Difference between revisions of "Team:HZAU-China/Description"

 
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{{HZAU-China}}
 
{{HZAU-China}}
 
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
  
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
 
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
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+
  </style>
+
 
</head>
 
</head>
  
<body data-spy="scroll" data-target="#myScrollspy" data-offset="20">
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<body>
   <div class="container">
+
   <div class="HZAU_div_main">
     <div class="row">
+
     <a class="HZAU_title">Description</a>
      <nav class="col-sm-3" id="myScrollspy">
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    <a class="zhengwen_disblock">The chromosome replication of bacteria can be divided into three phases: B C and D</a>
        <div class="container-fluid">
+
          <div class="container-fluid">
+
            <ul class="nav nav-pills nav-stacked">
+
              <li class="active" id="change_top">
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                <a href="#section1">Background of Cell Replication</a>
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              </li>
+
              <li style="margin:-2px">
+
                <a href="#section2">Inspiration & Development of Our Idea</a>
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              </li>
+
              <li style="margin:0px">
+
                <a href="#section3">The computer-controlled cell cycle</a>
+
              </li>
+
            </ul>
+
          </div>
+
        </div>
+
      </nav>
+
      <div class="col-sm-9">
+
        <div>
+
          <div id="section1" class="jiaozheng">
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          </div>
+
        </div>
+
        <a class="biaoti">Description</a>
+
        <a class="zhengwen_disblock" style="margin:0 0 0 30px;">The chromosome replication of bacteria can be divided into three phases: B C and D</a>
+
 
         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1-3]}$</a>
 
         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1-3]}$</a>
 
         <a class="zhengwen_disblock">, and meanwhile multi-rounds of replication exist simultaneously in one cell</a>
 
         <a class="zhengwen_disblock">, and meanwhile multi-rounds of replication exist simultaneously in one cell</a>
 
         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1]}$</a>
 
         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1]}$</a>
 
         <a class="zhengwen_disblock">. So both the replication phase and the copy number of chromosome are heterogeneous in a culture.</a>
 
         <a class="zhengwen_disblock">. So both the replication phase and the copy number of chromosome are heterogeneous in a culture.</a>
        <div>
+
    <div>
          <label for="HZAUmenu-toggle" class="zhengwen">To know more about replication
+
      <label for="HZAUmenu-toggle" class="zhengwen" style="font-weight:bold;">To know more about replication
            <span class="caret_black"></span>
+
        <span class="caret_black"></span>
          </label>
+
      </label>
          <input type="checkbox" id="HZAUmenu-toggle" />
+
      <input type="checkbox" id="HZAUmenu-toggle" />
          <ul id="HZAUmenu">
+
      <ul id="HZAUmenu">
            <a style="margin:0 0 0 30px;">The replication process of E. coli can be divided into three phases, phase B, phase C and phase D. B is also
+
        <a class="zhengwen">The replication process of E. coli can be divided into three phases; phase B, phase C and phase D. Phase B is also called
              called pre-replication phase in which cells are preparing for DNA replication, like G1 phase of eukaryotes.
+
          pre-replication phase, in which cells are preparing for DNA replication, like G1 phase of eukaryotes. Phase C is also
              C is also called replication phase in which the genome is under replication corresponding to phase S in eukaryotic
+
          called replication phase, in which the genome is under replication, corresponding to phase S in eukaryotic cell cycle.
              cell cycle. The last D phase, of course, is called post-replication phase, in which chromosome separates and
+
          The last phase D, of course, is called post-replication phase, in which chromosome separates and one cell divides
              one cell divides into two corresponding to G2 and M phase in eukaryotes. Among the three phases, C and D are
+
          into two, corresponding to G2 and M phases in eukaryotes. Among the three phases, C and D are relatively constant,
              relatively constant, about 40 min and 20 min separately, so when to initiate a replication determines the whole
+
          about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle. Recent work
              cell cycle. Recent research reveals a relationship between replication initiation and cell volume, but many
+
          revealed a relationship between replication initiation and cell volume, but many details still remain unknown.  
              details still remain unknown. But what we know is that a protein, DnaA, plays an important role in this process.
+
          What we know is that a protein, DnaA, plays an important role in this process. DnaA is a versatile protein possessing
              DnaA is a versatile protein possessing many different functions related to cell cycle, among which the most
+
          many different functions related to cell cycle, among which the most important one is to attach to the OriC,
              important one is to attached to the OriC, the origins of chromosome replication, and initiates replication.
+
          the origins of chromosome replication, and initiates replication. So controlling cell cycle by interrupting the
              So controlling cell cycle by interrupting the attachment of DnaA and corresponding DNA sequence with dCas9
+
          attachment of DnaA and the corresponding DNA sequence with dCas9 is an efficient approach.
              is an efficient approach.
+
          <br>
              <br></a>
+
              <a style="margin:0 0 0 30px;">The whole cell cycle of eukaryotes and prokaryotes show a certain similarity, but there is difference between
+
              them. The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before
+
              the last replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown
+
              that even an isogenetic bacteria grown in the same culture show a difference in both replication phase and
+
              genome copy numbers and this becomes a huge noise when constructing the 3D genome structure and building up
+
              a circuit related to genome gene. Besides, the development of synthetic biology requires a system to control
+
              the reproduction of engineered organisms. So we believe that our project would be a useful tool no matter in
+
              theoretical areas or application areas.</a>
+
          </ul>
+
        </div>
+
        <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
+
        <img src="https://static.igem.org/mediawiki/2017/1/19/T--HZAU-China--description_Figure2.png" class="tu_2">
+
        <div>
+
          <div id="section2" class="jiaozheng">
+
          </div>
+
        </div>
+
        <a class="zhengwen_disblock" style="margin:0 0 0 30px;">Our problem arises from a research about constructing 4D genome of eukaryote. So we begin to wonder why there isn’t
+
          a 4D genome project of prokaryote. After research we find that due to its complicated replication mechanism, there
+
          will be a huge noise while detecting its structure, which hinder the research on prokaryotic genome
+
 
