Team:HIT-Harbin/project/notebook/diary

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<p>&nbsp;&nbsp;&nbsp;&nbsp;Staphylococcus aureus infections are major causes of morbidity and mortality in community and hospital settings. Consequently, the emergence of methicillin-resistant and, more recently, vancomysin-resistant strains of S.aureus represents an enormous threat to public health. Since bacterial sensors are attracting more and more biologists' attention owing to its' specific, fast and accurate detecting, we plan to construct a E.coli biofilm consisting of two different engineered populations(namely biosensor and killer), which are designed to detect and eradicate S.aureus, respectively. The two engineered populations communicate with each other by AHL signal transduction. We hope that compartmentalization of functions can lessen metabolism load and cross-reactions interfere, and achieve the assembly of different functions in bacterial level. The whole system comprises sensing, killing and biofilm formation devices. </p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;Detecting device: to detect the existence of S.aureus through sensing the AIPs secreted only from S.aureus, and the report will be shown by the expression of GFP.</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;Killing device: to eradicate S.aureus through the production and release of lysostaphin.</p>
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<p>&nbsp;&nbsp;&nbsp;&nbsp;Biofilm formation device: to enhance biofilm formation by over-expression of yddV, a di-guanylate cyclase, which catalyzes GTP into c-di-GMP.</p>
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DIARY</div>
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<div id="main-container">
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<div class="post-title">
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<a>Brainstorm1</a>
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</div>
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<div class="post-excerpt">
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<p>Light controlling protein as a switch to regulate expression.  –Ying ZHANG
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<br>Application for water pollution.  –Yongqian HE
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<br>Engineering helicobacter pylori for medical application.  –Yubo YANG
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<br>Synthesis biology of plant hormones. –Yifan WU
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<br>On 04/21
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</p></div>
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<div class="post-title">
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<a>Brainstorm2</a>
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</div>
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<div class="post-excerpt">
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<p>Biology compass. --Lei QIAO<br>
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Engineering bacteria for carbon dioxide fixation.  –Fangping XIE<br>
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Biosensor.  –Borong CHENG<br>
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Culture of magnetotactic bacteria, heavy work.  –Kunming ZHAO<br>
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On 04/28
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</p></div>
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<div class="post-title">
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<a>Brainstorm3</a>
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</div>
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<div class="post-excerpt">
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<p>Introduction of Matlab, Cell Designer, Biosimulation for modeling. –Yue YU<br>
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miRNA for mRNA silence, for anticancer usage. –Fangping XIE<br>
 +
Microbial electricity generation. –Minghui HUANG<br>
 +
Protein modification for cancer treating.  –Xiangmiao ZENG<br>
 +
Quorum sensing to detect enterovirus. –Lei QIAO<br>
 +
0n 05/12</p>
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</div>
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<div class="post-title">
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<a>Human Practice1</a>
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</div>
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<div class="post-excerpt">
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<p>Invitation of a professor from Zhejiang University researching in synthesis biology.<br>
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A database software for everyone who’d like to collect the data of previous team information. <br>
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Create a flash showing the sprite of iGEM and the team of HIT.<br>
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Cartoon for spread of iGEM and synthesis biology around Harbin Institute of Technology.<br>
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In early June
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</p></div>
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<div class="post-title">
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<a>Human Practice2</a>
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</div>
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<div class="post-excerpt">
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<p>Song adaptation have done by Yifan WU, also made a flash linked to the Internet for sharing the iGEM happiness.<br>
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Made the first version of database software, which provides for SQL querying. But the database only includes teams from America.<br>
 +
In mid-July
 +
</p></div>
 +
<div class="post-title">
 +
<a>Project selections</a>
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</div>
 +
<div class="post-excerpt">
