Difference between revisions of "Team:HUST-China/Experiments"

 
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                                 <h3>2.  Lactate contrast.</h3>
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                                 <h3><b>2.  Lactate contrast.</h3>
 
                                 <p>MFC anode: Shewanella</p>
 
                                 <p>MFC anode: Shewanella</p>
 
                                 <p>MFC anode: Shewanella+lactate</p>
 
                                 <p>MFC anode: Shewanella+lactate</p>
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                                 <h3>3. Demonstrate that carbon cloth has higher electricity production efficiency than carbon rod.</h3>
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                                 <h3><b>3. Demonstrate that carbon cloth has higher electricity production efficiency than carbon rod.</h3>
 
                                 <p>MFC anode: carbon cloth</p>
 
                                 <p>MFC anode: carbon cloth</p>
 
                                 <p>MFC anode: carbon rod</p>
 
                                 <p>MFC anode: carbon rod</p>
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                                 <h3>4.  Study the effects of oxygen on Co-culture power systems.</h3>
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                                 <h3><b>4.  Study the effects of oxygen on Co-culture power systems.</h3>
 
                                 <p>MFC anode: anaerobic</p>
 
                                 <p>MFC anode: anaerobic</p>
 
                                 <p>MFC anode: aerobic</p>
 
                                 <p>MFC anode: aerobic</p>
 
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                                 <h3>5. Contrast the symbiotic effect of wild-type strains</h3>
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                                 <h3><b>5. Contrast the symbiotic effect of wild-type strains</h3>
 
                                 <p>MFC anode: Synechocystis PCC6803 (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Synechocystis PCC6803 (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella</p>
 
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                                 <h3>6. Functional verification of engineered Rhodopseudomonas palustris</h3>
+
                                 <h3><b>6. Functional verification of engineered Rhodopseudomonas palustris</h3>
 
                                 <p>MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Rhodopseudomonas palustris(engineered type) + Shewanella</p>
 
                                 <p>MFC anode: Rhodopseudomonas palustris(engineered type) + Shewanella</p>
 
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                                 <h3>7.  Functional verification of engineered Synechococcus PCC6803</h3>
+
                                 <h3><b>7.  Functional verification of engineered Synechococcus PCC6803</h3>
 
                                 <p>MFC anode: Synechocystis PCC6803 (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Synechocystis PCC6803 (wild type) + Shewanella</p>
 
                                 <p>MFC anode: Synechocystis PCC6803 (engineered type) + Shewanella</p>
 
                                 <p>MFC anode: Synechocystis PCC6803 (engineered type) + Shewanella</p>

Latest revision as of 03:11, 18 October 2018

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Experiments

1.1 Synechocystis sp.

1.1.1 Plasmid Construction in E.coli

We constructed following vectors carrying our parts and transformed these vectors into corresponding host strains.

Part Plasmid Construction Transformation to Host Strain
RBS-ldhD-RBS-lldP pSB1C3 E.coli DH5α
RBS-ldhDC-RBS-lldP pSB1C3 E.coli DH5α
RBS-ldhDnARSdR-RBS-lldP pSB1C3 E.coli DH5α
RBS-ldhDARSdR-RBS-lldP pSB1C3 E.coli DH5α
RBS-TH-RBS-gldA-RBS-lldp pSB1C3 E.coli DH5α

1.1.2 Add Flag Sequence into parts

The constructed plasmid was transformed into E.coli Top 10.

Part Plasmid Construction Transformation to Host Strain
RBS-ldhD-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDC-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDnARSdR-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDARSdR-RBS-lldP pSB1C3 E.coli Top 10

1.1.3 Add 6×His Sequence into parts

The constructed plasmid was transformed into E.coli Top 10.

Part Plasmid Construction Transformation to Host Strain
RBS-ldhD-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDC-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDnARSdR-RBS-lldP pSB1C3 E.coli Top 10
RBS-ldhDARSdR-RBS-lldP pSB1C3 E.coli Top 10

1.1.4 pCK360 Plasmid Conjugation

We constructed following vectors carrying our parts and transformed these vectors into E.coli Top 10 to transformed into cynobacteria.

Part Plasmid Construction Transformation to Host Strain
RBS-ldhD-RBS-lldP pck306 E.coli Top 10; cynobacteria
RBS-ldhDC-RBS-lldP pck306 E.coli Top 10; cynobacteria
RBS-ldhDnARSdR-RBS-lldP pck306 E.coli Top 10; cynobacteria
RBS-ldhDARSdR-RBS-lldP pck306 E.coli Top 10; cynobacteria

Figure 6. modified circuit of ldhD-lldP.

Figure 7. modified circuit of ldhDC-lldP.

Figure 8. modified circuit of ldhDnARSdR-lldP.

Figure 9. modified circuit of ldhDARSdR-lldP.

