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

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{{HZAU-China}}
 
{{HZAU-China}}
 
<html>
 
<html>
 
 
<head>
 
<head>
     <style type="text/css">
+
     <meta charset="utf-8">
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    <!--公式编辑器-->
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    <style>
 +
        /*改变超链接的位置*/
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 +
        .jiaozheng {
 +
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            top: -66px;
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 +
    <!--内容的样式-->
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    <style>
 +
        /*总样式*/
 +
 
 
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         body {
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+
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            text-align: justify;
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         .team_title {
+
        /*内容框子的样式*/
             width: 100%;
+
 
             min-width: 1250px;
+
         .HZAU_div_main {
             height: auto;
+
             margin: 64px auto 0 auto;
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             padding: 0 30px 0 30px;
 +
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         .div_row {
+
        /*内容中几种文体的样式*/
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 +
         .HZAU_div_main a:hover {
 +
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            text-decoration: none;
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        .HZAU_title {
 +
            font-size: 50px;
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            font-weight: bold;
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            width: 360px;
 
             display: block;
 
             display: block;
             width: 1250px;
+
             margin: 0 auto;
             margin: 0 auto 0 auto;
+
             padding-bottom: 50px;
             padding: 100px 0 100px 0;
+
             padding-top: 50px;
 +
            color: #000;
 +
            background-image: url(https://static.igem.org/mediawiki/2017/9/95/T--HZAU-China--datitle.png);
 +
            background-repeat: no-repeat;
 +
            background-size: 360px 80px;
 +
            background-position: center;
 
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         .div_col {
+
         .biaoti {
             float: left;
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             font-size: 35px;
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+
            font-weight: bold;
             height: 370px;
+
            text-align: center;
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 +
            display: block;
 +
            padding-bottom: 30px;
 +
            padding-top: 30px;
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             color: #000;
 
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         .div_col_left {
+
         .fubiaoti {
             float: left;
+
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+
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            padding-bottom: 30px;
 +
            padding-top: 30px;
 +
            color: #000;
 +
            background-image: url(https://static.igem.org/mediawiki/2017/e/e7/T--HZAU-China--xiaotitle.png);
 +
            background-repeat: no-repeat;
 +
            background-size: 65px 50px;
 +
            background-position: left;
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 +
        .fufubiaoti{
 +
            display: block;
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            font-style: arial;
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            font-size: 19px;
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         .div_col_right {
+
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+
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            text-align: justify;
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            margin-bottom: 9px;
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            margin-top: 7.2px;
 
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         .zhaopian {
+
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+
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             margin-bottom: 9px;
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            margin-top: 7.2px;
 
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         }
  
         .mingzi {
+
         .yinzhu {
             position: absolute;
+
             color:blue;
            margin: 16px 0 0 70px;
+
            font-size: 19px;
+
            font-weight: bold;
+
            font-family: "Arial", Helvetica, sans-serif;
+
 
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         .jieshao {
+
         .yinzhu:hover .yinzhu {
 +
            color:black;
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 +
        .yinwen {
 
             display: block;
 
             display: block;
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+
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+
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+
             line-height: 34px;
             background-repeat: no-repeat;
+
             background-size: 500px auto;
+
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+
 
             text-align: justify;
 
             text-align: justify;
             font-family: "Arial", Helvetica, sans-serif;
+
             color: #000;
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            margin-bottom: 9px;
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 +
            margin-top: 7.2px;
 +
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 +
 
 +
        /*图片的样式*/
 +
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 +
          display: block;
 +
            font-style: arial;
 
             font-size: 17px;
 
             font-size: 17px;
 +
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 +
            text-align: justify;
 +
            color: #000;
 +
            margin-bottom: 9px;
 +
            margin-left: 0px;
 +
            margin-right: 0px;
 +
            margin-top: 7.2px;
 +
        }
  
 +
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 +
            width: 600px;
 +
            margin: 0 auto;
 +
            display: block;
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 +
 +
        .tu_2 {
 +
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 +
            margin: 0 auto;
 +
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 +
 +
        .tu_3 {
 +
            width: 555px;
 +
            margin: 0 auto;
 +
            display: block;
 
