Difference between revisions of "Team:CMUQ/Notebook"

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{{CMUQ}}
 
 
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<html>
  
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<meta name="viewport" content="width=device-width, initial-scale=1">
  
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<div class="column full_size">
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    <link href="https://fonts.googleapis.com/css?family=Montserrat" rel="stylesheet">
  
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<h1>Notebook</h1>
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    <link href="//2015.igem.org/Team:Oxford/Assets/Bootstrap?action=raw&ctype=text/css" rel="stylesheet">
−
<p> Document the dates you worked on your project. This should be a detailed account of the work done each day for your project.</p>
+
    <link href="//2015.igem.org/Team:Oxford/Assets/stylesheet?action=raw&ctype=text/css" rel="stylesheet">
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 +
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 +
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<!--- THIS IS WHERE THE HTML BEGINS --->
 +
 
 +
 
 +
 
 +
<head>
 +
 
 +
<!-- This tells the browser that your page is responsive -->
 +
<meta name="viewport" content="width=device-width, initial-scale=1">
 +
 
 +
</head>
 +
<nav id="mainNav" class="navbar navbar-default navbar-fixed-top">
 +
    <div class="container">
 +
      <!-- Brand and toggle get grouped for better mobile display -->
 +
      <div class="navbar-header">
 +
        <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1">
 +
          <span class="sr-only">Toggle navigation</span>
 +
          <span class="icon-bar"></span>
 +
          <span class="icon-bar"></span>
 +
          <span class="icon-bar"></span>
 +
        </button>
 +
        <a class="navbar-brand" href="https://2017.igem.org/Team:CMUQ" >CMUQ</a>
 +
      </div>
 +
 
 +
      <!-- Collect the nav links, forms, and other content for toggling -->
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      <div class="collapse navbar-collapse" id= "expand">
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        <ul class="nav navbar-nav navbar-right">
 +
            <li class="dropdown">
 +
                <a class="dropdown-toggle" data-toggle="dropdown" href="#">PROJECT <span class="caret"> </span></a>
 +
                <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/descritpion">Description</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/design">Design</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/safety">Safety</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/Demonstrate">Demonstrate</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/Model">Model</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/Collaborations">Collaborations</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/achievments">Achievements</a></li>
 +
                </ul>
 +
            </li>
 +
            <li class="dropdown">
 +
                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> PRACTICES <span class="caret"> </span></a>
 +
                <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/humanpractices">Human Practices</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/HP/Silver"> Silver HP </a></li>
 +
                </ul>
 +
            </li>
 +
            <li class="dropdown">
 +
                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> WET LAB <span class="caret"> </span></a>
 +
                <ul class="dropdown-menu">
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/results">Overview & Results</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/notebook">Notebook</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/protocols">Protocols</a></li>
 +
                            <li><a href="https://2017.igem.org/Team:CMUQ/InterLab">InterLab</a></li>
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                    <li><a href="https://2017.igem.org/Team:CMUQ/modelling">Modelling</a></li>
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                <a class="dropdown-toggle" data-toggle="dropdown" href="#"> TEAM <span class="caret"> </span></a>
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                    <li><a href="https://2017.igem.org/Team:CMUQ/team">Team</a></li>
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                            <li><a href="https://2017.igem.org/Team:CMUQ/attributions">Attributions</a></li>
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                </ul>
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            <li><a href="https://2017.igem.org/Team:CMUQ/gallery">GALLERY</a></li>
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<div class="mainn">
  
 
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<body>
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<div class="container">
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  <div class="page-header">
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  </div>
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      <div class="timeline-panel">
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          <h4 class="timeline-title">Sunday 7/2</h4>
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        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">Dina, Najla and Maya discussed lab space, reagents and work time, as well as future meetings: </p>
 +
          <ul><li>Main Lab Space: 2033</li>
 +
<li>Days and Times: based on experiments and is specific to each group, need to inform Bernadette beforehand </li>
 +
<li>Regents: all reagents needed for the next two weeks are available, need to know more about SRB.</li>
 +
<li>iGEM group meetings will be held on Sundays: update logs during the weekend, present work on Sunday for the whole team</li></ul>
 +
         
