Difference between revisions of "Team:BGU Israel/Notebook"

 
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{{BGU_Israel}}
 
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   <title>OriginALS</title>
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          <h1 class="animated fadeInUp">Notebook</h1>
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<a href="#february" class="btn btn-info" role="button" >February</a>
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<a href="#march" class="btn btn-info" role="button" >March</a>
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<a href="#april" class="btn btn-info" role="button" >April</a>
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<a href="#may" class="btn btn-info" role="button" >May</a>
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<a href="#july" class="btn btn-info" role="button" >July</a>
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<a href="#august" class="btn btn-info" role="button" >August</a>
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<a href="#experiments" class="btn btn-info" role="button" >Experiments</a>
  
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     </div>
 
     </div>
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</div>
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      <ul class="nav navbar-nav navbar-right">
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<div class="arrowdown "></div>
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        <li><a href="index.html">Home</a></li>
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<!-- February -->
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        <li class="dropdown">
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<div id="february" class="bg-white text-center">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="https://2018.igem.org/Team:BGU_Israel/Description">Project
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        </a>
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        <ul class="dropdown-menu pull-right">
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/Description ">Description</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/Design">Design</a></li>
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            <li><a href="https://2018.igem.org/Team:BGU_Israel/Results">Results</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/Protocols">Protocols</a></li>
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            <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/Notebook">Notebook</a></li>
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        </ul>
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      </li>
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          <li class="dropdown">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="https://2018.igem.org/Team:BGU_Israel/Description">Team
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        </a>
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        <ul class="dropdown-menu pull-right">
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/Team">Members</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/Collaborations">Collaborations</a></li>
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          <li class="dropdown">
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/Parts">Team Parts</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/BasicParts ">Basic Parts</a></li>
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            <li><a href="https://2018.igem.org/Team:BGU_Israel/PartImprovement">Part Improvement</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_Israel/PartCollection">Part Collection</a></li>
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        </ul>
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      </li>
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  <li class="dropdown">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="https://2018.igem.org/Team:BGU_Israel/Description">Practices
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        </a>
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        <ul class="dropdown-menu pull-right">
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          <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/ALSConference">ALS Conference</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/ALSFunding">Funding Race</a></li>
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            <li><a href="https://2018.igem.org/Team:BGU_Israel/InterLab">InterLab</a></li>
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          <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/EthicsAndSafety">Ethics and Safty</a></li>
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        </ul>
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      </li>
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        <li><a href="https://2018.igem.org/Team:BGU_ISRAEL/Attributions">Attributions</a></li>
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          <!--<li><a href="https://2018.igem.org/Team:BGU_ISRAEL/Achievments">Achievments</a></li>-->
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      </ul>
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    </div>
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  </div>
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</nav>
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  <header  class="sub-page-header text-center">
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      <div class="container my-auto">
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          <h1>Notebook</h1>
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      </div>
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    </header>
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−
<!-- Container (About Section) -->
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<div id="abstract" class="container-fluid text-center">
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   <div class="row">
 
   <div class="row">
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<h1>February</h1>
 
<div class="col-sm-8 col-sm-offset-2">
 
<div class="col-sm-8 col-sm-offset-2">
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<p>We began working in our brand-new lab space! When we first arrived, the lab was nothing but two work benches. We had to collect and organize the equipment, materials, cell culture room, and work area; all according to lab safety standards. We also began cloning the plasmids for our experiments and learning how to work with cell culture by practicing on HEK293 cells.<br/>
−
      <p style="margin:0px !important; padding:0!important;"  class="mb-4 justified animated fadeInRight">It all began in the summer of 2017, the newly recruited iGEM-BGU team was tasked with choosing a topic for our iGEM project. Many ideas were proposed but one idea resonated with us. Liat Tsoran, one of our team members, told us her personal story. Liat’s father, Nir Tsoran, was diagnosed with ALS when Liat was only eleven years old. For seven years (longer than the average patient’s survival rate), Liat witnessed her father’s health, deteriorates from a fully functional adult to a man trapped inside his body. Throughout his ordeal, Nir did not let his disease prevent him from being an exemplary father and advocate. He served as the CEO of IsrALS, an Israeli non-profit organization committed to supporting ALS patients, their families, and promoting ALS research in Israel. Nir took this budding non-profit and the very small Israeli ALS scientific community and turned it into an influential strong local movement. Since her father’s diagnosis, Liat has been dedicating her life to understanding the disease and hopes, to one day contribute to finding a cure. Once we heard Liat’s story, the whole team enlisted to join her efforts. We suddenly understood that the “Ice Bucket Challenge” was not just a fun activity but a necessary step in bringing awareness to a devastating disease which has not received the exposure required to promote significant research for a cure.
+
<br/>
 +
<b>Highlights:</b> clone Steap4, Timp1, F4/80 into pGL4.17 and pGL3 plasmid for Promoter Assay.  
 