         }
 
         }
 
     </style>
 
     </style>
</head>
+
    <!--点击展开部分的样式-->
 +
    <style>
 +
        span.caret_black {
 +
            display: inline-block;
 +
            margin-left: 6px;
 +
            vertical-align: middle;
 +
            width: 0;
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 +
            border-right: 6px solid transparent;
 +
            border-top: 6px solid black;
 +
        }
  
<body>
+
         label {
    <div style="margin-top:50px">
+
             cursor: pointer;
         <img class="team_title" src="https://static.igem.org/mediawiki/2017/6/6d/T--HZAU-China--team.png">
+
         }
        <div class="div_row">
+
             <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/f/f1/T--HZAU-China--xiazhujun.png">
+
                <div class="mingzi">Zhujun Xia</div>
+
                <div class="jieshao">I'm Shane, the most brilliant member in the lab. Our team members call me teacher Xia, because I taught many
+
                    freshmen to do experiment. My idol is Jennifer Doudna. I take charge of work in wet lab where I met many
+
                    interesting people. I hope we can have a chance to discover the world in the future.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/a/a6/T--HZAU-China--yanghe.png">
+
                <div class="mingzi">He Yang</div>
+
                <div class="jieshao">Hello, My name is He Yang, majoring in bioengineer. This is my first time to participate in iGEM. I am good
+
                    at playing piano and practicing China traditional martial arts. I am also interested in learning everything
+
                    in lab. The past year in HZAU-China I gained valuable knowledge and friendship. I believe we'll achieve
+
                    good results this year.</div>
+
            </div>
+
         </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/6/6d/T--HZAU-China--Team_chengsongtao.png">
+
                <div class="mingzi">Songtao Cheng</div>
+
                <div class="jieshao">Hello! My name is Songtao Cheng. It's my first year to be an iGEMer. During the iGEM project I found that
+
                    synthetic biology is so charming. Joining iGEM is a good chance for me to learn knowledge and communicate
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                    with creative people to broaden my horizon. In short, I enjoy it!
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/6/61/T--HZAU-China--gengyingjie.png">
+
                <div class="mingzi">Yingjie Geng</div>
+
                <div class="jieshao">My name is Yingjie Geng. It is a great pleasure for me to be a member of HZAU-iGEM experiment group. My major
+
                    contribution is to test the protein expression of the pMag-split dCas9 and nMag-split dcas9, verify the
+
                    light-induced dimerization protein function by luciferase assay. I'm very happy to talk with others about
+
                    experimental design. So feel free to contact me.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/4/42/T--HZAU-China--guozhiqing.png">
+
                <div class="mingzi">Zhiqing Guo</div>
+
                <div class="jieshao">My name is Zhiqing Guo. I am a sophomore student now at HZAU. My hobby is widespread, such as reading, listening
+
                    to music, singing and watching anime. I am dreaming that I will be a super scientist saving the world.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/3/34/T--HZAU-China--dingzhangcheng.png">
+
                <div class="mingzi">Zhangcheng Ding</div>
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                <div class="jieshao">I'm a senior student in HZAU. My main job in the team is focusing on the result verification, most on the
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                    flow cytometry actually. It's my honour to participate in the competition which helped me to understand
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                    biology better. It's really nice to work with my partners.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/9/97/T--HZAU-China--hebincan.png">
+
                <div class="mingzi">Bingcan He</div>
+
                <div class="jieshao">It's so serious that I don't know what to say. Em, I'm Bincan He, an amusing girl.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/2/20/T--HZAU-China--miaoyini.png">
+
                <div class="mingzi">Yini Miao</div>
+
                <div class="jieshao">A girl who majors in Bioinformatics has great interest in biology and wants to be the force of it one day.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/5/5e/T--HZAU-China--xiongqiqi.png">
+
                <div class="mingzi">Qiqi Xiong</div>
+
                <div class="jieshao">Hi, I am a junior student from HZAU and it's my second year in HZAU-iGEM team. This year I worked as a member
