Difference between revisions of "Team:Kyoto/Project"

 
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     <span class="box-title"><font face="Segoe UI">Table of contents</font></span>
 
     <span class="box-title"><font face="Segoe UI">Table of contents</font></span>
 
           <ul class="index1">
 
           <ul class="index1">
             <li><a href="#Motivation"><b>●Motivation</b></a></li>
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             <li><a href="#Motivation">1) Motivation</a></li>
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            <li><a href="#Let's create a system that absorbs salt from a liquid using genetically modified yeast
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">2) Let's create a system that absorbs salt from a liquid using genetically modified yeast
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</a></li>
  
             <li><a href="#Na+濃度が関わる様々な生命現象">1)<b> Na+濃度が関わる様々な生命現象(RNAフォールディング、タンパク質の結合…と文献をつけながら挙げる。各々に細かくは触れない)</b></a></li>
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             <li><a href="#Aggregation system for increasing the efficiency of recollection and biosafety">3) Aggregation system for raising the efficiency of recollection and biosafety</a></li>
  
             <li><a href="#Pines are being lost due to pine-wilt disease"><font color="#fffafa"><font face="Segoe UI">2) <b>生物がもつトランスポーターの特異性(化学的な膜では特定のイオンを選択的に除くのは難しい)</b></font></a></li>
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             <li><a href="#Calculating the amount of yeast necessary to lower the concentration through mathematical modeling">4) Calculating the amount of yeast necessary to lower the concentration through mathematical modeling</a></li>
 
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            <li><a href="#The cause of pine-wilt disease is a tiny nematode">3) <b>酵母を用いた塩吸収システム(必要なエネルギーが小さいこと、エネルギー効率がいいこと、イオンの自由選択的除去ができること、フィルター交換がいらないこと、立地上の制限が小さいこと、など利点を挙げる)</b></a></li>
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            <li><a href="#It is difficult to prevent the spread of">4)<b>回収効率上昇のための凝集システム</b></font></a></li>
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            <li><a href="#RNAi is a powerful weapon to fight against the nematodes">5)<b> モデリングを介した目的濃度まで下げるのに必要な酵母量の算出</b></a></li>
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           </ul>
 
           </ul>
 
           </div>
 
           </div>
  
<ol style="margin-left:10%; size:80%"><img src="https://static.igem.org/mediawiki/2018/0/0d/T--Kyoto--Motivation.png" alt=""></ol>
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<h5 id="Motivation">1) Motivation</h5>
 
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<p>&emsp; Protein interactions, enzymatic reactions, folding of RNA, riboswitches... nearly all of these biological reactions are greatly affected by salt concentation. Salt concentration is also important for most biological devices designed by synthetic biologists. Synthetic biologist try to develope new devices that provide solutions to our daily problems in the world. However, the situations and circumstances vary greatly among each problem, often resulting in undesired salt concentrations. If the salt concentration is insufficient in the surrounding environment for a developing device, adding salt to the culture solution may solve a problem.<br><br>&emsp; But how about when salt concentrations are too high? This is a difficult problem to solve. Once devices that absorb salt from environment are developed, we can greatly support various functions of other devices, for example, sensing substances in the environment or bioremediation. Besides, if we can apply salt-absorbing device to the situation outside the laboratory, there is a possibility that it will be useful for purifying water in various scenes such as industrial wastewater and salt damage. <br>
<p>Na+濃度はRNAフォールディング(文献有)、DNAの2重鎖構造(文献つける必要)、タンパク質間の相互作用に大きな影響を与える。そしてiGEMerたちは海水中から重金属を回収したり、タンパク質間の作用を利用して何かを検出するデバイスを作成したりする。つまり、iGEMチームが開発するツールは、過酷な状況に置かれたり、Na+濃度を減らす必要があったりする。それらの効果を最大限に発揮するためにその生物の耐塩性を向上させたりNa+濃度を調節したりする必要がある。今年、私たちiGEM Kyotoは過酷な状況でも生育できたり、Na+を回収したりする酵母の作成に挑みました。(H&Pの意見を取り入れ)バイオセーフティーのために酵母を凝集させることも目指しました。</p>
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 Although this has a great possibility, the question of how feasible is this environmental desalination using synthetic biology principles has never been explored thoroughly. Therefore, we addressed this problem this year.
 
