Team:Bielefeld-Germany/Labjournal/June
From 2013.igem.org
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*Planning of our [[Team:Bielefeld-Germany/HumanPractice|Human Practice]] projects started and the first participations are fixed. | *Planning of our [[Team:Bielefeld-Germany/HumanPractice|Human Practice]] projects started and the first participations are fixed. | ||
*MFC: Designing of 3D models of MFC´s and visited a hacker space in order to print it in a 3D printer. | *MFC: Designing of 3D models of MFC´s and visited a hacker space in order to print it in a 3D printer. | ||
- | + | <br><br> | |
===Week 5=== | ===Week 5=== | ||
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====MFC==== | ====MFC==== | ||
- | + | *Constructed a resistor box with different potentiometers and LEDs in order to be able to test our fuel cells | |
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====Porines==== | ====Porines==== | ||
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**Forward GSU Promoter-1496-1505 (52 bp):<br> GAATTCGCGGCCGCTTCTAGAGGATAGGATCCGTCACCGAGTGCGAACTGCC | **Forward GSU Promoter-1496-1505 (52 bp):<br> GAATTCGCGGCCGCTTCTAGAGGATAGGATCCGTCACCGAGTGCGAACTGCC | ||
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===Week 6=== | ===Week 6=== | ||
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====MFC==== | ====MFC==== | ||
- | + | *Connected film canister cells in series and parallel to increase voltage/current | |
+ | *Tested different redox mediators in our fuel cell | ||
====Mediators==== | ====Mediators==== | ||
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**[[Team:Bielefeld-Germany/Labjournal/Molecular#Used Kits | Plasmid isolation]] of <partinfo>BBa_J04450</partinfo>. | **[[Team:Bielefeld-Germany/Labjournal/Molecular#Used Kits | Plasmid isolation]] of <partinfo>BBa_J04450</partinfo>. | ||
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===Week 7=== | ===Week 7=== | ||
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====MFC==== | ====MFC==== | ||
- | + | *Constructed a stack of five film canister cells which was able to make a LED glow faintly | |
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====Cytochromes==== | ====Cytochromes==== | ||
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*Anaerobic cultivation of ''Geobacter sulfurreducens'' strain DSM-12127 in nitrogen-gassed [https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/Molecular#Geobacter_Medium ''Geobacter''-medium], which was suggested by the strain-supplier: German Collection of Microorganisms and Cell Cultures DSMZ, using 30 mL cultivation-tubes and silicone stoppers with upending rim. | *Anaerobic cultivation of ''Geobacter sulfurreducens'' strain DSM-12127 in nitrogen-gassed [https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/Molecular#Geobacter_Medium ''Geobacter''-medium], which was suggested by the strain-supplier: German Collection of Microorganisms and Cell Cultures DSMZ, using 30 mL cultivation-tubes and silicone stoppers with upending rim. | ||
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===Week 8=== | ===Week 8=== | ||
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====MFC==== | ====MFC==== | ||
- | + | *Started planning a new, air tight fue cell model with improved geometry. | |
====Mediators==== | ====Mediators==== | ||
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<div align="center"> | <div align="center"> | ||
{| class="wikitable" style="text-align: center" | {| class="wikitable" style="text-align: center" | ||
- | |+ | + | |+Table3: Standard Phusion PCR Master Mix for amplification of ''Geobacter sulfurreducens'' gene cluster GSU 1491-1495 and GSU 1496-1505. |
|Component || Volume | |Component || Volume | ||
|- | |- | ||
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<div align="center"> | <div align="center"> | ||
{| class="wikitable" style="text-align: center" | {| class="wikitable" style="text-align: center" | ||
- | |+Table | + | |+Table 4: Standard two-step Phusion PCR program for amplification of ''Geobacter sulfurreducens'' gene cluster GSU 1491-1495 and GSU 1496-1505. |
|'''Step''' || '''Temperature''' || '''Time''' || '''Cycles''' | |'''Step''' || '''Temperature''' || '''Time''' || '''Cycles''' | ||
|- | |- | ||
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*GSU 1491-1495 and GSU 1496-1505 PCR products were isolated and purified by gel extraction. | *GSU 1491-1495 and GSU 1496-1505 PCR products were isolated and purified by gel extraction. | ||
<br> | <br> | ||
- | [[File:iGEM_Bielefeld_2013_26.06.13_Wires.jpg|left|300px|thumb|'''Figure | + | [[File:iGEM_Bielefeld_2013_26.06.13_Wires.jpg|left|300px|thumb|'''Figure 3:''' Agarose gel from PCR on the gene-clusters GSU 1491-1495 and GSU 1496-1505 of ''Geobacter sulfurreducens'' strain. Ladder: GeneRuler™ 1 kb DNA Ladder from Thermo Scientific.]] |
<br> | <br> | ||
*Inoculation of new cultivation tubes, containing [https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/Molecular#Geobacter_Medium ''Geobacter''-medium] with ''Geobacter sulfurreducens'' culture for higher concentrated PCR-template production by whole genome isolation. Cultivation at 35°C on a rotary shaker with 110 rpm. | *Inoculation of new cultivation tubes, containing [https://2013.igem.org/Team:Bielefeld-Germany/Labjournal/Molecular#Geobacter_Medium ''Geobacter''-medium] with ''Geobacter sulfurreducens'' culture for higher concentrated PCR-template production by whole genome isolation. Cultivation at 35°C on a rotary shaker with 110 rpm. |
Latest revision as of 23:57, 28 October 2013
June
Milestones
- Starting lab work on the sub-project Porins.