+
                    of Wet Lab in our project. Hope our studys can lead a promising prospect in controlling cells to be synchronized
+
                    by optical control system.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/4/4e/T--HZAU-China--wangjinyu.png">
+
                <div class="mingzi">Jinyu Wang</div>
+
                <div class="jieshao">I'm jinyu wang, a boy who likes animals. I'm a HZAU-iGEMer, I'm working for the things I'm eager to work
+
                    for life. So I'm always happy.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/c/ce/T--HZAU-China--huangwenqi.png">
+
                <div class="mingzi">Wenqi Huang</div>
+
                <div class="jieshao">You can call me Johnson Huang, and I am a senior student majoring in Biotechnology. Every French soldier
+
                    carries a marshal's baton in his knapsack, and I'm definitely not a French soldier. But anyway, the marvel
+
                    projects in iGEM always inspire me a lot and this year in iGEM I learned a lot as a team leader. Feel
+
                    free to contact me if you have any question about our project.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/b/b8/T--HZAU-China--zengyinqing.png">
+
                <div class="mingzi">Yinqing Zeng</div>
+
                <div class="jieshao">I am Yinqing Zeng and my major is biotech. I like to conduct my experiment because it can make my concentration.
+
                    I love this team and I hope what I learn this year could be uesful for them in the future. In another
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                    hand, my dream is opening a dessert shop though I don't like eating dessert.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/8/82/T--HZAU-China--haimengli.png">
+
                <div class="mingzi">Haimeng Li</div>
+
                <div class="jieshao">Hello! My name is Haimeng Li, I'm from a beautiful coastal city. My major is bioscience. I like doing experiments.
+
                    I am the head of human practice but responsible for logistics of the team. I'm very glad to join in this
+
                    competition to enrich my university life.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/c/ce/T--HZAU-China--zhouanqi.png">
+
                <div class="mingzi">Anqi Zhou</div>
+
                <div class="jieshao">Hi, I'm Anqi Zhou, a member of wet experiment group. This year, it is my second time attending iGEM. After
+
                    two years working with iGEMers, I gain happiness and friendship, also get attracted by the fascination
+
                    of synthetic biology which may be my future reseach field. It's a long way to be a exellent SynBiology
+
                    scientist but I would put in my best effort.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/d/d9/T--HZAU-China--guoweitong.png">
+
                <div class="mingzi">Weitong Guo</div>
+
                <div class="jieshao">Bioinformatics. Leader of dry lab. Designer of mathematical model and software.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/5/5d/T--HZAU-China--chenkening.png">
+
                <div class="mingzi">Chen Kening</div>
+
                <div class="jieshao">This is Kening! It sounds like cunning but not really... I have been in this team for two years and my best
+
                    reward is a well trained turtle. Besides, I'm the art designer and the conductor of qPCR experiment.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/2/20/T--HZAU-China--moqiqin.png">
+
                <div class="mingzi">Qiqin Mo</div>
+
                <div class="jieshao">I am Qiqin Mo, a boy (or Sister Qin? ) with a strong willing to change the world. l love science and literature.
+
                    In the IGEM lab, I was lucky to make acquaintance with so many interesting friends while gaining plenty
+
                    scientific thoughts. I'm happy here, thank you, IGEM.
+
                </div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/5/57/T--HZAU-China--bianhao.png">
+
                <div class="mingzi">Hao Bian</div>
+
                <div class="jieshao">Hello! My name is Hao Bian. It is my first time to participate in iGEM. I'm a curious otaku, like watching
+
                    anime and reading books. My interested areas are Neural science and Computer science.</div>
+
            </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/2/21/T--HZAU-China--lingyuzhong.png">
+
                <div class="mingzi">Lingyu Zhong</div>
+
                <div class="jieshao">My name is Lingyu Zhong. It's my first year in HZAU-iGEM team. I love sicence, and iGEM allowed me to get
+
                    closer to it. It's happy to do experiment with Mr.Summer Bamboo and Mother Anqi and Shabi Tissue and
+
                    Shabi Miu and others, hahahahahahahaha I love my team, I love iGEM, I love science.
+
  
