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Team:Bielefeld-CeBiTec/Notebook/Journal/rMFC/Sep
From 2014.igem.org
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<li>This week we arranged the complete <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Results/rMFC/Construction">H-cell reactor </a> for the first time to start first trials. Therefore we prepare the<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#H-cell%20buffer" target="_blank"> H-cell buffers</a> and the <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Nafion%C2%AE%20membrane" target="_blank">Nafion® membrane</a> which ensures the division of the two compartments.</li> | <li>This week we arranged the complete <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Results/rMFC/Construction">H-cell reactor </a> for the first time to start first trials. Therefore we prepare the<a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#H-cell%20buffer" target="_blank"> H-cell buffers</a> and the <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#Nafion%C2%AE%20membrane" target="_blank">Nafion® membrane</a> which ensures the division of the two compartments.</li> | ||
| - | + | </ul> | |
| + | <ul><li>Additionally we started to cultivate in the H-cell reactor to evaluate the growth of <i>E. coli</i> under the current intesity which is according to the literature needed to reduce neutral red and bromphenol blue.</li> | ||
</ul> | </ul> | ||
</ul> | </ul> | ||
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<li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> of all constructs with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionEnzymes" target="_blank"><i>EcoR</i>I</a> and <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionEnzymes" target="_blank"><i>Pst</i>I</a> </li> | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Protocols#RestrictionDigestion" target="_blank">Restriction digestion</a> of all constructs with <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionEnzymes" target="_blank"><i>EcoR</i>I</a> and <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/KitsAndEnzymes#RestrictionEnzymes" target="_blank"><i>Pst</i>I</a> </li> | ||
<ul> | <ul> | ||
| - | <li>Bands | + | <li>Bands as expected (~3300 bp and ~2070 bp)</li> |
</ul> | </ul> | ||
</ul> | </ul> | ||
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<ul> | <ul> | ||
<li><b><i>ccm</i></b></li> | <li><b><i>ccm</i></b></li> | ||
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</ul> | </ul> | ||
<br> | <br> | ||
| + | <ul> | ||
| + | <li><b>Electrobiochemical reactor system</b></li> | ||
| + | <ul> | ||
| + | <li> This week we performed several cyclic voltammetric measurements to characterize different electrode materials and mediators. Therefore the system was purged with nitrogen to remove any oxygen.</li> | ||
| + | <li> Measurements were performed under the following conditions and the the following experimental setup</li> | ||
| + | <ul> | ||
| + | <li> Cathode space: <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#H-cell%20buffer" target="_blank">cathode buffer</a> or <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#M9medium" target="_blank">M9 medium</a></li> | ||
| + | <li> Anode space: <a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/Media#H-cell%20buffer" target="_blank">anode buffer</a> | ||
| + | <li> Working electrode: platinic plate or graphite electrode</li> | ||
| + | <li> Counter electrode: platinic wire </li> | ||
| + | <li> Reference electrode: Ag/AgCl- electrode</li> | ||
| + | <li> Scan rate: 10 mV/s</li> | ||
| + | <li> Scan Limit: was varied among the different measurements</li> | ||
| + | <li> Cycle number: 3, 10 or 500</li> | ||
| + | <li> Mediators: neutral red or bromphenol blue</li> | ||
| + | <li> Temperature: 37°C</li> | ||
| + | </ul> | ||
| + | |||
</div> | </div> | ||
</div> | </div> | ||
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</ul> | </ul> | ||
</ul> | </ul> | ||
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</ul> | </ul> | ||
<ul> | <ul> | ||
| - | <li> | + | <li>Induction was performed by adding 0,1% Rhamnose</li> |
| + | <li>To document the growth curve and the consumption of substrate daily samples were taken for OD<sub>600</sub> measurement and HPLC analytics | ||
| + | </ul> | ||
| + | </ul> | ||
| + | </ul> | ||
| + | <br> | ||
| + | <ul> | ||
| + | <li><b>anaerobic cultivation for characterization of the antiporter δdcuB</b></li> | ||
| + | <ul> | ||
| + | <li>We tested all combinations of the following media and strains for the characterization of pSB1C3_T7_<i>frd</i></li> | ||
| + | <ul> | ||
| + | <li>Strains</li> | ||
| + | <ul> | ||
