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

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       <a class="biaoti">Description</a>
 
       <a class="biaoti">Description</a>
−
       <a class="zhengwen">In the long history of life evolution, different species living in different environment developed the most adaptive
+
       <a class="zhengwen">The replication of prokaryotes can be divided into three phases, B C and D, while there are multi-rounds of replication
−
         surviving mechanism for them under the selection pressure, among which some unmatchable become widly preserved in
+
        happened in one cell. So both the phase and the copy number of genome is various in a culture.</a>
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         different creatures, and the mechanism of replication is one of them. The majority of prokaryote share the same mechanism
+
      <div>
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        of self-replication including DNA replication, chromosome seperation and cell division. These three parts comprised
+
         <label for="menu-toggle" class="zhengwen" style="color:blue">To know more about replication
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        the whole cell cycle, and the main model creature for researching the replication process is E.coli, which at the
+
          <span class="caret_black"></span>
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         same time is the main object of our project.</a>
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 +
        <ul id="menu">
 +
          <a>The replication process of E.coli can be divided into three phases, phase B, phase C and phase D. B is also called
 +
            pre-replication phase in which cells are preparing for DNA replication, like G1 phase of eukaryotes. C is also
 +
            called replication phase in which the genome is under replication corresponding to phase S in eukaryotic cell
 +
            cycle. The last D phase, of course, is called post-replication phase, in which chromosome separates and one cell
 +
            divides into two corresponding to G2 and M phase in eukaryotes. Among the three phases, C and D are relatively
 +
            constant, about 40 min and 20 min separately, so when to initiate a replication determines the whole cell cycle.
 +
            Recent research reveals a relationship between replication initiation and cell volume, but many details are still
 +
            remain unknown. But what we know is that a protein, DnaA, plays an important role in this process.
 +
            <br> DnaA is a versatile protein possessing many different functions related to cell cycle, among which the most
 +
            important one is to attached to the OriC, the origins of chromosome replication, and initiates replication. So
 +
            controlling cell cycle by interrupting the attachment of DnaA and corresponding DNA sequence with dCas9 is an
 +
            efficient approach.
 +
            <br> 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>
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      <div class="jiaozheng">
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        <a id="item2_1"></a>
 +
      </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>
−
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−
 
−
    <div class="item" id="item2">
 
−
      <div id="item2_1" class="jiaozheng"></div>
 
−
      <a class="zhengwen">The replication process of E.coli replication can be devided into phase B,C and D, three phases. Phase B, also called
 
−
        pre-replication phase, is for DNA replication proparation similar as G1 phase in eukaryote cell cycle. Phase C is
 
−
        regarded as replication phase during which the chromosome is replicating corespond to the S phase in eukaryote. The
 
−
        last phase, phase D, is called post-replication phase, in which the behave of chromosome seperation and cell division
 
−
        happend just like what happened in G2 and M phase of eukaryote cells. the time of C phase and D phase in a generation
 
−
        is relative constant, so what actually determines the cell cycle is the initiation of genome replication. We know
 
−
        that cell have to garantee that each cell should have at least one chormosome, and this requires a highly coordination
 
−
        between DNA replication and cell divsion. Though the delicate mechanism of the corrdination is still a puzzle, it
 
−
        is clear that DnaA protein plays a significant role in this event. DnaA is a versatile protein, it can not only behave
 
−
        like a helicase opening the duble-helix of replication initiation site, OriC, while have the function of raising
 
−
        other proteins forming into the replisome to prolong the replication, but also can anchor the replicationg choromosome
 
−
        on the cell membrane leading the following seperation of chromosome. But what makes it the linker between replication
 
−
        and division is that its concentration determines the initiation volume of replication. So according to these information,
 
−
        we think that regulating the combination of DNA and DnaA protein will be an efficient method to regulate cell replication.
 
−
        <a href="">For more information please click here.</a>
 
−
      </a>
 
−
    </div>
 
−
    <img src="https://static.igem.org/mediawiki/2017/5/51/HZAU_2017_tu2_1.png" class="tu_2">
 
−
 
−
    <div class="item" id="item3">
 
−
      <div id="item3_1" class="jiaozheng"></div>
 
−
      <a class="zhengwen">There will be about 1h for an entire genome replication, but cell division can reach about 20min per generation. this
 
−
        reflects the multi-copy number of bacterial genome and only with this mechanism can E.coli reproduce in such a high
 
−
        speed. what's worse is that even isogenic cells grow in the same culture have a scattering distribution not only
 
−
        in phase but also in genome copy number. the strong heterogenic in cell cycle and genome copy number hinds the 3D
 
−
        genome research and may be a potential noise on genome gene expression. At the same time, the developing synthetic
 
−
        biology requires an approach that can control cell reproduction and can be easily incorporated into circuits, so
 
−
        that the whole system can be more safe and controlable. taking these into consider, we decided to use CRISPRi to
 
−
        inhibit its cell cycle, for more details please see design.</a>
 
−
        <br>
 
−
      <a class="zhengwen">But barely pause the replication in some circumstance can't satisfy our needs, and long time inhibition will prolong
 
−
        its length, so there is a need to totally control its replication, not only block but also open. with that purpose
 
−
        we decided to use optogentic to control this system, and the operablity of light to computer makes our system programable,
 
−
        which can be called 4C.</a>
 
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Revision as of 11:21, 29 October 2017

Description The replication of prokaryotes can be divided into three phases, B C and D, while there are multi-rounds of replication happened in one cell. So both the phase and the copy number of genome is various in a culture.
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.
Besides, the heterogenicity of cells are gathering importance recently in different fields.
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?
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.