- Successful PCR on oprF gene from Pseudomonas fluorescens. The oprF with pre- and suffix overlaps could be amplified from genome.
- Planning of our Human Practice projects started and the first participations are fixed.
- MFC: Designing of 3D models of MFC´s and visited a hacker space in order to print it in a 3D printer.
Week 5
Organization
- iGEM-Team Bielefeld will support the ‘CeBiTec Student Academy’ from August 26th to 30th with an own experiment.
MFC
- Constructed a resistor box with different potentiometers and LEDs in order to be able to test our fuel cells
Porines
- Primer design for isolation of oprF from Pseudomonas fluorescens strain, with overlaps for BioBrick Prefix and Suffix:
- Forward primer oprF (49 bp): GAATTCGCGGCCGCTTCTAGATGAAACTGAAAAACACCTTGGGCTTTGC
- Reverse primer oprF (51 bp): CTGCAGCGGCCGCTACTAGTATTACTTAGCTTGGGCTTCAACCTGCGCTTC
Nanowires
- Primer design for isolation of gene-cluster GSU 1491-1495, GSU 1496-1505 and GSU Promoter-1496-1505 from Geobacter sulfurreducens, containing overlaps for BioBrick Prefix and Suffix:
- Forward GSU 1491-1495 (45 bp):
GAATTCGCGGCCGCTTCTAGATGCAGGCTAGCAGACTGGGAGAAC - Reverse GSU 1491-1495 (38 bp):
CTGCAGCGGCCGCTACTAGTATCACTCCTCATCCATGC - Forward GSU 1496-1505 (42 bp):
GAATTCGCGGCCGCTTCTAGAGTTGGCCAATTACCCCCATAC - Reverse GSU 1496-1505 (51 bp):
CTGCAGCGGCCGCTACTAGTATCATAAACGAACCTCGTCCCAAGGCATCAG - Forward GSU Promoter-1496-1505 (52 bp):
GAATTCGCGGCCGCTTCTAGAGGATAGGATCCGTCACCGAGTGCGAACTGCC
- Forward GSU 1491-1495 (45 bp):
Week 6
Organization
- Thanks to NEB for the [http://www.neb-online.de/index.php/en/neb-announcements/231-igem-2013 free iGEM kit] with many useful laboratory things for all german iGEM teams.
- We are working on our first press release.
- Having a short radio contribution in the Bielefeld university campus radio ([http://www.radiohertz.de/beta-site radio 87.9 hertz]).
MFC
- Connected film canister cells in series and parallel to increase voltage/current
- Tested different redox mediators in our fuel cell
Mediators
- Glycerol dehydrogenase
- Isolation of shipping vector pSB1C3 out of 2013 Distribution Kit Plate 5 Well 3A with insert Part RFP (<bbpart>J04450</bbpart>) for better transformation characterization ([http://parts.igem.org/Help:2013_DNA_Distribution Distribution Kit BioBrick isolation]).
- Transformation of <partinfo>BBa_J04450</partinfo> into Escherichia coli KRX strain.
- Plasmid isolation of <partinfo>BBa_J04450</partinfo>.
