Difference between revisions of "Team:Lethbridge"

 
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     <div class="carousel-item white-text -webkit-text-stroke: 3px black; CB2 center" href="#two!">
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       <h1 class="thin">Nanoresponder</h1>
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       <h1 class="thin">Microbiome Study</h1>
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       <h2 class="grey-text thin center">EMS Microbiome Study</h2>
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       <h2 class="black-text thin center"></h2>
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       <div style="padding-top: 50px;"></div>
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       <div style="padding-top: 100px;"></div>
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       <a class="btn-large waves-effect white grey-text darken-text-2">explore</a>
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       <a href="https://2016.igem.org/Team:Lethbridge/Design" class="btn-large waves-effect white grey-text darken-text-2">Read More</a>
 
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     <div class="carousel-item white-text CB3 center" href="#three!">
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     <div class="carousel-item black-text CB3 center" href="#three!">
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       <h1 class="thin">Nanoresponder</h1>
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       <h1 class="thin">Antibody Development</h1>
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       <h2 class="grey-text thin center">Antibody Development</h2>
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       <a class="btn-large waves-effect white grey-text darken-text-2">explore</a>
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       <a href="https://2016.igem.org/Team:Lethbridge/Results" class="btn-large waves-effect white grey-text darken-text-2">Read More</a>
 
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     <div class="carousel-item white-text CB4 center" href="#four!">
 
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       <h1 class="thin">Nanoresponder</h1>
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       <h1 class="thin"></h1>
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       <h2 class="grey-text thin center">SDAB-DB: Single Domain Antibody Database</h2>
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       <h2 class="black-text thin center"> </h2>
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       <div style="padding-top: 100px;"></div>
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       <a class="btn-large waves-effect white grey-text darken-text-2">explore</a>
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       <a href="http://www.sdab-db.ca" class="btn-large waves-effect white grey-text darken-text-2">Visit SDAB-DB.ca</a>
 
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           <h3 class="white-text thin">Introduction</h3>
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           <h2 class="white-text thin center">Nanoresponder - Call to Action!</h2>
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           <p class="grey-text text-lighten-4">The prevalence of virulent and multiple antibiotic resistant pathogens in healthcare facilities has resulted in ongoing reassessment of best practices to prevent their transmission. However, whether pathogen reservoirs exist in emergency medical services (EMS) vehicles, remains largely unknown. Our iGEM team developed a custom bacterial two hybrid system to select single-domain antibodies (nanobodies) that recognize human pathogens. Informed by our Nanopore next generation sequencing of DNA samples from ambulance vehicles, antibodies targeting important pathogens were then used to develop a rapid and low cost ELISA-based testing kit that may be employed on-site by EMS workers. Our project provides a framework for rapid detection of emergent pathogens and a practical and rapid solution for monitoring their presence in and outside of the healthcare system.</p>
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           <h5 class="thin grey-text text-lighten-4"><b>With ever increasing threats from emergent pathogens and multiple resistant bacteria</b>, hospitals are cracking down with more rigorous monitoring and decontamination procedures to prevent pathogen spread.</h5>
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<h5 class="thin grey-text text-lighten-4">Emergency Medical Service (EMS) vehicles and workers are often the first point of patient care, however, <b>little is known about the importance of EMS vehicles for the transmission of pathogens</b>, and detection methods lag behind those of hospitals.</h5>
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<h5 class="thin grey-text text-lighten-4">We are Nanoresponder!<b> A team dedicated to the advancement of pathogen detection and monitoring in EMS vehicles.</b> We have taken a dual approach to pathogen detection: (1) <u><a href="#Nanopore">Nanopore Next Generation Sequencing (NGS)</a></u> of DNA samples from EMS vehicles; and (2) A rapid <u><a href="#Antibody">single-domain antibody detection system</a></u> to generate antibodies that may be <b>implemented in simple and reliable testing kits for fast, on-site pathogen detection.</b></h5>
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          <h3 class="white-text thin">EMS Vehicle Microbiome Investigation</h3>
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          <h5 class="thin grey-text text-lighten-4">Upon conducting an in-depth review of literature surrounding EMS vehicle pathogen detection and interviews with EMS officials, we discovered that <b>no published study utilizes a Next Generation Sequencing</b> approach to pathogen detection in EMS vehicles and instead solely cell culturing techniques were used. This is surprising considering that <b>many microbes are unculturable</b> in a laboratory setting and would otherwise escape detection. Moreover, cell culturing techniques may require many days before test results are available.</p>
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<h5 class="grey-text text-lighten-4">Recognizing the need for high-throughput and inclusive pathogen detection methods, we developed a detection platform, utilizing the <b>MinION</b> - a novel NGS sequencing technology from <b><u><a href="http://www.nanoporetech.com/">Oxford Nanopore Technologies</a></u></b>.</h5>
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<center><img class="responsive-img" src="https://static.igem.org/mediawiki/2016/5/5c/T--Lethbridge--NanoporeSeq.jpg" style="max-height=400px;">
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<h5 class="thin grey-text text-lighten-4">The MinION Next Geneneration Sequencing Platform</h5></center>
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<br>
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<h5 class="thin grey-text text-lighten-4">In collaboration with our local EMS department, we devised a sampling strategy, DNA extraction procedure and amplification procedure that is compatible with the MinION sequencing technology.</h5>
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<br>
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<center><img class="responsive-img" src="https://static.igem.org/mediawiki/2016/9/9d/T--Lethbridge--SamplingLoc.jpg" style="max-height:400px;">
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<h6 class="thin grey-text text-lighten-4">Sampling locations for the EMS Microbiome Study</h6></center>
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<br>
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<h5 class="thin grey-text text-lighten-4">Using polymerase chair reaction, we amplified ribosomal small subunit gene sequences from extracted sample DNA and subjected them to MinION deep sequencing. We found marked differences in microbial community structure between sample and control DNAs, with many EMS vehicles samples containing a large proportion of opportunistic pathogens.</h5>
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<center><img src="https://static.igem.org/mediawiki/2016/7/7c/T--Lethbridge--NpResult.jpg" width=50%>
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<h6 class="thin grey-text text-lighten-4">Sampling locations for the EMS Microbiome Study</h6></center>
  