</p>
 
</p>
 +
<button class="accordion">Week 1</button>
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<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/a/a6/T--BGU_Israel--notebook_week1.pdf" width="100%" height="500">
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</div>
−
   
+
 
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  </div>
+
<button class="accordion">Week 3 </button>
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−
    <div class="bg-grey">
+
 
−
<div class="container text-center">
+
<button class="accordion">Week 4</button>
−
  <div class="row">
+
<div class="panel2">
−
      <h1>Image right</h1>
+
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−
<div class="col-sm-6">
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−
      <p style="margin:0px !important; padding:0!important;" class="mb-4 justified animated fadeInRight">Recent research studies of Amyotrophic Lateral Sclerosis (ALS) suggest that brain cells that have become toxic, directly contribute to the progression of the disease. These cells change their gene expression pattern and possess distinguishing genetic markers. In addition, they drive the death of other cells in the brain among them the motor neurons. <br><br>
+
</object>
−
Our objective, as the BGU-IGEM team OriginALS, is to prolong survival of ALS patients via a novel genetic engineering approach. In order to reach this objective, we combine two separate strategies as our therapeutic approach: </p>
+
</div>
−
 
+
 
 
</div>
 
</div>
−
      <div class="col-sm-6">
 
−
          <img src="dark-lab.jpg" class="img-responsive" alt="Responsive image">
 
−
       
 
−
      </div>
 
−
   
 
 
   </div>
 
   </div>
 
</div>
 
</div>
 
</div>
 
</div>
−
        <div class="bg-white">
+
 
−
<div class="container text-center">
+
<!-- March -->
 +
<div id="march" class="bg-grey text-center">
 
   <div class="row">
 
   <div class="row">
−
      <h1>Image Left</h1>
+
<h1>March</h1>
−
      <div class="col-sm-5">
+
<div class="col-sm-8 col-sm-offset-2">
−
          <img src="dark-lab.jpg" class="img-responsive">
+
<p>
−
       
+
In March, we experienced our first little success. We cloned our promoters into the pGL3 vector and were able to begin our first experiment, the Promoter Assay. Meanwhile, so far, our practice cells were alive and well.
−
      </div>
+
<br/>
−
<div class="col-sm-7">
+
<br/>
−
      <p style="margin:0px !important; padding:0!important;" class="mb-4 justified animated fadeInRight">Recent research studies of Amyotrophic Lateral Sclerosis (ALS) suggest that brain cells that have become toxic, directly contribute to the progression of the disease. These cells change their gene expression pattern and possess distinguishing genetic markers. In addition, they drive the death of other cells in the brain among them the motor neurons. <br><br>
+
<b>Highlights:</b> A decision was made to concentrate our efforts on the pGL3 plasmid expression assay. Because, then we could compare the expression among the promoters and we wouldn’t have to use two sets of luciferase kits.
−
Our objective, as the BGU-IGEM team OriginALS, is to prolong survival of ALS patients via a novel genetic engineering approach. In order to reach this objective, we combine two separate strategies as our therapeutic approach: </p>
+
</p>
−
 
+
<button class="accordion">Week 5</button>
 +
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</div>
−
     
+
 
−
   
+
<button class="accordion">Week 6</button>
−
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+
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 +
<object data="https://static.igem.org/mediawiki/2018/1/10/T--BGU_Israel--notebook_week6.pdf" width="100%" height="500">
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 +
 +
<button class="accordion">Week 7</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/9/97/T--BGU_Israel--notebook_week7.pdf" width="100%" height="500">
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 +
</object>
 
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</div>
−
   
 
−
      <div class="bg-grey">
 
−
<div class="container text-center">
 
−
  <div class="row">
 
−
      <h1>Thumbnails</h1>
 
  
−
      <p style="margin:0px !important; padding:0!important;" class="mb-4 justified animated fadeInRight">Recent research studies of Amyotrophic Lateral Sclerosis (ALS) suggest that brain cells that have become toxic, directly contribute to the progression of the disease. These cells change their gene expression pattern and possess distinguishing genetic markers. In addition, they drive the death of other cells in the brain among them the motor neurons.: <br><br><br></p>
+
<button class="accordion">Week 8</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/d/de/T--BGU_Israel--notebook_week8.pdf" width="100%" height="500">
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 +
</div>
 
   </div>
 
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−
    <div class="row">
 
−
    <div class="col-sm-4">
 
−
        <img src="dark-lab.jpg" class="img-responsive">
 
−
        <h3>title</h3>
 
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        <p>lorem ipsum bf fd kdfdfkdflsdf</p>
 
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        </div>
 
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        <div class="col-sm-4">
 
−
        <img src="dark-lab.jpg" class="img-responsive">
 
−
            <h3>title</h3>
 
−
        <p>lorem ipsum bf fd kdfdfkdflsdf</p>
 
−
        </div>
 
−
        <div class="col-sm-4">
 
−
        <img src="dark-lab.jpg" class="img-responsive">
 
−
            <h3>title</h3>
 
−
        <p>lorem ipsum bf fd kdfdfkdflsdf</p>
 
−
        </div>
 
−
       
 
−
    </div>
 
−
</div>
 
 
</div>
 
</div>
  
−
<style>
 
−
    .footer-list {
 
−
        list-style: none;
 
−
        color:#fff;
 
−
    }
 
−
    .footer-list-item {
 
−
        padding:20px 0 20px 0 !important;
 
−
        border-bottom: 1px solid #fff;
 
−
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−
    .footer-list .footer-list-item:last-child {
 
−
        border:0;
 
−
    }
 
−
    .container-fluid {
 
−
      padding: 60px 50px;
 
