Team:Bielefeld-Germany/Labjournal
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- | [[Image:Bielefeld-Germany-2011 6FAM-signaltobackgroundratio-490-530nm target.png|450px|thumb|left| '''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 | + | [[Image:Bielefeld-Germany-2011 6FAM-signaltobackgroundratio-490-530nm target.png|450px|thumb|left| '''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).''']] |
- | [[Image:Bielefeld-Germany-2011 6FAM-signaltobackgroundratio-490-530nm split-target.png|450px|thumb|right| '''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 | + | [[Image:Bielefeld-Germany-2011 6FAM-signaltobackgroundratio-490-530nm split-target.png|450px|thumb|right| '''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).''']] |
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- | [[Image:Bielefeld-Germany-2011 TAMRA-signaltobackgroundratio-552-590nm target.png|450px|thumb|left| '''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 | + | [[Image:Bielefeld-Germany-2011 TAMRA-signaltobackgroundratio-552-590nm target.png|450px|thumb|left| '''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).''']] |
- | [[Image:Bielefeld-Germany-2011 TAMRA-signaltobackgroundratio-552-590nm split-target.png|450px|thumb|right| '''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 | + | [[Image:Bielefeld-Germany-2011 TAMRA-signaltobackgroundratio-552-590nm split-target.png|450px|thumb|right| '''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).''']] |
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Revision as of 00:52, 18 September 2011
Labjournal: On this page we summarize the (successful) results and achievements of our teamwork.
Week 1: 2nd - 8th may
- 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]
- 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
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.
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.
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.
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 (<partinfo>K525710</partinfo>) from E. coli (results shown below)
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)
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 KRX.
Week 16: 15th august - 21st august
S-layer:
- finally found our S-layer proteins in E. coli by analyzing the range of sizes in the polyacrylamid with a MALDI-TOF method-> 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 inclusion bodies formation 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
- Searching new purification methods for sgsE fusion proteins.
Bisphenol A:
- successful cloning of polycistronic FNR + BisdA + BisdB
NAD+ detection:
- Successful overexpression of NAD+-dependent DNA ligase (<partinfo>K525710</partinfo>) 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 silica 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
- cultivations of fusion protein between NADP+-ferredoxin oxidoreductase and SgsE / SbpA
- also SbpA | mCitrine fusion protein
Bisphenol A:
NAD+ detection:
- Suitibility of autonomously produced DNA ligase (<partinfo>K525710</partinfo>) from E. coli for the NAD+ bioassay could be demonstrated after treatment with NMN for deadenylation. Checking out the limit of detection right now.
Week 20: 12th september - 18th september
S-layer:
- testing a purification and coating protocol for S-layer fusion protein SbpA | mCitrine.
- characterizing immobilization behaviour of SbpA | mCitrine on silica beads
- optimizing purification and coating protocol for SgsE fusion proteins.
- Successful Ni-NTA purification of <partinfo>K525323</partinfo> (SbpA + mCerulean + his-tag).
Bisphenol A:
- successful cloning of fusion protein FNR + BisdA | BisdB and polycistronic FNR + BisdA + BisdB behind constitutive promoter -> characterizing these last constructs
NAD+ detection:
- NAD+ assay works :)