Team:Waterloo

From 2013.igem.org

(Difference between revisions)
(More team members and some project page changes.)
Line 1: Line 1:
<html>
<html>
   <!--
   <!--
-
     TODO:
+
     Notes:
     - Notebook file: https://2013.igem.org/File:Waterloo_notebook.txt
     - Notebook file: https://2013.igem.org/File:Waterloo_notebook.txt
 +
 +
    TODO:
 +
    - New team page with art and zooming photos.
 +
    - Slideshow view for the gallery.
 +
    - Biobrick sections.
 +
    - Full names.
 +
    - Remove dark background.
   -->
   -->
   <head>
   <head>
Line 346: Line 353:
   function createNavBar(notebook_sublinks, show_notebook) {
   function createNavBar(notebook_sublinks, show_notebook) {
-
    // Create NavBar
 
     navBar = new NavBar();
     navBar = new NavBar();
-
     //navBar.addLink(new Link('#/Home', 'Home'));
+
     // navBar.addLink(new Link('#/Home', 'Home'));
     navBar.addLink(
     navBar.addLink(
       new Link('#/Project', 'Project'),
       new Link('#/Project', 'Project'),
       [
       [
         new Link('#/Project/Abstract', 'Abstract'),
         new Link('#/Project/Abstract', 'Abstract'),
 +
        new Link('#/Project/Design', 'Design'),
 +
        new Link('#/Project/Ottawa', 'Ottawa\'s Collaboration'),
         new Link('#/Project/Video', 'Video'),
         new Link('#/Project/Video', 'Video'),
         new Link('#/Project/Results', 'Results'),
         new Link('#/Project/Results', 'Results'),
Line 405: Line 413:
         new Link('#/Team/MathModelling', 'Mathematical Modelling'),
         new Link('#/Team/MathModelling', 'Mathematical Modelling'),
         new Link('#/Team/Advisors', 'Advisors')
         new Link('#/Team/Advisors', 'Advisors')
 +
        // new Link('#/Team/GradStudentAdvisors', 'Graduate Student Advisors')
       ]
       ]
     );
     );
Line 451: Line 460:
     setupGroup('#administratorPhotos', 3, 150,
     setupGroup('#administratorPhotos', 3, 150,
       {
       {
-
         'Peter': 'https://static.igem.org/mediawiki/2013/5/5b/Waterloo_Peter_Hong.jpg',
+
         'Peter Hong': 'https://static.igem.org/mediawiki/2013/5/5b/Waterloo_Peter_Hong.jpg',
-
         'Linda': 'https://static.igem.org/mediawiki/2013/d/d1/Waterloo_Linda_Yang.jpg'
+
         'Linda Yang': 'https://static.igem.org/mediawiki/2013/d/d1/Waterloo_Linda_Yang.jpg'
       }
       }
     );
     );
-
     setupGroup('#advisorPhotos', 4, 150,
+
     setupGroup('#labTeamPhotos', 4, 150,
       {
       {
 +
        'Paul Reginato': 'https://static.igem.org/mediawiki/2013/b/bd/Waterloo_paul.JPG',
 +
        'Aaron Bender': 'https://static.igem.org/mediawiki/2013/5/59/Waterloo_aaron.JPG',
 +
        'Hina Bandukwala': 'https://static.igem.org/mediawiki/2013/0/0b/Waterloo_hina.JPG',
 +
        'Emily Li': 'https://static.igem.org/mediawiki/2013/b/bd/Waterloo_emily.JPG',
 +
        'Rummy Chowdhury': 'https://static.igem.org/mediawiki/2013/0/07/Waterloo_rummy.JPG',
 +
        'Julia Manalil': 'https://static.igem.org/mediawiki/2013/a/ae/Waterloo_julia.JPG',
 +
        'Steven ten Holder': 'https://static.igem.org/mediawiki/2013/4/4f/Waterloo_steven.JPG',
 +
        'Urooj Kishor': 'https://static.igem.org/mediawiki/2013/0/04/Waterloo_Urooj_2.jpg',
 +
        'Jama Hagi-Yusuf': 'https://static.igem.org/mediawiki/2013/a/a1/Waterloo_jama.jpg',
 +
        'Chris Morcos': 'https://static.igem.org/mediawiki/2013/6/65/Waterloo_chris.JPG',
 +
        'Peivand Sadat Mousavi': 'https://static.igem.org/mediawiki/2013/7/7a/Waterloo_Peivand_2.jpg',
 +
      }
 +
    );
 +
    setupGroup('#mathModellingTeamPhotos', 3, 150,
 +
      {
 +
        'Drew Neish': 'https://static.igem.org/mediawiki/igem.org/2/21/Waterloo_Drew_Neish.png',
 +
        'James Hawley': 'https://static.igem.org/mediawiki/igem.org/1/10/Waterloo_James_Hawley.jpg',
 +
        'Matt Smart': 'https://static.igem.org/mediawiki/igem.org/5/54/Waterloo_Matt_Smart.jpg',
 +
        'Paul Reginato': 'https://static.igem.org/mediawiki/2013/b/bd/Waterloo_paul.JPG',
 +
