Difference between revisions of "Team:HUST-China/Notebook"
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<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Results">Results</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Results">Results</a></li> | ||
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/wetlab/protocols">Protocols</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/wetlab/protocols">Protocols</a></li> | ||
| − | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/InterLab">Interlab | + | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/InterLab">Interlab</a></li> |
| − | + | ||
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Notebook">Notebook</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Notebook">Notebook</a></li> | ||
</ul> | </ul> | ||
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<ul class="dropdown-menu"> | <ul class="dropdown-menu"> | ||
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Modeling overview">Modeling overview</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Modeling overview">Modeling overview</a></li> | ||
| − | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/ | + | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/model_of_systems">Model of systems</a></li> |
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Sort of three genes">Sort of three genes</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Sort of three genes">Sort of three genes</a></li> | ||
| − | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Software"> | + | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Software">Software</a></li> |
</ul> | </ul> | ||
</li> | </li> | ||
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<ul class="dropdown-menu"> | <ul class="dropdown-menu"> | ||
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Human Practices">Human Practices</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Human Practices">Human Practices</a></li> | ||
| − | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/ | + | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Education_Engagement">Education&Engagement</a></li> |
</ul> | </ul> | ||
</li> | </li> | ||
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<a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">TEAM<b class="caret"></b></a> | <a href="#" data-toggle="dropdown" class="dropdown-toggle waves-effect waves-dark">TEAM<b class="caret"></b></a> | ||
<ul class="dropdown-menu"> | <ul class="dropdown-menu"> | ||
| − | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Team | + | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Team">Team Members</a></li> |
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Collaborations">Collaborations</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Collaborations">Collaborations</a></li> | ||
<li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Attributions">Attributions</a></li> | <li><a class="waves-effect waves-dark" href="https://2018.igem.org/Team:HUST-China/Attributions">Attributions</a></li> | ||
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<div class="row"> | <div class="row"> | ||
<div class="col-lg-12"> | <div class="col-lg-12"> | ||
| − | <h2 class="pageTitle"> | + | <h2 class="pageTitle">NoteBook</h2> |
</div> | </div> | ||
</div> | </div> | ||
| Line 188: | Line 187: | ||
<div class="col-md-12"> | <div class="col-md-12"> | ||
<p><span class="red-content">Ziyang Xiao, Haotian Ren, Yan Chen, Hao Qiu</span><br> | <p><span class="red-content">Ziyang Xiao, Haotian Ren, Yan Chen, Hao Qiu</span><br> | ||
| − | + | synechocystis Group took the responsibility of doing the Interlab. Preparation for the experiment. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 240: | Line 239: | ||
Restriction enzyme digestion of psb1c3<br> | Restriction enzyme digestion of psb1c3<br> | ||
<span class="red-content">Ziyang Xiao, Yan Chen, Haotian Ren</span><br> | <span class="red-content">Ziyang Xiao, Yan Chen, Haotian Ren</span><br> | ||
| − | Testing the cultivation ways of | + | Testing the cultivation ways of synechocystis PCC6803 |
</p> | </p> | ||
</div> | </div> | ||
| Line 249: | Line 248: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<p><span class="red-content">Ziyi Li, Jiayi Liu, Yizhe Zeng</span><br> | <p><span class="red-content">Ziyi Li, Jiayi Liu, Yizhe Zeng</span><br> | ||
| − | Construction of pYYDT-gapA, | + | Construction of pYYDT-gapA, pYYDT-mdh<br> |
