Template:Team:Sheffield/Content:WetLabJournal

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Wet Lab Journal

Week 1

Monday 23rd June

Make up 100ml of LB Broth and 100ml LB Agar.

Make an overnight starter culture of BBa_K258008 to test sterile technique.

Tuesday 24th June

Generate Chemically competent E.Coli.

  1. Make up 8 flasks of 100ml starter culture.
  2. 4 flasks (A-D) were checked each time to take the OD600 readings.
  3. OD600 readings to show when the cells are in exponential growth phase and so ready to be made competent.
    A B C D
    1.25h 0.077 0.078 0.082 0.096
    3.25h 0.567 0.674 0.714 0.809
  4. Aliquot into 24 falcon tubes. The cells will need to be spun down in 2 rounds.
  5. 72 eppendorf tubes will be produced, labelled ch. comp, dh5alpha.
  6. Store at -80°C.

Week 2

Monday 30th June

  1. Make 5mL overnight starter cultures of the following:
    Tube BioBrick Antibiotic
    1 BBa_K258008 Chloramphenicol
    2 BBa_K215107 Tetracycline
    3 BBa_K861061 Chloramphenicol
    4 BBa_K215002 Ampicillin
    5 BBa_K1149021 Chloramphenicol
    6 BBa_K861060 Chloramphenicol
  2. 5μl of an appropriate antibiotic was added to each culture to allow selection for cells containing biobrick plasmids.

Tuesday 1st July

Conduct 6 mini-preps, one for each of the biobrick cultures, to produce 6 Eppendorfs containing purified DNA.

Wednesday 2nd July

Run a DNA gel using the purified DNA collected yesterday to check DNA is pure.

  1. Use an 8 well comb to produce the gel.
  2. The table below shows the placement of each DNA sample within the Gel.
    Well Biobrick Part Function
    1 1kb gene ruler
    2 BBa_K1149021 Promoter, RBS, Lipase
    3 BBa_K258008 ABC transporter
    4 BBa_K861060 pFadR promoter
    5 BBa_K861061 pFadR Promoter + RFP
    6 BBa_K215107 ABC transporter (strong)
    7 BBa_K215002 pLAC +RBS +secretion signal + streptavidin binding tag
  3. The gel was run at 100v for 45 minutes (due to time constrains).

Below is the image taken of the Gel on the Gel dock.

4 LB agar plates were made, 2 ampicillin (100 μl) and 2 chloramphenicol (25 μl).

Nanodrop the DNA gained from the Mini-prep to generate concentrations of extracted DNA for all 6 biobricks.

Results are shown below:

Biobrick Concentration (ng/μl)
BBa_K1149021 115.0
BBa_K258008 075.9
BBa_K861060 100.3
BBa_K861061 130.7
BBa_K215107 043.3
BBa_K215002 125.0

Transform cells to confirm competency

  • For this transformation We used the BioBricks BBa_K258008 and BBa_K215002 to check if the cells were competent.
  • Calculations are shown below:

    BBa_K258008
    75.9ng x X = 10ng x 100μl
    X = 13.2μl

    BBa_K215002
    125.0ng x X = 10ng x 100μl
    X = 8.0μl

Friday 4th July

The linearised TliA and KerUS synthesised DNA is cloned into a pJet1.2 plasmid using blunt end ligation.

This ligation mix was then used to transform 3 eppendorfs of chemically competant cells (made on tuesday 25th):

  • Into eppendorf 1, pipette 5μl of the ligation mix containing TliA DNA.
  • Into eppendorf 2, pipette 5μl of the ligation mix containing KerUs DNA.
  • Into eppendorf 3, pipette 5μl of dH2O
  • Incubated for 45 minutes due to time constraints.
  • Constructs plated on ampicillin LB agar plates to select for the correct colonies.
  • Plates were checked on saturday AM and positive colonies were observed

Week 3

Monday 7th July

Make 200ml LB Agarand 200ml LB Broth.