        'Seyed Ali Madani Tonekaboni': 'https://static.igem.org/mediawiki/igem.org/e/eb/Waterloo_Seyed_Ali_Madani_Tonekaboni.jpg',
 +
        'Vedang Vyas': 'https://static.igem.org/mediawiki/igem.org/2/2b/Waterloo_Vedang_Vyas.jpg'
 +
      }
 +
    );
 +
    setupGroup('#humanPracticesTeamPhotos', 3, 150,
 +
      {
 +
        'Anjali Arya': 'https://static.igem.org/mediawiki/igem.org/b/b6/Anjali_Arya.jpg',
 +
        'Daniel Zhang': 'https://static.igem.org/mediawiki/igem.org/a/a2/Waterloo_Daniel_Zhang.jpg',
 +
        'Lucy Hu': 'https://static.igem.org/mediawiki/igem.org/9/9f/Waterloo_Lucy_Hu.jpeg',
 +
        'Mudit Kalia': 'https://static.igem.org/mediawiki/igem.org/2/22/Waterloo_Mudit_Kalia.jpg',
 +
        'Suzie Alexander': 'https://static.igem.org/mediawiki/igem.org/c/c3/Waterloo_Suzie_Alexander.jpg'
 +
      }
 +
    );
 +
    setupGroup('#advisorPhotos', 3, 150,
 +
      {
 +
        'Trevor Charles': 'https://static.igem.org/mediawiki/2013/7/74/Trevor_Charles.jpg',
         'Brian Ingalls': 'https://static.igem.org/mediawiki/2013/b/be/Brian_Ingalls.jpg',
         'Brian Ingalls': 'https://static.igem.org/mediawiki/2013/b/be/Brian_Ingalls.jpg',
         'Marc Aucoin': 'https://static.igem.org/mediawiki/2013/b/ba/Marc_Aucoin.jpg',
         'Marc Aucoin': 'https://static.igem.org/mediawiki/2013/b/ba/Marc_Aucoin.jpg',
-
         'Trevor Charles': 'https://static.igem.org/mediawiki/2013/7/74/Trevor_Charles.jpg',
+
         'Andrew Doxey': 'https://static.igem.org/mediawiki/igem.org/f/f5/Waterloo_Andrew_Doxey.jpg',
         'Barbara Moffatt': 'https://static.igem.org/mediawiki/igem.org/e/e3/Barbara_Moffatt.jpg'
         'Barbara Moffatt': 'https://static.igem.org/mediawiki/igem.org/e/e3/Barbara_Moffatt.jpg'
       }
       }
     );
     );
-
     setupGroup('#labTeamPhotos', 4, 150,
+
     setupGroup('#gradStudentPhotos', 2, 150,
       {
       {
-
         'Paul': 'https://static.igem.org/mediawiki/2013/b/bd/Waterloo_paul.JPG',
+
         'John Heil': 'https://static.igem.org/mediawiki/igem.org/6/62/Waterloo_John_Heil.jpg',
-
        'Aaron': 'https://static.igem.org/mediawiki/2013/5/59/Waterloo_aaron.JPG',
+
         'Maya D\'Alessio': 'https://static.igem.org/mediawiki/igem.org/0/0c/Waterloo_Maya_D%27Alessio.jpg'
-
        'Hina': 'https://static.igem.org/mediawiki/2013/0/0b/Waterloo_hina.JPG',
+
-
        'Emily': 'https://static.igem.org/mediawiki/2013/b/bd/Waterloo_emily.JPG',
+
-
        'Rummy': 'https://static.igem.org/mediawiki/2013/0/07/Waterloo_rummy.JPG',
+
-
        'Julia': 'https://static.igem.org/mediawiki/2013/a/ae/Waterloo_julia.JPG',
+
-
        'Steven': 'https://static.igem.org/mediawiki/2013/4/4f/Waterloo_steven.JPG',
+
-
        'Urooj': 'https://static.igem.org/mediawiki/2013/0/04/Waterloo_Urooj_2.jpg',
+
-
         'Jama': 'https://static.igem.org/mediawiki/2013/a/a1/Waterloo_jama.jpg',
+
-
        'Chris': 'https://static.igem.org/mediawiki/2013/6/65/Waterloo_chris.JPG',
+
-
        'Peivand': 'https://static.igem.org/mediawiki/2013/7/7a/Waterloo_Peivand_2.jpg',
+
-
        'Annas': 'https://static.igem.org/mediawiki/2013/0/0a/Waterloo_annas.jpg'
+
       }
       }
     );
     );
-
    // TODO
+
     setupGroup('#intentToInventPhotos', 2, 400, {});
-
    setupGroup('#mathModellingTeamPhotos', 1, 150, {});
+
-
    setupGroup('#humanPracticesTeamPhotos', 1, 150, {});
+
-
     setupGroup('#intentToInventPhotos', 1, 400, {});
+
     setupGroup('#labPhotos', 1, 350,
     setupGroup('#labPhotos', 1, 350,
       {
       {
Line 691: Line 722:
         var notebook_sublinks = createNotebook(data);
         var notebook_sublinks = createNotebook(data);
         createNavBar(notebook_sublinks, true);
         createNavBar(notebook_sublinks, true);
 +
        checkHash();
       },
       },
       error: function() {
       error: function() {
         // On failure create the navbar anyway.
         // On failure create the navbar anyway.
         createNavBar([], false);
         createNavBar([], false);
 +
        checkHash();
       }
       }
     });
     });
     setupPhotos();
     setupPhotos();
-
    checkHash();
 