                </div>
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            </div>
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             display: none;
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                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/0/09/T--HZAU-China--yuwentao.png">
+
                <div class="mingzi">Wentao Yu</div>
+
                <div class="jieshao">My name is Wentao Yu. wet lab. change linker, rbs, split check.</div>
+
             </div>
+
        </div>
+
        <div class="div_row">
+
            <div class="div_col div_col_left">
+
                <img class="zhaopian" src="https://static.igem.org/mediawiki/2017/0/0c/T--HZAU-China--Hongyu_Zhang.png">
+
                <div class="mingzi">Hongyu Zhang</div>
+
                <div class="jieshao"></div>
+
            </div>
+
            <div class="div_col div_col_right">
+
                <img class="zhaopian" src="">
+
                <div class="mingzi">Binguang Ma</div>
+
                <div class="jieshao">Prof. Ma is our direct instructor. He has seen us through thick and thin, and has been with us in times of
+
                    happiness and sorrow. His field of research is systems biology and synthetic biology, and this time,
+
                    the inspiration of our project is from him. We all love him, for he is not only our instructor, but also
+
                    our friends.
+
                </div>
+
            </div>
+
         </div>
+
  
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+
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 +
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 +
 +
<body>
 +
  <div class="HZAU_div_main">
 +
    <a class="HZAU_title">Model</a>
 +
    <a class="zhengwen">For control cell cycle, our wet lab sign genetic circuit to control initiation location -- OriC. Finally Replication
 +
      initiation switch. Finally, we will get the bacterium with Replication initiation switch. It’s obviously better chosing
 +
      Oric as the controlled target cause the physiological states of germs won’t be severely effected compared with being
 +
      disposed with starvation method. But it also brings us two questions:</a>
 +
    <a class="zhengwen">① How to observe OriC situation in time</a>
 +
    <a class="zhengwen">After Dry Lab’s analysis, we can tell you that switch OriC is enough to control cell cycle, even better. Because we can
 +
      create more new status such as one E,coli has 8 volume but has 1 DNA.</a>
 +
    <a class="zhengwen">② How to observe OriC situation in time?</a>
 +
    <a class="zhengwen">Cause of the limiting of our lab, we couldn’t observe the OriC in single cell directly. So Dry Lab build a model based
 +
      on a series of previous published rules to describe the coordination among chromosome replication, cell growth and
 +
      division. And now we original catch three goals: ①improve it to Mathematical formula level. ② find its inaptitude during
 +
      repressed ,define a new parameter “d” to supply it. ③ only needs one kind data so easy to obtain--Volume,enough to
 +
      calculate E.coli’s every replication process (OriC situation) and other cell cycle information in single cell level.
 +
    </a>
 +
    <a class="zhengwen">In the process of modeling we encounter many challenges, such as Bacteria initiates multi-replication process during
 +
      one cycle.</a>
 +
    <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
 +
    <a class="zhengwen">Figure 1. The different stages of synchronization. Ton: the light triggering the synchronization system is on. And CRISPER
 +
      system will block Oric. Tri: It won’t exert any effect when Oric is not blocked since it can’t initiate new replication
 +
      fork. Ts:time of becoming single chromosome.</a>
 +
    <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
 +
    <a class="zhengwen">Figure 2. The different stages of the bacterium’s returning to normal. Toff: the time it takes from turning of the light
 +
      to Oric is unblocked. Tr2: time it takes for the bacteria returning to the normal state since Oric is unblocked.</a>
 +
    <a class="zhengwen">Volume and replication model</a>
 +
    <a class="zhengwen">There’s a lot of attributes for a single bacteria such as volume, weight, concentration of different kinds of proteins