Make overnight cultures of positive colonies of pJet 1.2 with TliA and KerUS.

Make overnight cultures of E. coli MC1000.

Tuesday 8th July

Miniprep the Tlia and KerUS cultures to produce purified plasmid DNA.

Nanodrop the purified DNA to determine the concentration of DNA.

  • TliA - 5.2ng/μl
    KerUS - 3.4ng/μl

    • Produce glycerol stocks of the Tlia and KerUS cells for storage (retain only if insert confirmed).

    Make chemically competent MC1000.

  • Measure the OD600 of the MC1000 cells using spectrophotometer
  • Flask 1 - 0.803
  • Flask 2 - 0.624
  • Blank - 0.066
  • Decant the flasks of MC1000 into 50ml falcon tubes. We have 4 tubes of full MC1000, the 5th one is 21ml MC1000 and 9ml water, the 6th one is all water -to ensure the centrifuge is balanced (weight checked too).

    Make 10ml overnight cultures of pJet 1.2 containing TliA or KerUS

    Wednesday 9th July

    Repeat yesterdays miniprep as it didn't yield enough DNA.

  • Began with two 10ml starter cultures, one of pJet 1.2 TliA and one of pJet 1.2 KerUS.
  • Decanted by hand into falcon tubes to give four 5ml cultures.

    A Restriction Digest was carried out on the Tlia and KerUS minipreps, as well as the FadR vector that was miniprepped last week.

    TliA and KerUS were cut with xbaI and pstI, whilst FadR was cut with speI and pstI.

    Thursday 10th July

    Run Vector, TliA and KerUS DNA on a gel to ensure it has been cut correctly. Once confirmed the DNA was then extracted from the gel.

    Add 12.5μl 5X loading buffer to the DNA samples (50μl each) - total of 62.5μl in each eppendorf tube.
    Load each sample, using two wells each if necessary.
    Run at 100V for 60 minutes.

    Visualise the gel.

    The bands for TliA and Vector DNA were the correct size.
    The band for KerUS showed that the DNA had been cut incorrectly.

    The two samples of DNA that have been cut correctly are now extracted from the gel.

    The gel extraction was then nanodropped to determine DNA concentration.

    Vector: 14.3ng/μL
    Tlia: 190.9ng/μL

    A ligation reaction was carried out using the following amounts of reactants;

    3.5 μl vector
    0.2 μl lipase
    2 μl buffer
    1 μl ligase
    13.3 μl dH2O

    leave for 10 minutes at room temperature

    Add 5μl ligation reaction mix to 200μl DH5α and transform.

    NOTE: did not work -no positve colonies following antibiotic resistance selection on an LB agar plate

    We also did some work to help us characterise the pFadR promoter.

    Due to a mistake over biobrick numbers, our overnight contained pFadR without RFP, and so we used the day to test our experimental procedures.

    Day cultures were made.

    1 x 5ml of empty DH5α
    3 x 5ml of DH5α containing BBa_K861060
    Day cultures were placed in the incubator at 37°C, 170rpm for 3 hours

    Lipid stocks were made using Triton to solubilise.

    12 samples were made to be assayed;

    1: 5ml DH5α + 0% lipid
    2: 5ml DH5α + 1.0% olive oil
    3: 5ml DH5α + 1.0% oleic acid
    4: 5ml DH5α + BBa_K861060 + 0% lipid
    5: 5ml DH5α + BBa_K861060 + 0.1% olive oil
    6: 5ml DH5α + BBa_K861060 + 1.0% olive oil
    7: 5ml DH5α + BBa_K861060 + 0.1% oleic acid
    8: 5ml DH5α + BBa_K861060 + 1.0% oleic acid
    9: 5ml LB + 1% olive oil
    10: 5ml LB + 1% olive oil + chloramphenicol
    11: 5ml LB + 1% oleic acid
    12: 5ml LB + 1% oleic acid + chloramphenicol