 +
        </div>
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<h5>What should this page have?</h5>
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    <li class="timeline-inverted">
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      <div class="timeline-badge warning"></div>
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 7/3</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">Dina:</p>
 +
          <ul><li>Email Dr. Vincent with updates</li>
 +
<li>Re-read protocols, and write them by hand into lab notebook for next day  </li>  </ul>
 +
        </div>
 +
      </div>
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    </li>
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      <div class="timeline-badge danger"></div>
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      <div class="timeline-panel">
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        <div class="timeline-heading">
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          <h4 class="timeline-title">Tuesday 7/4</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">Dina:</p>
 +
          <ul> <li>Prepared LB-Agar Chloramphenicol plates  </li>
 +
            <li>Protocol:  </li>
 +
            <li> Work on presentation for tomorrow's team meeting </li></ul>
 +
        </div>
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      </div>
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    </li>
 +
    <li class="timeline-inverted">
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      <div class="timeline-badge"></div>
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          <h4 class="timeline-title">Wednesday 7/5</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">iGEM team meeting </p>
 +
          <p style="color:#92989C  ;">Interlab:</p>
 +
          <ul> <li>Obtained DH5α cells (Genetics Lab 2013) from Maya </li>
 +
<li>Start preparing competent DH5α cells:  </li> </ul>
 +
 
 +
        </div>
 +
      </div>
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    </li>
 +
    <li>
 +
      <div class="timeline-badge info"></div>
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      <div class="timeline-panel">
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thurday 7/6</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">Interlab</p>
 +
          <ul> <li>Continue preparing competent DH5α cells </li>
 +
            <li> Obtain regents needed for next week preparation of competent cells
 
<ul>
 
<ul>
−
<li>Chronological notes of what your team is doing.</li>
+
<li>MgCl2 (third floor lab) </li>
−
<li> Brief descriptions of daily important events.</li>
+
<li>CaCl2 (2033 cab)</li>
−
<li>Pictures of your progress. </li>
+
<li>ddH2O (Maria, Chemlab)</li>
−
<li>Mention who participated in what task.</li>
+
  <li>Glycerol (2033 Flammable cab)</li> </ul></ul>
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</ul>
+
         
  
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    <li class="timeline-inverted">
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      <div class="timeline-badge success"></div>
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          <h4 class="timeline-title">Sunday 7/9</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">DspB Lab:</p>
 +
          <ul><li>Meeting with  Dr. Vincent: changed protocol for the preparation of competent cells  as Cheryl mentioned in her email, need to use ultra competent cells (from Dr. Ihab's lab) → will start next week </li> </ul>
 +
          <p style="color:#4B8837;"> Biofilm Lab:</p>
 +
          <ul><li> Meeting with Bernadette and Maya to discuss materials and applinces being used in the lab for Biofilm Production.</li>
 +
          <li>Meeting with Professor Vincent to discuss how to proceed with porject:  </li>
 +
            <ul><li>96 well plates. </li>
 +
            <li> Add samples of SRB directly onto the wells (no inoculation); see if media is required for biofilm formation. </li>
 +
              <li>Possible simulation using appratus in lab (Bioflux 2000; https://bioflux.fluxionbio.com/microbiology )  </li>
 +
            </ul>
 +
          </ul>
 +
<p> To do: </p>
 +
          <ul><li> Write up protocol for biofilm production on plastic pipe.</li>
 +
          <li>SRB media recipe (just in case wemay need to use it)
 +
            </li><li>
 +
            Appratus set up
 +
            </li>
 +
            </ul>
 +
        </div>
 +
      </div>
 +
     
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    </li>
 +
    <li>
 +
      <div class="timeline-badge warning"></div>
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      <div class="timeline-panel">
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 7/10</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">Interlab:</p>
 +
          <ul><li>
 +
Continue preparing competent DH5α cells  </li>
 +
            <li>Preparation of MgCl2 and CaCl2 solutions for CaCl2 competent cells preparation  </li>
 +
            <li> LB media preparation </li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
    <li class= "timeline-inverted">
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      <div class="timeline-badge danger"></div>
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      <div class="timeline-panel">
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 7/11</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">Interlab:</p>
 +
          <ul><li>
 +
Finish preparing competent DH5α cells  </li>
 +
            <li>Prepare CaCl2 w/ Glycerol solution  </li>
 +
            <li> Filter sterilize all solutions</li></ul>
 +
          <p style ="color:#E74C3C;">Group meeting:</p>
 +
          <ul><li>Test for DspB secretion outside after successful transformation </li> </ul>
 +
          <p style ="color:#E74C3C;">Skype meeting with Chyrl</p>
 +
        </div>
 +
      </div>
 +
    </li>
 +
         
