Difference between revisions of "Team:Newcastle/Protocols"

 
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                 <h3>Experiments</h3>
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                 <h3>Alternative Roots</h3>
  
 
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                     <a href="#protocol" class="smoothscroll btn btn--stroke">
 
                         Overview
 
                         Overview
 
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                    <span>Scroll Down</span>
 
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     <section id='protocol' class="s-services">
  
 
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                             <h3 class="subhead">2018</h3>
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                             <h3 class="subhead">EXPERIMENTS</h3>
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                 <h1 class="display-2">The Newcastle Team</h1>
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                 <h1 class="display-2">PROTOCOLS</h1>
 
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                    <a href="https://2018.igem.org/Team:Newcastle/Team" onclick="location.href='https://2018.igem.org/Team:Newcastle/Team'"><font face="verdana" color="green">MEET FULL TEAM</font> </a>             
 
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<table id="protocols">
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                <div class="service-icon">
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      <thead>
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                    <i class="icon-paint-brush"></i>
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        <tr>
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                </div>
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          <th>Protocol</th>
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                <div class="service-text">
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          <th>Author</th>
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                    <h3 class="h2">Luke Waller</h3>
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          <th>Category</th>
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                    <img src="https://static.igem.org/mediawiki/2018/b/bc/T--Newcastle--Luke.png">
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          <th>PDF File</th>
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                    <p><br> Luke’s my name, Conner is my game. I am the engineering part Conner wants to intertwine with. Having finished my
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        </tr>
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                    third year I am staying on at Newcastle to complete my masters, hopefully getting into robotics.  
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      </thead>
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I took this role as I wanted to explore an avenue of engineering I was not familiar with and work with a multi-disciplined team. </p>
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      <tbody>
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        <tr>
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          <td>Glycerol Stock Preserves</td>
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                </div>
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          <td>Connor Trotter</td>
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            </div>
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          <td>General</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/5/5a/T--Newcastle--GlycerolStock1.pdf" style="color:green">View</a></td>
 +
        </tr>
 +
        <tr>
 +
          <td>Bacterial Isolation from Freeze-Dried Pellet</td>
 +
          <td>Connor Trotter</td>
 +
          <td>General</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/7/72/T--Newcastle--BacIsolation1.pdf" style="color:green">View</a></td>
 +
        </tr>
 +
        <tr>
 +
          <td>Cell Counting</td>
 +
          <td>Connor Trotter</td>
 +
          <td>Chemotaxis</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/8/89/T--Newcastle--Haemocytometer1.pdf" style="color:green">View</a></td>
 +
        </tr>
 +
<tr>
 +
        <td>Seeding Cells in ibidi µ-Slide III 3-in-1 Chemotaxis Microscopy Slide</td>
 +
        <td>Connor Trotter</td>
 +
        <td>Chemotaxis</td>
 +
        <td><a href="https://static.igem.org/mediawiki/2018/7/7d/T--Newcastle--ibidiprotocol.pdf" style="color:green">View<a/></td>
 +
        </tr>
 +
        <tr>
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          <td>Minimal A Salt Agar Chemotaxis Assay</td>
 +
          <td>Connor Trotter</td>
 +
          <td>Chemotaxis</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/7/7f/T--Newcastle--MinAgar.pdf" style="color:green">View</a></td>
 +
        </tr>
 +
       
 +
        <tr>
 +
        <td>0.75 % Agar Chemotaxis Assay</td>
 +
        <td>Connor Trotter</td>
 +
        <td>Chemotaxis</td>
 +
        <td><a href="https://static.igem.org/mediawiki/2018/4/47/T--Newcastle--0.5ProtocolRedone.pdf" style="color:green">View<a/></td>
 +
        </tr>
 +
        <tr>
 +
        <td>0.50 % Agar Chemotaxis Assay</td>
 +
        <td>Connor Trotter</td>
 +
        <td>Chemotaxis</td>
 +
        <td><a href="https://static.igem.org/mediawiki/2018/2/2a/T--Newcastle--0.5%25ProtocolRedoneTrue.pdf" style="color:green">View<a/></td>
 +
        </tr>
 +
        <tr>
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        <td>Growth Curve in Liquid Culture</td>
 +
          <td>Sadiya Quazi</td>
 +
          <td>Chemotaxis</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/6/6a/T--Newcastle--GCIL.pdf" style="color:green">View</a></td>
 +
        </tr>
 +
        <tr>
 +
        <tr>
 +
        <td>Quantitative Capillary Assay</td>
 +
          <td>Connor Trotter</td>
 +
          <td>Chemotaxis</td>
 +
          <td><a href="https://static.igem.org/mediawiki/2018/a/a1/T--Newcastle--CapillaryAssayChemo.pdf" style="color:green">View</a></td>
 +
        </tr>
  
