Difference between revisions of "Team:Dalhousie/Experiments"

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<h1>Experiments</h1>
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<p>Describe the research, experiments, and protocols you used in your iGEM project. These should be detailed enough for another team to repeat your experiments.</p>
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Please remember to put all characterization and measurement data for your parts on the corresponding Registry part pages.  
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<h5>What should this page contain?</h5>
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<li> Protocols </li>
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<li> Experiments </li>
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<li> Documentation of the development of your project </li>
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<h5>Inspiration</h5>
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<body>
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<li><a href="https://2014.igem.org/Team:Colombia/Protocols">2014 Colombia </a></li>
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<li><a href="https://2014.igem.org/Team:Imperial/Protocols">2014 Imperial </a></li>
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<li><a href="https://2014.igem.org/Team:Caltech/Project/Experiments">2014 Caltech </a></li>
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    <ul class="nav navbar-nav navbar-center">
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      <li class="active" ><a href="https://2017.igem.org/Team:Dalhousie" style=" color: white;">Home</a></li>
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<li class="dropdown" >
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        <a class="dropdown-toggle" data-toggle="dropdown" href="#" style=" color: white;">Project
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        </a>
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        <ul class="dropdown-menu" style=" background-color: rgba(193,211,93,0.8);">
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Description" >Description</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Design">Design</a></li>
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<li><a href="https://2017.igem.org/Team:Dalhousie/Requirements">Requirements</a></li>
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      </li>
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<li class="dropdown">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="#" style=" color: white;">Results
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        <ul class="dropdown-menu" style=" background-color: rgba(193,211,93,0.8);">
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          <li><a href="https://2017.igem.org/Team:Dalhousie/InterLab">Interlab</a></li>
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  <li><a href="https://2017.igem.org/Team:Dalhousie/Results">Results</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="#" style=" color: white;">Team
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Team">Team</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Collaborations">Collaborations</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Attributions">Attributions</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Sponsors">Sponsors</a></li>
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        </ul>
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<li class="dropdown">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="#" style=" color: white;">Human Practices
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        </a>
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        <ul class="dropdown-menu" style=" background-color: rgba(193,211,93,0.8);">
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        <li><a href="https://2017.igem.org/Team:Dalhousie/Human_Practices">Summary</a></li>
 +
          <li><a href="https://2017.igem.org/Team:Dalhousie/HP/Silver">Science Communication</a></li>
 +
          <li><a href="https://2017.igem.org/Team:Dalhousie/HP/Gold_Integrated">Integrated and Gold</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Engagement">Public Engagement</a></li>
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<li><a href="https://2017.igem.org/Team:Dalhousie/SocialMedia">Social Media</a></li>
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      </li>
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<li class="dropdown">
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        <a class="dropdown-toggle" data-toggle="dropdown" href="#" style=" color: white;">Lab
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        <ul class="dropdown-menu" style=" background-color: rgba(193,211,93,0.8);">
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Parts">Parts</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Safety" >Safety</a></li>
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            <li><a href="https://2017.igem.org/Team:Dalhousie/Experiments">Experiments</a></li>
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          <li><a href="https://2017.igem.org/Team:Dalhousie/Notebook">Notebook</a></li>
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<li><a href="https://2017.igem.org/Team:Dalhousie/Improve">Improve</a></li>
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        </ul>
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      </li>
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<ul class="nav navbar-nav navbar-right">
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    <div class="navbar-header">
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      <a class="navbar-brand" style=" color: white;">Contact us today </a>
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    </div>
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                        <a href="mailto:igemdalhousie@gmail.com" ><i class="fa fa-envelope-o fa-fw" style=" color: white;"  ></i> <span class="network-name"></span></a>
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                        <a target="_blank" href="https://twitter.com/dalhousie_igem?lang=en" ><i class="fa fa-twitter fa-fw" style=" color: white;" ></i> <span class="network-name"></span></a>
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<div class="top" ><div class="title" >Experiments</div></div>
  
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    <h1 id="FecalSamples" style="color: white;"> Protocols </br></br></h1>
 +
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  <div class="container">
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 +
    <div class="col-md-4">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/f/fa/Dalfluoro.pdf" style="color: rgba(193,211,93,0.8);"> Fluorophore Assessment of Glycosidase Activity </a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to assess the enzymatic activity of glycosidases using fluorophores conjugated to substrates of interest (such as cellobiose or xylobiose). Once the enzyme of interest cleaves substrate, the fluorophore is released enabling quantification of enzymatic activity.
 +
<p>
 +
  </div>
 +
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    <div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
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    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/a/af/Dalcosmid.pdf" style="color: rgba(193,211,93,0.8);">Cosmid Library Generation </br></br>
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to generate a library of cosmid clones that are representative of the microbiome of the porcupine for screening for novel enzymes.</br></br></br><p>
 +
  </div>
 +
 +
    <div class="col-md-4">
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    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/2/2a/Dalcoomassie.pdf" style="color: rgba(193,211,93,0.8);"> Coomassie Blue Stain </br></br>
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>To visual total protein in a given sample.</br></br></br></br></br><p>
 +
  </div>
 +
 +
<div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
 +
    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/7/79/DalWB.pdf" style="color: rgba(193,211,93,0.8);"> Western Blot
 +
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>To identify specific amino acid sequences of a protein, or tag, using fluorescently-tagged antibodies.</br></br></br><p>
 +
  </div>
 +
 +
    <div class="col-md-4">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/8/89/Dalbatch.pdf" style="color: rgba(193,211,93,0.8);"> Overnight Bacterial Batch Culture
 +
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to grow up single colonies of bacteria for use.</br><p>
 +
  </div>
 +
 +
<div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/9/93/Dalcloning.pdf" style="color: rgba(193,211,93,0.8);"> Cloning Overview
 +
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this overview is to isolate and clone genes of interest into an appropriate plasmid and then introduce the recombinant DNA molecule into <i>E. coli</i>. </br></br>
 +
<p>
 +
  </div>
 +
 