 +
         
 +
              <li>
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Wednesday 7/12</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">Biofilm lab:</p>
 +
          <ul><li>
 +
LB Apmicilin/Arabinose plates were made.  </li></ul>
 +
          <p style="color:#3EC8F1 ;">Interlab:</p>
 +
          <ul><li>TPrepare SOC media for competency test (Obtained SOC from Bernadette, didn't make our own)</li>
 +
            <li>
 +
Competent cell test using Kit</li></ul>
 +
          <p style="color:#3EC8F1 ;">Skype meeting with Pittsburgh for collaboration </p>
 +
        </div>
 +
      </div>
 +
    </li>
 +
   
 +
         
 +
          <li class="timeline-inverted">
 +
      <div class="timeline-badge success"></div>
 +
      <div class="timeline-panel">
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thursday 7/13</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">Interlab:</p>
 +
          <ul><li>Competent cells test: there was no growth on any of the plates except for tiny colonies on the 100 pb/µL plate. Another method to prepare competent DH5α cells should be utilized. </li> </ul>
 +
          <p style="color:#4B8837;"> Meeting to discuss Wiki with Yasmin</p>
 +
         
 +
<p style="color:#4B8837;"> Biofilm lab: </p>
 +
          <ul><li> Plated flouresent DH5α were incoulated on LB Ampicilin/Arabinose broth on 50 ml kleftt flask; left over 2 days in shaker at 37°C.</li>
 +
            </ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
         
 +
         
 +
          <li>
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 7/16</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">Biofilm lab: </p>
 +
          <ul><li>Using spechtophotometer, OD of inoculated cultre was found to be ~ 375. 3 dilutions were made at 7.5X, 13X and  26X. Dilutions and culture were left to incubate overnight in the air shaker at 37°C.</li></ul>
 +
        </div>
 +
        </div>
 +
    </li>
 +
       
 +
          <li class="timeline-inverted">
 +
      <div class="timeline-badge warning"></div>
 +
      <div class="timeline-panel">
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        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 7/17</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">DspB Lab:</p>
 +
          <ul><li>Obtain cells from Dr. Ihab lab, alongside the protocol</li>
 +
<li>Cells from competent cell test grew after ≈ 5 days  </li></ul>
 +
          <p style = "color:#F1A23E;"> Biofilm Lab:</p>
 +
          <ul><li>Dilutions and original culture in broth were checked under UV and no fluorescence was found. Plated GFP-DH5α cells  were found to be fluorescent. Cultures in broth were scrapped and new LB Ampicilin/Arabinose broth was planned to be made. </li> </ul>
 +
                    <img src='https://static.igem.org/mediawiki/2017/f/ff/Monday7-17.JPG' width="50%" hieght="50%" >  </img>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 
 +
          <li>
 +
      <div class="timeline-badge danger"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 7/14</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">Biofilm Lab:</p>
 +
          <ul> <li>LB Ampicilin/Arabinose broth was made. </li></ul>
 +
          <p style ="color:#E74C3C;"> DspB Lab:</p>
 +
          <ul><li>Prepared more Chl LB plates for transformations </li> </ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
   
 +
          <li class = "timeline-inverted">
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 7/23</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">DspB Lab:</p>
 +
          <ul><li>
 +
Transform DspB (BBa_K1659200 | Kit plate 7 | well 15C) into ultra competent cells  </li></ul>
 +
          <p style="color:#3EC8F1 ;">Biofilm Lab:</p>
 +
          <ul><li>Inoculate GFP-DH5α cells in 50 ml LB Amp/Arab broth in 150 ml Kelft flask. Left in shaker at 37 overnight to culture.</li></ul>
 +
           
 +
        </div>
 +
      </div>
 +
    </li>
 +
         
 +
  <li >
 +
      <div class="timeline-badge success"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 7/25</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">DspB Lab:</p>
 +
          <ul><li>Transformation of DspB (BBa_K1659200 | Kit plate 7 | well 15C) into ultra competent cells.</li>
 +
            <li>  Result: three colonies observed on LB Chl plate, no red fluorescence. </li></ul>
 +
          <p style="color:#4B8837;"> Biofilm Lab:</p>
 +
          <ul><li> Dilute by 10-fold GFP-DH5α culture and plate in 96 well plate. Left to incubate over 2 days.</li>
 +
          </ul>
 +
                    <img src='https://static.igem.org/mediawiki/2017/e/ec/Tuesday_7-25.JPG' width="50%" hieght="50%" >  </img>
 +
       