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            <div class="col-block service-item" data-aos="fade-up">
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        <tr>
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                <div class="service-icon">
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          <td>Naringenin Kill Curve in Liquid Culture</td>
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                    <i class="icon-group"></i>
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          <td>Sadiya Quazi</td>
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                </div>
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          <td>Chemotaxis</td>
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                <div class="service-text">
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          <td><a href="https://static.igem.org/mediawiki/2018/7/76/T--Newcastle--NarKillCurves.pdf" style="color:green">View</a></td>
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                    <h3 class="h2">Frank Eardley</h3>
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        </tr>
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                    <img src="https://static.igem.org/mediawiki/2018/0/04/T--Newcastle--Frank.png">
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        <tr>
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                    <p><br>I am a 4th year MBiol Cellular & Molecular Biology student. I joined iGEM
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          <td>Planting Seeds in Agar-Filled Microcentrifuge Tubes</td>
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                    for the opportunity to work with students from other academic fields and learn
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          <td>Lewis Tomlinson</td>
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                    more about synthetic biology. Outside of my degree, I am a scuba diving instructor
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          <td>Root Colonisation</td>
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                    and enjoy jumping in the North Sea whatever the weather.</p>
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          <td><a href="https://static.igem.org/mediawiki/2018/e/e3/T--Newcastle--MCPlant.pdf" style="color:green">View</a></td>
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        </tr>
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        <tr>
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                </div>
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          <td>Preparation and Staining of Microscopy Samples</td>
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            </div>
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          <td>Lewis Tomlinson</td>
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          <td>Root Colonisation</td>
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            <div class="col-block service-item" data-aos="fade-up">
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          <td><a href="https://static.igem.org/mediawiki/2018/b/bd/T--Newcastle--MScopy.pdf" style="color:green">View</a></td>
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                <div class="service-icon">
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        </tr>
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                    <i class="icon-megaphone"></i>
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        <tr>
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                </div>
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          <td>Planting Seeds in Agar-Filled Pipette-Tip Racks</td>
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                <div class="service-text">
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          <td>Lewis Tomlinson</td>
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                    <h3 class="h2">Will Tankard</h3>
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          <td>Root Colonisation</td>
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                    <img src="https://static.igem.org/mediawiki/2018/0/00/T--Newcastle--Will.png">
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          <td><a href="https://static.igem.org/mediawiki/2018/7/7d/T--Newcastle--RCK.pdf" style="color:green">View</a></td>
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                    <p><br>I’ve just completed my second year as an Architecture student. iGEM was a step
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        </tr>
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                    into the dark for me, the last time I did anything biology related was during my GCSE’s.  
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        <tr>
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                    I’m interested how the architecture and biology disciplines can merge. Synthetic Biology
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          <td>Re-isolating Endophytes</td>
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                    offers a new perspective on design starting with a bottom up approach.</p>
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          <td>Lewis Tomlinson</td>
−
                   
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          <td>Root Colonisation</td>
−
                   
