Team:Bielefeld-Germany/Labjournal

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Labjournal: On this page we summarize the (successful) results and achievements of our teamwork.

Contents

Week 1: 2nd - 8th may

Bisphenol A:

  • cloning of <partinfo>K123000</partinfo> and <partinfo>K123001</partinfo> behind weak (<partinfo>J23103</partinfo>) and medium strong (<partinfo>J23110</partinfo>) constitutive promoter (each part and both parts polycistronic)
  • cloning of fusionprotein between <partinfo>K123000</partinfo> and <partinfo>K123001</partinfo>, also assembly behind weak and medium strong constitutive promoter
  • testing and establishing of HPLC method for [http://en.wikipedia.org/wiki/Bisphenol_A BPA] detection
  • expression of the successfully assembled BPA degrading BioBricks in E. coli [http://openwetware.org/wiki/E._coli_genotypes#TOP10_.28Invitrogen.29 TOP10]

S-layer:

  • successful PCR on the S-layer genes of [http://expasy.org/sprot/hamap/CORGL.html Brevibacterium flavum] and Corynebacterium crenatum
  • successful cloning of the S-layer gene of B. flavum without TAT-sequence

Organizational:

  • meeting with [http://www.bielefeld-marketing.de/de/index.html Bielefeld Marketing] to discuss our participation at the science festival [http://www.geniale-bielefeld.de/ GENIALE] in Bielefeld

Week 2: 9th - 15th may

Figure 1: HPLC results of the first experiment on BPA degradation in E. coli TOP10. Cultivations were carried out in LB medium with 100 mg L-1 BPA at 30 °C. Samples were taken at the beginning of the cultivation and after one day. The HPLC results are shown above (area of the BPA peak). BisdA + BisdB is the polycistronic gene and BisdABisdB is the fusion protein.

Bisphenol A:

  • assembly of <partinfo>K157011</partinfo> behind existing BPA degrading parts (for purification and testing of <partinfo>K123000</partinfo> and <partinfo>K123001</partinfo> in a cell free system)
  • HPLC results: fusionprotein between <partinfo>K123000</partinfo> and <partinfo>K123001</partinfo> can degrade BPA and seems to work better than the polycistronic version (compare fig. 1)

S-layer:

  • expression of the S-layer gene without TAT-sequence of B. flavum in E. coli [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/single-step-_krx_-competent-cells/ KRX] and [http://openwetware.org/wiki/E._coli_genotypes#BL21.28DE3.29 BL21-Gold(DE3)] after sequencing gave correct results
  • successful PCR on the S-layer gene of [http://ijs.sgmjournals.org/cgi/content/abstract/54/3/779 Corynebacterium halotolerans]

Organizational:

  • moving to our own room in the [http://www.cebitec.uni-bielefeld.de/ CeBiTec]


Week 3: 16th - 22nd may

Bisphenol A:

  • successful PCR on the [http://www.brenda-enzymes.org/php/result_flat.php4?ecno=1.18.1.2 NADP oxidoreductase] gene from E. coli TOP10

S-layer:

  • successful cloning of the complete S-layer gene cspB of B. flavum, C. crenatum and C. halotolerans
  • successful cloning of the S-layer genes of B. flavum and C. halotolerans without TAT-sequence, without lipid anchor and without both (only self-assembly domain)

Organizational:


Week 4: 23rd - 29th may

Bisphenol A:

  • establishing a new method for analysis of BPA concentrations (extraction + LC-ESI-QTOF-MS)

S-layer:


Organizational:

  • arrange a BBQ for our workgroup in the CeBiTec to get to know our coworkers
  • substantiating our contribution to the GENIALE


Week 5: 30th may - 5th june

Bisphenol A:

  • beginning of first characterization experiments for BPA degrading BioBricks (<partinfo>K123000</partinfo> and <partinfo>K123001</partinfo>)

S-layer:


Organizational:

  • meeting with Prof. [http://de.wikipedia.org/wiki/Alfred_Pühler Alfred Pühler] to plan our contribution to the [http://www.cebitec.uni-bielefeld.de/content/view/209/88/ CeBiTec symposium] in july


Week 6: 6th - 12th june

Organizational:

  • presentation of the iGEM competition at the [http://www.bio.nrw.de/studentconvention 2nd BIO.NRW (PhD) Student Convention]


