Team:XMU-China/brainstorm

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<title>XMU-Brainstorm</title>
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<p class="tit">MINUTES OF THE FIRST BRAINSTORM MEETING</p>
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<p class="tit">MINUTES OF BRAINSTORM MEETING</p>
-
held at Chemistry Building 104<br>
+
<b>Place:</b> Chemistry Building 104. <br>
-
at 7:00pm, Mar 10th ~11th , 2012<br>
+
<b>Time:</b> 7:00 p.m., March 10th and 11th, 2012. <br>
-
In attendance: Zhaoshou Wang, former members &current members of XMU iGEM<br>
+
<b>In attendance:</b> Zhaoshou Wang, former and current members of XMU iGEM team.<br>  
-
To discuss the feasibility of all the ideas raised by members<br><hr>
+
<b>Aim:</b> To discuss the feasibility of all the ideas put forward by members.
-
<p class="subtitle">Group 1 : regulating cell regeneration </p>
+
<br><hr>
-
Speaker: Muxin Yu, Ruosang Qiu, Yunxin Long<br>
+
-
1.-Yu
+
-
<br>    Cell aging is related to telomerase. Telomerase may help supply a gap of the DNA synthesis mechanism. Research about cancer cell activation.<br>
+
-
2. -Qiu
+
-
Expands our project in 2011 <br>
+
-
a) Using AiiA to restrain AHL synthesis<br>
+
-
b) CcdA&CcdB:CcdA &gt;CcdB, function of CcdB is restrained;CcdA&lt;CcdB CcdB inhibit DNA gyrase<br>
+
-
3. -Long <br>
+
-
The concept of Rehabilitation, Stem cell, iPS cell, Cell Reprogramming. But there would be much obstruction using stem cells or reprogamming cells to perform iGEM experiments.<br>
+
-
Conclusion: <br>
+
-
Considering our experiment condition, the second idea is most practical. To control cells density, we can use CcdA to restraint CcdB and then release the DNA gyrase astricted by CcdB. Compared with site-directed mutagenesis and sequentialermr-PronePCR, controlling cells density in such way would be more labour-saving.<br><hr>
+
-
<p class="subtitle">Group 2:Bioscreen</p><br>
+
-
Speaker: Qingshu Wu, Yizhen Yan, Yuan He<br>
+
-
1. –Wu<br>
+
-
Literature summarize<br>
+
-
a) Circuit with Boolean logic:simple circuitintricate circuit<br>
+
-
b) About signal molecule<br>
+
-
2. –Yan<br>
+
-
a) Binary transferencoderNAND gatedigital tubes<br>
+
-
b) Density display device: A/D converter encoder digital tubes<br>
+
-
Special difficulties: constructing an operational amplifier<br>
+
-
3. –He<br>
+
-
a) How to decompose fluorescent proteins in order to recycle the displayer device? One of the idea is to use pigment to excitation fluorescence, then add some enzymes to decompose it.<br>
+
-
b) Cells immobilization embedding cells<br>
+
-
Conclusion: <br>
+
-
Some intricate circuit may be too long to express, in this case, connecting expressive gene with promoter in series or in parallel can help.
+
-
To construct recycling fluorescent device, fluorescent proteins should decompose themselves. How can we attain that?
+
-
After studying a lot of literatures, members knew more about biocomputer, and about how to transfer signals on biologic units. Yan simply drew a logic circuit which turns input signals (1 or 0) into corresponding numbers (1-9). In that way, our plan of constructing a display device will be easier to achieve. To fix the fluorescent cells, they primarily decided to embed cells in special tubes.  
+
-
Yet how to switch the number show on the screen, namely how to decompose fluorescent proteins is the primary problem. Group 2 and group 7 have started finding a solution to this problem.<br><hr>
+
-
<p class="subtitle">Group 3: Constructing engineering bacteria to produce cellulase</p>
+
-
Speaker: Chaoqun Hu, Xinzhu Tong<br>
+
-
1. It's hard to make use of cellulose<br>
+
<p class="subtitle"><a name="_Toc01" id="_Toc01"></a>Group1: Regulating Cell Regeneration</p><dl><dt>
-
2. Cellulose—endoglucanase, exoglucanase, β-1,4-glucosidase<br>
+
<b>Speakers: Muxin Yu, Ruosang Qiu, Yunxin Long</b></dt><br><b>
-
3. The case of University of Edinburgh in 2007: Intracellular proteins are not able to excrete by themselves. How to solve this problem? <br>
+
1. –Muxin Yu</b></dt>
-
To do research about:<br>
+
<dd>Cell aging is related to telomerase. Telomerase may help supply a gap of the DNA synthesis mechanism. Besides, she described some research about cancer cell activation.</dd><br>
-
a) Ways of cells secreting proteins <br>
+
<dt><b>2. –Ruosang Qiu</b></dt>
 +
<dd>Expands the project of 2011 XMU iGEM team.<br>
 +
a) Using AiiA to restrain AHL synthesis.<br>
 +
b) CcdA and ccdB: If ccdA&gt;ccdB, the function of ccdB is restrained; If ccdA&lt;ccdB, ccdB will inhibit DNA gyrase. </dd><br>
 +
<dt><b>3. –Yunxin Long</b></dt>
 +
<dd>The concept of rehabilitation, stem cell, IPS cell, cell reprogramming. And there would be many obstructionusing stem cells or reprogamming cells to perform iGEM experiments. </dd><br>
 +
<dt><b>Conclusion:</b></dt><br>
 +
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Considering our experiment condition, the second idea is the most practical. To control cells density, we can use ccdA to restraint ccdB and then release the DNA gyrase astricted by ccdB. Compared with site-directed mutagenesis and sequentialermr prone PCR, controlling cells density in that way would be more labour-saving.</dd></dl><hr>
 +
 
