Difference between revisions of "Team:Jiangnan/Design"

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<h1>Design</h1>
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Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.
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p{
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This page is different to the "Applied Design Award" page. Please see the <a href="https://2018.igem.org/Team:Jiangnan/Applied_Design">Applied Design</a> page for more information on how to compete for that award.
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<div class="Jnav">
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<div class="Jnavtitle">
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<a href="https://2018.igem.org/Team:Jiangnan/Safety">Safety</a>
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</div>
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<div class="Jnavtitle">
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<a href="https://2018.igem.org/Team:Jiangnan/Hardware">Hardware</a>
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</div>
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<div class="Jnavtitle" onmouseover="Jnavshow(this)" onmouseleave="Jnavhide(this)">
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<a href="https://2018.igem.org/Team:Jiangnan/Team">Team</a>
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<div class="Jnavdrag">
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<ul>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Team">Team Members</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Attributions">Attribution</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Collaborations">Collaboration</a></li>
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</ul>
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</div>
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</div>
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<div class="Jnavtitle" onmouseover="Jnavshow(this)" onmouseleave="Jnavhide(this)">
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<a href="https://2018.igem.org/Team:Jiangnan/Human_Practices">Human Practice</a>
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<div class="Jnavdrag">
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<ul>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Human_Practices">Overview</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Silver">Silver</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Entrepreneurship">Gold</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Public_Engagement">Public Engagement</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Entrepreneurship">Entrepreneurship</a></li>
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</ul>
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</div>
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</div>
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<div class="Jnavtitle">
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<a href="https://2018.igem.org/Team:Jiangnan/Model">Model</a>
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</div>
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<div class="Jnavtitle" onmouseover="Jnavshow(this)" onmouseleave="Jnavhide(this)">
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<a href="https://2018.igem.org/Team:Jiangnan/Notebook">Notebook</a>
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<div class="Jnavdrag">
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<ul>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Notebook">Lab Book</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Protocol">Protocol</a></li>
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</ul>
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</div>
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</div>
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<div class="Jnavtitle" onmouseover="Jnavshow(this)" onmouseleave="Jnavhide(this)">
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<a href="https://2018.igem.org/Team:Jiangnan">Project</a>
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<div class="Jnavdrag">
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<ul>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Background">Background</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Design">Design</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Demonstrate">Demonstration</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Results">Result</a></li>
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<li class="divider"></li>
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<li><a href="https://2018.igem.org/Team:Jiangnan/Parts">Part</a></li>
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</ul>
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</div>
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</div>
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<div class="navlogo" style="float: left;width: 20%;text-align: center;">
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<a href="https://2018.igem.org/Team:Jiangnan"><img src="https://static.igem.org/mediawiki/2018/d/d7/T--Jiangnan--igemJN_logo.png" style="width: 3em;"></a>
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</div>
 
</div>
 
</div>
  
  
  
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<div class="column two_thirds_size">
 
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<h3>What should this page contain?</h3>
 
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<ul>
 
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<li>Explanation of the engineering principles your team used in your design</li>
 
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<li>Discussion of the design iterations your team went through</li>
 
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<li>Experimental plan to test your designs</li>
 
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</ul>
 
  
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</div>
 
  
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<div class="column third_size">
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<div class="highlight decoration_A_full">
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<div style="width:100%;background-color: #f0ebea">
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<h3>Inspiration</h3>
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<img src="https://static.igem.org/mediawiki/2018/5/59/T--Jiangnan--design_top.png" width="100%" style="margin-top: -7em;">
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<ul>
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<div class="row">
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<li><a href="https://2016.igem.org/Team:MIT/Experiments/Promoters">2016 MIT</a></li>
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<div class="col s1" style="position: absolute;right: 0px; top: 30%;padding-right: 0;">
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<li><a href="https://2016.igem.org/Team:BostonU/Proof">2016 BostonU</a></li>
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<img src="https://static.igem.org/mediawiki/2018/7/71/T--Jiangnan--design_rightcircle1.png" width="100%">
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<li><a href="https://2016.igem.org/Team:NCTU_Formosa/Design">2016 NCTU Formosa</a></li>
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</div>
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</ul>
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</div>
 
