Team:Osaka/Human practice

From 2013.igem.org

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<p class="aaaa2">Although we did not encounter any issues with biosafety during the course of this project, a discussion of safety is mandated by the iGEM requirements so we included it here.</p>
 
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<br>
<br>
<br>
<p class="aaaa">
<p class="aaaa">
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Q1. Would any of your project ideas raise safety issues in terms of researcher safety, public safety or environmental safety ?</p>
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<FONT size="6"> E.col-Interior </FONT>
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<br>With this kit , people can enjoy the beautiful pattern E.coli make.
 +
Then maybe you wonder why E.coli can make patterns.
 +
Actually the condition of the plate (agar gel) is a bit special.
 +
It is hard (not as soft as usual plate) and there is little nutrition on it.
 +
So E.colis differ slowly consuming nutrition. And when nutrition around the front line of the colony is little , E.coli have to wait for nutrition coming from far away.
 +
When nutrition came to the front line , E.coli consume it immediately. And as the nutrition is not enough for all the E.coli , there is “E.coli which can catch and consume nutrition” and “E.coli which cannot catch nor consume” .
 +
So , the first type of E.coli grow more and more though the second type cannot grow so much.
 +
This is why we can see a “branch-like” patterns.
 +
And theoretically , we can get this pattern by computer simulation of differential equations. And , the fractal dimension of the “branch-like” colony is almost always 1,72.
 +
We hope that many people are interested not only in the beauty of the patterns but also the biological ,physical and mathematical beauty of the mechanism.
 +
</p>
<br>
<br>
<p class="aaaa">
<p class="aaaa">
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No, our project ideas do not raise any safety issue in terms of researcher safety, public safety or environmental safety. We use E.coli(K12) strain DH5α, DH10b, DH1, and DNA used in our laboratory were all of safe genes, moreover, our experiment was controlled under P1 level room. They are safe for the researcher and the environment, and they do not have any hazard outside the lab.</p>
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We have made this rearing kit for E.coli "E.CO-INTERIOR".
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<br><br>
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This year iGEM Osaka has a theme for projects.
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<p class="aaaa">
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It is "E.co-exist".
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Q2. Can your project auses risks to security through malicious misuse by individuals, groups, or countries?</p>
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People usually don't think E.coli is good.
 +
So we tried to show that E.coli can live helping each other just
 +
like human beings do. And our message is "Let's coexist with E.coli!!"
 +
Throught "E.COL-INTERIOR" ,we want everyone to enjoy beauty that E.coli naturally have.
<br>
<br>
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<p class="aaaa">
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The mind  in the name "E.COL-INTERIOR"
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No, within the compass of our imagination, our project ideas cannot be used for some malicious misuse.</p>
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<br><br>
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<p class="aaaa">
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Q3, If your project moved from a small-scale lab study to become widely used as a commercial/industrial product, what new risks might arise?</p>
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<br>
<br>
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<p class="aaaa">
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I study art persuing "beauty" of everything.
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Our project idea contains drug resistance gene. So if our project ideas widely used in society, they can accelerate the evolution of the drug-resistant bacterium.</p>
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There are many beautiful works and they have impressed me.
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<br><br>
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And there is a certain kind of arts which impress me best.
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<p class="aaaa">
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It is the God's art = the nature.
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Q4, Does your project include any design features to address safety risks?</p>
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We are mysteriously attracted by nature.
 +
"E.COL-INTERIOR" is a good example of this.
 +
"E.COL-INTERIOR" means E.coli as inteiror goods.
 +
Also, it means you can enjoy the beauty which E.coli naturally have.
 +
And this kit is the first thing that uncover Ecoli's beauty not only to scientists but also everyone.
 +
<br>Tatsuya Matsumura (iGEM OSAKA Designing Member)
 +
</p>
<br>
<br>
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<p class="aaaa">
 
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In our project, we use –ilvE E.coli strain which cannot produce isoleucine. In addition to that, we have construct apart that codes ilvE in biobrick format. They canbe used to construct an auxotrophic chassis system to prevent bio-hazard.</p>
 