1.1.5 Detection of yellow fluorescent protein

Since plasmid pCK306 has yellow fluorescent protein sequence, we cultivated the engineering cynobacteria induced by rhamnose for 24h. And put them under the fluorescence microscope at the wave of 488nm excitation light

1.2 Rhodopseudomonas palustris

1.2.1 Plasmid Construction in E.coli

We constructed following vectors carrying our parts and transformed these vectors into corresponding host strains.

Part Plasmid Construction Transformation to Host Strain
RBS-mleS pSB1C3 E.coli TOP10
RBS-ldhA pSB1C3 E.coli TOP10
RBS-lldP pSB1C3 E.coli TOP10
RBS-mleS-RBS-lldP pSB1C3 E.coli TOP10
RBS-lldP-RBS-ldhA-TT pSB1C3 E.coli TOP10
RBS-ldhA-RBS-lldP-TT pSB1C3 E.coli TOP10
RBS-mleS-RBS-ldhP-RBS-ldhA-TT pSB1C3 E.coli TOP10
RBS-mleS pMG105 E.coli TOP10
RBS-ldhA pMG105 E.coli TOP10
RBS-lldP pMG105 E.coli TOP10
RBS-mleS-RBS-lldP pMG105 E.coli TOP10
RBS-lldP-RBS-ldhA-TT pMG105 E.coli TOP10
RBS-ldhA-RBS-lldP-TT pMG105 E.coli TOP10
RBS-mleS-RBS-ldhP-RBS-ldhA-TT pMG105 E.coli TOP10

1.2.2 Transformation into E.coli BL21

The constructed plasmid was transformed into E.coli BL21.

Part Plasmid Construction Transformation to Host Strain
RBS-mleS pMG105 E.coli BL21
RBS-ldhA pMG105 E.coli BL21
RBS-lldP pMG105 E.coli BL21
RBS-mleS-RBS-lldP pMG105 E.coli BL21
RBS-lldP-RBS-ldhA-TT pMG105 E.coli BL21
RBS-ldhA-RBS-lldP-TT pMG105 E.coli BL21
RBS-mleS-RBS-ldhP-RBS-ldhA-TT pMG105 E.coli BL21

1.2.3 Transformation into Rhodopseudomonas palustris DSM5859

The constructed plasmid was transformed into Rhodopseudomonas palustris DSM5859.

Part Plasmid Construction Transformation to Host Strain
RBS-mleS pMG105 Rhodopseudomonas palustris DSM5859
RBS-ldhA pMG105 Rhodopseudomonas palustris DSM5859
RBS-lldP pMG105 Rhodopseudomonas palustris DSM5859
RBS-mleS-RBS-lldP pMG105 Rhodopseudomonas palustris DSM5859
RBS-lldP-RBS-ldhA-TT pMG105 Rhodopseudomonas palustris DSM5859
RBS-ldhA-RBS-lldP-TT pMG105 Rhodopseudomonas palustris DSM5859
RBS-mleS-RBS-ldhP-RBS-ldhA-TT pMG105 Rhodopseudomonas palustris DSM5859

1.2.4 Verification the expression at mRNA level

We did RT-qPCR to test the relative expression levels of each genes.

1.2.5 Detection of Lactate

We detect lactate by Lactic Acid assay kit.

Shewanella oneidensis MR-1

2.1 Plasmid Construction in E.coli

We constructed following vectors carrying our parts and transformed these vectors into corresponding host strains.

Part Plasmid Construction Transformation to Host Strain
RBS-dld pSB1C3 E.coli TOP10
RBS-lldEFG pSB1C3 E.coli TOP10
RBS-dld-TT -Ptac -RBS-lldEFG pSB1C3 E.coli TOP10
RBS-gapA pSB1C3 E.coli TOP10
RBS-mdh pSB1C3 E.coli TOP10
RBS-gapA-RBS-mdh-TT pSB1C3 E.coli TOP10
RBS-Ptac -RBS-pflB pSB1C3 E.coli TOP10
RBS-fdh pSB1C3 E.coli TOP10
RBS-pflB-RBS-fdh pSB1C3 E.coli TOP10
RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB pSB1C3 E.coli TOP10
RBS-dld pYYDT E.coli TOP10
RBS-lldEFG pYYDT E.coli TOP10
RBS-dld-TT -Ptac -RBS-lldEFG pYYDT E.coli TOP10
RBS-gapA pYYDT E.coli TOP10
RBS-mdh pYYDT E.coli TOP10
RBS-gapA-RBS-mdh-TT pYYDT E.coli TOP10
RBS-Ptac -RBS-pflB pYYDT E.coli TOP10
RBS-pflB-RBS-fdh pYYDT E.coli TOP10
RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB pYYDT E.coli TOP10

2.2 Transformation into E.coli WM3064

The constructed plasmid was transformed into a 2,6-diaminopimelic acid deficiency type E.coli WM3064.