</div>
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<div class="row" style="position: relative; margin-top: 5em;margin-bottom: 5em;">
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<div class="col s10 offset-s1">
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<h4>Broad Spectrum</h4>
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</div>
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<div class="col s10 offset-s1">
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<p>The key for a cell line to be sensitive to the infection of a broad spectrum of viruses is to have the corresponding receptors expressed on the cell surface. We established an association between virus Baltimore subtyping and cell surface receptors mediating virus infection, and found that given the current sensitivity spectrum of our chassis cell line MDBK, only Nectin4 and TfR need to be artificially expressed on cell surface to make it sensitive to, in principle, all commonly encountered animal viruses. The sequence design is as below, where the sequences encoding each receptor are inserted into the designed cassette,respectively, and the proteins are expressed after cell transfection.</p>
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</div>
 
</div>
 
</div>
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<div class="row" style="position: relative;margin-top: 5em;margin-bottom: 5em;">
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<div class="col s8 offset-s3">
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<img src="https://static.igem.org/mediawiki/2018/0/05/T--Jiangnan--design_Jiangnan.png" width="100%">
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<div class="col s3" style="position: absolute;left: 0;bottom: -60%;padding-left: 0;">
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<img src="https://static.igem.org/mediawiki/2018/9/92/T--Jiangnan--design_leftcircle1.png" width="100%">
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<div class="row" style="position: relative;margin-top: 5em;margin-bottom: 5em;">
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<div class="col s8 offset-s3" style="text-align: right;">
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<h4>Suspension Culture</h4>
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<p>Through comparing two sets (CHO and BHK-21) of transcriptome of suspended and adherent cells with the same origin, we obtained a list of candidate genes responsible for cell suspension. Following computational modeling of these genes, we identified the target gene “PABPC 1” and conducted wet lab experiments to verify our assumption. The gene regulatory network is constructed as below.</p>
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</div>
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<div class="row" style="position: relative;margin-top: 5em;margin-bottom: 5em;">
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<div class="col s12" style="text-align: center;">
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<img src="https://static.igem.org/mediawiki/2018/d/da/T--Jiangnan--design_suspension.png" width="40%">
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</div>
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<div class="col s1" style="position: absolute;right: 0;padding-right: 0;">
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<img src="https://static.igem.org/mediawiki/2018/6/6e/T--Jiangnan--design_rightcircle2.png" width="100%">
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</div>
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<div class="row" style="position: relative;margin-top: 5em;margin-bottom: 0;">
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<div class="col s10 offset-s1">
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<h4>High Titer</h4>
 +
<p>We conducted two sets of work to increase virus titer.</p>
 +
<p>First, we constructed the computational network and identified the key gene (IRF7) responsible for virus multiplication, which is shown as below.</p>
 +
</div>
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<div class="col s11" style="text-align: center;">
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<img src="https://static.igem.org/mediawiki/2018/5/58/T--Jiangnan--design_hightiter.png" width="40%">
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</div>
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<div class="col s10 offset-s1">
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<p>Second, we established an approach, namely cold atmospheric plasma, with the device manufactured to further increase virus titre. Plasma is the fourth fundamental state of matter, and a cocktail of ions, free electrons, reactive species, etc. Plasma may increase virus titre by increasing the permeability of cell membrane or stimulating cell receptors mediating virus internalization.</p>
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</div>
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<div class="col s10 offset-s1">
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<h4 style="text-align: center;"><br>Reference</h4>
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<p>
 +
1. Talekar A, Moscona APorotto M. Measles virus fusion machinery activated by sialic acid binding globular domain [J]. J Virol, 2013, 87(24): 13619-13627.<br>
  
