Difference between revisions of "Team:Tokyo Tech/Experiments"

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<section class="engine"><a href="https://mobirise.info/s">free bootstrap theme</a></section><section class="mbr-section content5 cid-r5GSXpxhLK mbr-parallax-background" id="content5-n">
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<section class="engine"><a href="https://mobiri.se/k">develop your own website</a></section><section class="header9 cid-r5el55DVH6 mbr-fullscreen mbr-parallax-background" id="header9-g">
  
  
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            <h1 class="mbr-section-title align-left mbr-bold pb-3 mbr-fonts-style display-1">Experiment</h1>
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            <h3 class="mbr-section-subtitle align-left mbr-light pb-3 mbr-fonts-style display-2">Establishment of dengue virus serotype detection system</h3>
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                <h3 class="mbr-section-subtitle align-center mbr-light mbr-white pb-3 mbr-fonts-style display-5">In wet lab section, we developed the detection system to identify which type the patient is infected with.&nbsp;</h3>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Abstract</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">To identify which serotype of dengue virus your target patient is infected with, many methods have been explored and established. Since our prediction model requires the certain number of consensus time-scale data, it has been urgent to develop a high-throughput and cost-efficient tool for the serotype identification.<br><br>With the assistance of Dr. Suzuki at National Institute of Infectious Diseases, our team designed a new detection system with fluorescence protein. Three types of constructs (Genetic feactures: 1. C, 2. prM-E and 3. Fluorescence protein-FMDV2a-NS) should be prepared first. After that, they are introduced into HEK293T cells and pseudo-viruses are produced after a certain interval. They are added to cultured Vero cells to check the infectivity by measuring the intensity of fluorescence emitted from fluorescence protein that works as mono-cistron.<br><br>Since each one of the constructs contains either structural or non-structural region, the pseudo-virus just causes single-round infection. In terms of biosafety, our system and products that apply this system can be demonstrated even in the real world.<br><br></p>
  
 
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Background</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">RT-PCR, ELISA and neutrilization assay - these methods have been widely used to identify infection experience and its serotype. However, RT-PCR is valid only for 0 to 5 days after infection and ELISA and neutralization assay have problem with cost-efficiency.<br></p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 1: Change in viral load and antibodies (Source: <a href="https://www.nature.com/scitable/topicpage/host-response-to-the-dengue-virus-22402106">Guzman, M. G. et al., 2010</a>)</p>
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                <h1 class="mbr-section-title mbr-white pb-3 mbr-fonts-style display-1">Pseudovirus Production</h1>
 
  
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                    <p class="mbr-text mbr-fonts-style display-5">The pseudovirus production phase consists of the following parts: construction, transfection and collection of pseudoviruses.</p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 2: Comparison of dengue detection system with existing ones<br></p>
  
 
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Experiment Overview</h1>
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                    <li><strong>Construction</strong> <br><br>- For the pseudovirus production, we prepared structural gene, and non-structural gene with fluorescence protein gene.<br><br>About structural gene, capsid (C), membrane (prM) and envelope (E) are necessary for the formation of viral structure. We prepared pCAG-C and pCAG-prM-E for Serotype I to IV.<br><br>About non-structural gene with fluorescence protein gene, we prepared EGFP-FMDV2a, DsRed-Express-FMDV2a, ZsYellow-FMDV2a and AmCyan-FMDV2a, and inserted each of them to non-structural genes of dengue virus.<br><br></li>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Our experiment consists of three parts: 1. Construction, 2. Pseudo-virus Production and 3. Pseudo-virus Infection. After three types of constructs are introduced into HEK293T cells, pseudo-viruses are produced. They are added to cultured Vero cells, and you can check the infection after a certain interval.<br></p>
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                    <li><strong>Transfection and collection of pseudoviruses&nbsp;<br></strong><br>- We introduced pCAG-C, pCAG-prM-E and FP-FMDV2a (FP: Fluorescence Protein) into HEK293T cells. After cell culture for about 2 days, we collect the supernatant that contains pseudoviruses produced from HEK293T cells.</li>
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                 <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 3: Experiment Overview (iGEM Tokyo Tech 2018)<br></p>
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                    <p class="mbr-text mbr-fonts-style display-5">After collecting pseudoviruses from HEK293T cells, we added them to Vero cells. When they can successfully infect the cells, the enclosed fluorescence protein gene is coded and we tried to estimate the amount by measuring the fluorescence intensity.<br><br>Since we split up the structural region and non-structural region, the pseudoviruses produced in our system can infect host cells only once. Thus, it will not spread out of the system and will not be harmful.<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-5">1. Construction</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">For the pseudo-virus production, we prepared structural gene, and non-structural gene with fluorescence protein gene.<br><br>About structural gene, capsid (C), membrane (prM) and envelope (E) are necessary for the formation of viral structure. We prepared pCAG-C and pCAG-prM-E for Serotype I to IV.<br><br>About non-structural gene with fluorescence protein gene, we prepared EGFP-FMDV2a, DsRed-Express-FMDV2a, ZsYellow-FMDV2a and AmCyan-FMDV2a, and inserted each of them to non-structural genes of dengue virus.</p>
  