−
  }
 
  
−
    .bg-grey {
+
<!-- April -->
−
        background-color:#ededed;
+
<div id="april" class="bg-white text-center">
−
        color:#000;
+
  <div class="row">
−
        padding: 60px 50px;
+
<h1>April</h1>
−
    }
+
<div class="col-sm-8 col-sm-offset-2">
−
    .bg-white {
+
<p>
−
        background-color:#fff;
+
Our long-awaited microglia and astrocytes arrived! While our cell lines were getting used to their new home, we began cloning our crisper and gRNA plasmids for our two-component system.
−
        color:#000;
+
<br/>
−
        padding: 60px 50px;
+
<br/>
−
    }
+
<b>Highlights:</b> Received microglia and astrocytes cell lines, px601, H1, H2 CMV-dCas9-VPR, building plasmids with Gibson assembly.
−
    .bg-dark {
+
</p>
−
        background-color:#262626;
+
<button class="accordion">Week 9</button>
−
       
+
<div class="panel2">
−
        padding: 60px 50px;
+
<object data="https://static.igem.org/mediawiki/2018/4/46/T--BGU_Israel--notebook_week9.pdf" width="100%" height="500">
−
    }
+
                        <embed src="https://static.igem.org/mediawiki/2018/4/46/T--BGU_Israel--notebook_week9.pdf" type="application/pdf" width="100%" height="600" />
−
      .bg-dark h1 {
+
</object>
−
        color:#fff !important;
+
</div>
−
       
+
−
    }
+
−
    footer.bg-dark p {
+
−
        color:#ededed !important;
+
−
    }
+
−
    .social-icons {
+
−
        display: inline;
+
−
        height:20px;
+
−
        width:20px;
+
−
        margin-right:10px;
+
−
    }
+
  
−
</style>
+
<button class="accordion">Week 10</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/e/ea/T--BGU_Israel--notebook_week10.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/e/ea/T--BGU_Israel--notebook_week10.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
<footer class="bg-dark">
+
<button class="accordion">Week 11</button>
−
    <div  class="container my-auto">
+
<div class="panel2">
−
<div class="row">
+
<object data="https://static.igem.org/mediawiki/2018/7/78/T--BGU_Israel--notebook_week11.pdf" width="100%" height="500">
−
    <div class="col-md-4">
+
                        <embed src="https://static.igem.org/mediawiki/2018/7/78/T--BGU_Israel--notebook_week11.pdf" type="application/pdf" width="100%" height="600" />
−
        <h3>About OrignALS</h3>
+
</object>
−
        <p><br>Established in 2006, EchoSense Ltd. develops innovative ultrasound Doppler systems for the diagnosis and monitoring of cardiac and pulmonary diseases. EchoSense delivers a fast,reliable and non-invasive method of diagnosis and our technology has undergone successful clinical trials in the United States, Europe and Israel. The Echosense research and development center is based in Haifa, Israel.</p>
+
−
        <img class="responsive-img" src="https://static.igem.org/mediawiki/2018/f/f0/T--BGU_Israel--originals_white.png" width="50%">
+
−
       
+
−
        <img class="img-responsive" src="">
+
−
    </div>
+
−
    <div class="col-md-4">
+
−
    <ul class="footer-list">
+
−
        <h3>Keep in Touch</h3>
+
−
       
+
−
  <li class="footer-list-item"><img class="img-responsive social-icons" src="https://static.igem.org/mediawiki/2018/3/3c/T--BGU_Israel--facebook.png" > @iGEMBGU</li>
+
−
  <li class="footer-list-item"><img class="img-responsive social-icons" src="https://static.igem.org/mediawiki/2018/e/e9/T--BGU_Israel--instagram.png" >@igem_2018_bgu</li>
+
−
  <li class="footer-list-item"><img class="img-responsive social-icons" src="https://static.igem.org/mediawiki/2018/2/26/T--BGU_Israel--twitter.jpg" > @originalsbgu</li>
+
−
        <li class="footer-list-item"><img class="img-responsive social-icons" src="https://static.igem.org/mediawiki/2018/8/83/T--BGU_Israel--email.png" > bgu_israel@gmail.com</li>
+
−
</ul>
+
−
    </div>
+
−
    <div class="col-md-4">
+
−
    <ul class="footer-list">
+
−
        <h3>Address</h3>
+
−
  <li class="footer-list-item">Ben-Gurion University of the Negev<br>
+
−
Ben Gurion 1, Beer Sheva 8410501, Israel</li>
+
−
 
+
−
          <li class="footer-list-item"><img class="responsive-img" src="https://static.igem.org/mediawiki/2018/a/a5/T--BGU_Israel--bgu_white.png"></li>
+
−
</ul>
+
−
    </div>
+
−
   
+
 
</div>
 
</div>
−
        </div>
 
−
</footer>
 
  
−
<script>
+
<button class="accordion">Week 12</button>
−
$(document).ready(function(){
+
<div class="panel2">
−
  // Add smooth scrolling to all links in navbar + footer link
+
<object data="https://static.igem.org/mediawiki/2018/d/db/T--BGU_Israel--notebook_week12.pdf" width="100%" height="500">
−
  $(".navbar a, #myBtn[href='#top']").on('click', function(event) {
+
                        <embed src="https://static.igem.org/mediawiki/2018/d/db/T--BGU_Israel--notebook_week12.pdf" type="application/pdf" width="100%" height="600" />
−
    // Make sure this.hash has a value before overriding default behavior
+
</object>
−
    if (this.hash !== "") {
+
</div>
−
      // Prevent default anchor click behavior
+
−
      event.preventDefault();
+
  
−
      // Store hash
+
</div>
−
      var hash = this.hash;
+
  </div>
 +
</div>
  