         </a>
 
         </a>
         <a class="yinzhu" href="#yinwen_jiaozheng">$^{[4]}$</a>
+
         <a  class="zhengwen">The whole cell cycles of eukaryotes and prokaryotes show a certain similarity, but there is difference between them.
        <a class="zhengwen_disblock">. </a>
+
          The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before the last
        <a class="zhengwen_disblock">Besides, the heterogenicity of cells are gathering importance recently in different fields, like industrial fermentation,
+
          replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown that even
          antidrug resistance research and synthetic biology</a>
+
          an isogenic bacteria growing in the same culture show differences in both replication phase and genome copy numbers
        <a class="yinzhu" href="#yinwen_jiaozheng">$^{[5-7]}$</a>
+
          and this becomes a huge noise when constructing the 3D genome structure and building up a circuit related to genome
        <a class="zhengwen_disblock">.</a>
+
          . Besides, the development of synthetic biology requires a system to control the reproduction of engineered
        <img src="https://static.igem.org/mediawiki/2017/a/a6/T--HZAU-China--computorHand.png" class="tu_3">
+
          organisms. So we believe that our project would be a useful tool no matter in theoretical areas or application
        <div>
+
          areas.</a>
          <div id="section3" class="jiaozheng">
+
      </ul>
          </div>
+
    </div>
        </div>
+
    <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
        <a class="zhengwen" style="text-indent:30px;">Therefore we begin to think if there could be a methods to eliminate the heterogeneity. While thinking deeper into
+
    <img src="https://static.igem.org/mediawiki/2017/1/19/T--HZAU-China--description_Figure2.png" class="tu_2">
          this problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a
+
    <a class="zhengwen_disblock">Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a
          new phenomenon that can change the traditional statements?
+
      4D genome project of prokaryote. After investigation we find that due to the complicated mechanisms of bacteria chromosome replication, there will be a huge noise while detecting its chromosome structure, which hinders the research on prokaryotic 4D genome
          <br>So in our mind the ideal synchronization methods should be not only simply inhibit the cell cycle but at the same
+
    </a>
          time can free the inhibition according to our decision. As we all know, the manipulation of machine is much more
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[4]}$</a>
          accurate than hum beings, and there is a trend to let machine help us to control the organisms, so we want our
+
    <a class="zhengwen_disblock">. </a>
          synchronization system can also be controlled by machine, by program.</a>
+
    <a class="zhengwen_disblock">Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation,
        <a class="zhengwen" style="text-indent:30px;">Therefore we begin to think if there could be a method to eliminate the heterogeneity. While thinking deeper into
+
      antidrug resistance research and synthetic biology</a>
          this problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[5-7]}$</a>
          new phenomenon that can change the traditional statements?</a>
+
    <a class="zhengwen_disblock">.</a>
        <a class="zhengwen" style="text-indent:30px;">So in our mind the ideal synchronization methods should be not only simply inhibit the cell cycle but at the same
+
    <img src="https://static.igem.org/mediawiki/2017/a/a6/T--HZAU-China--computorHand.png" class="tu_3">
          time can free the inhibition according to our decision. As we all know, the manipulation of machine is much more
+
    <a class="zhengwen">Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this
          accurate than hum beings, and there is a trend to let machine help us to control the organisms, so we want our
+
      problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon
          synchronization system can also be controlled by machine, by program.</a>
+
      that can change the traditional opinions?  
          <a class="zhengwen" style="text-indent:30px;"> <br></a>
+
      In our mind, the ideal synchronization methods should not only simply inhibit the cell cycle but at the same time
        <div>
+
      can free the inhibition according to our requirements. As we all know, the manipulation of machine is much more accurate
          <div id="yinwen_jiaozheng" class="jiaozheng">
+
      than living beings, and there is a trend to let machine help us to control the organisms, so we want our synchronization
          </div>
+
      system can also be controlled by machine and program.</a>  
        </div>
+
    <a class="zhengwen">
        <a class="yinwen">1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968
+
      <br>
          Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5.</a>
+
    </a>
        <a class="yinwen">2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry.
+
    <div>
          J Bacteriol. 1983 May;154(2) 656-662.</a>
+
      <div id="yinwen_jiaozheng" class="jiaozheng">
        <a class="yinwen">3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The
+
          three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2),
+
          252-264.</a>
+
        <a class="yinwen">4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia
+
          coli with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990).</a>
+
        <a class="yinwen">5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population.
+
          Nature Genetics. 49. . 10.1038/ng.3915.</a>
+
 