    Samples were incubated at 37°c

    OD600 Readings were taken at hourly time points

    100μl of each sample was pipetted into wells in a Transparent Greiner 96 microtitre plate.
    As well as the 12 samples, 5 Control Wells (blanks) were created, without cells:

    A: LB only
    B: 0.1% Oleic Acid only
    C: 1.0% Oleic Acid only
    D: 0.1% Olive Oil only
    E: 1.0% Olive Oil only

    How to use the Plate Reader

    Turn on computer
    Select ...
    Select open plate icon
    Place microtitre plate into cassette holder
    Select close plate icon
    Open lid of plate reader
    Twist wheels - for OD select white and red wires, for fluorescence select yellow and blue wires
    Select spanner icon on program to choose between OD and fluorescence
    Select Measure icon
    Edit ….
    Select Excel icon
    Open A600 for OD, RFP Charlotte for Fluoresence
    Select update icon
    Scroll down to Table 2 to view results

    Friday 11th July

    FadR assay analysis

    Week 4

    Monday 14th July

    Make overnight cultures.

  • DH5a + pSB3k3
  • DH5a + BBa_K861061
  • DH5a + BBa_K861060 x2
  • DH5a
  • DH5a + pJeT 1.2 TliA
  • DH5a + pJeT 1.2 KerUS

    • Tuesday 15th July

    Overnights of pJet 1.2 KerUS and TliA containing cells didn't grow, and so the time was used to make DNA stocks of BBa_K861060 and BBa_K861061.
    Overnights were Miniprepped and then Nanodropped.
    dH2O was used instead of the elution buffer in the miniprep kit.


    FadR - 80.6ng/μl
    FadR - 75.9ng/μl
    RFP - 50.3ng/μl

    Make Overnights of pJet 1.2 + TliA and KerUS.

    Wednesday 16th July

    Miniprep Tlia and KerUS cells.
    Nanodrop

    TliA - 522.0ng/μl
    Kerus - 264.9ng/μl

    Restriction Digests were made with TliA, KerUS and FadR containing plasmids.
    The following amounts of DNA were cut with restriction enzymes and the final reaction mixture bought up to 50μl.

    2μl Tlia
    4μl KerUS
    12.5μl FadR

    Run a Gel to seperate out the restriction fragments.
    Do a Gel extraction on the bands which are the correct size. The DNA was eluted into dH2O. Nanodrop

    TliA - 5.7ng/μl
    KerUS - 7.0ng/μl
    FadR - 5.7ng/μl

    A Ligation reaction was set up containing either cut TliA or KerUS and FadR vector.
    After an hour, the reaction mix was added to chemically competent DH5α which were transformed and plated on antibiotic containing LB agar plates.
    Plates were incubated overnight at 37°C

    Thursday 17th July

    No positve colonies from the TliA and KerUS with FadR vector transformation

    Day cultures of BBa_861060, BBa_861061 and pSB3k3 were made.
    Once grown (leave for around 5 hours), 10μl of these cells were then plated onto either 25μl 1% Oleic Acid, 25μl 1% Olive Oil or 25μl LB agar plates.
    Cells were left in the incubator overnight.

    Thursday 17th July

    No zone of clearing observed on olive oil containing plates

    Week 5

    Tecan data A second run was done on the Tecan. Three different cells were used;

    BBa_k861060
    BBa_k861061
    pSB3k3

    Each of these cells were added to solutions containing 0.5% Olive oil, 1% Olive oil and 2% Olive oil. Solutions without cells added were also used as a control.
    200μl of each solution was pipetted into a 96 well plate with a clear bottom and white wells.
    All unused wells were filled with LB to prevent evaporation of samples in the central wells. Fluorescence Microscopy

    Set up overnights of the following;

    PSB3K3
    pSB3K3 + 1% Olive Oil
    pSB3K3 + 1% Oleic Acid
    BBa_K861060
    BBa_K861060 + 1% Olive Oil
    BBa_K861060 + 1% Oleic Acid


    Add 10μl overnight cultures to microscope slide cover slips, allow to dry.
    add 10μl 4% paraformaldehyde, dry for 30 minutes.
    Wash 3 x with PBS buffer. Apply 10μl Prolong Gold Antifade Mountant with DAPI (Life Technologies). Fix to microscope slide, leave to dry overnight.
    Use fluorescence Microscope to visualise cells with DAPI and RFP suitable channels. Maintain the same exposure time between images so they are comparable.