+
          <td><a href="https://static.igem.org/mediawiki/2018/e/ef/T--Newcastle--RIso.pdf" style="color:green">View</a></td>
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                </div>
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        </tr>
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            </div>
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        <tr>
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          <td>Electroporation of <I>Pseudomonas</I> sp.</td>
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            <div class="col-block service-item" data-aos="fade-up">
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          <td>Frank Eardley</td>
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                <div class="service-icon">
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          <td>Endophytic Chassis Development</td>
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                    <i class="icon-earth"></i>
+
          <td><a href="https://static.igem.org/mediawiki/2018/b/bc/T--NEWCASTLE--Electroporation.pdf" style="color:green">View</a></td>
−
                </div>
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        </tr>
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                <div class="service-text">
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        <tr>
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                    <h3 class="h2">Heather Bottomley</h3>
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          <td>MIC Opentrons Code (2 Plates)</td>
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                    <img src="https://static.igem.org/mediawiki/2018/8/81/T--Newcastle--Heather.png">
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          <td>Frank Eardley</td>
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                    <p><br> Heather's the name, not doing the wiki is my game. I've just finished my                  third year of MBiol Cellular and Molecular Biology. I joined iGEM as an opportunity to formulate
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          <td>Endophytic Chassis Development</td>
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                    a novel idea and work in a multi - disciplinary team enhancing my biological knowledge.</p>
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          <td><a href="https://static.igem.org/mediawiki/2018/a/af/T--Newcastle--KillCurveCodes.pdf" style="color:green">View</a></td>
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        </tr>
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        <tr>
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                </div>
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          <td>MIC Protocol</td>
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            </div>
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          <td>Frank Eardley</td>
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          <td>Endophytic Chassis Development</td>
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            <div class="col-block service-item" data-aos="fade-up">
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          <td><a href="https://static.igem.org/mediawiki/2018/3/39/T--Newcastle--MICProtocol.pdf" style="color:green">View</a></td>
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                <div class="service-icon">
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        </tr>
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                    <i class="icon-cube"></i>
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        <tr>
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                </div>
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          <td>MIC Plate Layout</td>
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                <div class="service-text">
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          <td>Frank Eardley</td>
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                    <h3 class="h2">Connor Trotter</h3>
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          <td>Endophytic Chassis Development</td>
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                    <img src="https://static.igem.org/mediawiki/2018/d/dc/T--Newcastle--Connor.png">
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          <td><a href="https://static.igem.org/mediawiki/2018/b/bb/T--Newcastle--MICPlateLayout.pdf" style="color:green">View</a></td>
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                    <p><br> Connor is the name, getting my name misspelled is the game. I'm currently entering my third year
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        </tr>
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                    of Biology which has, so far, been fuelled by an excess of caffeine and binge watching a lot
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        <tr>
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                    of Rupaul's Drag Race. I joined Newcastle's team to apply what I have learned in a unique fashion by intertwining elements of Engineering and Architecture into biological concepts.</p>
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          <td>2-Part Gibson Assembly</td>
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          <td>Frank Eardley</td>
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                </div>
+
          <td>Endophytic Chassis Development</td>
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            </div>
+
          <td><a href="https://static.igem.org/mediawiki/2018/7/78/T--Newcastle--2PartGibson.pdf" style="color:green">View</a></td>
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        </tr>
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            <div class="col-block service-item" data-aos="fade-up">
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        <tr>
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                <div class="service-icon"><i class="icon-lego-block"></i></div>
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          <td>Amplification of gBlocks and Gradient PCR</td>
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                <div class="service-text">
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          <td>Heather Bottomley</td>
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                    <h3 class="h2">Patrycja Ubysz</h3>
+
          <td>Naringenin Operon Biosynthesis</td>
−
                    <img src="https://static.igem.org/mediawiki/2018/3/30/T--Newcastle--Patrycja.png">
+
          <td><a href="https://static.igem.org/mediawiki/2018/8/87/T--Newcastle--GBAmp.pdf" style="color:green">View</a></td>
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                    <p><br>I'm Pat, no game with my name. Just finished first year of Chemistry, I
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        </tr>
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                    probably liked it too much. I believe being interdisciplinary is crucial for research, especially
+
        <tr>
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                    in Synthetic Biology. I want to contribute to the team using my chemical/physical approach. I
+
          <td>Colony PCR of Transformed DH5α Cells</td>
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                    love working in the lab, however, would be happier without microbes. Basic coffee addict, bad
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          <td>Heather Bottomley</td>
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                    experience with BBQ parties. Probably follow every single NASA team account on Twitter.</p>
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          <td>Naringenin Operon Biosynthesis</td>
−
                   
+
          <td><a href="https://static.igem.org/mediawiki/2018/a/a9/T--Newcastle--PCTransform.pdf" style="color:green">View</a></td>
−
                </div>
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        </tr>
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            </div>
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        <tr>
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                <div class="col-block service-item" data-aos="fade-up">
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          <td>DpnI Digestion and Purification</td>
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                <div class="service-icon"><i class="icon-lego-block"></i></div>
+
          <td>Heather Bottomley</td>
−
                <div class="service-text">
+
          <td>Naringenin Operon Biosynthesis</td>
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                    <h3 class="h2">Lewis Tomlinson</h3>
+
          <td><a href="https://static.igem.org/mediawiki/2018/b/b0/T--Newcastle--DPN1Diges.pdf" style="color:green">View</a></td>
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                    <img src="https://static.igem.org/mediawiki/2018/0/0e/T--Newcastle--Lewis.png">
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        </tr>
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                    <p><br>Name: Lewis. Likes: llamas, guinea pigs, rock hyrax, all other animals, molecular biology, dungeons and dragons, science fiction and fantasy.
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        <tr>
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                    Life goal: llama sanctuary (including birds and rodents).</p>
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          <td>Gel Extraction and Purification of the gBlocks</td>
−
                   