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<br><br>
 
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<p class="aaaa">
 
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Q5, What safety training have you received?</p>
 
<br>
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<p class="aaaa">
<p class="aaaa">
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Our faculty adviser Prof. Kakimoto gave us safety training. It was about how we safely conduct experiments in a lab, and how we treat and dispose genetically engineered orginisms to prevent bio-hazard.</p>
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<FONT size="6"> Open Campus </FONT>
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<br><br>
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<br>We have been taught that DNA carries genetic information in school.
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<p class="aaaa">
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But, some may have had wandered if DNA really exist. And we thought it is partly because few students have experienced to extract DNA. Then, we presented a booth where students can do experiments to extract DNA from juice and plants.
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Q6, Does your institution have an Institutional Biosafety Committee, or an equivalent group? If yes, have you discussed your project with them? Describe any concerns they raised with your project, and any changes you made to your project plan based on their review.</p>
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At the same time , we introduced “what iGEM is” and our projects(2012 and 2013) by a poster. To introduce our project in 2013 , we showed a picture showing the relationship between A-type and B-type Ecoli (see “Project” page). Also we showed some mathematical models to describe how bacteria diffuse and increase on a plate.  
<br>
<br>
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<p class="aaaa">
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Ⅱ. experiments<br>
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Yes, our university has a biosafety committee which requires students and faculty alike to take a biosafety course as well as submit an application before engaging in any research activity involving genetically-modified organisms. In general, as we stuck to the 'safe' organisms of E. coli , the committee did not show any objection to our project. Here is the link to biosafety guidelines of our institution. ( http://www.osaka-u.ac.jp/jp/about/kitei/reiki_honbun/u035RG00000478.html )</p>
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i. extracting DNA from juice<br>
 +
All you need is a cup of juice and ethanol. It’s pretty easy.
 +
<br>Preparations <br>
 +
・transparent glass
 +
・20ml of 100%ethanol(cooled)
 +
・5ml of 100%juice<br>
 +
Processes<br>
 +
1. add ethanol to a glass<br>
 +
2. add juice to a glass<br>
 +
3. You can see DNA. They look like white threads.<br>
 +
<br>
 +
ⅱ. extract DNA from wild grass<br>
 +
To extract DNA from wild grass, it takes much longer and more processes than that of juice. So students have much more time to think many things to understand biology more.For example, what the procedure they are doing means or if the result of the experiment differs between one kind and another.
 +
<br>
 +
Preparations<br>
 +
・25ml of water ・1.0g of salt ・2ml of surfactant<br>
 +
・2ml of 100%ethanol ・mortar ・tea strainer<br>
 +
・two glasses<br>
 +
Processes<br>
 +
1. add wild grass to powdered dry ice and mash it in mortar <br>
 +
melt it at room temperature after freeze it<br>
 +
2. mix water, salt and surfactant <br>
 +
3. add 1 to 2 and mix softly with chopsticks<br>
 +
4. filter mixed material with tea strainer<br>
 +
5. pour filtered liquid in Eppendorf tube(1.5ml)
 +
centrifuge it at 3 minutes(precipitate　imprities)<br>
 +
6. pour supernatant liquid(6) in another Eppendorf tube(1.5ml)
 +
pour enough ethanol in it <br>
 +
7. You can see DNA that looks like white threads after a while<br>
 +
<br>
 +
Ⅲ. generalization
 +
Through these experiments, we are sure that students have more interest in biology.
 +
Actually , over 100 students came to our booth in 7hours.
 +
Almost all of iGEM OSAKA members were working for this experiment booth during the time. And all of the students said they were impressed to extract and see DNA with their hands and the experiments were really good. Some even said they want to join iGEM OSAKA someday.
 +
Our Human Practice Project in Open Campus was very successful !!
 +
</p>
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Latest revision as of 03:56, 28 September 2013