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</p>
  <h5 id="Na+濃度が関わる様々な生命現象"> Na+濃度が関わる様々な生命現象</h5>
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<center><img src="https://static.igem.org/mediawiki/2018/5/58/T--Kyoto--Description.png" width="30%"></center>
<p>イントロダクションで述べたようにNa+濃度はmacromoleculeの反応性にとても重要な影響を及ぼす。濃度が適切でないとRNAフォールディングはうまくなされないし、濃度が高いと分子同士の結合が阻害される一方で、低いと非特異的な結合が多くなる。例えば、私たちが数種類の塩濃度条件下でGPFのpull down assayを行ったところ、そのような結果が得られた(More detail is Here (GFPパーツE1010へのリンク))</p>
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<center>RNAフォールディングとか、タンパク質間の作用のイラスト</center>
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<h5 id="Let's create a system that absorbs salt from a liquid using genetically modified yeast"> <b>2) Let's create a system that absorbs salt from a liquid using genetically modified yeast</h5></b>
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<p>&emsp; Some salt-tolerant plants have developed systems that sequester Na+ from the cytoplasm to vacuoles in order to protect themselves from Na+ flowing in. In addition, some plants have gained Na+ tolerance system by producing compatible solutes. In the process of searching papers, we noticed that many genes involved in Na+ sequestration were also shown to function in budding yeast and give them salt tolerance. The budding yeast itself also has a mechanism for exporting Na+ out of the cell.  It is also known that budding yeasts, in which Na+-exporting genes have been destroyed and the mechanism are failed, are very sensitive to the high salt concentration in the medium, suggesting that these genes contribute to salt-tolerance of budding yeast. Hence, we assume that if these mechanisms can be combined, it is possible to develope a "biological desalination" device that stores Na+ in the vacuoles of budding yeast and lowers the salt concentration of the environment.<br><br>
  
  <h5 id="生物がもつトランスポーターの特異性(化学的な膜では特定のイオンを選択的に除くのは難しい)</"> <b>生物がもつトランスポーターの特異性(化学的な膜では特定のイオンを選択的に除くのは難しい)</h5>
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&emsp; We further investigated and noticed that team Aachen 2017, tried to create a similar budding yeast. We contacted the team Aachen and heard a detailed story. Here we proposed a question to ourselves. Can we combine genes of salt-tolerant plants and genes of salt-resistant and build a desalination system which team Aachen did not develop? We started to create budding yeast by expressing various genes and set "creating the device that minimizes the salt concentration of medium in the test tube" as the primary goal.
 +
</p>
  
 +
<h5 id="Aggregation system for increasing the efficiency of recollection and biosafety"> <b>3)  Aggregation system for increasing the efficiency of recollection and biosafety</h5></b>
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<p>&emsp; As mentioned above, we initially aimed to create a yeast that removes salt in "test tubes" in order to promote the usage of the biosensor, which detects trace elements contained in test samples such as blood and waste liquid, without being inhibited their function by salt in solution. However, from the activities in Human Practice, we have found a new goal that this system can also be used to solve the social problems such as a salt damage. In order to use our device in the real environment, we have to incorporate a mechanism that prevents genetically modified yeast from diffusing into the environment. For this purpose, we tried introducing an aggregation system to collect yeast efficiently after lowering the salt concentration in the environment.
 +
</p>
  
 +
<h5 id="Calculating the amount of yeast necessary to lower the concentration through mathematical modeling"> <b>4) Calculating the amount of yeast necessary to lower the concentration through mathematical modeling</h5></b>
 +
<p>&emsp; The advantage of a salt removal system is that you can easily control the amount and combination of components because they are artificially defined. You can use different factors depending on the situations, such as a difference in initial salt concentration of an extracellular fluid, a difference in target salt concentration, a difference in time required for salt concentration manipulation, a difference in a required amount of yeast etc. In order to enable this flexible application, it is necessary that our system is sufficiently understood, and mathematical modeling is properly done. By using the results of this modeling it is possible to estimate the optimalamount of yeast input when using our device.
  