 +
<p class="subtitle"><a name="_Toc02" id="_Toc02"></a>Group 2: Bioscreen</p>
 +
<dl><dt><b>
 +
Speakers: Qingshu Wu, Yizhen Yan, Yuan He</b></dt><br>
 +
<dt><b>1. –Qingshu Wu</b></dt>
 +
<dd>Literature summarize. <br>
 +
a) Circuit with Boolean logic: simple circuit &rarr; intricate circuit. <br>
 +
b) About signal molecule. </dd><br>
 +
<dt><b>2. –Yizhen Yan</b></dt>
 +
<dd>a) Binary transfer &rarr; encoder &rarr; nand gate &rarr; digital tubes. <br>
 +
b) Density display device: A/D converter &rarr; encoder&rarr; digital tubes.
 +
Special difficulties: Constructing an operational amplifier. </dd><br>
 +
<dt><b>3. –Yuan He</b></dt><dd>
 +
a) How to decompose fluorescent proteins in order to recycle the displayer device? One of the ideas is to use pigment to stimulate fluorescence, and then add some enzymes to decompose it.<br>
 +
b) Cells immobilization &rarr; embedding cells. </dd><br>
 +
<dt><b>Conclusion: </b></dt><br>
 +
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Some intricate circuit may be too long to express. In this case, connecting expressive gene with promoter in series or in parallel can help.
 +
<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;To construct recycling fluorescent device, fluorescent proteins should decompose themselves. How can we attain that?<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;After studying a lot of literatures, members knew more about biocomputer and how to transfer signals in biologic units. Yan drew a logic circuit simply which turns input signals (1 or 0) into corresponding numbers (1-9). In this way, our goal of constructing a display device will be easier to reach. To fix the fluorescent cells, they primarily decided to embed cells in special tubes.<br>
 +
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;But how to switch the number showing on the screen, namely how to decompose fluorescent proteins is the primary problem. Group 2 and Group 7 have started to find a solution to this problem.</dd></dl><hr>
 +
 
 +
<p class="subtitle"><a name="_Toc03" id="_Toc03"></a>Group 3: Constructing Engineering Bacteria to Produce Cellulose</p><dl>
 +
<dt><b>Speakers:  Chaoqun Hu, Xinzhu Tong</b></dt><br>
 +
<dd>1. It's hard to make use of cellulose. <br>
 +
2. Cellulose — endoglucanase, exoglucanase, β-1,4-glucosidase. <br>
 +
3. The project of University of Edinburgh in 2007: Intracellular proteins are not able to excrete by themselves. How to solve this problem? </dd>
 +
<p>To do research about: <dd>
 +
a) Ways of cells secreting proteins. <br>
b) How do original cells excrete cellulose?<br>
b) How do original cells excrete cellulose?<br>
-
c) In nature, how do living beings utilize cellulose ?<br>
+
c) In nature, how do living beings utilize cellulose?</dd><br></dd>
-
What's the advantages of this plan?<br>
+
What are the advantages of this plan?<br></p>
-
Conclusion:<br>
+
<dt><b>Conclusion: </b></dt><br><dd>
-
After studying literatures, members of group 3 learn about ege gene and Bgat1 gene that published in2012, which can be used to produce cellulase. Generally in the process of producing cellulose, some enzymes must be added for lysis, and then release cellulase out of cells. <br>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;After studying literatures, the members of Group 3 learned about ege gene and Bgat1 gene that published in 2012, which can be used to produce cellulose. Generally in the process of producing cellulose, some enzymes must be added for lysis, and then release cellulose out of cells. <br>
-
Group 3 members hoped to utilize the device controlling cell density which were constructed last year, and exchange ccdB to another gene which will let cells decompose themselves. Thus our engineering bacteria will not only produce cellulase with quorum sensing, and release it out of cells. Besides, group 3 are trying to construct a secreting routeway, hoping to produce cellulase without cell discruption.<br><hr>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The members of Group 3 hoped to utilize the device controlling cell density which was constructed last year, and exchange ccdB to another gene which will let cells themselves decompose. Thus our engineering bacteria will not only produce cellulose with quorum sensing but also release it out of cells. Besides, the members of Group 3 are trying to construct a secreting route way and hoping to produce cellulose without cell disruption. </dd></dl><hr>
-
<p class="subtitle">Group 4: photosynthetic bacterium(PSB) utilization</p>
+
 