Week 7: 13th - 19th june

S-Layer:

  • successful fusion of modified cspB genes of [http://hamap.expasy.org/proteomes/CORGL.html B. flavum] and [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans] with a monomeric RFP ([http://partsregistry.org/Part:BBa_E1010 BBa_E1010]) using Gibson assembly.
  • B. flavum:
    • K525131: fusion of cspB including lipid anchor and TAT-sequence (K525101) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010]
    • K525133: fusion of cspB including lipid anchor without TAT-sequence (K525103) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010]
  • C. halotolerans:
    • K525233: fusion of cspB including lipid anchor without TAT-sequence (K525203) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010]
    • K525224: fusion of cspB including TAT-sequence without lipid anchor (K525204) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010]
  • First expression of K525133 in [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/single-step-_krx_-competent-cells/ E. coli KRX] to test different induction time points und L-rhamnose concentrations. A higher inducer concentration results in a decreasing maximum and final optical density (OD600) but in a higher fluorescence level. K525133. The variations of the induction time point has no significant influence on growth and the progression of fluorescence.
Figure 2: Growth curve of [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/single-step-_krx_-competent-cells/ E. coli KRX] expressing K525133 using different inducer (L-rhamnose) concentrations and varying the time point of induction. Cultivations were carried out in LB medium. Inducing time points and inducer concentration are named with following indices: (E1) induced early (cultivation time = 2,75 h) L-rhamnose end concentration = 0,1 %; (E2) induced early (cultivation time = 2,75 h) L-rhamnose end concentration = 0,2 %; (L1) induced late (cultivation time = 4,25 h) L-rhamnose end concentration = 0,1 %; (L2) induced late (cultivation time = 4,25 h) L-rhamnose end concentration = 0,2 %
Figure 3: Fluorescence developmet of [http://www.promega.com/products/cloning-and-dna-markers/cloning-tools-and-competent-cells/bacterial-strains-and-competent-cells/single-step-_krx_-competent-cells/ E. coli KRX] expressing K525133 during cultivation using different inducer (L-rhamnose) concentrations and varying the time point of induction. Cultivations were carried out in LB medium. Inducing time points and inducer concentration are named with following indices: (E1) induced early (cultivation time = 2,75 h) L-rhamnose end concentration = 0,1 %; (E2) induced early (cultivation time = 2,75 h) L-rhamnose end concentration = 0,2 %; (L1) induced late (cultivation time = 4,25 h) L-rhamnose end concentration = 0,1 %; (L2) induced late (cultivation time = 4,25 h) L-rhamnose end concentration = 0,2 %

Bisphenol A:

  • cloning of NADP oxidoreductase in [http://www.bioinfo.pte.hu/f2/pict_f2/pJETmap.pdf pJET1.2] finally successful -> waiting for sequencing results to remove illegal restriction sites

Week 8: 20th - 26th june

S-layer:

  • successful cloning of K525232 using Gibson assembly.
    • K525232: fusion of modified cspB of [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans] without lipid anchor and TAT-sequence (K525203) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010].


Organizational:

  • finishing our first press release
  • all devices (thermocycler etc.) and materials (competent cells, polymerase, kits) from our sponsors arrived

Week 9: 27th june - 3rd july

S-Layer:

Week 10: 4th july - 10th july

Bisphenol A:

  • experiments on the influence of temperature, promotor intensity and the characteristics of the fusion protein <partinfo>K123000</partinfo> || <partinfo>K123001</partinfo> on BPA degradation

S-Layer:

  • Expression of K525131 (with TAT-sequence and lipid anchor), K5252133 (with lipid anchor), K525232 (nothing); K525233 (with lipid anchor) and K525234 (with TAT-sequence) in E. coli KRX to test the functional efficiency of Corynebacterium TAT-sequence in E.coli and the effect of the autoinduction protocol. After one day of cultivation an increased fluorescence in all periplasm fractions of E. coliexpressing S-layer constructs with TAT-sequence could be recognized. This is an indication that the Corynebacterium TAT-signal sequence is functional in E. coli. Comparing the manual and the autoinduction protocol, no significant changes in fluorescence (after 14 h) are identifiable.
Figure 4: Relative fluorescence of the S-layer/mRFP fusion proteins in the cell suspension less the distinct fluorescence of E. coli KRX. All cultivations were carried out in LB medium at 37 ˚C except K525131Glc which was in autoinduction medium. The expression of the S-layers in LB medium were induced adding 0,1 % L-rhamnose at OD600 = 0,6.
Figure 5: Relative fluorescence of the S-layer/mRFP fusion proteins in the periplasm less the distinct fluorescence of E. coli KRX periplasm. All cultivations were carried out in LB medium at 37 ˚C except K525131Glc which was in autoinduction medium. The expression of the S-layers in LB medium were induced adding 0,1 % L-rhamnose at OD600 = 0,6.