   });
   });
   $(document).keydown(function(e) {
   $(document).keydown(function(e) {
Line 750: Line 782:
           <h1 id="s_Project_Abstract">Abstract</h1>
           <h1 id="s_Project_Abstract">Abstract</h1>
           <p>
           <p>
-
            <!-- TODO abstract -->
 
             <p>Due to its nature as an information-encoding molecule, the use of DNA as an intercellular messaging molecule would enable more information-rich communication between populations of cells than traditional AHL-based messaging. The first demonstration of DNA messaging was published by the Endy group at Stanford University in late 2012, wherein DNA encoding instructions for expression of fluorescence and antibiotic resistance were transmitted from one bacterial population to another, carried by M13 bacteriophage particles.</p>
             <p>Due to its nature as an information-encoding molecule, the use of DNA as an intercellular messaging molecule would enable more information-rich communication between populations of cells than traditional AHL-based messaging. The first demonstration of DNA messaging was published by the Endy group at Stanford University in late 2012, wherein DNA encoding instructions for expression of fluorescence and antibiotic resistance were transmitted from one bacterial population to another, carried by M13 bacteriophage particles.</p>
-
<p>Incorporation of well-established <i>in vivo</i> DNA modification techniques into DNA messaging will diversify and extend potential intercellular communication programs, and will enable the integration of recent developments in DNA digital logic with DNA messaging.</p>
+
            <p>Incorporation of well-established <i>in vivo</i> DNA modification techniques into DNA messaging will diversify and extend potential intercellular communication programs, and will enable the integration of recent developments in DNA digital logic with DNA messaging.</p>
-
 
+
-
<p>The goal of our project is to place on a DNA message a switch that can be flipped in receiver cells under inducible conditions, and whose state determines whether or not the DNA message is retransmitted from receiver cells to a population of secondary receiver cells. The switch consists of a promoter that can be inverted using a serine integrase, leading to transcription of different genes. It is directly inspired by the recombinase addressable data (RAD) module published by the Endy group in early 2012.</p>
+
-
<p>We have synthesized four such DNA switches and will soon test the ability of PhiC31 and Bxb1 serine integrases, along with the respective recombination directionality factors (RDFs), to control their states. We have also produced constructs that we will use to attempt to control the production of M13 viral particles containing a DNA message and we will test these soon. We will integrate these efforts to demonstrate our goal of incorporating digital DNA logic into DNA messaging. Through this work, we will broaden the horizons of engineered intercellular communication.</p>
+
            <p>The goal of our project is to place on a DNA message a switch that can be flipped in receiver cells under inducible conditions, and whose state determines whether or not the DNA message is retransmitted from receiver cells to a population of secondary receiver cells. The switch consists of a promoter that can be inverted using a serine integrase, leading to transcription of different genes. It is directly inspired by the recombinase addressable data (RAD) module published by the Endy group in early 2012.</p>
 +
            <p>We have synthesized four such DNA switches and will soon test the ability of PhiC31 and Bxb1 serine integrases, along with the respective recombination directionality factors (RDFs), to control their states. We have also produced constructs that we will use to attempt to control the production of M13 viral particles containing a DNA message and we will test these soon. We will integrate these efforts to demonstrate our goal of incorporating digital DNA logic into DNA messaging. Through this work, we will broaden the horizons of engineered intercellular communication.</p>
           </p>
           </p>
 +
          <h1 id="s_Project_Design">Design</h1>
 +
          <h1 id="s_Project_Ottawa">Ottawa's Collaboration</h1>
           <h1 id="s_Project_Video">Video</h1>
           <h1 id="s_Project_Video">Video</h1>
           <div>
           <div>
Line 766: Line 798:
           <h1 id="s_Project_Results">Results</h1>
           <h1 id="s_Project_Results">Results</h1>
           <p>
           <p>
-
          Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results
 