-
Speaker: Zhao Ma, Hong Sun, Youbin Mo<br>
+
<p class="subtitle"><a name="_Toc04" id="_Toc04"></a>Group 4: Photosynthetic Bacterium (PSB) Utilization</p><dl><dt><b>
-
1. –Ma<br>
+
Speakers: Zhao Ma, Hong Sun, Youbin Mo</b></dt><br>
-
a) photosynthetic bacteria<br>
+
<dt><b>1. –Zhao Ma</b></dt>
-
b) Mechanism of photosynthesis of purple bacterium<br>
+
<dd>
-
c) The case of California Institute of Technology in 2011<br>
+
a) Photosynthetic bacteria. <br>
-
2. –Sun<br>
+
b) Mechanism of photosynthesis of purple bacterium. <br>
-
a) Cyclic photophosphorylation<br>
+
c) The case of California Institute of Technology in 2011. </dd><br>
-
b) Nitrogen fixation<br>
+
<dt><b>2. –Hong Sun</b></dt>
-
3. –Mo<br>
+
<dd>
-
a) Metabolism of acrylamide<br>
+
a) Cyclic photophosphorylation. <br>
-
b) Utilize of light energy: bacteriaamylose/proteinenergy<br>
+
b) Nitrogen fixation. </dd><br>
-
c) Finding usable bacteria<br>
+
<dt><b>3. –Youbin Mo</b></dt><dd>
-
Conclusion:<br>
+
a) Metabolism of acryl amide. <br>
-
Group 4 firstly introduced photosynthesis and its 3 major metabolic pathways. It's arduously to clone these pathways, so they are considering constructing some biobricks, which help to transform the organics that photosynthetic bacteria cannot utilize to another matter that can be utilize. Thus some organics can be decomposed by our engineering bacteria.<br><hr>
+
b) Utilize of light energy: bacteria &rarr;  amylase/protein &rarr;  energy. <br>
-
<p class="subtitle">Group 5: Utilizing engineering bacteria of quorum sensing (QS) system to increase Natamycin production </p>
+
c) Finding usable bacteria. </dd><br>
-
Speaker: Rong Fan, Qian Liang, Xinyi Yao<br>
+
<dt><b>Conclusion: </b></dt><br>
-
1. –Fan<br>
+
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Group 4 firstly introduced photosynthesis and its 3 major metabolic pathways. It's arduously to clone these pathways, so they are considering constructing some Biobricks, which help to transform the organics that photosynthetic bacteria cannot utilize to another matter that can be utilized. Thus some organics can be decomposed by our engineering bacteria. </dd></dl><hr>
-
a) Mechanism of bacteria quorum sensing (QS)<br>
+
 