−
      // Using jQuery's animate() method to add smooth page scroll
 
−
      // The optional number (900) specifies the number of milliseconds it takes to scroll to the specified area
 
−
      $('html, body').animate({
 
−
        scrollTop: $(hash).offset().top
 
−
      }, 500, function(){
 
−
 
 
−
        // Add hash (#) to URL when done scrolling (default click behavior)
 
−
        window.location.hash = hash;
 
−
      });
 
−
    } // End if
 
−
  });
 
−
 
 
−
  $(window).scroll(function() {
 
−
    $(".slideanim").each(function(){
 
−
      var pos = $(this).offset().top;
 
  
−
      var winTop = $(window).scrollTop();
+
<!-- May -->
−
        if (pos < winTop + 600) {
+
<div id="may" class="bg-grey text-center">
−
          $(this).addClass("slide");
+
  <div class="row">
−
        }
+
<h1>May</h1>
−
    });
+
<div class="col-sm-8 col-sm-offset-2">
−
  });
+
<p>
−
})
+
After a tireless journey, we successfully cloned most of our system’s plasmids. Now we began attempts to transfect these plasmids into our cell lines with different transfection reagents. Additionally, we began the promoter assay and astrocyte reactivity assay.
−
</script>
+
<br/>
−
<script type="text/javascript">
+
<br/>
−
    /*!
+
<b>Highlights:</b> Began Promoter assay, transfection attempts with reagents, ELISA for astrocyte reactivity assay.
−
* parallax.js v1.5.0 (http://pixelcog.github.io/parallax.js/)
+
</p>
−
* @copyright 2016 PixelCog, Inc.
+
<button class="accordion">Week 13</button>
−
* @license MIT (https://github.com/pixelcog/parallax.js/blob/master/LICENSE)
+
<div class="panel2">
−
*/
+
<object data="https://static.igem.org/mediawiki/2018/3/34/T--BGU_Israel--notebook_week13.pdf" width="100%" height="500">
 +
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 +
</object>
 +
</div>
  
−
;(function ( $, window, document, undefined ) {
+
<button class="accordion">Week 14</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/7/7d/T--BGU_Israel--notebook_week14.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/7/7d/T--BGU_Israel--notebook_week14.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
  // Polyfill for requestAnimationFrame
+
<button class="accordion">Week 15</button>
−
  // via: https://gist.github.com/paulirish/1579671
+
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/0/0c/T--BGU_Israel--notebook_week15.pdf" width="100%" height="500">
 +
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 +
</object>
 +
</div>
  
−
  (function() {
+
<button class="accordion">Week 16</button>
−
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+
<div class="panel2">
−
    var vendors = ['ms', 'moz', 'webkit', 'o'];
+
<object data="https://static.igem.org/mediawiki/2018/2/2d/T--BGU_Israel--notebook_week16.pdf" width="100%" height="500">
−
    for(var x = 0; x < vendors.length && !window.requestAnimationFrame; ++x) {
+
                        <embed src="https://static.igem.org/mediawiki/2018/2/2d/T--BGU_Israel--notebook_week16.pdf" type="application/pdf" width="100%" height="600" />
−
      window.requestAnimationFrame = window[vendors[x]+'RequestAnimationFrame'];
+
</object>
−
      window.cancelAnimationFrame = window[vendors[x]+'CancelAnimationFrame'] || window[vendors[x]+'CancelRequestAnimationFrame'];
+
</div>
−
    }
+
  
−
    if (!window.requestAnimationFrame)
+
</div>
−
      window.requestAnimationFrame = function(callback) {
+
  </div>
−
        var currTime = new Date().getTime();
+
</div>
−
        var timeToCall = Math.max(0, 16 - (currTime - lastTime));
+
−
        var id = window.setTimeout(function() { callback(currTime + timeToCall); },
+
−
          timeToCall);
+
−
        lastTime = currTime + timeToCall;
+
−
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+
−
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+
  
−
    if (!window.cancelAnimationFrame)
 
−
      window.cancelAnimationFrame = function(id) {
 
−
        clearTimeout(id);
 
−
      };
 
−
  }());
 
  
 +
<!-- June -->
 +
<div id="june" class="bg-white text-center">
 +
  <div class="row">
 +
<h1>June</h1>
 +
<div class="col-sm-8 col-sm-offset-2">
 +
<p>
 +
In June we had to face the music; our transfection was not working. We began exploring alternatives ways to insert our plasmids into our cells, such as electroporation, calcium phosphate transfection, and additional transfection reagents.
 +
<br/>
 +
<br/>
 +
<b>Highlights:</b> Astrocyte Western blot, Electroporation of microglia.
 +
</p>
 +
<button class="accordion">Week 17</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/6/6e/T--BGU_Israel--notebook_week17.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/6/6e/T--BGU_Israel--notebook_week17.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
  // Parallax Constructor
+
<button class="accordion">Week 18</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/7/7c/T--BGU_Israel--notebook_week18.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/7/7c/T--BGU_Israel--notebook_week18.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
  function Parallax(element, options) {
+
<button class="accordion">Week 19</button>
−
    var self = this;
+
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/2/22/T--BGU_Israel--notebook_week19.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/2/22/T--BGU_Israel--notebook_week19.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    if (typeof options == 'object') {
+
<button class="accordion">Week 20</button>
−
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+
<div class="panel2">
−
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+
<object data="https://static.igem.org/mediawiki/2018/7/79/T--BGU_Israel--notebook_week20.pdf" width="100%" height="500">
−
      $.extend(this, options);
+
                        <embed src="https://static.igem.org/mediawiki/2018/7/79/T--BGU_Israel--notebook_week20.pdf" type="application/pdf" width="100%" height="600" />
−
    }
+
</object>
 +
</div>
  