 
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                 <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 4: Construct line-up and original genes derived from dengue virus<br></p>
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                    <p class="mbr-text mbr-fonts-style display-5">To achieve parts validation in iGEM sliver medal criteria, we registered three parts: DENV2 C, EGFP-FMDV2a and DsRed-Express-FMDV2a. Capsid protein (C) is necessary for the formation of pseudovirus structure in the system.<br><br> EGFP-FMDV2a or DsRed-Express-FMDV2a is packed in the pseudovirus and codes fluorescence protein after the virus infects host cells.<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-5">2. Pseudo-virus Production</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">We introduced pCAG-C, pCAG-prM-E and FP-FMDV2a (FP: Fluorescence Protein) into HEK293T cells. After cell culture for about 2 days, we collect the supernatant that contains pseudo-viruses produced from HEK293T cells.</p>
  
 
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 5: Basic flow of transfection and pseudo-virus production<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-5">3. Pseudo-virus Infection and Functional Evaluation of Pseudo-virus</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">After collecting pseudo-viruses from HEK293T cells, we added them to Vero cells. When they can successfully infect the cells, the enclosed fluorescence protein gene is coded and we tried to estimate the amount by measuring the fluorescence intensity.</p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Since we split up the structural region and non-structural region, the pseudo-viruses produced in our system can infect host cells only once. Thus, it will not spread out of the system and will not be harmful.</p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 6: Basic flow of pseudo-virus infection and how fluorescence protein works
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-5">Note: Validated Parts (Silver Medal Criteria)</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">DENV2 C, EGFP-FMDV2a and DsRed-Express-FMDV2a are essential for pseudo-virus production. As one of the structural genes, DENV2 C plays an important role in virus structural formation. EGFP-FMDV2a and DsRed-Express-FMDV2a are enclosed in pseudo-virus and programmed to code functional fluorescence proteins after infecting the host cells.</p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">To get specific sequence and charanterization information, please see the following Parts Pages.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_K2729001">Parts Page: DENV2 C</a></p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_K2729006">Parts Page: EGFP-FMDV2a</a></p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="http://parts.igem.org/cgi/partsdb/part_info.cgi?part_name=BBa_K2729007">Parts Page: DsRed-Express-FMDV2a</a></p>
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                <img src="https://static.igem.org/mediawiki/2018/9/9c/T--Tokyo_Tech--silver_val_parts.png" width="1400" alt="Mobirise" title="">
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 7: List of validated parts and the features<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Progress of Our Experiment (~Oct. 17th, 2018)</h1>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Our team successfully validated that all the necessary constructs are produced by using electrophoresis (please refer to our Parts Pages).</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">After completing the construction, our team shifted to the transfection into HEK293T cells for pseudo-virus production. Using lipofection, the constructs have been already introduced into the cells and the pseudo-viruses will be collected in a few days.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">After collecting the pseudo-viruses, they will be added to cultured Vero cells. Our team will test the infectivity by measuring the fluorescence intensity at the end.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">The whole results will be announced in Giant Jamboree, so please do not miss it!</p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Our Goal</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">We successfully validated that the pseudo-viruses are produced, and they can infect the host cells. Making the most of our system and lab experience, our team will make a kit to identify which type your target patient was infected with before.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">As you can see in Fig. 8, if the patient was infected with type II virus before, type II-specific antibodies in blood serum decrease the infectivity of type II pseudo-virus. As a result, fluorescence protein programmed in the pseudo-virus would not be coded so much due to the decrease in the number of infectious viruses.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Thus, you can identify the infection experience and its type by measuring or observing the fluorescence intensity for each type/color.</p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 8: Mechanism of colorimetric type detection system with different fluorescence proteins<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Feedback to Modeling</h1>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Since our detection system enables us to collect more samling data in many areas quickly and with low cost, our prediction model can be more precise thanks to the increase in the consensus time-scale data of dengue-affected patients and serotype ratio.</p>
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            </div>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Biosafety</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">As you can see in Fig. 9, on native virus genome, structural genes and non-structural genes are integrated on the same sequence. Thus, the whole genome are replicated and that make viruses possible to replicate themselves in host cells.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">However, as you can see our construct design in Fig. 10, structural and non-structural regions are splitted so that the pseudo-virus cannot replicate themselves in host cells because RNA polymerase from non-structural V gene cannot replicate structural genes.</p>
 +
                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">To sum up, our system starts and ends in one place and doesn't harm environment.</p>
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                <img src="https://static.igem.org/mediawiki/2018/7/76/T--Tokyo_Tech--infectious_particle_ex.png" width="1400" alt="Mobirise" title="">
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 9: Infection process of native virus and production of infectious pseudo-virus<br></p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7">Figure 10: Infection process of our pseudo-virus for validating biosafety<br></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Reference</h1>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="https://www0.niid.go.jp/">National Institute of Infectious Diseases HP</a></p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="https://www.nature.com/scitable/topicpage/host-response-to-the-dengue-virus-22402106">Scitable: Host Response to the Dengue Virus</a></p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="https://www.ncbi.nlm.nih.gov/pubmed/28794181">Neutralization Assay for Zika and Dengue Viruses by Use of Real-Time-PCR-Based Endpoint Assessment.</a></p>
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                <p class="mbr-text align-center display-5 pb-3 mbr-fonts-style display-7"><a href="http://www.who.int/denguecontrol/en/">WHO: Dengue control</a></p>
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                <h1 class="mbr-section-title align-center pb-3 mbr-fonts-style display-2">Protocol</h1>
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                <div class="mbr-section-btn align-center"><a class="btn btn-primary display-4" href="https://2018.igem.org/Team:Tokyo_Tech/InterLab" target="_blank">InterLab Page</a>
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                    <a class="btn btn-black-outline display-4" href="https://2018.igem.org/Team:Tokyo_Tech/Model" target="_blank">Modeling</a></div>
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Revision as of 21:06, 17 October 2018