 +
2. Delpeut S, Noyce R SRichardson C D. The Tumor-Associated Marker, PVRL4 (Nectin-4), is the Epithelial Receptor for Morbilliviruses [J]. Viruses, 2014, 6(6): 2268-2286.<br>
 +
 +
3. Lofling J, Lyi S M, Parrish C R, et al. Canine and feline parvoviruses preferentially recognize the non-human cell surface sialic acid N-glycolyl neuraminic acid [J]. Virology, 2013, 440(1): 89-96.<br>
 +
 +
4. Vicentemanzanares M, Choi C KHorwitz A R. Integrins in cell migration - the actin connection [J]. Journal of Cell Science, 2009, 122(Pt 2): 199-206.<br>
 +
 +
5. Forzan M, Marsh MRoy P. Bluetongue Virus Entry into Cells [J]. J Virol, 2007, 81(9): 4819-4827.<br>
 +
 +
6. Schneider-Schaulies J, Meulen VSchneider-Schaulies S. Measles virus interactions with cellular receptors: Consequences for viral pathogenesis [J]. J NeuroVirol, 2001, 7(5): 391-399.<br>
 +
 +
7. Von Messling V, Oezguen N, Zheng Q, et al. Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry in peripheral blood mononuclear cells [J]. J Virol, 2005, 79(9): 5857-5862.<br>
 +
 +
8. Pratakpiriya W, Seki F, Otsuki N, et al. Nectin4 is an epithelial cell receptor for canine distemper virus and involved in neurovirulence [J]. J Virol, 2012, 86(18): 10207-10210.</p>
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Latest revision as of 03:02, 18 October 2018

Safety
Hardware
Team
Human Practice
Model
Notebook
Project

Broad Spectrum

The key for a cell line to be sensitive to the infection of a broad spectrum of viruses is to have the corresponding receptors expressed on the cell surface. We established an association between virus Baltimore subtyping and cell surface receptors mediating virus infection, and found that given the current sensitivity spectrum of our chassis cell line MDBK, only Nectin4 and TfR need to be artificially expressed on cell surface to make it sensitive to, in principle, all commonly encountered animal viruses. The sequence design is as below, where the sequences encoding each receptor are inserted into the designed cassette,respectively, and the proteins are expressed after cell transfection.

Suspension Culture

Through comparing two sets (CHO and BHK-21) of transcriptome of suspended and adherent cells with the same origin, we obtained a list of candidate genes responsible for cell suspension. Following computational modeling of these genes, we identified the target gene “PABPC 1” and conducted wet lab experiments to verify our assumption. The gene regulatory network is constructed as below.

High Titer

We conducted two sets of work to increase virus titer.

First, we constructed the computational network and identified the key gene (IRF7) responsible for virus multiplication, which is shown as below.

Second, we established an approach, namely cold atmospheric plasma, with the device manufactured to further increase virus titre. Plasma is the fourth fundamental state of matter, and a cocktail of ions, free electrons, reactive species, etc. Plasma may increase virus titre by increasing the permeability of cell membrane or stimulating cell receptors mediating virus internalization.


Reference

1. Talekar A, Moscona APorotto M. Measles virus fusion machinery activated by sialic acid binding globular domain [J]. J Virol, 2013, 87(24): 13619-13627.
2. Delpeut S, Noyce R SRichardson C D. The Tumor-Associated Marker, PVRL4 (Nectin-4), is the Epithelial Receptor for Morbilliviruses [J]. Viruses, 2014, 6(6): 2268-2286.
3. Lofling J, Lyi S M, Parrish C R, et al. Canine and feline parvoviruses preferentially recognize the non-human cell surface sialic acid N-glycolyl neuraminic acid [J]. Virology, 2013, 440(1): 89-96.
4. Vicentemanzanares M, Choi C KHorwitz A R. Integrins in cell migration - the actin connection [J]. Journal of Cell Science, 2009, 122(Pt 2): 199-206.
5. Forzan M, Marsh MRoy P. Bluetongue Virus Entry into Cells [J]. J Virol, 2007, 81(9): 4819-4827.
6. Schneider-Schaulies J, Meulen VSchneider-Schaulies S. Measles virus interactions with cellular receptors: Consequences for viral pathogenesis [J]. J NeuroVirol, 2001, 7(5): 391-399.
7. Von Messling V, Oezguen N, Zheng Q, et al. Nearby clusters of hemagglutinin residues sustain SLAM-dependent canine distemper virus entry in peripheral blood mononuclear cells [J]. J Virol, 2005, 79(9): 5857-5862.
8. Pratakpiriya W, Seki F, Otsuki N, et al. Nectin4 is an epithelial cell receptor for canine distemper virus and involved in neurovirulence [J]. J Virol, 2012, 86(18): 10207-10210.