 +
      and RNA, the amount of DNA and etc.but the accurate concentration of the matters can’t be directly detected due to
 +
      limited experimental conditions.Which means the variates and the concentration data the genetic circuit model needed
 +
      can’t de detected.This is a huge obstacle for the model’s accuracy.After thinking carefully, we summarized that through
 +
      the concentration of dCas9 and gRNA of the single bacteria can’t be directly acquired, the volume of which is the easiest
 +
      parameter we can get with Microfluidic photography and Flow cytometry that our project can be evaluated on single cellular
 +
      level other than bacterial colony just because we took the advantage of the volume of the bacteria which is totally
 +
      measurable and reliable.</a>
 +
    <a class="zhengwen">Thus we improved our previous work and made it formulized and softwarelized.</a>
 +
    <a class="zhengwen">1.related basic rules</a>
 +
    <a class="zhengwen">We checked some papers in the relevant research fields and summarized some rules of bacterium’s replication growth and
 +
      division, And applied them on our project.</a>
 +
    <a class="zhengwen_disblock">bac’s rule of growth</a>
 +
    <a>$V_{new} =V_{old}e^{\mu T}$</a>
 +
    <a class="zhengwen_disblock">bac’s rule of triggering replication innitition</a>
 +
    <a>$V>2^{N}V_{std}$</a>
 +
    <a class="zhengwen_disblock">reason of division: bac will definitely divide after complete</a>
 +
    <a class="HZAU_gongshi">$T_{C}+T_{D}$</a>
 +
    <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
 +
    <a class="zhengwen">Figure 3. diagrammatic sketch of the coordination among chromosome replication, cell growth and division</a>
 +
    <a class="zhengwen">2. inferring the progress flow inner the bac</a>
 +
    <a class="zhengwen">① Take the bacteria’s photo to get the volume Vold, Wait for the twait and take one photo again to get the volume Vnew
 +
    </a>
 +
    <a class="zhengwen_disblock">② Calculate the growth rate according to the formula.</a>
 +
    <a class="HZAU_gongshi">$\mu =\dfrac {nV_{nen}-lnV_{old}} {t_{wait}}$</a>
 +
    <a class="zhengwen_disblock">
 +
      <br>③ it can be inferred out that the upper limit of the replication folk Nmax is </a>
 +
    <a class="HZAU_gongshi">$\lceil log_{2}V_{std}e^{\mu(T_{C}+T_{D})} \rceil$
 +
      <a class="zhengwen_disblock">when the volume of the bac is V</a>
 +
      <a class="zhengwen_disblock">
 +
        <br>④ The volume when the bac complete stage C and getting into stage D:</a>
 +
      <a class="HZAU_gongshi">$V_{D} =V_{std}e^{\mu T}$</a>
 +
      <a class="zhengwen">⑤ the progress of the smallest replication folk</a>
 +
      <a class="HZAU_gongshi">$$x= \begin{cases} \dfrac {lnV-lnV_{std}} {\mu T_{c}}- \lfloor \dfrac {lnV-lnV_{std}} {ln2} \rfloor \dfrac {ln2} {\mu
 +
        T_{C}} ,V>V_{std}\\ \\ 0,V
 +
        < V_{std} \end{cases} $$</a>
 +
          <a class="zhengwen">⑥ Replication process of the replication folks</a>
 +
          <a class="HZAU_gongshi">$$\begin{cases} \quad \ \ \ x\\ \\ \dfrac {1} {log_{2}e^{\mu T_{c}}} + x\\ \\ \dfrac {2} {log_{2}e^{\mu T_{c}}}
 +
            + x\\ \\ \quad \ \ \ .\\ \quad \ \ \ .\\ \quad \ \ \ .\\ \\ \dfrac {N_(max)} {log_{2}e^{\mu T_{c}}} + x \end{cases}
 +
            $$
 +
          </a>
 +
          <a class="zhengwen_disblock">⑦ Infer how long will the bac split</a>
 +
          <a class="HZAU_gongshi">$T_{C}+T_{D} - \dfrac {lnV-lnV_{std}}{\mu}$</a>
 +
          <a class="zhengwen_disblock">
 +
            <br>⑧ Infer how long will it take for the bac to form the haploid chromosome without replication forks if all the
 +
            Oric is blocked.</a>
 +
          <a class="HZAU_gongshi">$T_{C}+T_{D}-xT_{C}$</a>
 +
          <a class="zhengwen_disblock">
 +
            <br>⑨ The range of volume cyclical changes:</a>
 +
          <a class="HZAU_gongshi">$[\dfrac {V_{std}e^{\mu(T_{C}+T_{D})}}{2},V_{std}e^{\mu (T_{C}+T_{D})}]$</a>
 +
          <a class="zhengwen">⑩ The interval between splits under the current grow environment.</a>
 +
          <a class="zhengwen">3. when will the normal cells be really effected by Oric</a>
 +
          <img src="https://static.igem.org/mediawiki/2017/4/44/T--HZAU-China--BCDperiod.png" class="tu_1">
 +