| + | <li>KRX wildtype B0015</li> | ||
| + | <li>KRX wildtype with pSB1C3_T7_<i>frd</i> | ||
| + | <li>KRX ΔdcuB::oprF</li> | ||
| + | <li>KRX ΔdcuB::oprF with pSB1C3_T7_<i>frd</i></li> | ||
| + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/StrainsAndConstructs" target="_blank">JW4084-1</a> | ||
| + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/StrainsAndConstructs" target="_blank">JW4084-1</a> with pSB1C3_T7_<i>frd</i></li> | ||
| + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/StrainsAndConstructs" target="_blank">JW0506-1</a> | ||
| + | <li><a href="https://2014.igem.org/Team:Bielefeld-CeBiTec/Notebook/StrainsAndConstructs" target="_blank">JW0506-1</a> with pSB1C3_T7_<i>frd</i></li> | ||
| + | |||
| + | </ul> | ||
| + | </ul> | ||
| + | <ul> | ||
| + | <li>Media</li> | ||
| + | <ul> | ||
| + | <li>M9 with xylose (50 mM)</li> | ||
| + | <li>M9 with xylose (50 mM) and fumarate (50 mM)</li> | ||
| + | <li>M9 with fumarate (50 mM) | ||
| + | </ul> | ||
| + | </ul> | ||
| + | <ul> | ||
| + | <li>Induction was performed by adding 0,1% Rhamnose</li> | ||
<li>To document the growth curve and the consumption of substrate daily samples were taken for OD<sub>600</sub> measurement and HPLC analytics | <li>To document the growth curve and the consumption of substrate daily samples were taken for OD<sub>600</sub> measurement and HPLC analytics | ||
Latest revision as of 19:46, 15 October 2014
 |
September |
 |
- FumA
- This week we assembled FumA with different constitutive promotors
- Restriction digestion with EcoRI and PstI
- Bands as expected (~2070 bp and ~1800 bp) for pSB1C3_T7_FumA
- BioBrick Assembly (Suffix)
- Transformation of all constructs with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~2100 bp) for all constructs
- Plasmid isolation of the positive colonies
- Restriction digestion with EcoRI and PstI
- Bands as expected (~2070 bp and ~1800 bp)
- ccm
- Gibson Assembly with ccm and pSB1C3
- Transformation of pSB1C3_ccm with electrocompotetent cells
- GSU 3274
- This week we assembled GSU 3274 with different promotors
- BioBrick Assembly (Suffix)
- Transformation of all constructs with electrocompotetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55°C
- Bands as expected (~ bp) for pSB1C3_ptac and pSB1A2_T7
- Electrobiochemical reactor system
- This week we arranged the complete H-cell reactor for the first time to start first trials. Therefore we prepare the H-cell buffers and the Nafion® membrane which ensures the division of the two compartments.
- Additionally we started to cultivate in the H-cell reactor to evaluate the growth of E. coli under the current intesity which is according to the literature needed to reduce neutral red and bromphenol blue.
- NAD/NADH Assay
- This week we startet the first test with the Promega NAD/NADH-Glo™ Assay to evaluate later cultivations respectively.
- frd (E.coli)
- This week we transform pSB1C3_T7_frd with different E.coli strains for the characterization of it respectively
- Transformation of pSB1C3_T7_frd with electrocompotetent cells of KRX ΔdcuB::oprF, JW4084-1 as well as JW0506-1 from the KEIO collection
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55 °C
- Bands as expected (~3600 bp)
- Restriction digestion of all constructs with EcoRI and PstI
- Bands as expected (~3300 bp and ~2070 bp)
- Expression of frd (E.coli) for SDS-Page
- Induction was carried out with 0.1 % Rhamnose and 1 mM IPTG
- For the release of the periplasmatic protein fraction a cold osmotic shock was performed
- ccm
- Plasmid isolation of pSB1C3_ccm
- Restriction digestion with NotI
- Bands not as expected (~6611 bp)
- ccm
- This week we tried to get the ccm into the correct backbone
- Gibson Assembly with ccm and pSB1C3
- Transformation with electrocompotetent cells and Transformation with chemocompetent cells
- Plasmid isolation of ccm and Restriction digestion with EcoRI and PstI
- Bands mainly not as expected (~6281 bp and ~2070 bp ) because additional bands are visible.
- Therefore a restriction digestion with EcoRV and HindIII was done
- Bands not as expected because only two bands were visible
- Colony PCR with new primer(ccm_con1, VR-Primer)
- Annealing temperature: 55°C
- Bands as expected (~880 bp)
- Plasmid isolation of pSB1C3_ccm and restriction digestion with EcoRI and PstI
- Bands not as expected (~6281 bp and ~2070 bp)
- PCR amplification of ccm backbone(pSB1C3_pre_ccm, pSB1C3_suf_ccm)
- Annealing temperature: 61°C
- Bands as expected (~6281 bp)
- Electrobiochemical reactor system
- This week we performed several cyclic voltammetric measurements to characterize different electrode materials and mediators. Therefore the system was purged with nitrogen to remove any oxygen.