 +
        </div>
 +
      </div>
 +
    </li>
 +
   
 +
          <li class="timeline-inverted">
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 7/16</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">Biofilm lab: </p>
 +
          <ul><li>Using spechtophotometer, OD of inoculated cultre was found to be ~ 375. 3 dilutions were made at 7.5X, 13X and  26X. Dilutions and culture were left to incubate overnight in the air shaker at 37°C.</li></ul>
 +
        </div>
 +
        </div>
 +
    </li>
 +
       
 +
          <li>
 +
      <div class="timeline-badge warning"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thursday 7/27</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">Biofilm Lab:</p>
 +
          <ul><li>GFP-DH5α biofilm were shown on 96 well plate.</li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
     
 +
         
 +
          <li class="timeline-inverted">
 +
      <div class="timeline-badge danger"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 7/30</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">DspB Lab:</p>
 +
          <ul> <li>Overnight culture of DspB plate (from fridge) into LB Chl media, picked two colonies and left overnight shaking at 37˚C.</li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
     
 +
         
 +
          <li>
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 7/31</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">DspB Lab:</p>
 +
          <ul> <li>Mini prep to extract DspB (BBa_K1659200 | Kit plate 7 | well 15C) plasmid DNA.</li>
 +
            <li> Agarose mini-gel run of DspB plasmid to check size: successful transformation as the size was ≈ 3Kb as expected for DspB plasmid</ul>
 +
                    <img src='https://static.igem.org/mediawiki/2017/9/99/Monday_7-31_1.png' width="50%" hieght="50%" >  </img>
 +
                  <img src='https://static.igem.org/mediawiki/2017/b/b5/Monday_7-31_2.png' width="50%" hieght="50%" >  </img>
 +
</div>
 
</div>
 
</div>
 +
</li>
 +
         
 +
    <li class="timeline-inverted" >
 +
      <div class="timeline-badge success"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 8/15</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">DspB Lab:</p>
 +
          <ul><li>Plated the remaining ultra competent cells ≈ 20 µLon LB plate to make more ultra-competent cells</li>
 +
            <li>  Plated 50 µL of Saad's prepared DH5 Alpha on LB plate to make more competent cells </li>
 +
              <li>
 +
                Transformation of DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I ) into LB-Chl plate
 +
            </li>
 +
            <li>
 +
              Need to do this for gene expression: DspB-DspA contained in the pSB1C3 backbone, was extracted via Miniprep. The NcoI restriction site was introduced upstream of each of our gene sequences (except BBa_K1659501 and BBa_K1659601) via PCR to facilitate their insertion into the arabinose-inducible pBAD/HisB commercial expression vector, and the insert-containing expression vectors were subsequently cloned separately into the standard laboratory E. coli K-12 strain MG1655 as well as a chemotaxis knockout strain E. coli RP437 ∆FliC.
 +
            </li>
 +
            </ul>
 +
         
 +
        </div>
 +
      </div>
 +
    </li>
 +
       
 +
         
 +
      <li>
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Wednesday 8/16</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">DspB Lab: </p>
 +
          <ul><li>Ultracompetent cells growth, as well as DH5 Alpha cells.</li>
 +
            <li>Plate with transformed DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I) didn't show any colonies, will keep in incubator for longer </li>
 +
          </ul>
 +
        </div>
 +
        </div>
 +
    </li>
  
−
<div class="column half_size">
+
<li class="timeline-inverted">
−
<h5>Inspiration</h5>
+
      <div class="timeline-badge warning"></div>
−
<p>You can see what others teams have done to organize their notes:</p>
+
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thursday 8/17</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">DspB Lab:</p>
 +
          <ul><li>Growth on the DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I) plate, only 4 colonies, leave over weekend</li>
 +
            <li>Store other plates (cells) in the fridge</li>
 +
          </ul>
 +
          <img src='https://static.igem.org/mediawiki/2017/d/dc/Thursday_8-17.jpg' width="50%" hieght="50%" >  </img>
 +
        </div>
 +
      </div>
 +
    </li>
 +
     