<!DOCTYPE html> {{Tokyo_Tech/mobirise/nav-bar}} Experiments

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Experiment

Establishment of dengue virus serotype detection system

Abstract

To identify which serotype of dengue virus your target patient is infected with, many methods have been explored and established. Since our prediction model requires the certain number of consensus time-scale data, it has been urgent to develop a high-throughput and cost-efficient tool for the serotype identification.

With the assistance of Dr. Suzuki at National Institute of Infectious Diseases, our team designed a new detection system with fluorescence protein. Three types of constructs (Genetic feactures: 1. C, 2. prM-E and 3. Fluorescence protein-FMDV2a-NS) should be prepared first. After that, they are introduced into HEK293T cells and pseudo-viruses are produced after a certain interval. They are added to cultured Vero cells to check the infectivity by measuring the intensity of fluorescence emitted from fluorescence protein that works as mono-cistron.

Since each one of the constructs contains either structural or non-structural region, the pseudo-virus just causes single-round infection. In terms of biosafety, our system and products that apply this system can be demonstrated even in the real world.

Background

RT-PCR, ELISA and neutrilization assay - these methods have been widely used to identify infection experience and its serotype. However, RT-PCR is valid only for 0 to 5 days after infection and ELISA and neutralization assay have problem with cost-efficiency.

Mobirise

Figure 1: Change in viral load and antibodies (Source: Guzman, M. G. et al., 2010)

Mobirise

Figure 2: Comparison of dengue detection system with existing ones

Experiment Overview

Our experiment consists of three parts: 1. Construction, 2. Pseudo-virus Production and 3. Pseudo-virus Infection. After three types of constructs are introduced into HEK293T cells, pseudo-viruses are produced. They are added to cultured Vero cells, and you can check the infection after a certain interval.

Mobirise

Figure 3: Experiment Overview (iGEM Tokyo Tech 2018)

1. Construction

For the pseudo-virus production, we prepared structural gene, and non-structural gene with fluorescence protein gene.

