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

 
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{{HZAU-China}}
 
{{HZAU-China}}
 
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</head>
 
</head>
  
 
<body>
 
<body>
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   <div class="HZAU_2017_menu">
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   <div class="HZAU_div_main">
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     <img src="https://static.igem.org/mediawiki/2017/8/8e/HZAU_2017_background_1.png" class="beijin">
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     <a class="HZAU_title">Description</a>
−
    <ul class="daohang">
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    <a class="zhengwen_disblock">The chromosome replication of bacteria can be divided into three phases: B C and D</a>
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      <li id="HZAU_menu_1">
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        <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1-3]}$</a>
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        <a href="#" id="bianse_1">Background</a>
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         <a class="zhengwen_disblock">, and meanwhile multi-rounds of replication exist simultaneously in one cell</a>
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      </li>
+
        <a class="yinzhu" href="#yinwen_jiaozheng">$^{[1]}$</a>
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      <li id="HZAU_menu_2">
+
        <a class="zhengwen_disblock">. So both the replication phase and the copy number of chromosome are heterogeneous in a culture.</a>
−
        <a href="#item2_1" id="bianse_2">4D genome</a>
+
    <div>
−
      </li>
+
      <label for="HZAUmenu-toggle" class="zhengwen" style="font-weight:bold;">To know more about replication
−
      <li id="HZAU_menu_3">
+
        <span class="caret_black"></span>
−
         <a href="#item3_1" id="bianse_3">4C</a>
+
      </label>
−
      </li>
+
      <input type="checkbox" id="HZAUmenu-toggle" />
−
    </ul>
+
      <ul id="HZAUmenu">
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  </div>
+
        <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
−
  <div class="HZAU_content">
+
          pre-replication phase, in which cells are preparing for DNA replication, like G1 phase of eukaryotes. Phase C is also
−
    <div class="HZAU_item">
+
          called replication phase, in which the genome is under replication, corresponding to phase S in eukaryotic cell cycle.
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      <a class="biaoti">Description</a>
+
          The last phase D, of course, is called post-replication phase, in which chromosome separates and one cell divides
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      <a class="zhengwen">The replication of prokaryotes can be divided into three phases, B C and D, while there are multi-rounds of replication
+
          into two, corresponding to G2 and M phases in eukaryotes. Among the three phases, C and D are relatively constant,
−
        happened in one cell. So both the phase and the copy number of genome is various in a culture.</a>
+
          about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle. Recent work
−
      <div>
+
          revealed a relationship between replication initiation and cell volume, but many details still remain unknown.  
−
        <label for="menu-toggle" class="zhengwen" style="color:blue">To know more about replication
+
          What we know is that a protein, DnaA, plays an important role in this process. DnaA is a versatile protein possessing
−
          <span class="caret_black"></span>
+
          many different functions related to cell cycle, among which the most important one is to attach to the OriC,
−
        </label>
+
          the origins of chromosome replication, and initiates replication. So controlling cell cycle by interrupting the
−
        <input type="checkbox" id="menu-toggle" />
+
          attachment of DnaA and the corresponding DNA sequence with dCas9 is an efficient approach.
−
        <ul id="menu">
+
          <br>
−
          <a>The replication process of E.coli can be divided into three phases, phase B, phase C and phase D. B is also called
+
        </a>
−
            pre-replication phase in which cells are preparing for DNA replication, like G1 phase of eukaryotes. C is also
+
        <a  class="zhengwen">The whole cell cycles of eukaryotes and prokaryotes show a certain similarity, but there is difference between them.
−
            called replication phase in which the genome is under replication corresponding to phase S in eukaryotic cell
+
          The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before the last
−
            cycle. The last D phase, of course, is called post-replication phase, in which chromosome separates and one cell
+
          replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown that even
−