−
    this.$element = $(element);
+
</div>
 +
  </div>
 +
</div>
  
−
    if (!this.imageSrc && this.$element.is('img')) {
 
−
      this.imageSrc = this.$element.attr('src');
 
−
    }
 
  
−
    var positions = (this.position + '').toLowerCase().match(/\S+/g) || [];
+
<!-- July -->
 +
<div id="july" class="bg-grey text-center">
 +
  <div class="row">
 +
<h1>July</h1>
 +
<div class="col-sm-8 col-sm-offset-2">
 +
<p>
 +
In July we preformed further attempts to transfect our cells and reactivity assays, and let’s not forget exams period.
 +
<br/>
 +
<br/>
 +
<b>Highlights:</b> Electroporation of microglia, mycoplasma assay, colony PCR after the microglia electroporation, transfection attempts with reagents, astrocyte reactivity assay using western blot.
 +
</p>
 +
<button class="accordion">Week 21</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/4/47/T--BGU_Israel--notebook_week21.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/4/47/T--BGU_Israel--notebook_week21.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    if (positions.length < 1) {
+
<button class="accordion">Week 22</button>
−
      positions.push('center');
+
<div class="panel2">
−
    }
+
<object data="https://static.igem.org/mediawiki/2018/d/db/T--BGU_Israel--notebook_week22.pdf" width="100%" height="500">
−
    if (positions.length == 1) {
+
                        <embed src="https://static.igem.org/mediawiki/2018/d/db/T--BGU_Israel--notebook_week22.pdf" type="application/pdf" width="100%" height="600" />
−
      positions.push(positions[0]);
+
</object>
−
    }
+
</div>
  
−
    if (positions[0] == 'top' || positions[0] == 'bottom' || positions[1] == 'left' || positions[1] == 'right') {
+
<button class="accordion">Week 23</button>
−
      positions = [positions[1], positions[0]];
+
<div class="panel2">
−
    }
+
<object data="https://static.igem.org/mediawiki/2018/8/89/T--BGU_Israel--notebook_week23.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/8/89/T--BGU_Israel--notebook_week23.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    if (this.positionX !== undefined) positions[0] = this.positionX.toLowerCase();
+
<button class="accordion">Week 24</button>
−
    if (this.positionY !== undefined) positions[1] = this.positionY.toLowerCase();
+
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/f/f1/T--BGU_Israel--notebook_week24.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/f/f1/T--BGU_Israel--notebook_week24.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    self.positionX = positions[0];
+
</div>
−
    self.positionY = positions[1];
+
  </div>
 +
</div>
  
−
    if (this.positionX != 'left' && this.positionX != 'right') {
+
<!-- August -->
−
      if (isNaN(parseInt(this.positionX))) {
+
<div id="august" class="bg-white text-center">
−
        this.positionX = 'center';
+
  <div class="row">
−
      } else {
+
<h1>August</h1>
−
        this.positionX = parseInt(this.positionX);
+
<div class="col-sm-8 col-sm-offset-2">
−
      }
+
<p>
−
    }
+
The summer was in full swing and with it our iGEM team. Each team member worked full force on experiments to reach a proof of concept.
 +
<br/>
 +
<br/>
 +
<b>Highlights:</b> continued reactive astrocyte experiments.
 +
</p>
 +
<button class="accordion">Week 25</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/0/0b/T--BGU_Israel--notebook_week25.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/0/0b/T--BGU_Israel--notebook_week25.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    if (this.positionY != 'top' && this.positionY != 'bottom') {
 
−
      if (isNaN(parseInt(this.positionY))) {
 
−
        this.positionY = 'center';
 
−
      } else {
 
−
        this.positionY = parseInt(this.positionY);
 
−
      }
 
−
    }
 
  
−
    this.position =
+
</div>
−
      this.positionX + (isNaN(this.positionX)? '' : 'px') + ' ' +
+
  </div>
−
      this.positionY + (isNaN(this.positionY)? '' : 'px');
+
</div>
  
−
    if (navigator.userAgent.match(/(iPod|iPhone|iPad)/)) {
+
<!-- Experiments -->
−
      if (this.imageSrc && this.iosFix && !this.$element.is('img')) {
+
<div id="experiments" class="bg-grey text-center">
−
        this.$element.css({
+
  <div class="row">
−
          backgroundImage: 'url(' + this.imageSrc + ')',
+
<h1>Experiments</h1>
−
          backgroundSize: 'cover',
+
<div class="col-sm-8 col-sm-offset-2">
−
          backgroundPosition: this.position
+
<button class="accordion">Calcium Phosphate Transfection</button>
−
        });
+
<div class="panel2">
−
      }
+
<object data="https://static.igem.org/mediawiki/2018/3/34/T--BGU_Israel--notebook_exp_calcium_phosphate.pdf" width="100%" height="500">
−
      return this;
+
                        <embed src="https://static.igem.org/mediawiki/2018/3/34/T--BGU_Israel--notebook_exp_calcium_phosphate.pdf" type="application/pdf" width="100%" height="600" />
−
    }
+
</object>
 +
</div>
  