-
b) GBL(Gamma-butyrolactone) signaling molecules<br>
+
<p class="subtitle"><a name="_Toc05" id="_Toc05"></a>Group 5: Utilizing Engineering Bacteria of Quorum Sensing  System to Increase Natamycin Production</p>
-
c) About Natamycin<br>
+
<dl><dt><b>Speakers: Rong Fan, Qian Liang, Xinyi Yao</b></dt><br>
-
2. –Liang<br>
+
<dt><b>1. –Rong Fan</b></dt><dd>
-
a) Regulatory genes—pimM and pimR<br>
+
a) Mechanism of bacteria quorum sensing (QS). <br>
-
b) High-efficiency production of Natamycin<br>
+
b) GBL (gamma-butyrolactone) signaling molecules. <br>
-
Key points:<br>
+
c) About natamycin. </dd><br>
-
1) Is it viable for mass-producing?<br>
+
<dt><b>2. –Qian Liang</b></dt><dd>
-
2) Negative feedback& positive feedback<br>
+
a) Regulatory genes — <i>pimM</i> and <i>pimR</i>.  <br>
-
3) Association of quorum sensing and pimM expression<br>
+
b) High-efficiency production of natamycin. </dd><br>
-
Conclusion:<br>
+
<dt><b>Key points:</b></dt>
-
Group 5 mainly searched information about increasing the production of Natamycin. But they didn't study about E coli's intracellular expression. Besides, they didn't mention of the advantages of utilizing quorum sensing (QS) system to produce metabolite. Therefore, in the following days, group 5 members should find answers to the two questions through studying literatures.<br><hr>
+
<dd>
-
<p class="subtitle">Group 6: Secretive expression of recombinant Barnase by <i>E.coli</i></p>
+
1) Is it viable for mass-producing? <br>
-
Speaker: Que Huang, Zhibin Gu<br>
+
2) Negative feedback and positive feedback. <br>
-
1. barnase,barstar, RNase<br>
+
3) Association of quorum sensing and <i>pimM</i> expression. </dd><br>
-
2. Cancer cellsacidityseparationdeath<br>
+
<dt><b>Conclusion:</b></dt><br>
-
Normal cellsbasicity non separation<br>
+
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Group 5 mainly searched information about increasing the production of natamycin. But they didn't study about the intracellular expression of E coli. Besides, they didn't mention of the advantages of utilizing quorum sensing (QS) system to produce metabolite. Therefore, in the following days, the members of Group 5 should find answers to the two questions through studying literatures. </dd></dl><hr>
-
3. Cloning strategies of Barnase gene
+
 
-
high fidelity PCR, why any error?
+
<p class="subtitle"><a name="_Toc06" id="_Toc06"></a>Group 6: Secretive Expression of Recombinant Barnase by <i>E.coli</i></p><dl><dt><b>
-
4. Secretive expression and Kil-Km Secretive box<br>
+
Speakers: Que Huang, Zhibin Gu</b></dt><br><dd>
-
Conclusion:<br>
+
1. Barnase, barstar, RNase. <br>
-
Barnase is a kind of RNase. It's toxic and it will cause cells death. Barstar is the depressor of Barnase. These two proteins interact and then neutralize the toxicity of Barnase. Group 6 members introduced barnase and barstar from various aspects, and told their applied prospect. Whereas they didn't learn about any problem in the process of producing Barnase, so we don't know what Synthetic biology can help to improve it. What's more, just to construct a biobrick to produce Barnase seems of not much value. <br>
+
2. Cancer cells &rarr;  acidity &rarr;  separation &rarr;  death. <br>
-
After discussion, we suggest group 6 members study about some difficulty in the productive process of Barnase, and try to communicate with group 5, finding our advantages of utilizing quorum sensing. Besides, Huang introduced some information of Kil-Km Secretive box, which can accelerate secreting proteins out of cells. So we hope them to exchange information with group 3 and help them to find secretive pathways.<br><hr>
+
&nbsp;&nbsp;&nbsp;&nbsp;Normal cells &rarr;  basicity &rarr;  non separation. <br>
-
<p class="subtitle">Group 7: Modulating the concentration of tricolor fluorescent proteins to show different colors</p>
+
3. Cloning strategies of barnase gene. <br>
-
Speaker: Zhenan Zheng, Sifan Wang, Jianzhao Chi
+
&nbsp;&nbsp;&nbsp;&nbsp;Are there any errors in high fidelity PCR and why? <br>
-
1. –Zheng <br>
+
4. Secretive expression and Kil-Km secretive box</dd><br>
-
Fluorescence resonance energy transfer (FRET)<br>
+
<dt><b>Conclusion: </b></dt><br>
-
a) Dual color FRET: Constructing fusion proteins are required<br>
+
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Barnase is a kind of RNase. It's toxic and will cause cells death. Barstar is the depressor of barnase. These two proteins interact and then neutralize the toxicity of barnase. The members of Group 6 introduced barnase and barstar from various aspects, such as their applied prospect. Whereas they didn't learn about any problem in the process of producing barnase, so we don't know whether synthetic biology can help to improve it. What's more, just to construct a Biobrick to produce barnase seems of not much value.<br>
-
b) Multicolor FRET: To detect base mispairing<br>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;After discussion, we suggested the members of group 6 to study about some difficulties in the productive process of barnase and try to communicate with Group 5, in order to find our advantages of utilizing quorum sensing. Besides, Huang introduced some information of Kil-Km secretive box, which can accelerate secreting proteins out of cells. So we hoped them to exchange information with Group 3 and help them to find secretive pathways. </dd></dl><hr>
-
2. –Wang<br>
+
 