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<p>1. Memristor and some other electric devices by engineered bacteria.<br>
 +
2. Biofilm from cellulose degradation.<br>
 +
3. Microbial fuel cell from bacteria in industrial wastewater.<br>
 +
4. Environmental detection, Enterovirus.<br>
 +
On 05/18</p></div>
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<div class="post-title">
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<a>Lecture</a>
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</div>
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<div class="post-excerpt">
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<p>Speech given by Prof. CHEN from Zhejiang University<br>
 +
For introduce synthesis biology and iGEM latest hot research.<br>
 +
Two lectures in the Huanghe Road campus and the main campus.<br>
 +
After the lecture, we made recruitment of new members for iGEM_HIT.<br>
 +
In early March</p></div>
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<div class="post-title">
 +
<a>Modeling Training</a>
 +
</div>
 +
<div class="post-excerpt">
 +
<p>Prof. XU attending the meeting for biology modeling training.<br>
 +
Flux balance analysis (FBA) is a widely used approach for studying biochemical networks, in particular the genome-scale metabolic network reconstructions.<br>
 +
FBA is a powerful mean of biological metabolic networks.<br>
 +
The process of iGEM is design-modelling-experiment-design again.<br>
 +
Three methods:<br>
 +
System definition, Mass balance; Linear programming regulation<br>
 +
On 05/26</p></div>  
 +
<div class="post-title">
 +
<a>Human Practice2</a>
 +
</div>
 +
<div class="post-excerpt">
 +
<p>Song adaptation have done by Yifan WU, also made a flash linked to the Internet for sharing the iGEM happiness.<br>
 +
Made the first version of database software, which provides for SQL querying. But the database only includes teams from America.<br>
 +
In mid-July
 +
</p></div>
 +
<div class="post-title">
 +
<a>Modeling1</a>
 +
</div>
 +
<div class="post-excerpt">
 +
<p>We searched plenty of publications for which related to mathematical modeling. <br>
 +
And two modeling members took responsible of each main part, detecting and killing, begin with figure out gene expression regulation.<br>
 +
For the next step, learning modeling software is necessary; we decided to use Matlab for main platform combining with other tools, such as cell designer.<br>
 +
In mid-July</p></div>  
 +
<div class="post-title">
 +
<a>Modeling2</a>
 +
</div>
 +
<div class="post-excerpt">
 +
<p>Figure out the regulation of detecting device in mathematical method.<br>
 +
Peruse the related literatures to conclude the Ordinary Differential Equations for our novel design.<br>
 +
Simulation in matlab for getting the material curve and analyse the results.<br>
 +
In late July</p></div>  
 +
<div class="post-title">
 +
<a>Modeling3</a>
 +
</div>
 +
<div class="post-excerpt">
 +
<p>Work out the regulation of killing device in mathematical method.<br>
 +
Conclude the Ordinary Differential Equations for our novel design from literatures.<br>
 +
Analyse the results from matlab curves of species variation.<br>
 +
Model improvement of the former part. Change the parameter of ODEs.<br>
 +
In early August</p></div>
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<div class="post-title">
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<a>Column</a>
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</div>
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<div class="post-excerpt">
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<p>Ying ZHANG concluded the software team of Berkeley in 2009, who build the platform for tools development of other researchers and teams.<br>
 +
Fangping XIE introduced the software team of USTC 2011. He elaborated the novel data structure which is named “Chain Node” model.<br>
 +
In June</p></div>
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<div class="post-title">
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<a>Wiki</a>
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</div>
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<div class="post-excerpt">
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<p>Reference to the former HIT_Harbin team wiki: <br>
 +
https://2011.igem.org/Team:HIT-Harbin<br>
 +
Best wiki of three areas：<br>
 +
https://2011.igem.org/Team:Calgary<br>
 +
https://2011.igem.org/Team:HokkaidoU_Japan<br>
 +
https://2011.igem.org/Team:Imperial_College_London</p></div>
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<div class="post-title">
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</div>
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</div>
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</div>
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<div id="footer">
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<a id="backtotop" href="HOME.html#header">Back to Top</a>
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<img  src="https://static.igem.org/mediawiki/2012/0/09/Op.jpg">
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<font size="2"><p>Fig. 1 Schematic of “S.aureus monitor” system. The AgrA protein is phosphorylated when AIP binds to AgrC protein across the membrane. P2(P3) is activated by phosphorylated AgrA, leading the production and release of 3OC6HSL. PluxI promoter is induced by LuxR-3OC6HSL complex, causing the production of lysostaphin and starting the time-delay device(PKU iGEM 2010). After a certain time, lysis E7 protein(NTU iGEM 2009) is produced. After the E7 protein attains the threshold concentration that causes the chassis to lyse, the accumulated lysostaphin is released into the exogenous environment and kills S.aureus.
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T5:constitutive promoter; P2(P3):AgrA~P inducible promoter; Ptrc:IPTG inducible promoter; PluxI:LuxR-3OC6HSL complex inducible promoter; AIP: produced by Staphylococcus aureus<p><font>
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Revision as of 14:42, 23 September 2012