 +
<li>
 +
      <div class="timeline-badge danger"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 8/21</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">DspB Lab:</p>
 +
          <ul> <li>Overnight culture of DspB-DspA plate (from fridge) into LB Chl media, picked two colonies and left overnight shaking at 37˚C.</li>
 +
          </ul>
 +
          <p style ="color:#E74C3C;">Yasmin and Dina:</p>
 +
          <ul> <li>Lab Photoshoot for Wiki</li>
 +
          </ul>
 +
          <p style ="color:#E74C3C;">Saad and Dina:</p>
 +
          <ul><li>Discuss SRB tagetting, logo and abstract</li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 8/22</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">DspB Lab:</p>
 +
          <ul> <li>Mini prep to extract DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I) </li>
 +
            <li> Agarosegel run of DspB-DspA unsuccessful</ul>
 +
         
 +
                    <img src='https://static.igem.org/mediawiki/2017/4/47/Tuesday_8-22.jpeg' width="50%" hieght="50%" >  </img>
 +
        <p style="color:#3EC8F1 ;">iGEM Team meeting</p>
 +
                 
 +
</div>
 +
</div>
 +
</li>
  
−
<ul>  
+
<li>
−
<li><a href="https://2014.igem.org/Team:ATOMS-Turkiye/Notebook">2014 ATOMS-Turkiye</a></li>
+
      <div class="timeline-badge success"></div>
−
<li><a href="https://2014.igem.org/Team:Tec-Monterrey/ITESM14_project.html#tab_notebook">2014 Tec Monterrey</a></li>
+
      <div class="timeline-panel">
−
<li><a href="https://2014.igem.org/Team:Kyoto/Notebook/Magnetosome_Formation#title">2014 Kyoto</a></li>
+
        <div class="timeline-heading">
−
<li><a href="https://2014.igem.org/Team:Cornell/notebook">2014 Cornell</a></li>
+
          <h4 class="timeline-title">Wednesday 8/23</h4>
−
</ul>
+
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">DspB Lab:</p>
 +
          <ul><li>Individual meeting with Cheryl</li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
  
 +
<li class= "timeline-inverted">
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 9/3</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">Dina:</p>
 +
          <ul><li>Meeting with Oxy Qatar for human resources</li></ul>
 +
        </div>
 +
        </div>
 +
    </li>
 +
 +
<li>
 +
      <div class="timeline-badge warning"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 9/19</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">DNA sequences arrived from IDT</p>
 +
         
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge danger"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Friday 8/29</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">Interlab Study submission </p>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
<li>
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thursday 10/5</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">Photoshoot</p>
 +
          <p style="color:#3EC8F1 ;">Team meeting</p>
 +
          <p style="color:#3EC8F1 ;">Wiki updates</p>
 +
          <p style="color:#3EC8F1 ;">Transform pRSET emGFP into DH5 Alpha (max comp)</p>
 +
                    <img src='https://static.igem.org/mediawiki/2017/b/b3/Thursday_10-5_1.jpg' width="50%" hieght="50%" >  </img>
 +
        <img src='https://static.igem.org/mediawiki/2017/2/22/Thursday_10-5_2.jpg' width="50%" hieght="50%" >  </img>
 +
</div>
 
</div>
 
</div>
 +
</li>
 +
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge success"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 10/8</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">Dina and Albandari:</p>
 +
          <img src='https://static.igem.org/mediawiki/2017/7/70/Sunday_10-8_1.png' width="50%" hieght="50%" >  </img>
 +
        <p style="color:#4B8837;">Dina and Kawthar:</p>
 +
        <ul><li>Double digest of pRSET plasmid with EcoRI and BamHI successful </li></ul>
 +
        <img src='https://static.igem.org/mediawiki/2017/b/b4/Sunday_10-8_2.png' width="50%" hieght="50%" >  </img>
 +
        <p style="color:#4B8837;">Aisha:</p>
 +
        <ul><li>Digestion of 3 samples of DspB DspA plasmid with PstI to check size</li></ul>
 +
         
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
<li>
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 10/9</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">Aisha and Albandari:</p>
 +
          <ul><li>Transform pSB1C3 plasmid from kit (we will use for salt sensor)</li> </ul>
 +
          <p style="color:#92989C  ;">Dina and Alreem:</p>
 +
          <ul><li>Agarose gel run with pRSET digest to extract, undigested plasmids to check size</li>
 +
            <li>Agarose gel run with DspB -DspA digested (BBa_K1659211, BBa_K1659201, and Dina's prepared BBa_K1659211)</li>
 +
             