 +
<p class="subtitle"><a name="_Toc07" id="_Toc07"></a>Group 7: Modulating the Concentration of Tricolor Fluorescent Proteins to Show Different Colors</p><dl>
 +
<dt><b>Speakers: Zhenan Zheng, Sifan Wang, Jianzhao Chi</b></dt><br>
 +
<dt><b>
 +
1. –Zhenan Zheng</b></dt><dd>
 +
Fluorescence resonance energy transfer (FRET). <br>
 +
a) Dual color FRET: Constructing fusion proteins is required. <br>
 +
b) Multicolor FRET: To detect base mispairing. </dd><br>
 +
<dt><b>2. –Sifan Wang</b></dt><dd>
Unstable fluorescent protein<br>
Unstable fluorescent protein<br>
-
To add peptide tail after GFP so as to be identified and decomposed by intracellular proteinase. The key lies in controlling and modulating the fluorescence intensity and the degradation velocity.<br>
+
Add peptide tail after GFP so that it can be identified and decomposed by intracellular proteinase. The key lies in controlling and modulating the fluorescence intensity and the degradation velocity. </dd><br>
-
3. –Chi<br>
+
<dt><b>3. –Jianzhao Chi</b></dt><dd>
-
Function of some Nano antibiotics: Modifying GFP's character.<br>
+
Function of some nano antibiotics: Modifying GFP's character. </dd><br>
-
Conclusion:<br>
+
<dt><b>Conclusion: </b></dt><br>
-
Study of group 7 focused on the choke point of this project: The degradation of fluorescent proteins, i.e. how to switch from one color to another. This Problem was also mentioned by group 2. How to switch from number A to number B when constructing a bioscreen? After studying literatures, group 7 put forward three probable proposals.<br>
+
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Group 7 focused on the choke point of this project: The degradation of fluorescent proteins, i.e. how to switch from one color to another. This problem was mentioned by Group 2 as well. How to switch from number A to number B when constructing a bio-screen? After studying literatures, Group 7 put forward three probable proposals.<br><dd>
-
1) FRET mechanism<br>
+
1) FRET mechanism. <br>
-
2) Unstable fluorescent protein<br>
+
2) Unstable fluorescent protein. <br>
-
3) Utilizing Nano antibiotics to regulate fluorescent protein<br>
+
3) Utilizing nano antibiotics to regulate fluorescent protein. <br></dd>
-
After discussion, we thought the proposal two is relatively viable. For proposal one, mutual interference between yellow and blue lights is a hidden trouble. And the catabolic enzymes of Nano antibiotics mentioned in proposal three may be not easy to find.<br>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;After discussion, we thought the second proposal is relatively viable. For the first proposal, mutual interference between yellow and blue lights is a hidden trouble. And the catabolic enzymes of nano antibiotics mentioned in the third proposal may be not easy to find.<br>
-
So group 7 is suggested to study further about unstable fluorescent protein and peptide tail. But all of the three proposals are worth trying, and group 7's study results can act as reference of group 2's project—bioscreen.<br><hr>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;So the members of Group 7 are suggested to study further about unstable fluorescent protein and peptide tail. But all the three proposals are worth trying. And the study results of Group 7 can act as reference of the project of Group 2 — Bioscreen.  
-
<p class="subtitle">Group 8: Utilizing aptamers biobrick to construct biosensor</p>
+
</dd></dl><br><hr>
-
Speaker: Shuqin Hu, Mouzhe Xie, Zebo Hu<br>
+
 
-
1. – Shuqin<br>
+
 
-
a) Aptamers: widespread use in electrochemistry field, but it's application in biosome is still in initial stage.<br>
+
<p class="subtitle"><a name="_Toc08" id="_Toc08"></a>Group 8: Utilizing Aptamers Biobrick to Construct Biosensor</p><dl><dt><b>
-
b) Estrogen sensor<br>
+
Speakers: Shuqin Hu, Mouzhe Xie, Zebo Hu</b></dt><br><dt><b>1. –Shuqin Hu</b></dt><dd>
-
2. –Mouzhe<br>
+
a) Aptamer: It is widespread used in electrochemistry field, but its application in biosome is still in initial stage. <br>
-
in vitroin vivo<br>
+
b) Estrogen sensor. </dd><br>
-
     What's the relationship between the biosensor and Synthetic biology?
+
<dt><b>2. –Mouzhe Xie</b></dt><dd>
-
a) Constructing probe molecules. Whereas it may be difficult to construct, because single chains are not stable <br>
+
In vitro &rarr;  in vivo<br>
-
b) Application in microbe. Introducing unstable single chains may lead to degradation.<br>
+
     What's the relationship between the biosensor and synthetic biology? <br>
-
3. –Zebo<br>
+
a) Constructing probe molecules. Whereas it may be difficult to construct, because single chains are not stable<br>
 +
b) Application in microbe. Introducing unstable single chains may lead to degradation. </dd><br>
 +
<dt><b>3. –Zebo Hu</b></dt><dd>
Feasibility analysis<br>
Feasibility analysis<br>
-
a) SELEX (systematic evolution of ligands by exponential enrichment)<br>
+
a) SELEX ( systematic evolution of ligands by exponential enrichment ) <br>
-
b) Comparing aptamers with antibiotics<br>
+
b) Comparing aptamers with antibiotics Better in stability and affinity; more extensive and more sensitive targets. </dd><br>
-
Better in stable, affinity; more extensive and more sensitive targets.<br>
+
 