Standardization of gapA, mdh | Standardization of gapA, mdh | ||
</p> | </p> | ||
| Line 347: | Line 346: | ||
<div class="collapsible-body"><p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng </span><br> | <div class="collapsible-body"><p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng </span><br> | ||
Conjugation of E.coli WM3064 and Shewanella oneidensis MR-1: we transferred the targeted plasmid into E.coli WM3064 and conjugated WM3064 and Shewanella oneidensis MR-1 so that the Shewanella oneidensis MR-1 could finally get the targetted plasmid.<br> | Conjugation of E.coli WM3064 and Shewanella oneidensis MR-1: we transferred the targeted plasmid into E.coli WM3064 and conjugated WM3064 and Shewanella oneidensis MR-1 so that the Shewanella oneidensis MR-1 could finally get the targetted plasmid.<br> | ||
| − | Conjugation pYYDT and pYYDT-lldEFG this week | + | Conjugation pYYDT and pYYDT-lldEFG this week. |
</p> | </p> | ||
<div class="col-md-6 col-md-offset-1"> | <div class="col-md-6 col-md-offset-1"> | ||
| Line 353: | Line 352: | ||
</div> | </div> | ||
<div class="col-md-12"> | <div class="col-md-12"> | ||
| − | <p>Using device to produce electricity with Shewanella. We proved that Shewanella could produce more | + | <p>Using device to produce electricity with Shewanella. We proved that Shewanella could produce more electricity with the existence of lactate. |
</p> | </p> | ||
</div> | </div> | ||
| Line 428: | Line 427: | ||
Amplifying the gene and transforming in E. coli.<br> | Amplifying the gene and transforming in E. coli.<br> | ||
<span class="red-content">Ziyang Xiao</span><br> | <span class="red-content">Ziyang Xiao</span><br> | ||
| − | + | synechocystis culture. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 462: | Line 461: | ||
Checking the finial consequence by gene sequencing.<br> | Checking the finial consequence by gene sequencing.<br> | ||
<span class="red-content">Ziyang Xiao</span><br> | <span class="red-content">Ziyang Xiao</span><br> | ||
| − | + | synechocystis culture. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 493: | Line 492: | ||
<p> | <p> | ||
<span class="red-content">Yan Chen</span><br> | <span class="red-content">Yan Chen</span><br> | ||
| − | Transforming recombinant shuttle plasmid into | + | Transforming recombinant shuttle plasmid into synechocystis<br> |
<span class="red-content">Hao Qiu</span><br> | <span class="red-content">Hao Qiu</span><br> | ||
| − | Transforming ldhd sequence into | + | Transforming ldhd sequence into synechocystis.<br> |
<span class="red-content">Ziyang Xiao</span><br> | <span class="red-content">Ziyang Xiao</span><br> | ||
| − | + | synechocystis culture. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 507: | Line 506: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin</span><br> | <p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin</span><br> | ||
| − | Construction of pSB1C3-pflB-fdh:we found that there was no tac promotor before | + | Construction of pSB1C3-pflB-fdh:we found that there was no tac promotor before. |
</p> | </p> | ||
<div class="col-md-6 col-md-offset-1"> | <div class="col-md-6 col-md-offset-1"> | ||
| Line 526: | Line 525: | ||
<p> | <p> | ||
<span class="red-content">Hao Qiu</span><br> | <span class="red-content">Hao Qiu</span><br> | ||
| − | Using DNS to detect the condition of producing lactate by | + | Using DNS to detect the condition of producing lactate by synechocystis.<br> |
<span class="red-content">Yuanda Huang, Yan Chen</span><br> | <span class="red-content">Yuanda Huang, Yan Chen</span><br> | ||
| − | Transforming recombinant shuttle plasmid into | + | Transforming recombinant shuttle plasmid into synechocystis.<br> |
<span class="red-content">Ziyang Xiao</span><br> | <span class="red-content">Ziyang Xiao</span><br> | ||
| − | + | synechocystis culture. | |
</p> | </p> | ||
</div> | </div> | ||
| Line 541: | Line 540: | ||
<div class="collapsible-body"> | <div class="collapsible-body"> | ||
<p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin</span><br> | <p><span class="red-content">Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin</span><br> | ||
| − | Construction of | + | Construction of pYYDT-pflB-fdh |
</p> | </p> | ||
<div class="col-md-6 col-md-offset-1"> | <div class="col-md-6 col-md-offset-1"> | ||
| Line 561: | Line 560: | ||