            divides into two corresponding to G2 and M phase in eukaryotes. Among the three phases, C and D are relatively
+
          an isogenic bacteria growing in the same culture show differences in both replication phase and genome copy numbers
−
            constant, about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle.
+
          and this becomes a huge noise when constructing the 3D genome structure and building up a circuit related to genome
−
            Recent research reveals a relationship between replication initiation and cell volume, but many details are still
+
          . Besides, the development of synthetic biology requires a system to control the reproduction of engineered
−
            remain unknown. But what we know is that a protein, DnaA, plays an important role in this process.
+
          organisms. So we believe that our project would be a useful tool no matter in theoretical areas or application
−
            <br> DnaA is a versatile protein possessing many different functions related to cell cycle, among which the most
+
           areas.</a>
−
            important one is to attached to the OriC, the origins of chromosome replication, and initiates replication. So
+
      </ul>
−
            controlling cell cycle by interrupting the attachment of DnaA and corresponding DNA sequence with dCas9 is an
+
    </div>
−
            efficient approach.
+
    <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
−
            <br> The whole cell cycle of eukaryotes and prokaryotes show a certain similarity, but there is difference between
+
    <img src="https://static.igem.org/mediawiki/2017/1/19/T--HZAU-China--description_Figure2.png" class="tu_2">
−
            them. The cell cycle of prokaryotes can overlap, which means the next round of replication initiates before the
+
    <a class="zhengwen_disblock">Our project is inspired by the research about constructing 4D genomes of eukaryotes. We wonder why there isn’t a
−
            last replication complete, while eukaryotic cell cycle initiates one after another. Experiments have shown that
+
       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
−
            even an isogenetic bacteria grown in the same culture show a difference in both replication phase and genome
+
    </a>
−
            copy numbers and this becomes a huge noise when constructing the 3D genome structure and building up a circuit
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[4]}$</a>
−
            related to genome gene. Besides, the development of synthetic biology requires a system to control the reproduction
+
    <a class="zhengwen_disblock">. </a>
−
            of engineered organisms. So we believe that our project would be a useful tool no matter in theoretical areas
+
    <a class="zhengwen_disblock">Besides, the heterogenicity of cells are gathering more and more attentions in different fields, like industrial fermentation,
−
            or application areas.
+
      antidrug resistance research and synthetic biology</a>
−
           </a>
+
    <a class="yinzhu" href="#yinwen_jiaozheng">$^{[5-7]}$</a>
−
        </ul>
+
    <a class="zhengwen_disblock">.</a>
−
      </div>
+
    <img src="https://static.igem.org/mediawiki/2017/a/a6/T--HZAU-China--computorHand.png" class="tu_3">
−
      <img src="https://static.igem.org/mediawiki/2017/f/f1/HZAU_2017_BCDperiod.png" class="tu_1">
+
    <a class="zhengwen">Therefore, we begin to think if there could be a method to eliminate the heterogeneity. When thinking deeper into this
−
       <div class="jiaozheng">
+
      problem, it becomes interesting that what would happen if all the cells are synchronized, will there be a new phenomenon
−
        <a id="item2_1"></a>
+
      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.</a>   
 +
    <a class="zhengwen">
 +
      <br>
 +
    </a>
 +
    <div>
 +
      <div id="yinwen_jiaozheng" class="jiaozheng">
 
       </div>
 
       </div>
−
      <a class="zhengwen">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.
 
−
        <br>Besides, the heterogenicity of cells are gathering importance recently in different fields.</a>
 
−
      <img src="https://static.igem.org/mediawiki/2017/d/d2/HZAU_2017_computorHand.png" class="tu_2">
 
−
      <div class="jiaozheng">
 
−
        <a id="item3_1"></a>
 
−
      </div>
 
−
      <a class="zhengwen">Therefore we begin to think if there could be a methods to eliminate the heterogeneity. While 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 statements?
 
−
        <br>So in our mind the ideal synchronization methods should be not only simply inhibit the cell cycle but at the same
 
−
        time can free the inhibition according to our decision. As we all know, the manipulation of machine is much more
 
−
        accurate than hum 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, by program.</a>
 
 
     </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>
 
</body>
 
</body>
 +
 
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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.