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          <td>Heather Bottomley</td>
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                </div>
+
          <td>Naringenin Operon Biosynthesis</td>
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            </div>
+
          <td><a href="https://static.igem.org/mediawiki/2018/c/cc/T--Newcastle--GBlockGel.pdf" style="color:green">View</a></td>
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        </tr>
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                <div class="col-block service-item" data-aos="fade-up">
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        <tr>
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                <div class="service-icon"><i class="icon-lego-block"></i></div>
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          <td>Gibson Assembly of gBlocks and pSB1C3 Backbone</td>
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                <div class="service-text">
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          <td>Heather Bottomley</td>
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                    <h3 class="h2">Sadiya Quazi</h3>
+
          <td>Naringenin Operon Biosynthesis</td>
−
                    <img src="https://static.igem.org/mediawiki/2018/f/f2/T--Newcastle--Sadiya.png">
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          <td><a href="https://static.igem.org/mediawiki/2018/1/15/T--Newcastle--Gib.pdf" style="color:green">View</a></td>
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                    <p><br>Sadiya’s the name, which most can’t pronounce (despite it being totally phonetic). Just completed first year of Chemistry after switching from Fine Art,
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        </tr>
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                    and yes, it’s been a huge change, as people always exclaim when I tell them. Both benefit from having that alternative perspective and this is what drew me to
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        <tr>
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                      iGEM - working as part of a very cross-disciplinary team.</p>
+
          <td>Making Chemically Competent Cells</td>
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          <td>Heather Bottomley</td>
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                </div>
+
          <td>Naringenin Operon Biosynthesis</td>
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            </div>
+
          <td><a href="https://static.igem.org/mediawiki/2018/a/a6/T--Newcastle--CCell.pdf" style="color:green">View</a></td>
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          <td>Miniprep of Transformed Colonies</td>
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          <td>Heather Bottomley</td>
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                    <h3 class="h2">Umar Farooq</h3>
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          <td>Naringenin Operon Biosynthesis</td>
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          <td>Amplification, Purification and Quantification of the pSB1C3 Backbone by PCR</td>
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                    jokes, allergic to onions.
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          <td>Heather Bottomley</td>
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          <td>Naringenin Operon Biosynthesis</td>
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          <td><a href="https://static.igem.org/mediawiki/2018/5/5f/T--Newcastle--PCReaction.pdf" style="color:green">View</a></td>
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          <td>Quantifying DNA Concentration</td>
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          <td>Heather Bottomley</td>
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                <div class="service-icon"><i class="icon-lego-block"></i></div>
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          <td>Naringenin Operon Biosynthesis</td>
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          <td><a href="https://static.igem.org/mediawiki/2018/0/03/T--Newcastle--QuantifyingDNA.pdf" style="color:green">View</a></td>
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                    <h3 class="h2">Chris Carty</h3>
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                    <p><br>I’m Chris, 2nd year Architecture student, discovered iGEM when beginning my dissertation in the area  of Bio-Materialism. I want to take organisms that have been designed at the genetic scale and design them for use at the human scale - aiding the transition from biologically inspired to biologically engineered design. Better at architecture than Will.</p>
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          <td>Resuspending gBlocks and Primers</td>
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          <td>Heather Bottomley</td>
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          <td><a href="https://static.igem.org/mediawiki/2018/a/a0/T--Newcastle--GBlockFragmnt.pdf" style="color:green">View</a></td>
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          <td>SOC Media Preparation</td>
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          <td>Heather Bottomley</td>
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          <td>Naringenin Operon Biosynthesis</td>
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          <td><a href="https://static.igem.org/mediawiki/2018/4/4e/T--Newcastle--SOC1.pdf" style="color:green">View</a></td>
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          <td>Transformation of the Gibson assembly product into pSB1C3</td>
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          <td>Heather Bottomley</td>
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          <td>Naringenin Operon Biosynthesis</td>
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          <td><a href="https://static.igem.org/mediawiki/2018/1/15/T--Newcastle--GBTransform.pdf" style="color:green">View</a></td>
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                    <font size="4" font face="verdana" font color="green">Substantial time was spent carrying out extensive research, both inside and outside the lab, in order to optimise the system for the target audience. This included speaking with organisations and individuals in industry who are involved with hydroponics-based systems or those who may be interested in working with such a system in the future. Some of the individuals we liaised with include Chris Tapsell, the Research Director of KWS UK, one of the biggest seed companies in the world, and Richard Ballard, co-founder of Growing Underground in London where they hydroponically grow micro greens and salad leaves 33 metres below the ground. These potential clients helped us focus our product so that it can better meet the needs of our clients.</font><br><br>
 