About structural gene, capsid (C), membrane (prM) and envelope (E) are necessary for the formation of viral structure. We prepared pCAG-C and pCAG-prM-E for Serotype I to IV.

About non-structural gene with fluorescence protein gene, we prepared EGFP-FMDV2a, DsRed-Express-FMDV2a, ZsYellow-FMDV2a and AmCyan-FMDV2a, and inserted each of them to non-structural genes of dengue virus.

Mobirise

Figure 4: Construct line-up and original genes derived from dengue virus

2. Pseudo-virus Production

We introduced pCAG-C, pCAG-prM-E and FP-FMDV2a (FP: Fluorescence Protein) into HEK293T cells. After cell culture for about 2 days, we collect the supernatant that contains pseudo-viruses produced from HEK293T cells.

Mobirise

Figure 5: Basic flow of transfection and pseudo-virus production

3. Pseudo-virus Infection and Functional Evaluation of Pseudo-virus

After collecting pseudo-viruses from HEK293T cells, we added them to Vero cells. When they can successfully infect the cells, the enclosed fluorescence protein gene is coded and we tried to estimate the amount by measuring the fluorescence intensity.

Since we split up the structural region and non-structural region, the pseudo-viruses produced in our system can infect host cells only once. Thus, it will not spread out of the system and will not be harmful.

Mobirise

Figure 6: Basic flow of pseudo-virus infection and how fluorescence protein works

Note: Validated Parts (Silver Medal Criteria)

DENV2 C, EGFP-FMDV2a and DsRed-Express-FMDV2a are essential for pseudo-virus production. As one of the structural genes, DENV2 C plays an important role in virus structural formation. EGFP-FMDV2a and DsRed-Express-FMDV2a are enclosed in pseudo-virus and programmed to code functional fluorescence proteins after infecting the host cells.

To get specific sequence and charanterization information, please see the following Parts Pages.

Parts Page: DENV2 C

Parts Page: EGFP-FMDV2a

Parts Page: DsRed-Express-FMDV2a

Mobirise

Figure 7: List of validated parts and the features

Progress of Our Experiment (~Oct. 17th, 2018)

Our team successfully validated that all the necessary constructs are produced by using electrophoresis (please refer to our Parts Pages).

After completing the construction, our team shifted to the transfection into HEK293T cells for pseudo-virus production. Using lipofection, the constructs have been already introduced into the cells and the pseudo-viruses will be collected in a few days.

After collecting the pseudo-viruses, they will be added to cultured Vero cells. Our team will test the infectivity by measuring the fluorescence intensity at the end.

The whole results will be announced in Giant Jamboree, so please do not miss it!

Our Goal

We successfully validated that the pseudo-viruses are produced, and they can infect the host cells. Making the most of our system and lab experience, our team will make a kit to identify which type your target patient was infected with before.

As you can see in Fig. 8, if the patient was infected with type II virus before, type II-specific antibodies in blood serum decrease the infectivity of type II pseudo-virus. As a result, fluorescence protein programmed in the pseudo-virus would not be coded so much due to the decrease in the number of infectious viruses.

Thus, you can identify the infection experience and its type by measuring or observing the fluorescence intensity for each type/color.

Mobirise

Figure 8: Mechanism of colorimetric type detection system with different fluorescence proteins

Feedback to Modeling

Since our detection system enables us to collect more samling data in many areas quickly and with low cost, our prediction model can be more precise thanks to the increase in the consensus time-scale data of dengue-affected patients and serotype ratio.

Biosafety

As you can see in Fig. 9, on native virus genome, structural genes and non-structural genes are integrated on the same sequence. Thus, the whole genome are replicated and that make viruses possible to replicate themselves in host cells.

However, as you can see our construct design in Fig. 10, structural and non-structural regions are splitted so that the pseudo-virus cannot replicate themselves in host cells because RNA polymerase from non-structural V gene cannot replicate structural genes.

To sum up, our system starts and ends in one place and doesn't harm environment.

Mobirise

Figure 9: Infection process of native virus and production of infectious pseudo-virus

Mobirise

Figure 10: Infection process of our pseudo-virus for validating biosafety

Reference

National Institute of Infectious Diseases HP

Scitable: Host Response to the Dengue Virus

Neutralization Assay for Zika and Dengue Viruses by Use of Real-Time-PCR-Based Endpoint Assessment.

WHO: Dengue control

Protocol



InterLab Page Modeling

Address

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Contacts

Email: igem2018tokyotech@gmail.com

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