    Following fresh ligation and transformation positive colonies were achieved for lipase with fadR responsive promoter in vector. Folllowing restriction digestion with xbaI and pst1. Negative result.

    Overnights of BBa_k861060, BBa_k861061 x2, TliA x2, PSB3K3 pellets frozen for minipreps later

    Week 6

    Monday 28th July

    Miniprep of overnights from Friday (BBa_k861060, BBa_k861061 x2, TliA x2, PSB3K3)

    Plasmid DNA stored in -20

    Produce 6 flasks of LB agar.

    Overnights of the following;

    KerUS
    TliA
    BBa_k823017
    PSB3k3

    Tuesday 29th July

    Make up new stocks of soluble Olive oil (in Triton).

    Make up 8 of agar plates with tributyrin in order to test lipase activity:

    Differing concentrations of Tributyrin was added to either full strength or dilute LB agar. Any Olive oil was added to the empty plate and swirled to mix.

    0.5% tributyrin
    0.5% tributyrin + 2% Olive Oil
    1% tributyrin
    1% tributyrin + 2% Olive Oil



    Make M9 Media
    Too 800ml distilled H2O add;

    44g of Na2.2H2O
    15g of KH2.H2PO4
    2.5g of NaCl
    5g of NH4Cl

    Pour 800ml of distilled H2O into 1L measuring cylinder
    Disolve with magnetic flea and stirrer
    Transfer media into 2 durans and autoclave.

    To 10mL water add either;

    1.2g of MgSO4
    1.1g of CaCl2


    Shake/invert until salts dissolve
    Transfer into conical flasks, cover with cotton wool and foil, autoclave.

    Make Glycerol stocks of pJet 1.2 KerUS, pJet 1.2 TliA, PSB3K3, BBa_K823017.

    Made 6 LB Agar stocks.

    Nanodrop of pJet 1.2 TliA and pJet 1.2 Lipase, BBa_k861060
    Restriction and digest of pJet 1.2 TliA and pJet 1.2 Lipase with BBa_k861060. Transform into DH5a.

    Wednesday 30th July


    One positive colony for TliA in the FadR vector in DH5a -ovenight culture of this

    Thursday 31st July

    Miniprep the potential TliA in the FadR vector.
    Nanodrop 54ng/μl Restriction digest of potential TliA in the FadR vector with NdeI and EcoR1 to confirm - failed
    Make glycerol stocks of overnights potential TliA in the FadR vector

    Friday 1st August

    Restriction digest undertaken.
    TliA and a construct thought to contain the gene for TliA in the FadR vector were restricted using Xba1, Nde1 and both. A gel of the restriction digest was made
    The gel showed that the fadR plasmid did not contain the lipase.

    Week 7


    ABC transporters into cells Overnights of both ABC Transporters (BBa_K258008, BBa_K215107), T1SS signal-strep binding tag (BBa_K215002).
    Miniprep the above plasmids and transform into stocks of chemically competant DH5a.
    Grow overnights of positive colonies, make competant and store at -80 in preperation for the transformation of a lipase containing plasmid.
    Cloning
    Miniprep the pJet 1.2 TliA and promoters BBa_J23101, BBa_J23110 and BBa_J23100.
    Elute into 50&#956 of dH20.
    Nanodrop

    TliA - 103ng/μl
    BBa_J23101 - 278ng/μl
    BBa_J23110 - 408ng/μl
    BBa_J23100 - 380ng/μl


    Carry out a Restriction digest on the TliA and all three promoter plasmids - already had digested kerUS.