- Measurements were performed under the following conditions and the the following experimental setup
- Cathode space: cathode buffer or M9 medium
- Anode space: anode buffer
- Working electrode: platinic plate or graphite electrode
- Counter electrode: platinic wire
- Reference electrode: Ag/AgCl- electrode
- Scan rate: 10 mV/s
- Scan Limit: was varied among the different measurements
- Cycle number: 3, 10 or 500
- Mediators: neutral red or bromphenol blue
- Temperature: 37°C
- FumA
- This week we removed the the mutation of FumA by PCR
- PCR amplification of FumA using a gradient(FumA_mut_fwd, FumA_mut_rev)
- Annealing temperature: 50°C to 60°C
- Bands as expected (~4000 bp)
- Gibson Assembly with FumA and pSB1C3 and digestion with DpnI to remove the template
- Transformation with chemocompetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55°C
- Bands as expected (~2100 bp)
- Plasmid isolation of pSB1C3_FumA
- Sequencing of pSB1C3_FumA (Primer: FumA_seq) confirmed the correct construct
- FumBCD
- This week we amplified and transformed FumBCD
- PCR amplification of FumBCD of pJet-Vector (FumBCD_fwd, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (1579 bp)
- PCR products were purified out of the gel
- Gibson Assembly with FumBCD and pSB1C3
- Digestion with DpnI to remove the template
- Transformation with electrocompotetent cells and Transformation with chemocompetent cells
- Colony PCR (VF-Primer, VR-Primer)
- Annealing temperature: 55°C
- Bands not as expected (~1909 bp)
- Deletion of dcuB and integration of oprF into chromosome
- Controll of the strain KRX ΔdcuB::oprF with and without frd (E.coli)
- FumBCD
- This week we amplified and transformed FumBCD
- PCR amplification of FumBCD of pJet-Vector (FumBCD_fwd, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (1579 bp)
- PCR products were purified out of the gel
- PCR amplification of FumBCD backbone(pSB1C3_pre_Fum_BCD, pSB1C3_suf_Fum_BCD)
- Annealing temperature: 55°C
- Bands (not) as expected (~2070 bp)
- Gibson Assembly with FumBCD and pSB1C3
- Transformation with electrocompotetent cells and Transformation with chemocompetent cells
- Colony PCR (FumBCD_fwd, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (~1579 bp)
- Plasmid isolation of pSB1C3_FumBCD
- Restriction digestion with EcoRI and PstI
- Bands not as expected (~1579 bp and ~2070 bp)
- Cloning by restriction and ligation
- PCR amplification of FumBCD of pJet-Vector (FumBCD_fwd, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (1579 bp)
- Restriction digestion of FumBCD with XbaI and SpeI
- Restriction digestion of the backbone with XbaI and SpeI
- Ligation of both fragments and Transformation with electrocompotetent cells as well as Transformation with chemocompetent cells
- Colony PCR (FumBCD_fwd, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (~1579 bp)
- Verification of the FumBCD insertion in pSB1C3
- PCR amplification (VF-Primer, FumBCD_rev)
- Annealing temperature: 55°C
- Bands as expected (~1694 bp)
- Restriction digestion of FumBCD with EcoRI and PstI
- Bands as expected (~1579 bp)
- anaerobic cultivation for characterization of pSB1C3_T7_frd
- We tested all combinations of the following media and strains for the characterization of pSB1C3_T7_frd
- Media
- M9 with xylose (50 mM)
- M9 with xylose (50 mM) and fumarate (50 mM)
- M9 with fumarate (50 mM)
- Induction was performed by adding 0,1% Rhamnose
- To document the growth curve and the consumption of substrate daily samples were taken for OD600 measurement and HPLC analytics
- anaerobic cultivation for characterization of the antiporter δdcuB
- We tested all combinations of the following media and strains for the characterization of pSB1C3_T7_frd
- Strains
- Media
- M9 with xylose (50 mM)
- M9 with xylose (50 mM) and fumarate (50 mM)
- M9 with fumarate (50 mM)
- Induction was performed by adding 0,1% Rhamnose
- To document the growth curve and the consumption of substrate daily samples were taken for OD600 measurement and HPLC analytics
