Team:Bielefeld-Germany/Labjournal/week21

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Contents

Week 21 (09/17 - 09/23/12)

Monday September 17th

  • Team Cultivation & Purification:
    • Cell disruption of fermentation of E. coli Rosetta-Gami 2 with BBa_K863012 via high-pressure homogenization and purification via Ni-NTA column.
Activity of ECOL measured via oxidized ABTS at OD420 in relation to a MeOH gradient.
Activity of ECOL measured via oxidized ABTS at OD530 in relation to a MeOH gradient.
  • Team Activity Tests:
    • Another day full of measurements is over! Today we measured some more samples from Team Immobilization: check their labjournal. As well we went on with characterizing our laccases. ECOL was analyzed regarding its behavior in different concentrations of MeOH and acetonitrile. The activity was measured with concentrations of 2-16 µL, respectively. Since ABTS is changing it´s emission spectrum when being in contact with methanol we also detected the OD530. As expected ECOL is happier when only little MeOH is in its environment. We did the same measurements with acetonitrile and got the same result: the fewer acetonitrile, the better for ECOL. Again, we will hand over these results to Team Substrate Analytics.


Activity of ECOL measured via oxidized ABTS at OD420 in relation to a acetonitrile gradient.
Activity of ECOL measured via oxidized ABTS at OD530in relation to a acetonitrile gradient.

Tuesday September 18th

  • Team Cellulose Binding Domain:
    • Primer arrived:
    • Gradient-PCR with the CBDcex(T7)+GFP_His-plasmid and S3N10-CBDcex_RV and S3N10-GFP_FW primer-mix. the right product appeared only at 66,5°C; Lower: wrong product; Higher: no product
      • Following PCR at 66,5°C(50µL) had the wrong product (main product at 2 kbp); could be because of a different template concentration or not exact temperature.
      • Alternativly took the 20 µL-tube with right product and added 0,5 µL DpnI for over-night digestion.
    • Gradient-PCR with CBDcex(T7)+GFP_His-template and a CBDcex_Freiburg- + GFP_Freiburg_compl-primer-mix to amplify the whole fusion-protein and get rid of the His-tag.
    • Gradient-PCR with CBDclos(T7)+GFP_His-template and a CBDclos_Freiburg- + GFP_Freiburg_compl-primer-mix to amplify the whole fusion-protein and get rid of the His-tag.
  • Team Activity Tests:
Fig. 1: Measurements of ECOL in a CuCl gradient of 0,1 to 0,7 mM. The activity was measured via oxidized ABTS at OD420, (n=4).
    • Today we measured the activity of our ECOL laccase in a CuCl gradient to check whether another concentration than the one we usually incubated the laccases with might be more optimal. We chose a gradient from 0,1 mM to 0,7 mM (with an increment of 0,1) and measured the incubated samples as usual in 100 mM sodium acetate buffer, 0,1 mM ABTS (ad 200 µL H2O), respectively. Fig. 1 shows that the chosen concentration do influence ECOL, 0,4 mM seems like the best choice for incubation before the activity measurments. Thus the spectrum of OD420 maxima is not immensely wide so that ECOL seems to be satisfied with any CuCl concentration.
Fig. 2: Activity measurements of TTHL via OD420.
    • Additionally we measured the activity of TTHL at 25°C and in sodium acetate buffer (pH 5). TTHL finally also shows some activity, our favorite fractions of Team Cultivations output are number 1 and 2. Unfortunately TTHL couldn´t be indentified correctly via MALDI yet so that we will have to wait with further characterizing until we get the go through the MALDI results.
  • Team Substrate Anayltics:
    • We analyze Ethin estradiol and estradiol degradation with the Spectrofluorophotometer. The measure showed that the degradation product are detectable but the results weren't clear. We decide to do this measurement again to have better results so a new degradation of the two substrates were set.




Wednesday September 19th

  • Team Cellulose Binding Domain:
    • Stopped over-night-DpnI-digestion of S3N10-clos-GFP_his PCR-product and cleaned up in gel. Ligated the PCR-product with itself via Blunt-end-ligation and transformed it into KRX. Plated on Select-Agar.
    • Gradient-PCRs of the CBDcex(T7)+GFP_His-plasmid and a CBDclos(T7)+GFP_His-plasmid (unsequenced) with the CBDcex_Freiburg- and GFP_Freiburg-compl- and the CBDclos_Freiburg- and GFP_Freiburg_compl primers, respectively. The CBDcex-setup showed no correct product, but the CBDclos-setup had the right bands at temperatures from 57°C to 64°C; Merged the correct fractions and cleaned them up through the gel.
    • Digested the cleaned-up product with SpeI and XbaI and DpnI.
    • Ligated <partinfo>J61101</partinfo> and CBDclos_Freiburg with GFP_Freiburg and transformed it into KRX.
  • Team Activity Test:
    • What a day! The deadline is coming closer and we still had (!) a lot of measurements to do, so today was chosen to be a day full of important measurements. First we measured the activity of the TVEL0 and BPUL in a CuCl gradient. As well we examined what our BPUL laccase does when its supposed to work in different pHs. BPUL was additionally characterized regarding its behavior in different concentrations of MeOH and acetonitrile. This output is of course most interesting for Team Substrate Analytics.
      Comparison of activity of ECOL in sodium acetate buffer and Britton-Robinson buffer, measured at OD420 respectively.
      Since we already compared the behaviour of TVEL0 in the environment of sodium acetate buffer (pH 5) and Britton-Robinson buffer (pH 5), respectively, we also compared BPUL and ECOL in those buffers. ECOL is not impressed by the two different buffer systems and thus not influenced in it´s activity.