Overlap extension PCR of ldhDnARSdR and lldp. <br> | Overlap extension PCR of ldhDnARSdR and lldp. <br> | ||
<span class="red-content">Hao Qiu</span><br> | <span class="red-content">Hao Qiu</span><br> | ||
| − | Expansion culture of | + | Expansion culture of synechocystis. DNS detection of sugar production of synechocystis, YFP fluorescent protein detection of synechocystis.<br> |
<span class="red-content">Yan Chen</span><br> | <span class="red-content">Yan Chen</span><br> | ||
| − | Transforming recombinant shuttle plasmid into | + | Transforming recombinant shuttle plasmid into synechocystis. |
</p> | </p> | ||
</div> | </div> | ||
| Line 576: | Line 575: | ||
1. Construction of pSB1C3-Ptac-pflB-fdh<br> | 1. Construction of pSB1C3-Ptac-pflB-fdh<br> | ||
2. Reconjugation of pYYDT-lldEFG<br> | 2. Reconjugation of pYYDT-lldEFG<br> | ||
| − | 3. We did two groups of electrogenesis experiments. One of them included the engineering | + | 3. We did two groups of electrogenesis experiments. One of them included the engineering synechocystis and Shewanella, the other included the engineering Rhodopseudomonas palustris and Shewanella. It turned out that the later one worked better than the former one.<br> |
<span class="red-content">Yuanda Huang</span><br> | <span class="red-content">Yuanda Huang</span><br> | ||
Add the first tag to ldhDnARSdR-lldp /ldhDARSdR-lldp. <br> | Add the first tag to ldhDnARSdR-lldp /ldhDARSdR-lldp. <br> | ||
<span class="red-content">Hao Qiu</span><br> | <span class="red-content">Hao Qiu</span><br> | ||
| − | Detection of YFP fluorescent protein of | + | Detection of YFP fluorescent protein of synechocystis.<br> |
<span class="red-content">Yan Chen</span><br> | <span class="red-content">Yan Chen</span><br> | ||
| − | Detection of YFP fluorescent protein of | + | Detection of YFP fluorescent protein of synechocystis. Detection of Flag tag.<br> |
<span class="red-content">Ziyang Xiao</span><br> | <span class="red-content">Ziyang Xiao</span><br> | ||
| − | Detection of YFP fluorescent protein of | + | Detection of YFP fluorescent protein of synechocystis. Detection of 6× His tag and lactate.<br> |
Conjugation of pYYDT-pflB-fdh<br> | Conjugation of pYYDT-pflB-fdh<br> | ||
We proved that the engineering bacteria with pYYDT-gapA-mdh could produce more electricity than the bacteria with pYYDT.<br> | We proved that the engineering bacteria with pYYDT-gapA-mdh could produce more electricity than the bacteria with pYYDT.<br> | ||
| Line 590: | Line 589: | ||
Overlap extension PCR of ldhDnARSdR and lldp. <br> | Overlap extension PCR of ldhDnARSdR and lldp. <br> | ||
<span class="red-content">Hao Qiu</span><br> | <span class="red-content">Hao Qiu</span><br> | ||
| − | Expansion culture of | + | Expansion culture of synechocystis. DNS detection of sugar production of synechocystis, YFP fluorescent protein detection of synechocystis.<br> |
<span class="red-content">Yan Chen</span><br> | <span class="red-content">Yan Chen</span><br> | ||
| − | Transforming recombinant shuttle plasmid into | + | Transforming recombinant shuttle plasmid into synechocystis. |
</p> | </p> | ||
</div> | </div> | ||
Latest revision as of 23:02, 17 October 2018
NoteBook
-
April 1-30Ziyang Xiao, Junhao Xiong, Jingyu Ren, Yan chen, Qian Li
Pre-experiment of electrogenesis: tested and optimized the electrogenesis condition for MFC (Microbial Fuel Cell) -
May 1-31
Yiyan Yu, Ziyi Li, Junhao Xiong
Basic design of molecular experiments: design sequences, primers and the construction of Shewanella -
July 1-7
Junhao Xiong, Ziqi Yin, Jiayi Liu
Preparation for following experiments including preparing LB culture medium, antibiotics and optimizing culture condition of Shewanella oneidensis MR-1.
Bo Peng
Construction of pSB1C3-RBS-mleS
Ziyang Xiao, Haotian Ren, Yan Chen, Hao Qiu
synechocystis Group took the responsibility of doing the Interlab. Preparation for the experiment. -
July 8-21
Junhao Xiong, Ziqi Yin, Jiayi Liu
Construction of pYYDT-pflB: PCR, double enzyme digestion (with NdeI & SalI), ligation, transformation (into E.coli TOP10).
Qian Li
Construction of pSB1C3-RBS-lldp-RBS-ldhA-TT
Ziyang Xiao, Haotian Ren, Yan Chen, Hao Qiu
Finishing the cell cultures cultivation and using some machines to measure some related data. -
July 22-29
Junhao Xiong, Ziqi Yin, Jiayi Liu
Construction of pYYDT-gapA-mdh, pYYDT-lldEFG: PCR, double enzyme digestion (with NdeI & SalI), ligation, transformation (into E.coli TOP10).