 +
<div class="col-md-4">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/7/7a/DalCMC.pdf" style="color: rgba(193,211,93,0.8);"> Congo Red Media Generation </br></br>
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>The purpose of this protocol is to assay carboxymethyl cellulose degradation via a pH change detectable by the dye Congo Red as differentially coloured halos around colonies of bacteria.<p>
 +
  </div>
 +
 +
    <div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/1/1b/DalCongored.pdf" style="color: rgba(193,211,93,0.8);"> Congo Red Overlay Assay for Carboxymethylcellulose Degradation
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Concentration protocol to concentrate DNA isolating using the PowerFecal Extraction kit.</br></br></br><p>
 +
  </div>
 +
 +
   
 +
 +
<div class="col-md-4">
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    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/9/9d/Dalgelmaking.pdf" style="color: rgba(193,211,93,0.8);"> 0.8% Agarose Gel </br></br>
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to create an agarose gel for visualizing and extracting DNA.</br></br></br><p>
 +
  </div>
 +
 +
    <div class="col-md-4"style="background-color: rgba(61,85,28, 0.8);">
 +
    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/e/ee/Dalcelloise.pdf" style="color: rgba(193,211,93,0.8);"> Cellobiose Media Generation
 +
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>The purpose of this protocol is to create solid growth media containing cellobiose to measure beta-glucosidase activity.</br></br></br><p>
 +
  </div>
 +
 +
<div class="col-md-4">
 +
    <div class="row">
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      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/2/2d/Dalsell.pdf" style="color: rgba(193,211,93,0.8);"> LB Agar Selection Media Plate Generation
 +
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to generate solid growth media containing LB and an antibiotic of choice for selective growth of successful clones following transformation.
 +
<p>
 +
  </div>
 +
 +
<div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
 +
    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/2/24/Daltransform.pdf" style="color: rgba(193,211,93,0.8);"> Heat Shock Transformation
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to introduce plasmid DNA into <i>E. coli</i> cells.</br></br></br>
 +
<p>
 +
  </div>
 +
 +
<div class="col-md-4">
 +
    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/7/76/DalCMCCC.pdf" style="color: rgba(193,211,93,0.8);"> Carboxymethylcellulose Media Generation
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>The purpose of this protocol is to create solid growth media containing both carboxymethylcellulose and glucose for measuring endoglucanase activity.
 +
<p>
 +
  </div>
 +
 +
<div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
 +
    <div class="row">
 +
      <hr id="hr">
 +
      <h4><a href="https://static.igem.org/mediawiki/2017/0/09/Dalsalt.pdf" style="color: rgba(193,211,93,0.8);"> M9 Salts Generation
 +
</a></h4>
 +
      <hr id="hr">
 +
    </div>
 +
    <p>Purpose of this protocol is to generate a salt solution for <i>E. coli</i> growth. </br></br></br><p>
 +
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<a href="http://www.plosibilities.wordpress.com"><img src="https://static.igem.org/mediawiki/2017/archive/8/8c/20171031235427%21Dalscreen.png" height="20%" width="20%" ></a>
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<img src="https://static.igem.org/mediawiki/parts/d/d7/Porcupinelogo2017.png" height="20%" width="20%" >
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Latest revision as of 23:33, 1 November 2017

Experiments

Protocols

Fluorophore Assessment of Glycosidase Activity

Purpose of this protocol is to assess the enzymatic activity of glycosidases using fluorophores conjugated to substrates of interest (such as cellobiose or xylobiose). Once the enzyme of interest cleaves substrate, the fluorophore is released enabling quantification of enzymatic activity.

Cosmid Library Generation

Purpose of this protocol is to generate a library of cosmid clones that are representative of the microbiome of the porcupine for screening for novel enzymes.


Coomassie Blue Stain

To visual total protein in a given sample.




Western Blot

To identify specific amino acid sequences of a protein, or tag, using fluorescently-tagged antibodies.


Overnight Bacterial Batch Culture

Purpose of this protocol is to grow up single colonies of bacteria for use.

Cloning Overview

Purpose of this overview is to isolate and clone genes of interest into an appropriate plasmid and then introduce the recombinant DNA molecule into E. coli.

Congo Red Media Generation

The purpose of this protocol is to assay carboxymethyl cellulose degradation via a pH change detectable by the dye Congo Red as differentially coloured halos around colonies of bacteria.

Congo Red Overlay Assay for Carboxymethylcellulose Degradation

Concentration protocol to concentrate DNA isolating using the PowerFecal Extraction kit.


0.8% Agarose Gel

Purpose of this protocol is to create an agarose gel for visualizing and extracting DNA.


Cellobiose Media Generation

The purpose of this protocol is to create solid growth media containing cellobiose to measure beta-glucosidase activity.


LB Agar Selection Media Plate Generation

Purpose of this protocol is to generate solid growth media containing LB and an antibiotic of choice for selective growth of successful clones following transformation.

Heat Shock Transformation

Purpose of this protocol is to introduce plasmid DNA into E. coli cells.


Carboxymethylcellulose Media Generation

The purpose of this protocol is to create solid growth media containing both carboxymethylcellulose and glucose for measuring endoglucanase activity.

M9 Salts Generation

Purpose of this protocol is to generate a salt solution for E. coli growth.