          <a class="zhengwen_disblock">Figure 4. When the normal bac is going to form a new replication fork and Oric is blocked at this time, the replication
 +
            process is really inhibited. so when Oric is unblocked, the time bac is actually effected is the time it takes
 +
            to form the new replication fork:</a>
 +
          <a class="HZAU_gongshi">$T_{r1}=\dfrac {ln2}{\mu}-xT_{C}. $</a>
 +
          <a class="zhengwen_disblock">Equal with</a>
 +
          <a class="HZAU_gongshi">$T_{r1}=\dfrac {ln2}{\mu}-(\dfrac {lnV-lnV_{std}} {\mu}-\lfloor \dfrac {lnV-lnV_{std}} {ln2} \rfloor \dfrac {ln2}
 +
            {\mu})$
 +
          </a>
 +
          <a class="zhengwen">4. when will the abnormal cells recover to the normal, predictable stage.</a>
 +
          <a class="zhengwen">According to the Bacteria under the CRISPR control, cell Volume will become many times to normal one, but it only
 +
            have one chromosome. If we allow its initiate new replication process (release its OriC), it want to initiate
 +
            many OriC to recovery itself, but previous model didn’t describe this phenom, so we define a new parameter “d”
 +
            to supply.</a>
 +
          <a class="zhengwen_disblock">bac’s rule of growth</a>
 +
          <a class="HZAU_gongshi">$V_{new} =V_{old}e^{\mu T}$</a>
 +
          <a class="zhengwen_disblock"><br>bac’s rule of triggering replication innitition</a>
 +
          <a class="HZAU_gongshi">$V>2^{N}V_{std}$</a>
 +
          <a class="zhengwen_disblock"><br>reason of division: bac will definitely divide after complete</a>
 +
          <a class="HZAU_gongshi">$T_{C}+T_{D}$</a>
 +
          <a class="zhengwen">The triggercondition to initiate replication under abnormal situation: the shortest interval of forming two replication
 +
            forks.
 +
          </a>
 +
          <a class="zhengwen">①The time needs to wait is 0 if Oric is unblocked in Tr1 since the inhibition of Oric hasn’t cause real effect
 +
            to bac</a>
 +
          <a class="zhengwen">②If Oric is unblocked after Tr1, we have those analysis:</a>
 +
          <a class="zhengwen">the restrict limits of becoming backe to normal:</a>
 +
          <a class="HZAU_gongshi">$\dfrac{lnV-lnV_{std}}{\mu}-N\dfrac{ln2}{\mu}-k(\dfrac{ln2}{\mu}-d)
 +
            <0$</a>
 +
              <a class="zhengwen">K means the number of replication folks, d means minimum folk forming interval, N means the replication folks
 +
                exists in the bac.</a>
 +
              <a class="zhengwen">The above formula is transformed, so that it can be solved directly:</a>
 +
              <a class="HZAU_gongshi">$k>\dfrac{lnV-lnV_{std}-Nln2}{ln2-\mu d}$</a>
 +
              <a class="zhengwen">Because k is an integer, the formula add *** so it’s better for computer calculation.</a>
 +
              <a class="HZAU_gongshi">$k=\lceil\dfrac{lnV-lnV_{std}-Nln2}{ln2-\mu d}\rceil$</a>
 +
              <a class="zhengwen">We get the mean of k, the dividing time for the bac to become normal is:</a>
 +
              <a class="HZAU_gongshi">N+k</a>
 +
              <a class="zhengwen">Finally the time needed for the bac to recover to normal from the blocking method is removed.</a>
 +
              <a class="HZAU_gongshi">$T_{r2}=T_{C}+T_{D}+d(k-1)$</a>
 +
              <a class="zhengwen">It is worth noting that when the number of bacterial liabilities is less than 2, the minimum interval between
 +
                two bifurcation must be less than ln2 / u, otherwise the bacteria will be dragged down by the new debt on
 +
                the way of repayment and will not return to normal.</a>
 +
                <a class="biaoti">References</a>
 +
                <a class="yinwen">1. Stephen Cooper (2006). Distinguishing between linear and exponential cell growth during the division cycle: Single-cell studies, cell-culture studies, and the object of cell-cycle research. Theoretical Biology and Medical Modelling, 3:10</a>
 +
                <a class="yinwen">2. M Wallden, D Fange, EG Lundius, Ö Baltekin, J Elf (2016). The Synchronization of Replication and Division Cycles in Individual E.coli Cells. Cell, 166(3):729-739.</a>
 +
                <a class="yinwen">3. Cooper S, Helmstetter CE (1968). Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Biol 31(3):519–540.</a>
 +
  </div>
 +
</body>
 