 +
            </ul>
 +
<p style="color:#92989C  ;">Saad:</p>
 +
          <ul><li>Gel imaging</li></ul>
 +
          <img src='https://static.igem.org/mediawiki/2017/7/76/Monday_10-9.png' width="50%" hieght="50%" >  </img>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge danger"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 10/10</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style ="color:#E74C3C;">Saad:</p>
 +
          <ul><li>Extraction of pRSET plasmid from gel: concentration = 19.8 µg/mL</li></ul>
 +
          <p style ="color:#E74C3C;">Dina and Alreem:</p>
 +
          <ul><li>PCR of DspB DspA </li></ul>
 +
          <img src='https://static.igem.org/mediawiki/2017/9/98/Tuesday_10-10_1.png' width="50%" hieght="50%" >  </img>
 +
        <img src='https://static.igem.org/mediawiki/2017/0/0c/Tuesday_10-10_2.jpg' width="50%" hieght="50%" >  </img>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
 +
<li>
 +
      <div class="timeline-badge warning"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Tuesday 10/11</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style = "color:#F1A23E;">DspB DspA:</p>
 +
          <ul><li>Cleanup PCR products DspB DspA samples and combine samples</li>
 +
            <li>Digestion of PCR products with EcoRI and BamHI</li>
 +
            <li>Ran a gel to check size</li>
 +
            <li>Cleanup </li>
 +
            <li>Ligation into pRSET plasmid with instant sticky-end ligase mix NEB</li>
 +
            <li>Transformation</li>
 +
          </ul>
 +
          <p style = "color:#F1A23E;">gBLOCK:</p>
 +
          <ul><li>PCR samples  </li></ul>
 +
          <img src='https://static.igem.org/mediawiki/2017/2/2b/Wednesday_10-11.png' width="50%" hieght="50%" >  </img>
 +
        <p>gBLOCK 1: WT proU osmolarity promoter</p>
 +
        <p>gBLOCK 2: proU-B0034-mRFP-B001</p>
 +
        <p>gBLOCK 3: Consensus proU osmolarity promoter</p>
 +
        <p>gBLOCK 4: WT proU-RBS-mRFP-B0015</p>
 +
</div>
 +
      </div>
 +
    </li>
 +
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge info"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Thursday 10/12</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#3EC8F1 ;">PCR cleanup</p>
 +
          <p style="color:#3EC8F1 ;">Digestion</p>
 +
          <p style="color:#3EC8F1 ;">Cleanup</p>
 +
          <p style="color:#3EC8F1 ;">Ligation</p>
 +
          <p style="color:#3EC8F1 ;">Transformation</p>
 +
                   
 +
</div>
 +
</div>
 +
</li>
 +
 +
<li>
 +
      <div class="timeline-badge success"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Sunday 10/15</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#4B8837;">There was growth of pRSET em-GFP plasmid with insert DspB DspA</p>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
<li class="timeline-inverted">
 +
      <div class="timeline-badge"></div>
 +
      <div class="timeline-panel">
 +
        <div class="timeline-heading">
 +
          <h4 class="timeline-title">Monday 10/16</h4>
 +
        </div>
 +
        <div class="timeline-body">
 +
          <p style="color:#92989C  ;">DspBDspA in pRSET:</p>
 +
          <ul><li>Mini prep</li>
 +
            <li>Transform in BL21 </li></ul>
 +
          <p style="color:#92989C;">ProU:</p>
 +
          <ul><li>Inoculate into LB-Chl</li></ul>
 +
        </div>
 +
      </div>
 +
    </li>
 +
 +
  </ul>
 +
</div>
 +
 +
 +
 +
 +
 +
 +
 +
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Revision as of 13:09, 26 October 2017

  • Sunday 7/2

    Dina, Najla and Maya discussed lab space, reagents and work time, as well as future meetings:

    • Main Lab Space: 2033
    • Days and Times: based on experiments and is specific to each group, need to inform Bernadette beforehand
    • Regents: all reagents needed for the next two weeks are available, need to know more about SRB.
    • iGEM group meetings will be held on Sundays: update logs during the weekend, present work on Sunday for the whole team

  • Monday 7/3

    Dina:

    • Email Dr. Vincent with updates
    • Re-read protocols, and write them by hand into lab notebook for next day

  • Tuesday 7/4

    Dina:

    • Prepared LB-Agar Chloramphenicol plates
    • Protocol:
    • Work on presentation for tomorrow's team meeting

  • Wednesday 7/5

    iGEM team meeting

    Interlab:

    • Obtained DH5α cells (Genetics Lab 2013) from Maya
    • Start preparing competent DH5α cells:

  • Thurday 7/6

    Interlab

    • Continue preparing competent DH5α cells
    • Obtain regents needed for next week preparation of competent cells
      • MgCl2 (third floor lab)
      • CaCl2 (2033 cab)
      • ddH2O (Maria, Chemlab)
      • Glycerol (2033 Flammable cab)

  • Sunday 7/9

    DspB Lab:

    • Meeting with Dr. Vincent: changed protocol for the preparation of competent cells as Cheryl mentioned in her email, need to use ultra competent cells (from Dr. Ihab's lab) → will start next week

    Biofilm Lab:

    • Meeting with Bernadette and Maya to discuss materials and applinces being used in the lab for Biofilm Production.
    • Meeting with Professor Vincent to discuss how to proceed with porject:
      • 96 well plates.
      • Add samples of SRB directly onto the wells (no inoculation); see if media is required for biofilm formation.
      • Possible simulation using appratus in lab (Bioflux 2000; https://bioflux.fluxionbio.com/microbiology )

    To do:

    • Write up protocol for biofilm production on plastic pipe.
    • SRB media recipe (just in case wemay need to use it)
    • Appratus set up

  • Monday 7/10

    Interlab:

    • Continue preparing competent DH5α cells
    • Preparation of MgCl2 and CaCl2 solutions for CaCl2 competent cells preparation
    • LB media preparation

  • Tuesday 7/11

    Interlab:

    • Finish preparing competent DH5α cells
    • Prepare CaCl2 w/ Glycerol solution
    • Filter sterilize all solutions

    Group meeting:

    • Test for DspB secretion outside after successful transformation

    Skype meeting with Chyrl

  • Wednesday 7/12

    Biofilm lab:

    • LB Apmicilin/Arabinose plates were made.

    Interlab:

    • TPrepare SOC media for competency test (Obtained SOC from Bernadette, didn't make our own)
    • Competent cell test using Kit

    Skype meeting with Pittsburgh for collaboration

  • Thursday 7/13

    Interlab:

    • Competent cells test: there was no growth on any of the plates except for tiny colonies on the 100 pb/µL plate. Another method to prepare competent DH5α cells should be utilized.

    Meeting to discuss Wiki with Yasmin

    Biofilm lab:

    • Plated flouresent DH5α were incoulated on LB Ampicilin/Arabinose broth on 50 ml kleftt flask; left over 2 days in shaker at 37°C.

  • Sunday 7/16

    Biofilm lab:

    • Using spechtophotometer, OD of inoculated cultre was found to be ~ 375. 3 dilutions were made at 7.5X, 13X and 26X. Dilutions and culture were left to incubate overnight in the air shaker at 37°C.

  • Monday 7/17

    DspB Lab:

    • Obtain cells from Dr. Ihab lab, alongside the protocol
    • Cells from competent cell test grew after ≈ 5 days

    Biofilm Lab:

    • Dilutions and original culture in broth were checked under UV and no fluorescence was found. Plated GFP-DH5α cells were found to be fluorescent. Cultures in broth were scrapped and new LB Ampicilin/Arabinose broth was planned to be made.

  • Tuesday 7/14

    Biofilm Lab:

    • LB Ampicilin/Arabinose broth was made.

    DspB Lab:

    • Prepared more Chl LB plates for transformations

  • Sunday 7/23

    DspB Lab:

    • Transform DspB (BBa_K1659200 | Kit plate 7 | well 15C) into ultra competent cells

    Biofilm Lab:

    • Inoculate GFP-DH5α cells in 50 ml LB Amp/Arab broth in 150 ml Kelft flask. Left in shaker at 37 overnight to culture.

  • Tuesday 7/25

    DspB Lab:

    • Transformation of DspB (BBa_K1659200 | Kit plate 7 | well 15C) into ultra competent cells.
    • Result: three colonies observed on LB Chl plate, no red fluorescence.

    Biofilm Lab:

    • Dilute by 10-fold GFP-DH5α culture and plate in 96 well plate. Left to incubate over 2 days.

  • Sunday 7/16

    Biofilm lab:

    • Using spechtophotometer, OD of inoculated cultre was found to be ~ 375. 3 dilutions were made at 7.5X, 13X and 26X. Dilutions and culture were left to incubate overnight in the air shaker at 37°C.

  • Thursday 7/27

    Biofilm Lab:

    • GFP-DH5α biofilm were shown on 96 well plate.

  • Sunday 7/30

    DspB Lab:

    • Overnight culture of DspB plate (from fridge) into LB Chl media, picked two colonies and left overnight shaking at 37˚C.