Organizational:

  • presenting our posters from the teams of 2010 and 2011 at the congress [http://www.biotechnologie2020plus.de/BIO2020/Navigation/DE/root,did=121262.html Biotechnologie2020+] in Berlin hosted by the "Bundesministerium für Bildung und Forschung" (Federal Ministry of Education and Research).

Week 11: 11th july - 17th july

Bisphenol A / S-Layer:

  • our BioBrick order (some fluorescences proteins and cleavage sites) from iGEM HQ arrived

S-layer:

  • our synthesized S-Layers SgsE and SbpA finaly arrived


Organizational:

  • presenting the iGEM competition and our team project at the secondary school [http://www.rg-herford.de/ Ravensberger Gynmasium] in Herford ([http://www.flickr.com/photos/igem-bielefeld/sets/72157627214780020/ Photos])

Week 12: 18th july - 24th july

Organizational:

  • presenting our projects from 2010 and 2011 at the [http://www.cebitec.uni-bielefeld.de/content/view/209/88/ CeBiTec Symposium 2011] in Bielefeld
  • meeting and having fun with the iGEM teams from Delft/NL, Edinburgh/UK, Odense/DK. Freiburg/DE and Ljubljana/SL at the Symposium ([http://www.flickr.com/photos/igem-bielefeld/sets/72157627300144576/ Photos])


Bisphenol A / S-Layer:

  • removing illegal restiction sites to get valid BioBricks


NAD+ detection:

  • cloning the NAD+-dependent DNA ligase from E. coli into BioBrick backbones

Week 13: 25th july - 31th july

S-Layer:

  • fusing the synthesized S-Layers to a bunch of fluorescent proteins
  • successful cloning of K525231 using Gibson assembly.
    • K525231: fusion of modified cspB of [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans] including lipid anchor and TAT-sequence (K525201) with [http://partsregistry.org/Part:BBa_E1010 BBa_E1010].
  • testing the basal transcription of E. coli KRX by adding inducer (L-rhamnose) or not. The increasing RFU per OD600 reveals the basal transcription of E. coli KRX. L-rhamnose in the medium leads to up to a ten times higher RFU per OD600.
Figure 6: Growth curves of E. coli KRX expressing fluorescence tagged S-layer constructs of [http://expasy.org/sprot/hamap/CORGL.html B. flavum]. Cultivations were carried out in autoinduction medium at 37 ˚C with and without adding inducer (L-rhamnose). The induced cultivations are marked with index I and the uninduced are marked with index U.
Figure 7: Growth curves of E. coli KRX expressing fluorescence tagged S-layer constructs of [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans]. Cultivations were carried out in autoinduction medium at 37 ˚C with and without adding inducer (L-rhamnose). The induced cultivations are marked with index I and the uninduced are marked with index U.


Figure 8: Development of relative fluorescence per OD600 during cultivation of E. coli KRX expressing fluorescence tagged S-layer constructs of [http://expasy.org/sprot/hamap/CORGL.html B. flavum] and [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans]. Cultivations were carried out in autoinduction medium at 37 ˚C.
Figure 9: Development of relative fluorescence per OD600 during uninduced cultivation of E. coli KRX containing fluorescence tagged S-layer gens constructs of [http://expasy.org/sprot/hamap/CORGL.html B. flavum] and [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans]. Cultivations were carried out in autoinduction medium at 37 ˚C without adding inducer.
Figure 10: Development of relative fluorescence per OD600 in periplasm of E. coli KRX expressing fluorescence tagged S-layer constructs of [http://expasy.org/sprot/hamap/CORGL.html B. flavum] and [http://ijs.sgmjournals.org/content/54/3/779.abstract C. halotolerans] during cultivation. Cultivations were carried out in autoinduction medium at 37 ˚C.


