Team:Wageningen UR

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'''Project description Team Wageningen_UR'''
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'''Synthetic biological approach for the development of standardized medical delivery systems'''
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Our team will join the competition with a medically focussed project on Virus-Like Paricles (VLPs). VLPs are empty virusses that lack a genetic content, and can therefore not self-replicate. These VLPs can be modified to make vaccines or used as bio-nano carriers for site-specific drug delivery.  
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  <h2>Human Body Model</h2>
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  <p>To determine the effects of the VLPs and the medicine in the human body a human body model was constructed. With this model we are able to compare the traditional use of medicine with the use of our VLPs. If succesful it will open up a whole new era for the use of medicine.</p>
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  <h2>Human Practices</h2>
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  <p>For science to be applicable outside the confined area of a laboratory, its procedures and outcomes should be compatible with the rest of society. It is therefore important for any scientist to know which stakeholders play a role in applying VLPs in the clinic.</p>
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The development of conventional vaccines is slow, laborious and costly. VLPs can serve as a cheap and standardized platform for the development and production of vaccines, making preventive healthcare accessible worldwide.
 
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Three different viruses will serve as initial workhorses. Cowpea Chlorotic Mottle Virus (CCMV), Turnip Yellows Virus (TuYV) and Hepatitis B (HepB) have been selected for their promising properties in either packaging molecules or modification possibilities on the outside of the particle. The research done on these three VLPs should lead to one standardized tool.
 
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Charged coils applied on the outside of the VLP will serve as a docking site in order to obtain one standardized tool for medical delivery systems. The epitope of interest is fused to the oppositely charged coil designed to connect to the docking site. With this, a Plug and Apply system is designed, creating the desired standardized platform.
 