    Slight variation to usual protocol: After 2 hours, 3μl CIP was added to the promoter plasmids and then returned to the heat block for another hour.
    After 2 hours, the lipase was removed from the heat block. Make a gel
    Restriction digestion mixes were all run on a DNA agarose gel and the correct sized bands cut.
    DNA was extracted from the gel.
    The TliA and kerUS inserts were ligated into each of the three different promoter strength harbouring vectors.
    The ligation was left in the fridge overnight.
    Ligation mixes were transformed into NEB5a cells
    Positive colonies were seen for TliA and kerUS in the BBa_J23110 containing vectors
    Colony PCR confirmed that TliA and kerUS had successfully been cloned into the BBa_J23110 vector
    These colonies were grown in liquid culture and -80°C stocks were created

    Tecan run with minimal media
    DH5a plus the following plasmids were used for the tecan runs

    FadR-Rfp
    FadR
    J23110


    2 x 50ml falcon tubes of M9 media was made

    35ml of dH2O was added from duran
    10ml of M9 salts was added from duran
    2ml of casamino acids was added from falcon tube
    100µl of MgSO4 was added from 50ml conical flask
    1ml of 20% glucose solution was added to one falcon tube, 1ml of dH2O was added to the other
    5µl of CaCl2 was added from 50ml conical flask
    topped up with dH2O to make 50ml solution

    Lipid was added to the M9 Solution
    Total volume created = 4ml, in 6ml bijou tubes
    Since the Olive oil:Triton X-100 ratio was 1:2, the following concentrations were made:

    Solution 1% 2% 3% 4%
    M9 Media 4.0ml 3.88ml 3.76ml 3.52ml
    Olive oil:Triton 0μl 120μl 240μl 480μl
    The 4.0% stock was made from the falcon tube without glucose added as a supplementary carbon source.
    the 0.0%, 1.0% and 2.0% were made from the falcon tube with glucose added as a supplementary carbon source

    Transformed cells & antibiotics were added to all 4 concentrations of M9/Lipid media.

    96-Well plate was made.
    200μl of each solution containing the 3 different promoters were pipetted into 4 wells to create 4 technical repeats.
    200μl of each solution devoid of cells were pipetted into 3 wells in the region of the plate (B-G, 10-11)

    Week 9

    Monday 18th August

    Make overnights of kerUS and BBa_J23110

    Tuesday 19th August

    Make 4 day cultures;

    5ml KerUS + Nail
    5ml KerUS + Hair
    5ml BBa_J23110 + Nail
    5ml BBa_J23110 + Hair

    These were left in the shaking incubator for the cells to grow and produce and secrete keratinase.

    Autoclave hair, nail and feather samples to sterilise. This was done in glass beakers with foil 'lids'.

    Restreak KerUS and BBa_J23110.

    Make overnights of kerUS and BBa_J23110.

    Wednesday 20th August

    Overnights of BL21.

    Thursday 21st August

    Make 2 5ml day cultures of BL21.
    Allow around 3 hours for them to reach the exponential growth phase.
    Take an OD reading
    If the OD600 is over 0.6, use these innoculations to produce Chemically competant cells.

    Miniprep KerUS BBa_J23110

    Transform the chemically competant BL21 strain using 250ng of the purified KerUS BBa_J23110 DNA.

    Plate the following;

    100μl of control onto an antibiotic free plate.
    100μl of control onto an ampicillin plate.
    100μl of transformant onto an ampicillin plate.
    Remaining 900μl spun down and resuspended in 100μl of LB and plated onto an ampicillin plate.


    Transform TliA BBa_J23110 into stocks of ABC transporter (BBa_K258008) containing competent cells
    Pour plates containing Lb Agar, Lb Agar containing 1% casein, Lb Agar containing 1% gelatin and Agar containing 1% gelatin.