       </div>
 
       </div>
 
     </div>
 
     </div>
 +
    <a class="biaoti">References</a>
 +
    <a class="yinwen">1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968
 +
      Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5.</a>
 +
    <a class="yinwen">2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry.
 +
      J Bacteriol. 1983 May;154(2) 656-662.</a>
 +
    <a class="yinwen">3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The three-dimensional
 +
      architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2), 252-264.
 +
    </a>
 +
    <a class="yinwen">4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia coli
 +
      with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990).</a>
 +
    <a class="yinwen">5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population. Nature
 +
      Genetics. 49. . 10.1038/ng.3915.</a>
 +
  </div>
 
   </div>
 
   </div>
 
 
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Latest revision as of 12:27, 28 November 2017

Description The chromosome replication of bacteria can be divided into three phases: B C and D $^{[1-3]}$ , and meanwhile multi-rounds of replication exist simultaneously in one cell $^{[1]}$ . So both the replication phase and the copy number of chromosome are heterogeneous in a culture.
Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a 4D genome project of prokaryote. After investigation we find that due to the complicated mechanisms of bacteria chromosome replication, there will be a huge noise while detecting its chromosome structure, which hinders the research on prokaryotic 4D genome $^{[4]}$ . Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation, antidrug resistance research and synthetic biology $^{[5-7]}$ . Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon that can change the traditional opinions? In our mind, the ideal synchronization methods should not only simply inhibit the cell cycle but at the same time can free the inhibition according to our requirements. As we all know, the manipulation of machine is much more accurate than living beings, and there is a trend to let machine help us to control the organisms, so we want our synchronization system can also be controlled by machine and program.
References 1. Helmstetter CE. DNA synthesis during the division cycle of rapidly growing Escherichia coli B/r. J Mol Biol. 1968 Feb;31(3) 507-518. doi:10.1016/0022-2836(68)90424-5. 2. Skarstad K, Steen HB, Boye E. Cell cycle parameters of slowly growing Escherichia coli B/r studied by flow cytometry. J Bacteriol. 1983 May;154(2) 656-662. 3. Umbarger, M. A., Toro, E., Wright, M. A., Porreca, G. J., Bau, D., Hong, S. H., . . . Church, G. M. (2011). The three-dimensional architecture of a bacterial genome and its alteration by genetic perturbation. Mol Cell, 44(2), 252-264. 4. Paalme, T., Tiisma, K., Kahru, A., Vanatalu, K. & Vilu, R. Glucose-limited fed-batch cultivation of Escherichia coli with computer-controlled fixed growth rate. Biotechnol. Bioeng. 35, 312–319 (1990). 5. Baumgart, Leo & Mather, William & Hasty, Jeff. (2017). Synchronized DNA cycling across a bacterial population. Nature Genetics. 49. . 10.1038/ng.3915.