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</p>
  
 
<br><br><br><br><br>
 
<br><br><br><br><br>

Latest revision as of 22:47, 7 December 2018

Team:Kyoto/Project - 2018.igem.org

1) Motivation

  Protein interactions, enzymatic reactions, folding of RNA, riboswitches... nearly all of these biological reactions are greatly affected by salt concentation. Salt concentration is also important for most biological devices designed by synthetic biologists. Synthetic biologist try to develope new devices that provide solutions to our daily problems in the world. However, the situations and circumstances vary greatly among each problem, often resulting in undesired salt concentrations. If the salt concentration is insufficient in the surrounding environment for a developing device, adding salt to the culture solution may solve a problem.

  But how about when salt concentrations are too high? This is a difficult problem to solve. Once devices that absorb salt from environment are developed, we can greatly support various functions of other devices, for example, sensing substances in the environment or bioremediation. Besides, if we can apply salt-absorbing device to the situation outside the laboratory, there is a possibility that it will be useful for purifying water in various scenes such as industrial wastewater and salt damage.
 Although this has a great possibility, the question of how feasible is this environmental desalination using synthetic biology principles has never been explored thoroughly. Therefore, we addressed this problem this year.

2) Let's create a system that absorbs salt from a liquid using genetically modified yeast

  Some salt-tolerant plants have developed systems that sequester Na+ from the cytoplasm to vacuoles in order to protect themselves from Na+ flowing in. In addition, some plants have gained Na+ tolerance system by producing compatible solutes. In the process of searching papers, we noticed that many genes involved in Na+ sequestration were also shown to function in budding yeast and give them salt tolerance. The budding yeast itself also has a mechanism for exporting Na+ out of the cell. It is also known that budding yeasts, in which Na+-exporting genes have been destroyed and the mechanism are failed, are very sensitive to the high salt concentration in the medium, suggesting that these genes contribute to salt-tolerance of budding yeast. Hence, we assume that if these mechanisms can be combined, it is possible to develope a "biological desalination" device that stores Na+ in the vacuoles of budding yeast and lowers the salt concentration of the environment.

  We further investigated and noticed that team Aachen 2017, tried to create a similar budding yeast. We contacted the team Aachen and heard a detailed story. Here we proposed a question to ourselves. Can we combine genes of salt-tolerant plants and genes of salt-resistant and build a desalination system which team Aachen did not develop? We started to create budding yeast by expressing various genes and set "creating the device that minimizes the salt concentration of medium in the test tube" as the primary goal.

3) Aggregation system for increasing the efficiency of recollection and biosafety

  As mentioned above, we initially aimed to create a yeast that removes salt in "test tubes" in order to promote the usage of the biosensor, which detects trace elements contained in test samples such as blood and waste liquid, without being inhibited their function by salt in solution. However, from the activities in Human Practice, we have found a new goal that this system can also be used to solve the social problems such as a salt damage. In order to use our device in the real environment, we have to incorporate a mechanism that prevents genetically modified yeast from diffusing into the environment. For this purpose, we tried introducing an aggregation system to collect yeast efficiently after lowering the salt concentration in the environment.

4) Calculating the amount of yeast necessary to lower the concentration through mathematical modeling

  The advantage of a salt removal system is that you can easily control the amount and combination of components because they are artificially defined. You can use different factors depending on the situations, such as a difference in initial salt concentration of an extracellular fluid, a difference in target salt concentration, a difference in time required for salt concentration manipulation, a difference in a required amount of yeast etc. In order to enable this flexible application, it is necessary that our system is sufficiently understood, and mathematical modeling is properly done. By using the results of this modeling it is possible to estimate the optimalamount of yeast input when using our device.