    Friday 22nd August


    Positive colonies of all transformations
    Overnights of positive colonies of cells containing TliA/BBa_J23110/BBa_K258008, KerUs/BBa_J23110 and BBa_J23110

    Saturday 23nd August


    Plate out KerUs containing overnights onto Casein, Gelatin and Gelatin LB agar plates. BBa_J23110 was used as a negative control. Staphylococcus aureus was used as a positive control.
    Incubate for 8 hours, then flood plates in saturated ammonium sulphate.

    Week 10

    Monday 25th August

    Make overnights of KerUS/BBa_J23110, tliA/BBa_J23110, tliA/BBa_J23110/BBa_K258008 and BBa_J23110.
    Autoclave four 1 Litre conical flasks each containing 100ml of LB Broth.

    Tuesday 26th August

    Innoculate each of the autoclaved flasks with 1ml of each of the overnights. Add the correct antibiotic to each.
    Incubate at 30°C to promote protein expression.
    Give 5 or 6 hours for the cells to reach exponential growth phase and produce an adequate amount of protein to assay.

    After 6 hours, samples were taken for analysis by protein gel.

    Into 4 eppendorfs, pipette 1.5 ml of each innoculation.
    These are spun down and the supernatant removed into a second tube. Following the addition of 150μl trichloroacetic acid (TCA) and kept in the 4 degree overnight.

    Into 4 more eppendorfs, pipette 0.5ml of each innoculation.
    These are spun down, the supernatant poured away, the pellet labelled and kept in the -20 degree.

    Remaining culture was centrifuged, sterile filtered and loaded into Vivaspin 20 10,000 MWCO columns (GE Life Science) (tliA without exporter was excluded) add 5ml of culture supernatant. These were spun down at 3,500 rpm for 8 minutes.
    Supernatant that had passed through the column was discarded, and more supernatant was added into the top of the column. This was repeated until around 15ml of supernatant had passed through the column.
    Around 1ml of concentrated supernatant was then removed from the top of the column.

    Overnight liquid cultures of cells containing kerUS (no promoter), tliA/BBa_J23110 and pSB1C3

    Wednesday 27th August

    To prepare the protein sample to be loaded onto a gel

    To the cell pellet add 100μl 2X SDS buffer. Resuspend the cells in this solution.
    Centrifuge the 1.5ml of supernatant/TCA mix for 15 minutes at 13,300rpm, remove supernatant, resuspend pellet in 900μl acetone, repeat centrifugation step, remove supernatant, allow remaining acetone to evaporate then add 50μl of SDS buffer (a ratio of ~1:20)
    To the 1ml concentrated supernatant, add 1ml of SDS buffer (a ratio of 1:1)
    Place all of these samples into a heat block at 95°C for 5 minutes. The cell pellet may need to be vortexed and left for an additional 5 minutes.



    Make a 12% SDS-PAGE gel. Load 5μl cell lysate samples and 15μl supernatant (concentrated or non-concentrated) onto the gel
    Stain the SDS-PAGE gel with InstantBlue (Expedeon) overnight

    Miniprep plasmids from overnight cultures, set up restriction digests with EcoRI and PstI (add CIP to the acceptor vector). Run donor mixes on a DNA gel and isolate DNA from bands of correct size
    Ligate isolated cut kerUS and tliA/J23110 with cut pSB1C3 overnight

    Thursday 28th August


    Transform both ligation mixes into NEB5a and plate on chloramphenicol containing LB agar plates

    Friday 29th August


    Positive colonies on both LB agar plates. Colony PCR to confirm insertion of kerUS or tliA/J23110.
    Overnight liquid cultures of a positive colony from each.

    Saturday 30th August

    Miniprep overnight cultures. Send some for sequencing with sequencing primers. Once confirmed send on to the BioBricks Registry

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