Week 7
MFC
- Constructed a stack of five film canister cells which was able to make a LED glow faintly
Cytochromes
- Cultivation of Shewanella oneidensis MR-1 in liquid LB medium at 30 °C
- Isolation of genomic DNA from S. oneidensis and dilution to the subsequently used PCR template:
- 4-2006-453: 5.5ng/µl
- Amplification of the mtrCAB cluster with Phusion polymerase
- Annealing: Gradient [55.8 - 56.7 - 57.8 - 59.1 - 60.4 - 61.7 - 62.9 - 63.9]
- Elongation: 1:15 min
- Notes: Clear Bands at the expected 5.2 kb, the annealing temperature seems not to have an effect.
- PCR-CleanUp
- Lane2: 4-2106-451: 7.4 ng/µl
- Lane5: 4-2106-451: 8.5 ng/µl
Porines
- Starting first cultivation of Pseudomonas fluorescens strain for complete genome isolation.
- Successful genome isolation of Pseudomonas fluorescens.
- Successful PCR with forward and reverse primer oprF on the oprF gene of Pseudomonas fluorescens strain.
- oprF PCR product was isolated by agarose gel electrophoresis and purified.
- Bands are at expected size of 1300 bp.
Nanowires
- Anaerobic cultivation of Geobacter sulfurreducens strain DSM-12127 in nitrogen-gassed Geobacter-medium, which was suggested by the strain-supplier: German Collection of Microorganisms and Cell Cultures DSMZ, using 30 mL cultivation-tubes and silicone stoppers with upending rim.
Week 8
Organization
- Let’s go to Lyon, flights are booked for the European jamboree in Lyon from October 11 to 13, 2013.
- We will participate at [http://www.bio.nrw.de/studentconvention BioNRW pHD Student Convention] in Düsseldorf at July 13th.
MFC
- Started planning a new, air tight fue cell model with improved geometry.
Mediators
- Glycerol dehydrogenase
- Cloning of gldA into pSB1C3 shipping vector with NEB BioBrick assembly Kit did not work as expected.
- Screening of colonies with colony PCR and plasmid restriction analysis shows re-ligated pSB1C3 shipping vector.
- Bands are at size of 2000 bp, the length of linear pSB1C3.
- Primer design for pSB1C3 according an universal usable backbone for Gibson Assembly with Prefix and Suffix specific overlaps:
- Forward primer pSB1C3 (23 bp): TACTAGTAGCGGCCGCTGCAGTC
- Reverse primer pSB1C3 (23 bp): CTCTAGAAGCGGCCGCGAATTCC
- Primer design for pSB1C3 according an universal usable backbone for Gibson Assembly with Prefix and Suffix specific overlaps:
Porines
- Cloning of oprF into pSB1C3 shipping vector with NEB BioBrick assembly Kit did not work as expected.
- Screening of colonies with colony PCR and plasmid restriction analysis shows re-ligated pSB1C3 shipping vector as described for gldA cloning.
Nanowires
- Successful genomic DNA isolation of Geobacter sulfurreducens strain.
- Successful PCR with forward and reverse primer GSU 1491-1495 and GSU 1496-1505 on the appropriate gene-cluster of Geobacter sulfurreducens.
Component | Volume |
H2O | to 50 µL |
Template (100 ng) | 20 µL |
Betain 5 M | 12.5 µL |
5 x Phusion GC Buffer | 10 µL |
DMSO | 2.5 µL |
Primer-Mix 10 mM | 2.5 µL |
10mM dNTP´s | 2 µL |
Phusion DNA Polymerase | 0.5 µL |
Step | Temperature | Time | Cycles |
Denaturation | 98 °C | 30 sec | |
Denaturation | 98 °C | 30 sec | 10 |
Annealing | 55 °C | 60 sec | 10 |
Elongation | 72°C | 270 sec | 10 |
Denaturation | 98 °C | 30 sec | 25 |
Annealing | 60 °C | 60 sec | 25 |
Elongation | 72 °C | 270 sec | 25 |
Elongation | 72 °C | 300 sec |
- Clearly visible band at size of 7200 bp, the length of gene cluster GSU 1491-1495.
- Clearly visible band at size of 9000 bp, the length of gene cluster GSU 1496-1505.
- Several bands at smaller sizes suggest alternative primer binding sites in the genome of Geobacter sulfurreducens.
- GSU 1491-1495 and GSU 1496-1505 PCR products were isolated and purified by gel extraction.
- Inoculation of new cultivation tubes, containing Geobacter-medium with Geobacter sulfurreducens culture for higher concentrated PCR-template production by whole genome isolation. Cultivation at 35°C on a rotary shaker with 110 rpm.