</html>
 
</html>

Revision as of 01:10, 2 November 2017

Model For control cell cycle, our wet lab sign genetic circuit to control initiation location -- OriC. Finally Replication initiation switch. Finally, we will get the bacterium with Replication initiation switch. It’s obviously better chosing Oric as the controlled target cause the physiological states of germs won’t be severely effected compared with being disposed with starvation method. But it also brings us two questions: ① How to observe OriC situation in time After Dry Lab’s analysis, we can tell you that switch OriC is enough to control cell cycle, even better. Because we can create more new status such as one E,coli has 8 volume but has 1 DNA. ② How to observe OriC situation in time? Cause of the limiting of our lab, we couldn’t observe the OriC in single cell directly. So Dry Lab build a model based on a series of previous published rules to describe the coordination among chromosome replication, cell growth and division. And now we original catch three goals: ①improve it to Mathematical formula level. ② find its inaptitude during repressed ,define a new parameter “d” to supply it. ③ only needs one kind data so easy to obtain--Volume,enough to calculate E.coli’s every replication process (OriC situation) and other cell cycle information in single cell level. In the process of modeling we encounter many challenges, such as Bacteria initiates multi-replication process during one cycle. Figure 1. The different stages of synchronization. Ton: the light triggering the synchronization system is on. And CRISPER system will block Oric. Tri: It won’t exert any effect when Oric is not blocked since it can’t initiate new replication fork. Ts:time of becoming single chromosome. Figure 2. The different stages of the bacterium’s returning to normal. Toff: the time it takes from turning of the light to Oric is unblocked. Tr2: time it takes for the bacteria returning to the normal state since Oric is unblocked. Volume and replication model There’s a lot of attributes for a single bacteria such as volume, weight, concentration of different kinds of proteins and RNA, the amount of DNA and etc.but the accurate concentration of the matters can’t be directly detected due to limited experimental conditions.Which means the variates and the concentration data the genetic circuit model needed can’t de detected.This is a huge obstacle for the model’s accuracy.After thinking carefully, we summarized that through the concentration of dCas9 and gRNA of the single bacteria can’t be directly acquired, the volume of which is the easiest parameter we can get with Microfluidic photography and Flow cytometry that our project can be evaluated on single cellular level other than bacterial colony just because we took the advantage of the volume of the bacteria which is totally measurable and reliable. Thus we improved our previous work and made it formulized and softwarelized. 1.related basic rules We checked some papers in the relevant research fields and summarized some rules of bacterium’s replication growth and division, And applied them on our project. bac’s rule of growth $V_{new} =V_{old}e^{\mu T}$ bac’s rule of triggering replication innitition $V>2^{N}V_{std}$ reason of division: bac will definitely divide after complete $T_{C}+T_{D}$ Figure 3. diagrammatic sketch of the coordination among chromosome replication, cell growth and division 2. inferring the progress flow inner the bac ① Take the bacteria’s photo to get the volume Vold, Wait for the twait and take one photo again to get the volume Vnew ② Calculate the growth rate according to the formula. $\mu =\dfrac {nV_{nen}-lnV_{old}} {t_{wait}}$
③ it can be inferred out that the upper limit of the replication folk Nmax is
$\lceil log_{2}V_{std}e^{\mu(T_{C}+T_{D})} \rceil$ when the volume of the bac is V