  • Monday 7/31

    DspB Lab:

    • Mini prep to extract DspB (BBa_K1659200 | Kit plate 7 | well 15C) plasmid DNA.
    • Agarose mini-gel run of DspB plasmid to check size: successful transformation as the size was ≈ 3Kb as expected for DspB plasmid

  • Tuesday 8/15

    DspB Lab:

    • Plated the remaining ultra competent cells ≈ 20 µLon LB plate to make more ultra-competent cells
    • Plated 50 µL of Saad's prepared DH5 Alpha on LB plate to make more competent cells
    • Transformation of DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I ) into LB-Chl plate
    • Need to do this for gene expression: DspB-DspA contained in the pSB1C3 backbone, was extracted via Miniprep. The NcoI restriction site was introduced upstream of each of our gene sequences (except BBa_K1659501 and BBa_K1659601) via PCR to facilitate their insertion into the arabinose-inducible pBAD/HisB commercial expression vector, and the insert-containing expression vectors were subsequently cloned separately into the standard laboratory E. coli K-12 strain MG1655 as well as a chemotaxis knockout strain E. coli RP437 ∆FliC.

  • Wednesday 8/16

    DspB Lab:

    • Ultracompetent cells growth, as well as DH5 Alpha cells.
    • Plate with transformed DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I) didn't show any colonies, will keep in incubator for longer

  • Thursday 8/17

    DspB Lab:

    • Growth on the DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I) plate, only 4 colonies, leave over weekend
    • Store other plates (cells) in the fridge

  • Monday 8/21

    DspB Lab:

    • Overnight culture of DspB-DspA plate (from fridge) into LB Chl media, picked two colonies and left overnight shaking at 37˚C.

    Yasmin and Dina:

    • Lab Photoshoot for Wiki

    Saad and Dina:

    • Discuss SRB tagetting, logo and abstract

  • Tuesday 8/22

    DspB Lab:

    • Mini prep to extract DspB-DspA (BBa_K1659211 | Kit plate 7 | well 15I)
    • Agarosegel run of DspB-DspA unsuccessful

    iGEM Team meeting

  • Wednesday 8/23

    DspB Lab:

    • Individual meeting with Cheryl

  • Sunday 9/3

    Dina:

    • Meeting with Oxy Qatar for human resources

  • Tuesday 9/19

    DNA sequences arrived from IDT

  • Friday 8/29

    Interlab Study submission

  • Thursday 10/5

    Photoshoot

    Team meeting

    Wiki updates

    Transform pRSET emGFP into DH5 Alpha (max comp)

  • Sunday 10/8

    Dina and Albandari:

    Dina and Kawthar:

    • Double digest of pRSET plasmid with EcoRI and BamHI successful

    Aisha:

    • Digestion of 3 samples of DspB DspA plasmid with PstI to check size

  • Monday 10/9

    Aisha and Albandari:

    • Transform pSB1C3 plasmid from kit (we will use for salt sensor)

    Dina and Alreem:

    • Agarose gel run with pRSET digest to extract, undigested plasmids to check size
    • Agarose gel run with DspB -DspA digested (BBa_K1659211, BBa_K1659201, and Dina's prepared BBa_K1659211)

    Saad:

    • Gel imaging

  • Tuesday 10/10

    Saad:

    • Extraction of pRSET plasmid from gel: concentration = 19.8 µg/mL

    Dina and Alreem:

    • PCR of DspB DspA

  • Tuesday 10/11

    DspB DspA:

    • Cleanup PCR products DspB DspA samples and combine samples
    • Digestion of PCR products with EcoRI and BamHI
    • Ran a gel to check size
    • Cleanup
    • Ligation into pRSET plasmid with instant sticky-end ligase mix NEB
    • Transformation

    gBLOCK:

    • PCR samples

    gBLOCK 1: WT proU osmolarity promoter

    gBLOCK 2: proU-B0034-mRFP-B001

    gBLOCK 3: Consensus proU osmolarity promoter

    gBLOCK 4: WT proU-RBS-mRFP-B0015

  • Thursday 10/12

    PCR cleanup

    Digestion

    Cleanup

    Ligation

    Transformation

  • Sunday 10/15

    There was growth of pRSET em-GFP plasmid with insert DspB DspA

  • Monday 10/16

    DspBDspA in pRSET:

    • Mini prep
    • Transform in BL21

    ProU:

    • Inoculate into LB-Chl