−
    if (navigator.userAgent.match(/(Android)/)) {
+
<button class="accordion">Cytokine Inhibition</button>
−
      if (this.imageSrc && this.androidFix && !this.$element.is('img')) {
+
<div class="panel2">
−
        this.$element.css({
+
<object data="https://static.igem.org/mediawiki/2018/d/da/T--BGU_Israel--notebook_exp_qpcr.pdf" width="100%" height="500">
−
          backgroundImage: 'url(' + this.imageSrc + ')',
+
                        <embed src="https://static.igem.org/mediawiki/2018/d/da/T--BGU_Israel--notebook_exp_qpcr.pdf" type="application/pdf" width="100%" height="600" />
−
          backgroundSize: 'cover',
+
</object>
−
          backgroundPosition: this.position
+
</div>
−
        });
+
−
      }
+
−
      return this;
+
−
    }
+
  
−
    this.$mirror = $('<div />').prependTo(this.mirrorContainer);
+
<button class="accordion">Cell lines Infections with Lentivirus</button>
 +
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/0/0e/T--BGU_Israel--notebook_exp_lenti_infection.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/0/0e/T--BGU_Israel--notebook_exp_lenti_infection.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    var slider = this.$element.find('>.parallax-slider');
+
<button class="accordion">Promoter Assay</button>
−
    var sliderExisted = false;
+
<div class="panel2">
 +
<object data="https://static.igem.org/mediawiki/2018/5/51/T--BGU_Israel--notebook_exp_promoter_assay.pdf" width="100%" height="500">
 +
                        <embed src="https://static.igem.org/mediawiki/2018/5/51/T--BGU_Israel--notebook_exp_promoter_assay.pdf" type="application/pdf" width="100%" height="600" />
 +
</object>
 +
</div>
  
−
    if (slider.length == 0)
+
<button class="accordion">Reversed-Caspase-3 Induction</button>
−
      this.$slider = $('<img />').prependTo(this.$mirror);
+
<div class="panel2">
−
    else {
+
<object data="https://static.igem.org/mediawiki/2018/5/50/T--BGU_Israel--notebook_exp_caspase3.pdf" width="100%" height="500">
−
      this.$slider = slider.prependTo(this.$mirror)
+
                        <embed src="https://static.igem.org/mediawiki/2018/5/50/T--BGU_Israel--notebook_exp_caspase3.pdf" type="application/pdf" width="100%" height="600" />
−
      sliderExisted = true;
+
</object>
−
    }
+
</div>
  
−
    this.$mirror.addClass('parallax-mirror').css({
+
</div>
−
      visibility: 'hidden',
+
  </div>
−
      zIndex: this.zIndex,
+
</div>
−
      position: 'fixed',
+
−
      top: 0,
+
−
      left: 0,
+
−
      overflow: 'hidden'
+
−
    });
+
  
−
    this.$slider.addClass('parallax-slider').one('load', function() {
 
−
      if (!self.naturalHeight || !self.naturalWidth) {
 
−
        self.naturalHeight = this.naturalHeight || this.height || 1;
 
−
        self.naturalWidth  = this.naturalWidth  || this.width  || 1;
 
−
      }
 
−
      self.aspectRatio = self.naturalWidth / self.naturalHeight;
 
  
−
      Parallax.isSetup || Parallax.setup();
 
−
      Parallax.sliders.push(self);
 
−
      Parallax.isFresh = false;
 
−
      Parallax.requestRender();
 
−
    });
 
  
−
    if (!sliderExisted)
 
−
      this.$slider[0].src = this.imageSrc;
 
  
−
    if (this.naturalHeight && this.naturalWidth || this.$slider[0].complete || slider.length > 0) {
+
  <!-- accordion script -->
−
      this.$slider.trigger('load');
+
<script>
−
    }
+
var acc = document.getElementsByClassName("accordion");
 +
var i;
  
−
  }
+
for (i = 0; i < acc.length; i++) {
−
 
+
   acc[i].addEventListener("click", function() {
−
 
+
    this.classList.toggle("active");
−
  // Parallax Instance Methods
+
     var panel = this.nextElementSibling;
−
 
+
    if (panel.style.maxHeight){
−
  $.extend(Parallax.prototype, {
+
      panel.style.maxHeight = null;
−
    speed:    0.2,
+
    } else {
−
    bleed:    0,
+
       panel.style.maxHeight = panel.scrollHeight + "px";
−
    zIndex:  -100,
+
     }  
−
    iosFix:  true,
+
−
    androidFix: true,
+
−
    position: 'center',
+
−
    overScrollFix: false,
+
−
    mirrorContainer: 'body',
+
−
 
+
−
    refresh: function() {
+
−
      this.boxWidth        = this.$element.outerWidth();
+
−
      this.boxHeight      = this.$element.outerHeight() + this.bleed * 2;
+
−
      this.boxOffsetTop    = this.$element.offset().top - this.bleed;
+
−
      this.boxOffsetLeft  = this.$element.offset().left;
+
−
      this.boxOffsetBottom = this.boxOffsetTop + this.boxHeight;
+
−
 
+
−
      var winHeight = Parallax.winHeight;
+
−
      var docHeight = Parallax.docHeight;
+
−
      var maxOffset = Math.min(this.boxOffsetTop, docHeight - winHeight);
+
−
      var minOffset = Math.max(this.boxOffsetTop + this.boxHeight - winHeight, 0);
+
−
      var imageHeightMin = this.boxHeight + (maxOffset - minOffset) * (1 - this.speed) | 0;
+
−
      var imageOffsetMin = (this.boxOffsetTop - maxOffset) * (1 - this.speed) | 0;
+
−
      var margin;
+
−
 
