Difference between revisions of "Team:Dalhousie/Experiments"

 
(42 intermediate revisions by 3 users not shown)
Line 201: Line 201:
  
 
<div class="row">
 
<div class="row">
−
     <h3 id="FecalSamples" style="color:#674A8A;"> High-Throughput Sequencing </h3>
+
     <h1 id="FecalSamples" style="color: white;"> Protocols </br></br></h1>
 
   </div>
 
   </div>
  
Line 208: Line 208:
 
     <div class="col-md-4">
 
     <div class="col-md-4">
 
     <div class="row">
 
     <div class="row">
 +
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/d/d6/T--Dalhousie_Halifax_NS--PowerFecalProtocol.pdf"> Fecal Sample DNA Extraction </a></h4>
+
       <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">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>To extract environmental DNA from fecal samples. This extraction will purify genomic DNA from prokaryotic and eukaryotic cells found in the fecal sample.  
+
     <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>
 
<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/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>
  
Line 219: Line 230:
 
     <div class="row">
 
     <div class="row">
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/7/70/T--Dalhousie_Halifax_NS--PowerFecalConcentration.pdf"> DNA Concentration</a></h4>
+
       <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">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>Concentration protocol to concentrate DNA isolating using the PowerFecal Extraction kit.<p>
+
     <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>
  
Line 228: Line 251:
 
     <div class="row">
 
     <div class="row">
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/a/ae/T--Dalhousie_Halifax_NS--16IlluminaSeq.pdf"> 16S Illumina Miseq Sequencing </a></h4>
+
       <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">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>Illumina MiSeq Sequencing was used to identify the sequences of the 16S rRNA genes in the fecal samples. This step was undertaking by the Integrated Microbiome Resource at Dal. There protocol was provided to us.<p>
+
     <p>Purpose of this protocol is to grow up single colonies of bacteria for use.</br><p>
 
   </div>
 
   </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/2017/9/93/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">
 
<div class="col-md-4">
 
     <div class="row">
 
     <div class="row">
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/4/46/T--Dalhousie_Halifax_NS--MetagenomicSequencingIllumina.pdf"> Metagenomic Shotgun Illumina Miseq Sequencing </a></h4>
+
       <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);">
 +
    <div class="row">
 +
      <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">
 +
    <div class="row">
 +
      <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">
 +
      <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">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>This protocol was used by the Integrated Microbiome Resource to sequence the metagenomic DNA in our fecal samples from the porcupine, beaver, arctic wolf and coyote.
+
     <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>
 
<p>
 
   </div>
 
   </div>
  
−
    <div class="col-md-4">
+
<div class="col-md-4" style="background-color: rgba(61,85,28, 0.8);">
 
     <div class="row">
 
     <div class="row">
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/d/d1/T--Dalhousie_Halifax_NS--16SSequencingAnalysis.pdf"> 16S Sequencing Analysis
+
       <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>
 
</a></h4>
 
       <hr id="hr">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>This protocol was used for analyzing the 16S Illumina Sequencing data from the illumina sequencer. Provided by the Integrated Microbiome Resource at Dalhousie University.<p>
+
     <p>Purpose of this protocol is to introduce plasmid DNA into <i>E. coli</i> cells.</br></br></br>
 +
<p>
 
   </div>
 
   </div>
  
Line 257: Line 340:
 
     <div class="row">
 
     <div class="row">
 
       <hr id="hr">
 
       <hr id="hr">
−
       <h4><a href="https://static.igem.org/mediawiki/2016/d/d1/T--Dalhousie_Halifax_NS--16SSequencingAnalysis.pdf"> 16S Sequencing Analysis
+
       <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>
 
</a></h4>
 
       <hr id="hr">
 
       <hr id="hr">
 
     </div>
 
     </div>
−
     <p>This protocol was used for analyzing the 16S Illumina Sequencing data from the illumina sequencer. Provided by the Integrated Microbiome Resource at Dalhousie University.<p>
+
     <p>The purpose of this protocol is to create solid growth media containing both carboxymethylcellulose and glucose for measuring endoglucanase activity.
 +
<p>
 
   </div>
 
   </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>
 +
  </div>
 +
 
 +
 
 
</div>
 
</div>
 
</div>
 
</div>
Line 278: Line 373:
 
             <div class="inner">
 
             <div class="inner">
 
       <p style="text-align: center; ">
 
       <p style="text-align: center; ">
−
<img src="https://static.igem.org/mediawiki/2017/8/8c/Dalscreen.png" height="20%" width="20%" >
+
<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>
 
<img src="https://static.igem.org/mediawiki/parts/d/d7/Porcupinelogo2017.png" height="20%" width="20%" >
 
<img src="https://static.igem.org/mediawiki/parts/d/d7/Porcupinelogo2017.png" height="20%" width="20%" >
 
<img src="https://static.igem.org/mediawiki/2017/e/ef/Whitetigerlogo.png" height="20%" width="20%" >
 
<img src="https://static.igem.org/mediawiki/2017/e/ef/Whitetigerlogo.png" height="20%" width="20%" >
Line 370: Line 465:
 
#panel2{
 
#panel2{
 
width:100%;
 
width:100%;
−
height: 1900px;
+
height: 1300px;
 
margin-bottom:0px;
 
margin-bottom:0px;
 
background:  rgba(35,47,19,0.9);
 
background:  rgba(35,47,19,0.9);

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.