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          <h3 class="white-text thin">Single Domain Antibody Development System</h3>
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          <h5 class="grey-text text-lighten-4 thin">Recognizing that EMS vehicles may be reservoirs of pathogens, we next wished to meet the need for a rapid and on-site pathogen detection technology that uses specific antibodies for detection. Towards this we engineered a <b>library of synthetic single domain antibodies</b> (Nanobodies) as well as a <b>bacterial two hybrid system for antibody selection</b>.</h5>
  
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<center><img src="https://static.igem.org/mediawiki/2016/1/11/T--Lethbridge--construct1.jpg" width=50%>
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<h6 class="grey-text thin text-lighten-4">Engineered Bacterial-two-hybrid Antibody Selection System</h6></center>
  
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<h5 class="grey-text thin text-lighten-4">We successfully demonstrate an <b>integrated DNA sequencing plus antibody detection platform</b> for monitoring the presence of pathogens in EMS vehicles that may be ported to function in other portions of health, environment and other sectors.</h5>
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        <h5 class="white-text">Links</h5>
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          <li><a class="grey-text text-lighten-3" href="#!">Link 1</a></li>
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          <li><a class="grey-text text-lighten-3" href="#!">Link 2</a></li>
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          <li><a class="grey-text text-lighten-3" href="#!">Link 3</a></li>
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    Designed by Chris Isaac
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Latest revision as of 03:59, 20 October 2016

Lethbridge iGEM 2016

Microbiome Study

Read More

Antibody Development

Read More

Visit SDAB-DB.ca

Nanoresponder - Call to Action!

With ever increasing threats from emergent pathogens and multiple resistant bacteria, hospitals are cracking down with more rigorous monitoring and decontamination procedures to prevent pathogen spread.
Emergency Medical Service (EMS) vehicles and workers are often the first point of patient care, however, little is known about the importance of EMS vehicles for the transmission of pathogens, and detection methods lag behind those of hospitals.
We are Nanoresponder! A team dedicated to the advancement of pathogen detection and monitoring in EMS vehicles. We have taken a dual approach to pathogen detection: (1) Nanopore Next Generation Sequencing (NGS) of DNA samples from EMS vehicles; and (2) A rapid single-domain antibody detection system to generate antibodies that may be implemented in simple and reliable testing kits for fast, on-site pathogen detection.

EMS Vehicle Microbiome Investigation

Upon conducting an in-depth review of literature surrounding EMS vehicle pathogen detection and interviews with EMS officials, we discovered that no published study utilizes a Next Generation Sequencing approach to pathogen detection in EMS vehicles and instead solely cell culturing techniques were used. This is surprising considering that many microbes are unculturable in a laboratory setting and would otherwise escape detection. Moreover, cell culturing techniques may require many days before test results are available.

Recognizing the need for high-throughput and inclusive pathogen detection methods, we developed a detection platform, utilizing the MinION - a novel NGS sequencing technology from Oxford Nanopore Technologies.

The MinION Next Geneneration Sequencing Platform

In collaboration with our local EMS department, we devised a sampling strategy, DNA extraction procedure and amplification procedure that is compatible with the MinION sequencing technology.


Sampling locations for the EMS Microbiome Study

Using polymerase chair reaction, we amplified ribosomal small subunit gene sequences from extracted sample DNA and subjected them to MinION deep sequencing. We found marked differences in microbial community structure between sample and control DNAs, with many EMS vehicles samples containing a large proportion of opportunistic pathogens.

Sampling locations for the EMS Microbiome Study

Single Domain Antibody Development System

Recognizing that EMS vehicles may be reservoirs of pathogens, we next wished to meet the need for a rapid and on-site pathogen detection technology that uses specific antibodies for detection. Towards this we engineered a library of synthetic single domain antibodies (Nanobodies) as well as a bacterial two hybrid system for antibody selection.

Engineered Bacterial-two-hybrid Antibody Selection System
We successfully demonstrate an integrated DNA sequencing plus antibody detection platform for monitoring the presence of pathogens in EMS vehicles that may be ported to function in other portions of health, environment and other sectors.