Thursday September 20th

  • Team Cellulose Binding Domain:
    • No Colonies on the S3N10-CBDclos(T7)+GFP_His-transformations-dish with the blunt-end ligation; reason: forgotten to phosphorylate the PCR-product.
    • Two colonies on the CBDclos+GFP-dish with the constitutive J23100 + J61101 promoter. But none of them is glowing. And them shouldn't ... used the wrong selection-agar (since J61101 carries pSB1A2-backbone with AMP-resistence.
  • Team Activity Tests:
Temperatur measurements of ECOL at 10°C and 25°C. Measurements were done via optical density 420 nm.
    • Today we started another exciting measurement. Today was all about temperatures. Through our cooperation with the clarification plant we found out that the waster water here in Germany has a minimal temperature of 10°C throughout the year. We used this value together with our previous measurements at 25°C to complete the temperature gradient of our measurements. Eventhough ECOL shows an increased activity at 10°C, it does reach a comparable OD value as the samples measured at 25°C. The increased activity is expressed by achieving the maximal OD420 slower than the laccase measured at 25°C. This seems like good news for Team Modeling.
  • Team Substrate Analytics:
    • Degradation measure from Ethin estradiol and Estradiol with the Spectrofluorophotometer. Degradation was from the 18th September

Friday September 21st

  • Team Cellulose Binding Domain:
    • Transformated <partinfo>J61101</partinfo> with CBDclos+GFP again and plated on the right selection-agar this time!
ECOL activity with different concentration of ABTS.
  • Team Activity Tests:
    • Another part of the characterization of our ECOL and BPUL laccase was to measure their activity when exposed to different concentrations of ABTS. We choose an exponential gradient of 2 µL to 16 µL and measured with the usual laccase concentration of 0,003 mg/mL and 100 mM sodium acetate buffer (ad 200 µL H2O). Unfortunately the measurements that contained 16 µL ABTS could not be measured completely because the OD420 exceeded the maximal value that Tecan was able to measure. The results of ECOL (see. Fig. 1) show as well an exponential increase in the OD420 correlated to the ABTS concentrations, respectively. The negative control was chosen to contain the maximum of 16 µL ABTS in buffer and water that was incubated with CuCl.

Saturday September 22nd

  • Team Fungal Laccases:
  • Digest of <partinfo>BBa_K863204</partinfo> for cloning GFP in the vector and to show that the vector is working.
  • Team Cellulose Binding Domain:
    • Once again two colonies on the agar-dish: can not say if they have a green glow...
      • picked the colonies and them put into AMP-LB-Medium.
    • Also made a flask with 10 mL LB-Medium and cells with the CBDcex(J61101)+GFP_His-plasmid
  • Team Cultivation & Purification:
    • For collaboration with UCL London: Made precultures of E. coli KRX with <partinfo>BBa_K729006</partinfo>, with <partinfo>BBa_K863005</partinfo> and without plasmid.

Sunday September 23rd

  • Team Cellulose Binding Domain:
    • All cultures did not show any sign of GFP-glow under uv-light.
    • Gradient-PCR of <partinfo>BBa_K863104</partinfo> with S3N10_Cex_compl- and S3N10_GFP-primermix to generate a 13 amino acid-linker between the cellulose binding domain and the GFP.
    • Transformated CBDcex(T7)+GFP_His and CBDclos(T7)+GFP_His into BL21, to test if the problem is in the expression-system.
  • Team Cultivation & Purification:
Figure x: Growth kinetics of flask cultivation of E. coli KRX with <partinfo>BBa_K729006</partinfo> and without plasmid as negative control using LB-medium and of E. coli KRX with <partinfo>BBa_K863005</partinfo> using autoinduction medium. Further parameters: final volume of 60 mL, 60 µg/mL chloramphenicol, 37 °C, durance: 12 hours.
    • For collaboration with UCL London: Cultivation of E. coli KRX with <partinfo>BBa_K729006</partinfo> and E. coli KRX without plasmid as negative control
      • Settings: 250 mL flasks without baffles, final volume: 60 mL, LB-medium, 60 µg/mL chloramphenicol, 37 °C, durance: 12 hours.
      • We determined the OD600 for a growth kinetics (see figure X).
    • Cultivation of E. coli KRX with <partinfo>BBa_K863005</partinfo> for comparison.
      • Settings: 250 mL flasks without baffles, final volume: 60 mL, autoinduction medium, 60 µg/mL chloramphenicol, 37 °C, durance: 12 hours.