-
Conclusion:<br>
+
<dt><b>Conclusion: </b></dt><br>
-
Group 8 members told us the definition of aptamer and biosensor, and introduced the project of Pro. Yang Zhaoyong's group. Whereas they found that aptamer biosensors and Synthetic biology have little conjunction. At present, aptamer biosensors are usually selected in vitro, for example attaching on surface of an electrode.<br>
+
<dd>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;The members of Group 8 told us the definition of aptamer and biosensor, and introduced the project of Professor Zhaoyong Yang's group. Whereas they found that aptamer biosensors and synthetic biology had little conjunction. At present, aptamer biosensors are usually selected in vitro, such as attaching on surface of an electrode.<br>
-
If we want to do research of aptamer biosensors in vivo, there will be two ways:<br>
+
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;If we want to do research about aptamer biosensors in vivo, there will be two ways:<br><dd>
-
1) To construct it in microbe, and let it transcribe single chains we need for making biosensor. But single chains are not stable. So this plan needs further research.<br>
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1) Construct them in microbe, and let them transcribe single chains for making biosensor. But single chains are not stable. So this plan needs further research.<br>
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2) To select aptamers we need in vitro, then transform it in vivo, meanwhile its function of sensor should be maintained.<br>
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2) Select aptamers we need in vitro then transform it in vivo, meanwhile its function of sensor should be maintained.After discussion, we thought both of the two means are of great difficulty. The members of Group 8 can ask Teacher Wang and Professor Yang for help that seeking for the bonding point of aptamer biosensors and synthetic biology or Biobrick. </dd></dd></dl>
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After discussion, we thought the two means are both of great difficulty. Group 8 can ask teacher Wang and Pro. Yang for help, seeking for the bonding point of aptamer biosensor and Synthetic biology or biobrick.<br>
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<div id="fin">
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After the brainstorm meeting this week, members from different groups still keep doing paper research. Group meeting was held every week during which group members could share their ideas and disscuss their project. Finally, group 2's project 'cell display' stand out from the rest due to its fancy idea. We constructed and characterized our device over this summer so you can see the wonderful E.lumoli now.</div>

Latest revision as of 19:35, 26 September 2012

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Contents[hide][show]
  • Group 1: Regulating Cell Regeneration
  • Group 2: Bioscreen
  • Group 3: Cellulose produced in E.coli
  • Group 4: Photosynthetic E.coli
  • Group 5: Antibiotic produced in E.coli
  • Group 6: Barnase produced in E.coli
  • Group 7:Tricolor E.coli
  • Group 8:Aptamers Biobrick in Biosensor
  • XMU-Brainstorm

    MINUTES OF BRAINSTORM MEETING

    Place: Chemistry Building 104.
    Time: 7:00 p.m., March 10th and 11th, 2012.
    In attendance: Zhaoshou Wang, former and current members of XMU iGEM team.
    Aim: To discuss the feasibility of all the ideas put forward by members.

    Group1: Regulating Cell Regeneration

    Speakers: Muxin Yu, Ruosang Qiu, Yunxin Long

    1. –Muxin Yu
    Cell aging is related to telomerase. Telomerase may help supply a gap of the DNA synthesis mechanism. Besides, she described some research about cancer cell activation.

    2. –Ruosang Qiu
    Expands the project of 2011 XMU iGEM team.
    a) Using AiiA to restrain AHL synthesis.
    b) CcdA and ccdB: If ccdA>ccdB, the function of ccdB is restrained; If ccdA<ccdB, ccdB will inhibit DNA gyrase.

    3. –Yunxin Long
    The concept of rehabilitation, stem cell, IPS cell, cell reprogramming. And there would be many obstructionusing stem cells or reprogamming cells to perform iGEM experiments.

    Conclusion:

         Considering our experiment condition, the second idea is the most practical. To control cells density, we can use ccdA to restraint ccdB and then release the DNA gyrase astricted by ccdB. Compared with site-directed mutagenesis and sequentialermr prone PCR, controlling cells density in that way would be more labour-saving.