+
−
      if (imageHeightMin * this.aspectRatio >= this.boxWidth) {
+
−
        this.imageWidth    = imageHeightMin * this.aspectRatio | 0;
+
−
        this.imageHeight   = imageHeightMin;
+
−
        this.offsetBaseTop = imageOffsetMin;
+
−
 
+
−
        margin = this.imageWidth - this.boxWidth;
+
−
 
+
−
        if (this.positionX == 'left') {
+
−
          this.offsetLeft = 0;
+
−
        } else if (this.positionX == 'right') {
+
−
          this.offsetLeft = - margin;
+
−
        } else if (!isNaN(this.positionX)) {
+
−
          this.offsetLeft = Math.max(this.positionX, - margin);
+
−
        } else {
+
−
          this.offsetLeft = - margin / 2 | 0;
+
−
        }
+
−
      } else {
+
−
        this.imageWidth    = this.boxWidth;
+
−
        this.imageHeight  = this.boxWidth / this.aspectRatio | 0;
+
−
        this.offsetLeft    = 0;
+
−
 
+
−
        margin = this.imageHeight - imageHeightMin;
+
−
 
+
−
        if (this.positionY == 'top') {
+
−
          this.offsetBaseTop = imageOffsetMin;
+
−
        } else if (this.positionY == 'bottom') {
+
−
          this.offsetBaseTop = imageOffsetMin - margin;
+
−
        } else if (!isNaN(this.positionY)) {
+
−
          this.offsetBaseTop = imageOffsetMin + Math.max(this.positionY, - margin);
+
−
        } else {
+
−
          this.offsetBaseTop = imageOffsetMin - margin / 2 | 0;
+
−
        }
+
−
      }
+
−
     },
+
−
 
+
−
    render: function() {
+
−
      var scrollTop    = Parallax.scrollTop;
+
−
      var scrollLeft  = Parallax.scrollLeft;
+
−
      var overScroll  = this.overScrollFix ? Parallax.overScroll : 0;
+
−
      var scrollBottom = scrollTop + Parallax.winHeight;
+
−
 
+
−
      if (this.boxOffsetBottom > scrollTop && this.boxOffsetTop <= scrollBottom) {
+
−
        this.visibility = 'visible';
+
−
        this.mirrorTop = this.boxOffsetTop  - scrollTop;
+
−
        this.mirrorLeft = this.boxOffsetLeft - scrollLeft;
+
−
        this.offsetTop = this.offsetBaseTop - this.mirrorTop * (1 - this.speed);
+
−
      } else {
+
−
        this.visibility = 'hidden';
+
−
       }
+
−
 
+
−
      this.$mirror.css({
+
−
        transform: 'translate3d('+this.mirrorLeft+'px, '+(this.mirrorTop - overScroll)+'px, 0px)',
+
−
        visibility: this.visibility,
+
−
        height: this.boxHeight,
+
−
        width: this.boxWidth
+
−
      });
+
−
 
+
−
      this.$slider.css({
+
−
        transform: 'translate3d('+this.offsetLeft+'px, '+this.offsetTop+'px, 0px)',
+
−
        position: 'absolute',
+
−
        height: this.imageHeight,
+
−
        width: this.imageWidth,
+
−
        maxWidth: 'none'
+
−
      });
+
−
     }
+
 
   });
 
   });
−
 
+
}
−
 
+
$('.btn-info').click(function(){
−
  // Parallax Static Methods
+
     $('html, body').animate({
−
 
+
         scrollTop: $( $(this).attr('href') ).offset().top
−
  $.extend(Parallax, {
+
     }, 500);
−
    scrollTop:    0,
+
     return false;
−
    scrollLeft:  0,
+
−
    winHeight:    0,
+
−
    winWidth:    0,
+
−
    docHeight:    1 << 30,
+
−
    docWidth:    1 << 30,
+
−
    sliders:      [],
+
−
    isReady:      false,
+
−
    isFresh:      false,
+
−
    isBusy:      false,
+
−
 
+
−
    setup: function() {
+
−
      if (this.isReady) return;
+
−
 
+
−
      var self = this;
+
−
 
+
−
      var $doc = $(document), $win = $(window);
+
−
 
+
−
      var loadDimensions = function() {
+
−
        Parallax.winHeight = $win.height();
+
−
        Parallax.winWidth  = $win.width();
+
−
        Parallax.docHeight = $doc.height();
+
−
        Parallax.docWidth  = $doc.width();
+
−
      };
+
−
 
+
−
      var loadScrollPosition = function() {
+
−
        var winScrollTop  = $win.scrollTop();
+
−
        var scrollTopMax  = Parallax.docHeight - Parallax.winHeight;
+
−
        var scrollLeftMax = Parallax.docWidth  - Parallax.winWidth;
+
−
        Parallax.scrollTop  = Math.max(0, Math.min(scrollTopMax,  winScrollTop));
+
−
        Parallax.scrollLeft = Math.max(0, Math.min(scrollLeftMax, $win.scrollLeft()));
+
−
        Parallax.overScroll = Math.max(winScrollTop - scrollTopMax, Math.min(winScrollTop, 0));
+
−
      };
+
−
 