Part Plasmid Construction Transformation to Host Strain
RBS-dld pYYDT E .coli WM3064
RBS-lldEFG pYYDT E .coli WM3064
RBS-dld-TT -Ptac -RBS-lldEFG pYYDT E .coli WM3064
RBS-gapA pYYDT E .coli WM3064
RBS-mdh pYYDT E .coli WM3064
RBS-gapA-RBS-mdh-TT pYYDT E .coli WM3064
RBS-Ptac -RBS-pflB pYYDT E .coli WM3064
RBS-pflB-RBS-fdh pYYDT E .coli WM3064
RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB pYYDT E .coli WM3064

2.3 Conjugation between E.coli and Shewanella oneidensis MR-1

We did conjugation after the transformation to WM3064 to introduce the plasmid into Shewanella oneidensis MR-1.

Part Plasmid Construction Transformation to Host Strain
RBS-dld pYYDT Shewanella oneidensis MR-1
RBS-lldEFG pYYDT Shewanella oneidensis MR-1
RBS-dld-TT -Ptac -RBS-lldEFG pYYDT Shewanella oneidensis MR-1
RBS-gapA pYYDT Shewanella oneidensis MR-1
RBS-mdh pYYDT Shewanella oneidensis MR-1
RBS-gapA-RBS-mdh-TT pYYDT Shewanella oneidensis MR-1
RBS-Ptac -RBS-pflB pYYDT Shewanella oneidensis MR-1
RBS-pflB-RBS-fdh pYYDT Shewanella oneidensis MR-1
RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB pYYDT Shewanella oneidensis MR-1

2.4 Verification the expression on mRNA level

We did RT-qPCR to test the relative expression levels of each genes.

2.5 Electrogenesis detection

We cultivated the engineering bacteria and put them into the electrogenesis device to test the output votage. We also did the measurement of electrode-attached biomass.

Co-culture and electricity

Microorganism 1 Microorganism 2 Addition 1 Addition 2
E.coli LB medium
Shewanella oneidensis MR-1 LB medium
Shewanella oneidensis MR-1 LB medium Lactate
Shewanella oneidensis MR-1 Cynobacteria LB medium
Shewanella oneidensis MR-1 Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT- RBS-dld) LB medium Lactate
Shewanella oneidensis MR-1(pYYDT-RBS-lldEFG) LB medium Lactate
Shewanella oneidensis MR-1(pYYDT -RBS-dld-TT -Ptac -RBS-lldEFG) LB medium Lactate
Shewanella oneidensis MR-1(pYYDT-RBS-gapA-RBS-mdh-TT ) LB medium Lactate
Shewanella oneidensis MR-1(pYYDT -RBS-pflB-RBS-fdh) LB medium Lactate
Shewanella oneidensis MR-1(pYYDT-RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB LB medium Lactate
Shewanella oneidensis MR-1(pYYDT- RBS-dld) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT-RBS-lldEFG) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-dld-TT -Ptac -RBS-lldEFG) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-gapA-RBS-mdh-TT ) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-pflB-RBS-fdh) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB) Rhodopseudomonas palustris DSM5859 LB medium
Shewanella oneidensis MR-1(pYYDT- RBS-dld) Cynobacteria LB medium
Shewanella oneidensis MR-1(pYYDT-RBS-lldEFG) Cynobacteria LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-dld-TT -Ptac -RBS-lldEFG) Cynobacteria LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-gapA-RBS-mdh-TT ) Cynobacteria LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-pflB-RBS-fdh) Cynobacteria LB medium
Shewanella oneidensis MR-1(pYYDT -RBS-gapA-RBS-mdh-TT -RBS-Ptac -RBS-pflB) Cynobacteria LB medium

In this part, we mainly verify our vision by constructing MFC system and we detect the generated voltage. We did several parallel experiments to prove it:

1. Pre-experiment of electrogenesis.

MFC anode: Shewanella

MFC anode: Blank medium

MFC anode: E.coli

2. Lactate contrast.

MFC anode: Shewanella

MFC anode: Shewanella+lactate

3. Demonstrate that carbon cloth has higher electricity production efficiency than carbon rod.

MFC anode: carbon cloth

MFC anode: carbon rod

4. Study the effects of oxygen on Co-culture power systems.

MFC anode: anaerobic

MFC anode: aerobic

5. Contrast the symbiotic effect of wild-type strains

MFC anode: Synechocystis PCC6803 (wild type) + Shewanella

MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella

6. Functional verification of engineered Rhodopseudomonas palustris

MFC anode: Rhodopseudomonas palustris (wild type) + Shewanella

MFC anode: Rhodopseudomonas palustris(engineered type) + Shewanella

7. Functional verification of engineered Synechococcus PCC6803

MFC anode: Synechocystis PCC6803 (wild type) + Shewanella

MFC anode: Synechocystis PCC6803 (engineered type) + Shewanella