    Group 2: Bioscreen

    Speakers: Qingshu Wu, Yizhen Yan, Yuan He

    1. –Qingshu Wu
    Literature summarize.
    a) Circuit with Boolean logic: simple circuit → intricate circuit.
    b) About signal molecule.

    2. –Yizhen Yan
    a) Binary transfer → encoder → nand gate → digital tubes.
    b) Density display device: A/D converter → encoder→ digital tubes. Special difficulties: Constructing an operational amplifier.

    3. –Yuan He
    a) How to decompose fluorescent proteins in order to recycle the displayer device? One of the ideas is to use pigment to stimulate fluorescence, and then add some enzymes to decompose it.
    b) Cells immobilization → embedding cells.

    Conclusion:

         Some intricate circuit may be too long to express. In this case, connecting expressive gene with promoter in series or in parallel can help.
         To construct recycling fluorescent device, fluorescent proteins should decompose themselves. How can we attain that?
         After studying a lot of literatures, members knew more about biocomputer and how to transfer signals in biologic units. Yan drew a logic circuit simply which turns input signals (1 or 0) into corresponding numbers (1-9). In this way, our goal of constructing a display device will be easier to reach. To fix the fluorescent cells, they primarily decided to embed cells in special tubes.
         But how to switch the number showing on the screen, namely how to decompose fluorescent proteins is the primary problem. Group 2 and Group 7 have started to find a solution to this problem.

    Group 3: Constructing Engineering Bacteria to Produce Cellulose

    Speakers: Chaoqun Hu, Xinzhu Tong

    1. It's hard to make use of cellulose.
    2. Cellulose — endoglucanase, exoglucanase, β-1,4-glucosidase.
    3. The project of University of Edinburgh in 2007: Intracellular proteins are not able to excrete by themselves. How to solve this problem?

    To do research about:

    a) Ways of cells secreting proteins.
    b) How do original cells excrete cellulose?
    c) In nature, how do living beings utilize cellulose?

    What are the advantages of this plan?

    Conclusion:

         After studying literatures, the members of Group 3 learned about ege gene and Bgat1 gene that published in 2012, which can be used to produce cellulose. Generally in the process of producing cellulose, some enzymes must be added for lysis, and then release cellulose out of cells.
         The members of Group 3 hoped to utilize the device controlling cell density which was constructed last year, and exchange ccdB to another gene which will let cells themselves decompose. Thus our engineering bacteria will not only produce cellulose with quorum sensing but also release it out of cells. Besides, the members of Group 3 are trying to construct a secreting route way and hoping to produce cellulose without cell disruption.

    Group 4: Photosynthetic Bacterium (PSB) Utilization

    Speakers: Zhao Ma, Hong Sun, Youbin Mo

    1. –Zhao Ma
    a) Photosynthetic bacteria.
    b) Mechanism of photosynthesis of purple bacterium.
    c) The case of California Institute of Technology in 2011.

    2. –Hong Sun
    a) Cyclic photophosphorylation.
    b) Nitrogen fixation.

    3. –Youbin Mo
    a) Metabolism of acryl amide.
    b) Utilize of light energy: bacteria → amylase/protein → energy.
    c) Finding usable bacteria.

    Conclusion:

         Group 4 firstly introduced photosynthesis and its 3 major metabolic pathways. It's arduously to clone these pathways, so they are considering constructing some Biobricks, which help to transform the organics that photosynthetic bacteria cannot utilize to another matter that can be utilized. Thus some organics can be decomposed by our engineering bacteria.

    Group 5: Utilizing Engineering Bacteria of Quorum Sensing System to Increase Natamycin Production

    Speakers: Rong Fan, Qian Liang, Xinyi Yao

    1. –Rong Fan
    a) Mechanism of bacteria quorum sensing (QS).
    b) GBL (gamma-butyrolactone) signaling molecules.
    c) About natamycin.

    2. –Qian Liang
    a) Regulatory genes — pimM and pimR.
    b) High-efficiency production of natamycin.

    Key points:
    1) Is it viable for mass-producing?
    2) Negative feedback and positive feedback.
    3) Association of quorum sensing and pimM expression.

    Conclusion:

         Group 5 mainly searched information about increasing the production of natamycin. But they didn't study about the intracellular expression of E coli. Besides, they didn't mention of the advantages of utilizing quorum sensing (QS) system to produce metabolite. Therefore, in the following days, the members of Group 5 should find answers to the two questions through studying literatures.