+
−
      $win.on('resize.px.parallax load.px.parallax', function() {
+
−
          loadDimensions();
+
−
          self.refresh();
+
−
          Parallax.isFresh = false;
+
−
          Parallax.requestRender();
+
−
        })
+
−
        .on('scroll.px.parallax load.px.parallax', function() {
+
−
          loadScrollPosition();
+
−
          Parallax.requestRender();
+
−
        });
+
−
 
+
−
      loadDimensions();
+
−
      loadScrollPosition();
+
−
 
+
−
      this.isReady = true;
+
−
 
+
−
      var lastPosition = -1;
+
−
 
+
−
      function frameLoop() {
+
−
        if (lastPosition == window.pageYOffset) {  // Avoid overcalculations
+
−
          window.requestAnimationFrame(frameLoop);
+
−
          return false;
+
−
        } else lastPosition = window.pageYOffset;
+
−
 
+
−
        self.render();
+
−
        window.requestAnimationFrame(frameLoop);
+
−
      }
+
−
 
+
−
      frameLoop();
+
−
    },
+
−
 
+
−
    configure: function(options) {
+
−
      if (typeof options == 'object') {
+
−
        delete options.refresh;
+
−
        delete options.render;
+
−
        $.extend(this.prototype, options);
+
−
      }
+
−
    },
+
−
 
+
−
    refresh: function() {
+
−
      $.each(this.sliders, function(){ this.refresh(); });
+
−
      this.isFresh = true;
+
−
     },
+
−
 
+
−
    render: function() {
+
−
      this.isFresh || this.refresh();
+
−
      $.each(this.sliders, function(){ this.render(); });
+
−
    },
+
−
 
+
−
    requestRender: function() {
+
−
      var self = this;
+
−
      self.render();
+
−
      self.isBusy = false;
+
−
    },
+
−
    destroy: function(el){
+
−
      var i,
+
−
          parallaxElement = $(el).data('px.parallax');
+
−
      parallaxElement.$mirror.remove();
+
−
      for(i=0; i < this.sliders.length; i+=1){
+
−
        if(this.sliders[i] == parallaxElement){
+
−
          this.sliders.splice(i, 1);
+
−
        }
+
−
      }
+
−
      $(el).data('px.parallax', false);
+
−
      if(this.sliders.length === 0){
+
−
        $(window).off('scroll.px.parallax resize.px.parallax load.px.parallax');
+
−
        this.isReady = false;
+
−
        Parallax.isSetup = false;
+
−
      }
+
−
    }
+
−
  });
+
−
 
+
−
 
+
−
  // Parallax Plugin Definition
+
−
 
+
−
  function Plugin(option) {
+
−
    return this.each(function () {
+
−
      var $this = $(this);
+
−
      var options = typeof option == 'object' && option;
+
−
 
+
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Latest revision as of 16:34, 17 October 2018

OriginALS

OriginALS

Notebook

February March April May
June July August Experiments

February

We began working in our brand-new lab space! When we first arrived, the lab was nothing but two work benches. We had to collect and organize the equipment, materials, cell culture room, and work area; all according to lab safety standards. We also began cloning the plasmids for our experiments and learning how to work with cell culture by practicing on HEK293 cells.

Highlights: clone Steap4, Timp1, F4/80 into pGL4.17 and pGL3 plasmid for Promoter Assay.

March

In March, we experienced our first little success. We cloned our promoters into the pGL3 vector and were able to begin our first experiment, the Promoter Assay. Meanwhile, so far, our practice cells were alive and well.

Highlights: A decision was made to concentrate our efforts on the pGL3 plasmid expression assay. Because, then we could compare the expression among the promoters and we wouldn’t have to use two sets of luciferase kits.

April

Our long-awaited microglia and astrocytes arrived! While our cell lines were getting used to their new home, we began cloning our crisper and gRNA plasmids for our two-component system.

Highlights: Received microglia and astrocytes cell lines, px601, H1, H2 CMV-dCas9-VPR, building plasmids with Gibson assembly.

May

After a tireless journey, we successfully cloned most of our system’s plasmids. Now we began attempts to transfect these plasmids into our cell lines with different transfection reagents. Additionally, we began the promoter assay and astrocyte reactivity assay.

Highlights: Began Promoter assay, transfection attempts with reagents, ELISA for astrocyte reactivity assay.

June

In June we had to face the music; our transfection was not working. We began exploring alternatives ways to insert our plasmids into our cells, such as electroporation, calcium phosphate transfection, and additional transfection reagents.

Highlights: Astrocyte Western blot, Electroporation of microglia.

July

In July we preformed further attempts to transfect our cells and reactivity assays, and let’s not forget exams period.

Highlights: Electroporation of microglia, mycoplasma assay, colony PCR after the microglia electroporation, transfection attempts with reagents, astrocyte reactivity assay using western blot.

August

The summer was in full swing and with it our iGEM team. Each team member worked full force on experiments to reach a proof of concept.

Highlights: continued reactive astrocyte experiments.

Experiments

OriginALS

About Us


The BGU-iGEM team “OriginALS” hopes to develop an innovative therapeutic approach to prolong the life expectancy of ALS patients, using Synthetic Biology. We are dedicated to promoting ALS awareness and research in Israel through public engagement and educational activities.

    Keep in Touch

  • @iGEMBGU
  • @igem_2018_bgu
  • @originalsbgu
  • originalsbgu@gmail.com

    Address

  • Ben-Gurion University of the Negev
    Ben Gurion 1, Beer Sheva 8410501, Israel