) were transferred to eppendorf tube and centrifugated for 20s at 16000g.
    2. The supernatant was discarded, while the pellet was resuspended in buffer
    3. Lysing buffer was added to the sample and carefully mixed in 2min.
    4. Neutralizing buffer was added to the sample, and mixed until the colour of the solution became yellow.
    5. The solution was centrifugated for 2min at 16000g
    6. The supernatant was collected and transferred to column in a collection tube, and centrifugated for 30s at 16000g.
    7. The supernatant in the collection tube was discarded.
    8. Endo-wash buffer was added to the column and centrifugated for 1min at 16000g.
    9. Plasmid- wash buffer was added to the column and centrifugated for 1 min at 16000g.
    10. The solution in the collection tube was discarded, while the column with plasmids was transferred to a new collection tube.
    11. The plasmids in the column were eluted by adding 30μL distilled water, and centrifugated for 30s in 16000g.
    
    Transformation into TG1-cells:
    1. Thaw competent cells on ice for 10min.
    2. Use a pipette and transfer 2μL of mini-prepped plasmids into DH5α samples. Pipette up and down while stirring the pipette tip gently for 5-10s.
    3. Incubate the cells on ice for 20min
    4. Heat shock the cells for 45s at 42℃. Immediately put the samples on ice for 2min.
    5. Add 900μL LB medium to the cells. Incubate at 37℃, 200RPM for 1h.
    6. Plate out 100μL of the transformation medium into agar plates with selection agent (CM and AMP).
    7. Incubate the cells at 37℃.
    
    Results: No bacterial growth has been observed. We has been decided to redo miniprep and double transformation of TG1-cells, see Week 31, 30 July.
  • Jul

    26

    Preparations for biofilm measurements

    Goal:
    1. Make media for the biofilm measurements (LB and M63B1)
    2. Prepare TG1, TG2 buffers and Psi medium for supercompetent cells.
    
    Procedure:
    1. Made three versions of the two media with pH-values at 4.5, 7.2 and 9.5. The media was then autoclaved and sugar will be added before use of the media.
    2. Made TG1, TG2 buffers and Psi medium, see protocol.
    
    
  • Jul

    27

    Make supercompetent cells of TG1, second attempt

    Goal:
    1. Make supercompetent cells of TG1 by following an improved protocol.
    
• Week

  31

  Week 31

  • Jul

    30

    Miniprep and transformation of TG1-cells

    Goal:
    1. Transformation of TG1-cells with DNA that includes pdCas9 and pgRNA with antiluxS-gene.
    
    Procedure:
    pgRNA with antiluxS and pdCas9 has already been transformed into E.coli DH5α. The plasmid was isolated and extracted during the following miniprep protocol:
    ZR plasmid miniprep kit:
    1.1mL of each cell culture (which carry both pgRNA and pdCas9) were transferred to eppendorf tube and centrifugated for 20s at 16000g.
    2. The supernatant was discarded, while the pellet was resuspended in buffer
    3. Lysing buffer was added to the sample and carefully mixed in 2min.
    4. Neutralizing buffer was added to the sample, and mixed until the colour of the solution became yellow.
    5. The solution was centrifugated for 2min at 16000g
    6. The supernatant was collected and transferred to column in a collection tube, and centrifugated for 30s at 16000g.
    7. The supernatant in the collection tube was discarded.
    8. Endo-wash buffer was added to the column and centrifugated for 1min at 16000g.
    9. Plasmid- wash buffer was added to the column and centrifugated for 1 min at 16000g.
    10. The solution in the collection tube was discarded, while the column with plasmids was transferred to a new collection tube.
    11. The plasmids in the column were eluted by adding 30μL distilled water, and centrifugated for 30s in 16000g.
    
    Transformation into TG1-cells:
    1. Thaw competent cells on ice for 10min.
    2. Use a pipette and transfer 5μL of mini-prepped plasmids into DH5α samples. Pipette up and down while stirring the pipette tip gently for 5-10s.
    3. Incubate the cells on ice for 20min
    4. Heat shock the cells for 45s at 42℃. Immediately put the samples on ice for 2min.
    5. Add 900μL LB medium to the cells. Incubate at 37℃, 200RPM for 1h.
    6. Plate out 100μL of the transformation medium into agar plates with selection agent (CM and AMP).
    7. Incubate the cells at 37℃.
    
    Results: Noticeable bacterial growth was observed on all plates, with no apparent contamination.
  • Jul

    31

    title

    
    
  • Aug

    1

    title

    Goal:
    Procedure:
    
    Results:
  • Aug

    2

    title

    Goal:
    
  • Aug

    3

    title

    Goal:
    
• Week

  32

  Note title

  • Aug

    6

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    7

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    8

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    9

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    10

    Note title

    Lorem ipsum dolor sit amet.
• Week

  33

  Note title

  • Aug

    13

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    14

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    15

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    16

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    17

    Note title

    Lorem ipsum dolor sit amet.
• Week

  34

  Note title

  • Aug

    20

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    21

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    22

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    23

    Note title

    Lorem ipsum dolor sit amet.
  • Aug

    24

    Note title

    Lorem ipsum dolor sit amet.