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                    <font size="4" font face="verdana" font color="green">In addition to gathering external opinion on our system, we also did our own tests on system performance. This included tests to verify the optimal light intensity, wavelength and positioning. The graph below illustrates how the light intensity (measured in lux) varies over time (in seconds) when the system is operated under various wavelengths of light. The black line indicates the system running with the rainbow function loaded which cyclically varies the light wavelength. As the results showed that blue, red and purple light and provided the most lux we are currently using these in the system but plan to use the rainbow function too in future to see how this affects growth or the aesthetics of the plant.
 
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                <h1 class="display-2">References & Attributions</h1>
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<p class="about-para"><font size="2"><strong>Attributions: Connor Trotter, Sadiya Quazi, Lewis Tomlinson, Frank Eardley, Heather Bottomley
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Latest revision as of 00:50, 18 October 2018

Alternative Roots/Protocols

Alternative Roots

Protocols

Overview

EXPERIMENTS

PROTOCOLS

Protocol Author Category PDF File
Glycerol Stock Preserves Connor Trotter General View
Bacterial Isolation from Freeze-Dried Pellet Connor Trotter General View
Cell Counting Connor Trotter Chemotaxis View
Seeding Cells in ibidi µ-Slide III 3-in-1 Chemotaxis Microscopy Slide Connor Trotter Chemotaxis View
Minimal A Salt Agar Chemotaxis Assay Connor Trotter Chemotaxis View
0.75 % Agar Chemotaxis Assay Connor Trotter Chemotaxis View
0.50 % Agar Chemotaxis Assay Connor Trotter Chemotaxis View
Growth Curve in Liquid Culture Sadiya Quazi Chemotaxis View
Quantitative Capillary Assay Connor Trotter Chemotaxis View
Naringenin Kill Curve in Liquid Culture Sadiya Quazi Chemotaxis View
Planting Seeds in Agar-Filled Microcentrifuge Tubes Lewis Tomlinson Root Colonisation View
Preparation and Staining of Microscopy Samples Lewis Tomlinson Root Colonisation View
Planting Seeds in Agar-Filled Pipette-Tip Racks Lewis Tomlinson Root Colonisation View
Re-isolating Endophytes Lewis Tomlinson Root Colonisation View
Electroporation of Pseudomonas sp. Frank Eardley Endophytic Chassis Development View
MIC Opentrons Code (2 Plates) Frank Eardley Endophytic Chassis Development View
MIC Protocol Frank Eardley Endophytic Chassis Development View
MIC Plate Layout Frank Eardley Endophytic Chassis Development View
2-Part Gibson Assembly Frank Eardley Endophytic Chassis Development View
Amplification of gBlocks and Gradient PCR Heather Bottomley Naringenin Operon Biosynthesis View
Colony PCR of Transformed DH5α Cells Heather Bottomley Naringenin Operon Biosynthesis View
DpnI Digestion and Purification Heather Bottomley Naringenin Operon Biosynthesis View
Gel Extraction and Purification of the gBlocks Heather Bottomley Naringenin Operon Biosynthesis View
Gibson Assembly of gBlocks and pSB1C3 Backbone Heather Bottomley Naringenin Operon Biosynthesis View
Making Chemically Competent Cells Heather Bottomley Naringenin Operon Biosynthesis View
Miniprep of Transformed Colonies Heather Bottomley Naringenin Operon Biosynthesis View
Amplification, Purification and Quantification of the pSB1C3 Backbone by PCR Heather Bottomley Naringenin Operon Biosynthesis View
Quantifying DNA Concentration Heather Bottomley Naringenin Operon Biosynthesis View
Resuspending gBlocks and Primers Heather Bottomley Naringenin Operon Biosynthesis View
SOC Media Preparation Heather Bottomley Naringenin Operon Biosynthesis View
Transformation of the Gibson assembly product into pSB1C3 Heather Bottomley Naringenin Operon Biosynthesis View




References & Attributions

Attributions: Connor Trotter, Sadiya Quazi, Lewis Tomlinson, Frank Eardley, Heather Bottomley