team team team team team team team team
team


E.col-Interior
With this kit , people can enjoy the beautiful pattern E.coli make. Then maybe you wonder why E.coli can make patterns. Actually the condition of the plate (agar gel) is a bit special. It is hard (not as soft as usual plate) and there is little nutrition on it. So E.colis differ slowly consuming nutrition. And when nutrition around the front line of the colony is little , E.coli have to wait for nutrition coming from far away. When nutrition came to the front line , E.coli consume it immediately. And as the nutrition is not enough for all the E.coli , there is “E.coli which can catch and consume nutrition” and “E.coli which cannot catch nor consume” . So , the first type of E.coli grow more and more though the second type cannot grow so much. This is why we can see a “branch-like” patterns. And theoretically , we can get this pattern by computer simulation of differential equations. And , the fractal dimension of the “branch-like” colony is almost always 1,72. We hope that many people are interested not only in the beauty of the patterns but also the biological ,physical and mathematical beauty of the mechanism.


We have made this rearing kit for E.coli "E.CO-INTERIOR". This year iGEM Osaka has a theme for projects. It is "E.co-exist". People usually don't think E.coli is good. So we tried to show that E.coli can live helping each other just like human beings do. And our message is "Let's coexist with E.coli!!" Throught "E.COL-INTERIOR" ,we want everyone to enjoy beauty that E.coli naturally have.
The mind in the name "E.COL-INTERIOR"
I study art persuing "beauty" of everything. There are many beautiful works and they have impressed me. And there is a certain kind of arts which impress me best. It is the God's art = the nature. We are mysteriously attracted by nature. "E.COL-INTERIOR" is a good example of this. "E.COL-INTERIOR" means E.coli as inteiror goods. Also, it means you can enjoy the beauty which E.coli naturally have. And this kit is the first thing that uncover Ecoli's beauty not only to scientists but also everyone.
Tatsuya Matsumura (iGEM OSAKA Designing Member)



Open Campus
We have been taught that DNA carries genetic information in school. But, some may have had wandered if DNA really exist. And we thought it is partly because few students have experienced to extract DNA. Then, we presented a booth where students can do experiments to extract DNA from juice and plants. At the same time , we introduced “what iGEM is” and our projects(2012 and 2013) by a poster. To introduce our project in 2013 , we showed a picture showing the relationship between A-type and B-type Ecoli (see “Project” page). Also we showed some mathematical models to describe how bacteria diffuse and increase on a plate.
Ⅱ. experiments
i. extracting DNA from juice
All you need is a cup of juice and ethanol. It’s pretty easy.
Preparations
・transparent glass ・20ml of 100%ethanol(cooled) ・5ml of 100%juice
Processes
1. add ethanol to a glass
2. add juice to a glass
3. You can see DNA. They look like white threads.

ⅱ. extract DNA from wild grass
To extract DNA from wild grass, it takes much longer and more processes than that of juice. So students have much more time to think many things to understand biology more.For example, what the procedure they are doing means or if the result of the experiment differs between one kind and another.
Preparations
・25ml of water ・1.0g of salt ・2ml of surfactant
・2ml of 100%ethanol ・mortar ・tea strainer
・two glasses
Processes
1. add wild grass to powdered dry ice and mash it in mortar
melt it at room temperature after freeze it
2. mix water, salt and surfactant
3. add 1 to 2 and mix softly with chopsticks
4. filter mixed material with tea strainer
5. pour filtered liquid in Eppendorf tube(1.5ml) centrifuge it at 3 minutes(precipitate　imprities)
6. pour supernatant liquid(6) in another Eppendorf tube(1.5ml) pour enough ethanol in it
7. You can see DNA that looks like white threads after a while

Ⅲ. generalization Through these experiments, we are sure that students have more interest in biology. Actually , over 100 students came to our booth in 7hours. Almost all of iGEM OSAKA members were working for this experiment booth during the time. And all of the students said they were impressed to extract and see DNA with their hands and the experiments were really good. Some even said they want to join iGEM OSAKA someday. Our Human Practice Project in Open Campus was very successful !!

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