Haibo Huang
Construction of pSB1C3-RBS-lldP and pSB1C3-RBS-ldhA.
Haotian Ren
Restriction enzyme digestion of psb1c3
Ziyang Xiao, Yan Chen, Haotian Ren
Testing the cultivation ways of synechocystis PCC6803 -
July 30 - August 5
Ziyi Li, Jiayi Liu, Yizhe Zeng
Construction of pYYDT-gapA, pYYDT-mdh
Standardization of gapA, mdh
Kaiwen Liu
Construction of pmg105-PpckA-RBS-lldP-RBS-ldhA-TT
Yan Chen, Sijie Xu
Interlab Experiment 4 -
August 6-12
Ziyi Li, Jiayi Liu, Yizhe Zeng
Construction of pYYDT-dld
Standardization of dld, lldEFG
Haibo Huang
Construction of pSB1C3-RBS-ldhA-RBS-lldP-TT
Yan Chen, Yuanda Huang
Restriction enzyme digestion of psb-lldEFG
Yan Chen, Sijie Xu, Yuanda Huang, Ziyang Xiao
Constructing ldhDc-lldP, ldhDARSDR-lldP, ldhDnARSDR-lldPT -
August 13-19
Ziyi Li, Yizhe Zeng
Overlap extension PCR of dld and lldEFG: We got the right band but the sequencing result revealed a mutation of it.
Making competent cells of E.coli WM3064: we need the deficiency type WM3064 to conjugate with Shewanella oneidensis MR-1.
Bo Peng
Construction of pmg105-PpckA-RBS-lldP-TT, pmg105-PpckA-RBS-ldhA-RBS-lldP-TT and pmg105-PpckA-RBS-mleS-TT.
Yuanda Huang, Yan Chen, Sijie Xu, Tao Jian, Ziyang Xiao
PCR of ldhDnARSdR, PCR of ldhDARSdR,
Overlap extension PCR of ldhDnARSdR and lldp (Dn-L)
Overlap extension PCR of ldhDARSdR and lldp (DA-L)
Overlap extension PCR of ldhDC and lldp (DC-L) -
August 20-26
Ziyi Li, Junhao Xiong, Yizhe Zeng
Conjugation of E.coli WM3064 and Shewanella oneidensis MR-1: we transferred the targeted plasmid into E.coli WM3064 and conjugated WM3064 and Shewanella oneidensis MR-1 so that the Shewanella oneidensis MR-1 could finally get the targetted plasmid.
Conjugation pYYDT and pYYDT-lldEFG this week.
Using device to produce electricity with Shewanella. We proved that Shewanella could produce more electricity with the existence of lactate.
Yuanda Huang, Haotian Ren, Ziyang Xiao
PCR of ldhDnARSdR, PCR of ldhDARSdR,
PCR of ldhDnARSdR, extraction enzyme digestion of ldhDnARSdR,
Ligation of ldhDnARSdR and psb1c3, transformation
Hao Qiu
Constructing the pathway of TH-glad-lldp.
Insert sequence TH-glad-lldp to vector psb1c3. -
August 27 – September 2
Ziyi Li, Junhao Xiong, Yizhe Zeng
Redesigning about connecting dld and lldEFG: We decided to drop the idea about overlap extension PCR to connect dld and lldEFG and started to use isocaudamer (XbaI and SpeI) to connect these genes.
Conjugation of pYYDT-gapA and pYYDT-mdh.
By constructing Rhodopseudomonas palustris-Shewanella oneidensis mutualism system, we found that Shewanella could produce more electricity if Rhodopseudomonas palustris exists.
Qian Li
Construction of pSB1C3-RBS-mleS-RBS-lldp.
Yuanda Huang, Ziyang Xiao
Overlap extension PCR of ldhDnARSdR-lldp
Tao Jian
Adding Flag tag to ldhD-lldP.
Yan Chen
Adding Flag tag to ldhDc-lldP -
September 3-9
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
Conjugation of pYYDT-dld and pYYDT-Ptac-pflB.
New method to connect dld and lldEFG. However, we failed at the construction of pSB1C3-ptac-lldEFG because of the biobrick prefix on pYYDT.