-
          Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results
 
-
          Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results
 
-
          Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results Results.
 
           </p>
           </p>
           <h1 id="s_Project_Future">Future Aspirations</h1>
           <h1 id="s_Project_Future">Future Aspirations</h1>
           <h1 id="s_Project_Biobricks">Biobricks</h1>
           <h1 id="s_Project_Biobricks">Biobricks</h1>
 +
          <ul>
 +
            <li>Hpdo with no gene 8</li>
 +
            <li>Bxb1 rdf</li>
 +
            <li>Bxb1 int</li>
 +
            <li>Bxb1 switch</li>
 +
            <li>BXB1 switch flipped</li>
 +
            <li>ΦC31 rdf</li>
 +
            <li>ΦC31 int</li>
 +
            <li>ΦC31 switch</li>
 +
            <li>ΦC31 switch flipped</li>
 +
          </ul>
         </div>
         </div>
       </div>
       </div>
Line 869: Line 908:
           <h1 id="s_Team_Advisors">Advisors</h1>
           <h1 id="s_Team_Advisors">Advisors</h1>
           <div id="advisorPhotos" class="photoSection"></div>
           <div id="advisorPhotos" class="photoSection"></div>
 +
 +
          <div class="clearFix"></div>
 +
          <h1 id="s_Team_GradStudentAdvisors">Graduate Student Advisors</h1>
 +
          <div id="gradStudentPhotos" class="photoSection"></div>
         </div>
         </div>

Revision as of 05:51, 11 August 2013

Abstract

Due to its nature as an information-encoding molecule, the use of DNA as an intercellular messaging molecule would enable more information-rich communication between populations of cells than traditional AHL-based messaging. The first demonstration of DNA messaging was published by the Endy group at Stanford University in late 2012, wherein DNA encoding instructions for expression of fluorescence and antibiotic resistance were transmitted from one bacterial population to another, carried by M13 bacteriophage particles.

Incorporation of well-established in vivo DNA modification techniques into DNA messaging will diversify and extend potential intercellular communication programs, and will enable the integration of recent developments in DNA digital logic with DNA messaging.

The goal of our project is to place on a DNA message a switch that can be flipped in receiver cells under inducible conditions, and whose state determines whether or not the DNA message is retransmitted from receiver cells to a population of secondary receiver cells. The switch consists of a promoter that can be inverted using a serine integrase, leading to transcription of different genes. It is directly inspired by the recombinase addressable data (RAD) module published by the Endy group in early 2012.

We have synthesized four such DNA switches and will soon test the ability of PhiC31 and Bxb1 serine integrases, along with the respective recombination directionality factors (RDFs), to control their states. We have also produced constructs that we will use to attempt to control the production of M13 viral particles containing a DNA message and we will test these soon. We will integrate these efforts to demonstrate our goal of incorporating digital DNA logic into DNA messaging. Through this work, we will broaden the horizons of engineered intercellular communication.

Design

Ottawa's Collaboration

Video

Results

Future Aspirations

Biobricks

  • Hpdo with no gene 8
  • Bxb1 rdf
  • Bxb1 int
  • Bxb1 switch
  • BXB1 switch flipped
  • ΦC31 rdf
  • ΦC31 int
  • ΦC31 switch
  • ΦC31 switch flipped

Switch Modelling

x y z

Population & Infection Modelling

a b c

Phage Particle Production Modelling

a b c

Intent to Invent

Vlogs

Special Project

Intent to Invent

Laboratory

Safety

This page is still in progress

Sponsors

Administrators

Lab & Design

Human Practices

Mathematical Modelling

Advisors

Graduate Student Advisors

 

Retrieved from "http://2013.igem.org/Team:Waterloo"