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Modification of the monomere can inhibit multimerization and with it formation of the VLP. Therefore, tertiary and quarternary protein structure modelling is used to predict whether the modification will inhibit assembly. If the in silico results are positive, the construct will be made and cloned in Escherichia coli.
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= Abstract =
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Formation of VLPs is usually confirmed using Electron Microscopy (EM). This is rather time consuming and expensive, so Dynamic Light Scattering (DLS) is investigated as an alternative method. DLS can provide an indication of VLP formation but conclusive evidence should be obtained by EM.
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'''A standardized tool for site specific drug delivery using Virus-Like Particles'''
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Medicines are generally active in a non-site-specific fashion, affecting the whole patient, including healthy tissue. Therefore, we attempt to specifically target diseased areas by packaging medicines inside Virus-Like Particles (VLPs). VLPs are not infectious, as they are built solely from viral coat proteins. We designed a modular Plug and Apply system that enables modifications to these coat proteins. The system facilitates the linkage of numerous ligands to the coat protein, thereby creating site-specific carriers. After expression of coat protein genes in Escherichia coli the VLPs were assembled in vitro, yielding modified Virus-Like Particles. Medicines can be packed using the Plug and Apply system or simply by addition during VLP assembly. Concluding, VLPs can be used as universal carriers for site-specific drug delivery, which is confirmed by our human body model. The device allows customization to a variety of diseases while decreasing side effects for patients during treatment.
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The formation of the first VLP samples is confirmed by using these two detection methods, and the gene is standardized conform the rules of iGEM. This gene will now serve for further development of the standardized medical delivery systems, making mass development and production of new vaccines possible.
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<h2 class="ulc1">Abstract</h2>
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<h4>A standardized tool for site specific drug delivery using Virus-Like Particles</h4>
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<p align="justify">Medicines are generally active in a non-site-specific fashion, affecting the whole patient, including healthy tissue. Therefore, we attempt to specifically target diseased areas by packaging medicines inside Virus-Like Particles (VLPs). VLPs are not infectious, as they are built solely from viral coat proteins. We designed a modular Plug and Apply system that enables modifications to these coat proteins. The system facilitates the linkage of numerous ligands to the coat protein, thereby creating site-specific carriers. After expression of coat protein genes in <i>Escherichia coli</i> the VLPs were assembled in vitro, yielding modified Virus-Like Particles. Medicines can be packed using the Plug and Apply system or simply by addition during VLP assembly. Concluding, VLPs can be used as universal carriers for site-specific drug delivery, allowing customization to a variety of diseases while decreasing side effects for patients during treatment.</p>
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<b>The Constructor</b><br>
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An application that assists you in creating your cloning strategies for your iGem project.
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<h2 class="ulc3">Medal Achievements</h2>
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[http://socialwur.nl  The Constructor]
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We helped the iGEM community by providing <a href="https://2012.igem.org/Team:Wageningen_UR/TheConstructor">The Constructor</a>.
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<div class="achievement-desc">This a tool which makes constructing complicated Functional Genetic Modules build from many BioBrick child’s play. The trials showed a more efficient cloning strategy which saves time in the laboratory work.</div>
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We improved one of the most widely used BioBricks: GFP.
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<div class="achievement-desc">The reporter protein GFP (<a href="http://partsregistry.org/Part:BBa_I13522">old biobrick</a>) has been modified so that it can be utilized with the Plug 'n Apply System. The new BioBricks are <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K883700">BBa_K883700</a> and <a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K883701">BBa_K883701 (with His-tag)</a>. By using the PnA System, the GFP can be used to indicate the location of, for example, expressed receptors. </div>
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We turned the <a href="https://2012.igem.org/Team:Wageningen_UR/Human_Practices">Human Practices</a> into a national effort.
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<div class="achievement-desc">By cooperating with most of the Dutch iGEM teams, we managed to have a nation-wide appearance in three major cities during the <a href="https://2012.igem.org/Team:Wageningen_UR/DiscoveryFestival">Discovery Festivals</a>. Our team presents the science of iGEM in Rotterdam, while being analysed <a href="https://2012.igem.org/Team:Wageningen_UR/DiscoveryFestival_Communication">by a student in Applied Communication</a>.</div>
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Software: The Constructor<br />&nbsp;
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<div class="achievement-desc">We're not in iGEM's <a href="https://igem.org/Software">software track</a>, but still we think it is important to create and improve software tools for the iGEM community. Therefore we tried to fullfill the <a href="https://igem.org/Software#Software_Competition_Judging">medal requirements for the software track</a> with <a href="https://2012.igem.org/Team:Wageningen_UR/TheConstructor">The Constructor</a>.</div>
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|We're going to develop a new platform for synthetic biology.
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|[[Image:Wageningen_UR_logo.png|200px|right|frame]]
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We submitted a new and well characterised standard BioBrick: <a href="https://2012.igem.org/Team:Wageningen_UR/ModifyingtheCCMV">CCMV</a> (<a href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K883001">BBa_K883001</a>).
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<div class="achievement-desc">This BrioBrick can be used to produce <a href="https://2012.igem.org/Team:Wageningen_UR/ModifyingtheCCMV">CCMV</a> Virus-Like particles. Besides, it can serve as a template for modifications to pursue many new <a href="https://2012.igem.org/Team:Wageningen_UR/Applications">applications</a>. The sequence is confirmed.</div>
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We demonstrated that the production of VLPs using our own BioBricks works.
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<div class="achievement-desc">We produced both <a href="https://2012.igem.org/Team:Wageningen_UR/ModifyingtheCCMV">CCMV</a> and <a href="https://2012.igem.org/Team:Wageningen_UR/ModifyingtheHepatitisB">HepB VLPs</a> using the BioBricks we constructed ourselves. The protocol and detailed description of the machines used for production and detection of these VLPs <a href="https://2012.igem.org/Team:Wageningen_UR/Protocol">has been made available.</a></div>
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We <a href="http://partsregistry.org/Part:BBa_K883001">characterised the stability</a> of <a href="https://2012.igem.org/Team:Wageningen_UR/ModifyingtheCCMV">CCMV VLPs</a>.
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<div class="achievement-desc">We changed the conditions in which the VLPs were resuspended. By changing pH and temperature and taking samples over time, we indicated at which values the VLPs were not stable. This defines the borders at which the VLPs can be used.</div>
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- <a href="https://igem.org/Team.cgi">Team registration</a><br />
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- New submitted and highly-documented standard <a href="https://2012.igem.org/Team:Wageningen_UR/Parts">BioBrick Part or Device.</a><br />
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|align="center"|[[Team:Wageningen_UR | Team Wageningen_UR]]
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- Complete Judging form<br />
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Present a poster and a talk at the iGEM Jamboree
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<div class="achievement-desc">We are going to the European iGEM Jamboree from 5 to 7 October.</div>
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Latest revision as of 21:10, 26 October 2012


Home

Human Body Model

To determine the effects of the VLPs and the medicine in the human body a human body model was constructed. With this model we are able to compare the traditional use of medicine with the use of our VLPs. If succesful it will open up a whole new era for the use of medicine.