We proved that Shewanella could produce more electricty under anaerobic condition.
Yuanda Huang
Adding tags to ldhDnARSdR-lldp
Yan Chen
Adding his tag to ldhD-lldP and ldhDc-lldP
Hao Qiu
Amplifying the gene and transforming in E. coli.
Ziyang Xiao
synechocystis culture. -
September 10-16
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
Conjugation of pYYDT-gapA-mdh
Haibo Huang
Adding tags to ldhDnARSdR-lldp
Yan Chen
Construction of pmg105-PpckA-RBS-ldhA-TT.
Yuanda Huang
Adding tags to ldhDARSdR-lldp
Yan Chen
Recombination of ldhD-lldP and ldhDc-lldP to shuttle plasmid PCK306
Hao Qiu
Checking the finial consequence by gene sequencing.
Ziyang Xiao
synechocystis culture. -
September 17-23
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
Application of the electrogenesis: we used the device to charge an LED (1.7V), a cell phone (5V) and a small engine (5V). The success proved that we can put our device into practice.
We proved that carbon cloth has better effect than carbon rods.
Kaiwen Liu
Construction of pmg105-PpckA-RBS-mleS-RBS-lldP-TT
Haibo Huang
Inserting ldhDnARSdR-lldp biaoda into the plasmid called pck306 through recombinase,
Inserting ldhDARSdR-lldp biaoda into the plasmid called pck306 through recombinase
Yan Chen
Transforming recombinant shuttle plasmid into synechocystis
Hao Qiu
Transforming ldhd sequence into synechocystis.
Ziyang Xiao
synechocystis culture. -
September 24-30
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
Construction of pSB1C3-pflB-fdh:we found that there was no tac promotor before.
We proved that the electricity produced by Rhodopseudomonas palustrls could be ignored in the electrogenesis system.
At the same time, it was demonstrated that the lactate could be the only carbon source in the culture medium.
Qian Li
Construction of pSB1C3- RBS-mleS-RBS-lldP-RBS-ldhA-TT
Hao Qiu
Using DNS to detect the condition of producing lactate by synechocystis.
Yuanda Huang, Yan Chen
Transforming recombinant shuttle plasmid into synechocystis.
Ziyang Xiao
synechocystis culture. -
October 1-7
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
Construction of pYYDT-pflB-fdh
Conjugation of pYYDT-pflB-fdh
We proved that the engineering bacteria with pYYDT-gapA-mdh could produce more electricity than the bacteria with pYYDT.
Bo Peng
Construction of RBS-mleS-RBS-lldP-TT pmg105-PpckA-RBS-mleS-RBS-lldP-RBS-ldhA-tt.
Yuanda Huang
Overlap extension PCR of ldhDnARSdR and lldp.
Hao Qiu
Expansion culture of synechocystis. DNS detection of sugar production of synechocystis, YFP fluorescent protein detection of synechocystis.
Yan Chen
Transforming recombinant shuttle plasmid into synechocystis. -
October 8-14
Ziyi Li, Junhao Xiong, Yizhe Zeng, Ziqi Yin
1. Construction of pSB1C3-Ptac-pflB-fdh
2. Reconjugation of pYYDT-lldEFG
3. We did two groups of electrogenesis experiments. One of them included the engineering synechocystis and Shewanella, the other included the engineering Rhodopseudomonas palustris and Shewanella. It turned out that the later one worked better than the former one.
Yuanda Huang
Add the first tag to ldhDnARSdR-lldp /ldhDARSdR-lldp.
Hao Qiu
Detection of YFP fluorescent protein of synechocystis.
Yan Chen
Detection of YFP fluorescent protein of synechocystis. Detection of Flag tag.
Ziyang Xiao
Detection of YFP fluorescent protein of synechocystis. Detection of 6× His tag and lactate.
Conjugation of pYYDT-pflB-fdh
We proved that the engineering bacteria with pYYDT-gapA-mdh could produce more electricity than the bacteria with pYYDT.
Yuanda Huang
Overlap extension PCR of ldhDnARSdR and lldp.
Hao Qiu
Expansion culture of synechocystis. DNS detection of sugar production of synechocystis, YFP fluorescent protein detection of synechocystis.
Yan Chen
Transforming recombinant shuttle plasmid into synechocystis.