④ The volume when the bac complete stage C and getting into stage D:
$V_{D} =V_{std}e^{\mu T}$ ⑤ the progress of the smallest replication folk $$x= \begin{cases} \dfrac {lnV-lnV_{std}} {\mu T_{c}}- \lfloor \dfrac {lnV-lnV_{std}} {ln2} \rfloor \dfrac {ln2} {\mu T_{C}} ,V>V_{std}\\ \\ 0,V < V_{std} \end{cases} $$ ⑥ Replication process of the replication folks $$\begin{cases} \quad \ \ \ x\\ \\ \dfrac {1} {log_{2}e^{\mu T_{c}}} + x\\ \\ \dfrac {2} {log_{2}e^{\mu T_{c}}} + x\\ \\ \quad \ \ \ .\\ \quad \ \ \ .\\ \quad \ \ \ .\\ \\ \dfrac {N_(max)} {log_{2}e^{\mu T_{c}}} + x \end{cases} $$ ⑦ Infer how long will the bac split $T_{C}+T_{D} - \dfrac {lnV-lnV_{std}}{\mu}$
⑧ Infer how long will it take for the bac to form the haploid chromosome without replication forks if all the Oric is blocked.
$T_{C}+T_{D}-xT_{C}$
⑨ The range of volume cyclical changes:
$[\dfrac {V_{std}e^{\mu(T_{C}+T_{D})}}{2},V_{std}e^{\mu (T_{C}+T_{D})}]$ ⑩ The interval between splits under the current grow environment. 3. when will the normal cells be really effected by Oric Figure 4. When the normal bac is going to form a new replication fork and Oric is blocked at this time, the replication process is really inhibited. so when Oric is unblocked, the time bac is actually effected is the time it takes to form the new replication fork: $T_{r1}=\dfrac {ln2}{\mu}-xT_{C}. $ Equal with $T_{r1}=\dfrac {ln2}{\mu}-(\dfrac {lnV-lnV_{std}} {\mu}-\lfloor \dfrac {lnV-lnV_{std}} {ln2} \rfloor \dfrac {ln2} {\mu})$ 4. when will the abnormal cells recover to the normal, predictable stage. According to the Bacteria under the CRISPR control, cell Volume will become many times to normal one, but it only have one chromosome. If we allow its initiate new replication process (release its OriC), it want to initiate many OriC to recovery itself, but previous model didn’t describe this phenom, so we define a new parameter “d” to supply. bac’s rule of growth $V_{new} =V_{old}e^{\mu T}$
bac’s rule of triggering replication innitition
$V>2^{N}V_{std}$
reason of division: bac will definitely divide after complete
$T_{C}+T_{D}$ The triggercondition to initiate replication under abnormal situation: the shortest interval of forming two replication forks. ①The time needs to wait is 0 if Oric is unblocked in Tr1 since the inhibition of Oric hasn’t cause real effect to bac ②If Oric is unblocked after Tr1, we have those analysis: the restrict limits of becoming backe to normal: $\dfrac{lnV-lnV_{std}}{\mu}-N\dfrac{ln2}{\mu}-k(\dfrac{ln2}{\mu}-d) <0$ K means the number of replication folks, d means minimum folk forming interval, N means the replication folks exists in the bac. The above formula is transformed, so that it can be solved directly: $k>\dfrac{lnV-lnV_{std}-Nln2}{ln2-\mu d}$ Because k is an integer, the formula add *** so it’s better for computer calculation. $k=\lceil\dfrac{lnV-lnV_{std}-Nln2}{ln2-\mu d}\rceil$ We get the mean of k, the dividing time for the bac to become normal is: N+k Finally the time needed for the bac to recover to normal from the blocking method is removed. $T_{r2}=T_{C}+T_{D}+d(k-1)$ It is worth noting that when the number of bacterial liabilities is less than 2, the minimum interval between two bifurcation must be less than ln2 / u, otherwise the bacteria will be dragged down by the new debt on the way of repayment and will not return to normal. References 1. Stephen Cooper (2006). Distinguishing between linear and exponential cell growth during the division cycle: Single-cell studies, cell-culture studies, and the object of cell-cycle research. Theoretical Biology and Medical Modelling, 3:10 2. M Wallden, D Fange, EG Lundius, Ö Baltekin, J Elf (2016). The Synchronization of Replication and Division Cycles in Individual E.coli Cells. Cell, 166(3):729-739. 3. Cooper S, Helmstetter CE (1968). Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Biol 31(3):519–540.