Human Practices

For science to be applicable outside the confined area of a laboratory, its procedures and outcomes should be compatible with the rest of society. It is therefore important for any scientist to know which stakeholders play a role in applying VLPs in the clinic.
1. Introduction

The Wageningen UR team has worked on the modification of virus-like particles (VLPs) to make them interesting platforms for vaccine production and/or site specific drug delivery. VLPs are empty virus capsids, meaning that they do not contain any viral genome and proteins except for the coat proteins. Coat proteins of some viruses have shown the ability to self-assemble in absence of its viral genome and other viral proteins, and thus form VLPs. Our human body model gives us an inside about how our drug delivery system would improve drug application.

2. Plug 'n Apply
System

A big challenge of our project is the attachment of ligands and functional proteins on either the outside or inside of a virus-like particle (VLP). We decided to use a noncovalent anchor-like system, which consists of two different coiled-coil proteins. We call it the Plug-and-Apply-system (PnA-system).

3. Virus Like
Particles

A Virus-Like Particle (VLP) is a shell of viral Coat Proteins (CPs) that spontaneously assemble with the right conditions. Although a VLP resembles the original virus in shape and size, it lacks both the external sites that are usually required for the infection of cells and the internal machinery needed for viral replication. Moreover, they also lack the viral genetics to be transcribed and replicated.

4. Outside
Modification

The monomers of virus-like particles (VLPs) have been subject to many modifications of which some are aimed at changing the appearance of the particle. By changing the outside, the VLP acquires new properties which have been used mainly in vaccine development . The modification we pursue is adding a coil to the protein subunits, at any location that is exposed on the outside of the VLP. This can be a fusion to a C or N-terminal, but a modification in a loop is possible as well.

5. Inside
Modification

Since virus-like particles (VLPs) lack genetic content, they enclose an empty space. This space can be filled with proteins such as antibiotics, hormones, and all sorts of pharmaceuticals. Modifications on the inside of the VLPs can increase binding affinity to the loaded substance. The first modifications we pursue is adding the K-coil to the protein subunits at any location that is exposed on the inside of the VLP.

6. Detection

A key part of our project is the detection of VLPs. We need sufficient visualization to get conclusive evidence of VLP formation. Besides standard approaches, we will investigate alternative methods to detect the formation and stability of Virus-Like Particles.

7. Applications

The goal of our project is to construct standardized self-assembling particles with a simple and versatile attachment system for either packaging molecules, presenting ligands/epitopes, or both. By combining the PnA (Plug 'n Apply) System and Virus-Like Particles (VLPs), we create a tool that can be applied in numerous applications.

8. The Constructor

The registry is the substrate to make complex devices. We designed a web tool that facilitates an automatic cloning recommendation which outcompetes manual querying of the BioBrick parts from the registry. Besides constructing the best cloning strategy, The Constructor also allows the user to select for BioBrick quality and availability.

9. Final
Overview

"If it turns out that the combination of delivery and medicine has a superior ability to cure, everything is achievable in the modern world." Senior Project Leader in veterinary medicine at MSD. "Having in place a system that can rapidly develop a vaccine against unexpected viral agents would be of great importance for public health." ECDC Program Leader Vaccine Preventable Diseases


Abstract

A standardized tool for site specific drug delivery using Virus-Like Particles

Medicines are generally active in a non-site-specific fashion, affecting the whole patient, including healthy tissue. Therefore, we attempt to specifically target diseased areas by packaging medicines inside Virus-Like Particles (VLPs). VLPs are not infectious, as they are built solely from viral coat proteins. We designed a modular Plug and Apply system that enables modifications to these coat proteins. The system facilitates the linkage of numerous ligands to the coat protein, thereby creating site-specific carriers. After expression of coat protein genes in Escherichia coli the VLPs were assembled in vitro, yielding modified Virus-Like Particles. Medicines can be packed using the Plug and Apply system or simply by addition during VLP assembly. Concluding, VLPs can be used as universal carriers for site-specific drug delivery, which is confirmed by our human body model. The device allows customization to a variety of diseases while decreasing side effects for patients during treatment.

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