Bisphenol A:

  • testing new BPA extraction protocols for LC-MS including an internal standard (bisphenol F)

Week 14: 1st august - 7th august

Bisphenol A:

  • BPA analysis with extraction and LC-MS finally works and is very accurate
  • Better results for BPA degradation in E. coli -> our fusion protein (<partinfo>K123000</partinfo> to <partinfo>K123001</partinfo>) can completely degrade BPA
  • Measuring characterization results for different BPA degrading BioBricks

NAD+ detection:

  • Successful characterization of two differently labeled (6-FAM or TAMRA with Dabcyl) molecular beacons as a preparation for the NAD+ bioassay including autonomously produced NAD+-dependent DNA ligase from E. coli (results shown below)
Figure 11: Emission spectra of 6-FAM labeled molecular beacon in its closed and open state (target added) at an extinction wavelength 495 nm (n=3).
Figure 12: Emission spectra of 6-FAM labeled molecular beacon in its closed state (split target added) at an extinction wavelength 495 nm (n=3).


Figure 13: Extinction spectra of 6-FAM labeled molecular beacon in its closed and open state (target added) at an emission wavelength 530 nm (n=3).
Figure 14: Extinction spectra of 6-FAM labeled molecular beacon in its closed state (split target added) at an emission wavelength 530 nm (n=3).


Figure 15: Emission spectra of TAMRA labeled molecular beacon in its closed or open state (target added) at an extinction wavelength 544 nm (n=3).
Figure 16: Emission spectra of TAMRA labeled molecular beacon in its closed state (split target added) at an extinction wavelength 544 nm (n=3).


Figure 17: Extinction spectra of TAMRA labeled molecular beacon in its closed or open state (target added) at an emission wavelength 590 nm (n=3).
Figure 18: Extinction spectra of TAMRA labeled molecular beacon in its closed state (split target added) at an emission wavelength 590 nm (n=3).


Figure 19: Signal-to-background ratio (S/B) determination of 6-FAM labeled molecular beacon in its closed or open state at an extinction wavelength 495 nm and emission wavelength 530 nm. Molecular beacons and the target were added one after another (see gaps) each after equilibrium was reached. Calculated S/B: 45,52 (n=3).
Figure 20: Signal-to-background ratio (S/B) determination of 6-FAM labeled molecular beacon in its closed state at an extinction wavelength 495 nm and emission wavelength 530 nm. Molecular beacons and the split target were added one after another (see gaps) each after equilibrium was reached. Calculated S/B: 3,36 (n=3).


Figure 21: Signal-to-background ratio (S/B) determination of TAMRA labeled molecular beacon in its closed or open state at an extinction wavelength 552 nm and emission wavelength 590 nm. Molecular beacons and the target were added one after another (see gaps) each after equilibrium was reached. Calculated S/B: 18,21 (n=3).
Figure 22: Signal-to-background ratio (S/B) determination of TAMRA labeled molecular beacon in its closed state at an extinction wavelength 552 nm and emission wavelength 590 nm. Molecular beacons and the split target were added one after another (see gaps) each after equilibrium was reached. Calculated S/B: 2,31 (n=3).


Figure 23: Thermal profile of 6-FAM labeled molecular beacon alone and with either target or split target added (n=5).
Figure 24: Imaging 6-FAM labeled molecular beacon alone and with either target or split target added.


Week 15: 8th august - 14th august

Bisphenol A:

  • BPA analysis with extraction and HPLC with UV detector leads to very similar results as the analysis with LC-MS (except for low BPA concentrations -> LOD / LOQ of LC-MS is lower than that of "normal" HPLC, compare figure 24)
  • measuring of more samples from cultivations with BPA degrading BioBricks for further characterization
  • we discovered some interesting results in our MS data - soon more
  • testing methods to purify his-tagged BisdA and BisdB for cell free BPA degradation and further characterization of these proteins
  • testing the influence of BPA on the growth of E. coli
  • developing a modell for BPA degradation by E. coli (compare fig. 25)
Figure 24: HPLC results and optical density of experiments on BPA degradation of E. coli KRX. Cultivations were carried out in LB medium with ~ 100 mg L-1 BPA at 30 °C. Samples were taken every three hours over one day. BPA concentration was measured by HPLC with either UV detector or ESI-qTOF-MS. 502: negative control (<partinfo>K123000</partinfo>), 512: polycistronic <partinfo>K123001</partinfo> and <partinfo>K123000</partinfo>, 517: fusionprotein between <partinfo>K123001</partinfo> and <partinfo>K123000</partinfo>, every part behind medium strong constitutive promoter.
Figure 25: Modelling of BPA degradation (filled squares) by and OD600 (open squares) of E. coli KRX carrying genes for BisdA and BisdB (polycistronic bisdAB (black) and fusion protein between BisdA and BisdB (red)) behind the medium strong promoter <partinfo>J23110</partinfo>. Cultivations were carried out at 30 °C in LB + Amp + BPA medium for 24 h with automatic sampling every three hours in 300 mL shaking flasks without baffles with silicon plugs. Three biological replicates were analysed.


S-layer:

  • MALDI-TOF analysis of SDS-PAGEs to characterize the function of the TAT-sequence and the lipid anchor of PS2 (encoded by cspB gene) in E. coli

Week 16: 15th august - 21st august

S-layer:

  • finally found our S-layer proteins in E. coli -> now we can plan purification strategy
  • fusion of FPs to sgsE successful

Bisphenol A:

  • all metabolites of natural BPA degradation pathway found during degradation of BPA in E. coli by LC-MS -> now MS/MS to check structure of these metabolites to be sure
    • some "metabolites" could also be found due to fragmentation during ionization of the product of BPA degradation
  • testing whether E. coli can grow on BPA as the only carbon source (on M9 plates)
    • seems like they can't

Week 17: 22nd august - 28th august

S-layer:

  • cultivation and test purification of sgsE fusion proteins (<partinfo>K525304</partinfo>, <partinfo>K525305</partinfo> and <partinfo>K525306</partinfo>)
    • SDS-PAGEs showed that inclusion bodies are formed in E coli KRX expressing sgsE.

Bisphenol A:

  • purification of his-tagged BisdA and BisdB
  • first characterization results entered into partsregistry
  • cloning of fusion protein FNR:BisdA:BisdB successful

Week 18: 29th august - 4th september

S-layer:

  • developing IEX clean-up for S-layers from Corynebacterium halotolerans

Bisphenol A:

  • successful cloning of polycistronic FNR + BisdA + BisdB

NAD+ detection:

  • Successful overexpression of NAD+-dependent DNA ligase in E. coli KRX and purification with Ni-NTA columns utilizing the protein`s C-terminal His-tag. Trying out utility for the NAD+ bioassay now.

Organizational:

  • participating at the science festival [http://www.geniale-bielefeld.de/ GENIALE] in Bielefeld with a [http://www.geniale-bielefeld.de/programm/detail/date/456/show/Event/ lab tour] and a [http://www.geniale-bielefeld.de/programm/detail/date/295/show/Event/ presentation with public discussion afterwards (science café)]. Our participation is also mentioned in the regional newspaper [http://www.westfalen-blatt.de/nachricht/2011-08-30-wie-ein-hamster-im-laufrad/?cHash=b8421d55eb00ebf8532ebfa677a7e18f Westfalen Blatt] and in the internet on [http://www.direkt-bielefeld.de/Wissenschaft-im-Doppelpack-108856.html Bielefeld Direkt].


Week 19: 5th september - 11th september

S-layer:

  • coating beads with fluorescent S-layer fusion protein SgsE | mCitrine, remove these proteins again and find them in SDS-PAGE
  • characterizing immobilization behaviour of S-layers on silica beads -> seems to work (fig. X)
  • cultivate bigger amounts of and develop new purification strategy for S-layer fusion proteins
  • testing purification of S-layer fusion proteins with his-tag
Fig. X: Immobilization behaviour of fluorescent S-layer fusion protein SgsE :: mCitrine as a function of silica bead concentration. Data fitted with Michaelis-Menten function.

Bisphenol A:

  • characterization of polycistronic FNR + BisdA + BisdB

NAD+ detection:

  • Suitibility of autonomously produced DNA ligase from E. coli for the NAD+ bioassay could be demonstrated after treatment with NMN for deadenylation. Checking out the limit of detection right now.
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