HIT-Harbin

DIARY
DIARY
Brainstorm1

Light controlling protein as a switch to regulate expression. –Ying ZHANG
Application for water pollution. –Yongqian HE
Engineering helicobacter pylori for medical application. –Yubo YANG
Synthesis biology of plant hormones. –Yifan WU
On 04/21

Brainstorm2

Biology compass. --Lei QIAO
Engineering bacteria for carbon dioxide fixation. –Fangping XIE
Biosensor. –Borong CHENG
Culture of magnetotactic bacteria, heavy work. –Kunming ZHAO
On 04/28

Brainstorm3

Introduction of Matlab, Cell Designer, Biosimulation for modeling. –Yue YU
miRNA for mRNA silence, for anticancer usage. –Fangping XIE
Microbial electricity generation. –Minghui HUANG
Protein modification for cancer treating. –Xiangmiao ZENG
Quorum sensing to detect enterovirus. –Lei QIAO
0n 05/12

Human Practice1

Invitation of a professor from Zhejiang University researching in synthesis biology.
A database software for everyone who’d like to collect the data of previous team information.
Create a flash showing the sprite of iGEM and the team of HIT.
Cartoon for spread of iGEM and synthesis biology around Harbin Institute of Technology.
In early June

Human Practice2

Song adaptation have done by Yifan WU, also made a flash linked to the Internet for sharing the iGEM happiness.
Made the first version of database software, which provides for SQL querying. But the database only includes teams from America.
In mid-July

Project selections

1. Memristor and some other electric devices by engineered bacteria.
2. Biofilm from cellulose degradation.
3. Microbial fuel cell from bacteria in industrial wastewater.
4. Environmental detection, Enterovirus.
On 05/18

Lecture

Speech given by Prof. CHEN from Zhejiang University
For introduce synthesis biology and iGEM latest hot research.
Two lectures in the Huanghe Road campus and the main campus.
After the lecture, we made recruitment of new members for iGEM_HIT.
In early March

Modeling Training

Prof. XU attending the meeting for biology modeling training.
Flux balance analysis (FBA) is a widely used approach for studying biochemical networks, in particular the genome-scale metabolic network reconstructions.
FBA is a powerful mean of biological metabolic networks.
The process of iGEM is design-modelling-experiment-design again.
Three methods:
System definition, Mass balance; Linear programming regulation
On 05/26

Human Practice2

Song adaptation have done by Yifan WU, also made a flash linked to the Internet for sharing the iGEM happiness.
Made the first version of database software, which provides for SQL querying. But the database only includes teams from America.
In mid-July

Modeling1

We searched plenty of publications for which related to mathematical modeling.
And two modeling members took responsible of each main part, detecting and killing, begin with figure out gene expression regulation.
For the next step, learning modeling software is necessary; we decided to use Matlab for main platform combining with other tools, such as cell designer.
In mid-July

Modeling2

Figure out the regulation of detecting device in mathematical method.
Peruse the related literatures to conclude the Ordinary Differential Equations for our novel design.
Simulation in matlab for getting the material curve and analyse the results.
In late July

Modeling3

Work out the regulation of killing device in mathematical method.
Conclude the Ordinary Differential Equations for our novel design from literatures.
Analyse the results from matlab curves of species variation.
Model improvement of the former part. Change the parameter of ODEs.
In early August

Column

Ying ZHANG concluded the software team of Berkeley in 2009, who build the platform for tools development of other researchers and teams.
Fangping XIE introduced the software team of USTC 2011. He elaborated the novel data structure which is named “Chain Node” model.
In June

Wiki

Reference to the former HIT_Harbin team wiki:
https://2011.igem.org/Team:HIT-Harbin
Best wiki of three areas：
https://2011.igem.org/Team:Calgary
https://2011.igem.org/Team:HokkaidoU_Japan
https://2011.igem.org/Team:Imperial_College_London

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