    Group 6: Secretive Expression of Recombinant Barnase by E.coli

    Speakers: Que Huang, Zhibin Gu

    1. Barnase, barstar, RNase.
    2. Cancer cells → acidity → separation → death.
        Normal cells → basicity → non separation.
    3. Cloning strategies of barnase gene.
        Are there any errors in high fidelity PCR and why?
    4. Secretive expression and Kil-Km secretive box

    Conclusion:

         Barnase is a kind of RNase. It's toxic and will cause cells death. Barstar is the depressor of barnase. These two proteins interact and then neutralize the toxicity of barnase. The members of Group 6 introduced barnase and barstar from various aspects, such as their applied prospect. Whereas they didn't learn about any problem in the process of producing barnase, so we don't know whether synthetic biology can help to improve it. What's more, just to construct a Biobrick to produce barnase seems of not much value.
         After discussion, we suggested the members of group 6 to study about some difficulties in the productive process of barnase and try to communicate with Group 5, in order to find our advantages of utilizing quorum sensing. Besides, Huang introduced some information of Kil-Km secretive box, which can accelerate secreting proteins out of cells. So we hoped them to exchange information with Group 3 and help them to find secretive pathways.

    Group 7: Modulating the Concentration of Tricolor Fluorescent Proteins to Show Different Colors

    Speakers: Zhenan Zheng, Sifan Wang, Jianzhao Chi

    1. –Zhenan Zheng
    Fluorescence resonance energy transfer (FRET).
    a) Dual color FRET: Constructing fusion proteins is required.
    b) Multicolor FRET: To detect base mispairing.

    2. –Sifan Wang
    Unstable fluorescent protein
    Add peptide tail after GFP so that it can be identified and decomposed by intracellular proteinase. The key lies in controlling and modulating the fluorescence intensity and the degradation velocity.

    3. –Jianzhao Chi
    Function of some nano antibiotics: Modifying GFP's character.

    Conclusion:

         Group 7 focused on the choke point of this project: The degradation of fluorescent proteins, i.e. how to switch from one color to another. This problem was mentioned by Group 2 as well. How to switch from number A to number B when constructing a bio-screen? After studying literatures, Group 7 put forward three probable proposals.
    1) FRET mechanism.
    2) Unstable fluorescent protein.
    3) Utilizing nano antibiotics to regulate fluorescent protein.
         After discussion, we thought the second proposal is relatively viable. For the first proposal, mutual interference between yellow and blue lights is a hidden trouble. And the catabolic enzymes of nano antibiotics mentioned in the third proposal may be not easy to find.
         So the members of Group 7 are suggested to study further about unstable fluorescent protein and peptide tail. But all the three proposals are worth trying. And the study results of Group 7 can act as reference of the project of Group 2 — Bioscreen.


    Group 8: Utilizing Aptamers Biobrick to Construct Biosensor

    Speakers: Shuqin Hu, Mouzhe Xie, Zebo Hu

    1. –Shuqin Hu
    a) Aptamer: It is widespread used in electrochemistry field, but its application in biosome is still in initial stage.
    b) Estrogen sensor.

    2. –Mouzhe Xie
    In vitro → in vivo
    What's the relationship between the biosensor and synthetic biology?
    a) Constructing probe molecules. Whereas it may be difficult to construct, because single chains are not stable.
    b) Application in microbe. Introducing unstable single chains may lead to degradation.

    3. –Zebo Hu
    Feasibility analysis
    a) SELEX ( systematic evolution of ligands by exponential enrichment )
    b) Comparing aptamers with antibiotics Better in stability and affinity; more extensive and more sensitive targets.

    Conclusion:

         The members of Group 8 told us the definition of aptamer and biosensor, and introduced the project of Professor Zhaoyong Yang's group. Whereas they found that aptamer biosensors and synthetic biology had little conjunction. At present, aptamer biosensors are usually selected in vitro, such as attaching on surface of an electrode.
         If we want to do research about aptamer biosensors in vivo, there will be two ways:
    1) Construct them in microbe, and let them transcribe single chains for making biosensor. But single chains are not stable. So this plan needs further research.
    2) Select aptamers we need in vitro then transform it in vivo, meanwhile its function of sensor should be maintained.After discussion, we thought both of the two means are of great difficulty. The members of Group 8 can ask Teacher Wang and Professor Yang for help that seeking for the bonding point of aptamer biosensors and synthetic biology or Biobrick.
    After the brainstorm meeting this week, members from different groups still keep doing paper research. Group meeting was held every week during which group members could share their ideas and disscuss their project. Finally, group 2's project 'cell display' stand out from the rest due to its fancy idea. We constructed and characterized our device over this summer so you can see the wonderful E.lumoli now.