Difference between revisions of "Team:SIAT-SCIE/Results"

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           <p style="font-size: 20px"> We provide models aiming to provide better understanding of our project and result analysis</p>
 
           <p style="font-size: 20px"> We provide models aiming to provide better understanding of our project and result analysis</p>
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         <h1> The Structure and Domain of CjCas9 </h1>
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         <h1>1. The Structure and Domain of CjCas9 </h1>
 
         <p style="font-size: 20px"> To provide a better view of the structure and functional domain of CjCas9, we provide a 360-degree rotating graph of the protein with its sgRNA and target DNA. </p>
 
         <p style="font-size: 20px"> To provide a better view of the structure and functional domain of CjCas9, we provide a 360-degree rotating graph of the protein with its sgRNA and target DNA. </p>
 
              
 
              
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         <p style="font-size: 15px; margin-left: 150px;margin-right: 150px;"> <b>Figure.1 </b>Structural image of CjCas9 in complex with sgRNA(red) and target DNA(purple) sequence (with PAM AGAAACC). We have annotated the protein by color according to their specific functions[1]. The white REC1 domain and the grey REC2 domain form the REC (crRNA recognition) domain. The cyan RuvC domain, the blue PLL domain, the yellow WED domain and the incarnadine PI domain form the NUC(nuclease) domain. Further explanation about the functions of these region can be found at Yomada 2017.
 
         <p style="font-size: 15px; margin-left: 150px;margin-right: 150px;"> <b>Figure.1 </b>Structural image of CjCas9 in complex with sgRNA(red) and target DNA(purple) sequence (with PAM AGAAACC). We have annotated the protein by color according to their specific functions[1]. The white REC1 domain and the grey REC2 domain form the REC (crRNA recognition) domain. The cyan RuvC domain, the blue PLL domain, the yellow WED domain and the incarnadine PI domain form the NUC(nuclease) domain. Further explanation about the functions of these region can be found at Yomada 2017.
 
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         <p style="font-size: 20px">As natural kins to bacterial cell membranes, OMVs can be degraded easily while preserving the shape and bioactivity of sensitive Cas9 proteins within, as well as single guide RNAs (sg-RNAs). We expect this technique would open up new possibilities of in vitro genetic engineering, thus providing substantial aid in curing and preventing illnesses such as inflammatory bowel diseases by removing virulence genes from malignant bacteria with this technique.</p>
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         <p style="font-size: 20px"> The display is created using the free online software Jmol[1] to vistualize the 3D structure of CjCas9, with the help of PicGIF Lite to transform images into gif. </p>
 
          
 
          
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         <h1>Fusobacterium nucleatum</h1>
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         <h1> 2. Estimated Number of Cas9 Encapsulation by OMVs </h1>
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         <p style="font-size: 20px">Our project aims to test the efficiency of our system by applying it to knock out fadA gene of Fusobacterium nucleatum, a strain of bacteria that reside in human alimentary canal. </p>
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         <p style="font-size: 20px"> OMVs have diameters that vary from 20 to 250 nanometers[3], which allows it to carry great amount of substance. To provide a more statistical explanation of the Cas9 carrying ability of OMVs, we use a simulant model to calculate the amount of Cas9 proteins one OMV can carry. The approximate volume of CjCas9, approximately 700 nanometers cube(82x96x88), is determined by the bounding box volume obtained by Jmol. </p>
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         <p style="font-size: 20px">F. nucleatum is a gram-negative bacterium prevalently found in mammal oral cavity, and is frequently associated with oral inflammation diseases and various cancers (2).  Its virulence stems from its invasion of the human epithelial cells, which induces oncogenic gene expression. The main genetic culprit of its pathogenicity is its fadA gene, which is an adhesion virulence factor that insures the binding of F.nucleatum to the host epithelial cell, thereby enabling the bacterium to invading the host and causing inflammation and cancer. </p>
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         <p style="font-size: 20px"> In addition, as supplementary material for our choice in the type of Cas9s, we also estimated the number of SgCas9s[4] one OMV can cargo through the same method. The result shows an estimated bounding box volume of 1430 nanometers cube. The difference between the results is shown in Figure.2. As shown, CjCas9’s small size allows it to be carried in great amount during the transmission and is, therefore, more suitable to be used in OMV-mediated gene editing. </p>
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        <p style="font-size: 20px">F. nucleatum’s fadA gene is a congenial candidate for our project since, being gram-negative, F.nucleatum possesses abundant OMVs that are central to our designed system. Through knocking out the fadA gene, we are enabled to observe the efficacy of our system’s application in realistic setting.</p>
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        <p style="text-align: center"><img src="https://static.igem.org/mediawiki/2018/9/99/T--SIAT-SCIE--OMVrelationship.png" width="800px" height="400px"></p>
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        <p style="font-size: 20px"></p>
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        <p style="font-size: 15px; margin-left: 150px;margin-right: 150px;"> <b>Figure.2</b>Estimated quantity of Cas9s encapsulation by OMVs. The data is calculated assuming cuboid shape of Cas9 proteins and perfect sphere shape of OMVs.
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        </p>
 
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        <details>
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            <summary>Mechanism of FadA protein</summary>
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            <p style="text-indent: 20px;font-size: 20px; padding: 10px 10px 10px 10px;margin:40px 200px 0px 200px">The FadA protein is activated when its two forms combine and become internalized. The first form is a pre-FadA that is anchored in the cell membrane, whereas the second form is the mature FadA (mFadA) that is secreted out of F. nucleatum. When the two forms combine to form a complex, the protein is capable to help F. nucleatum bind to the host epithelial cell, thus allowing F. nucleatum embark on invading the host cells.</p>
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            <h3 style="margin: 20px 200px 30px 200px;font-size:30px">Overview (Fig. 1)</h3>
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              <p style="text-indent: 20px;font-size: 20px; padding: 10px 10px 10px 10px;margin:0px 200px 0px 200px">We will first express Cas9 and sgRNA in E.coli and then transport them to E.coli’s periplasm(Step 1). By then, they may be packaged by OMVs that bud off from E.coli’s outer membrane(Step 2). Those OMVs will be collected and mixed with our target bacteria, thereby allowing them to fuse with bacteria again, to release the Cas9 proteins and sgRNA(Step 3), and cleave the target gene (Step 4 & 5).  Afterwards, we will test whether the target gene is cleaved by Cas9.
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            </p>
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            <p style="text-align: center"><img src="https://static.igem.org/mediawiki/2018/3/30/T--SIAT-SCIE--SIAT_Description_Figure1.png" height="600px" width="900px"></p>
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        </details>
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      </article>
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<h1>Safety</h1>
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        <p style="font-size: 20px">Out of safety concerns, instead of using the pathogenic Fusobacterium nucleatum, we transform a section of FadA’s coding sequence — with sgRNA’s binding site — into E.coli to test our system’s efficiency.</p>
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Revision as of 03:44, 3 December 2018

We provide models aiming to provide better understanding of our project and result analysis

1. The Structure and Domain of CjCas9

To provide a better view of the structure and functional domain of CjCas9, we provide a 360-degree rotating graph of the protein with its sgRNA and target DNA.

Figure.1 Structural image of CjCas9 in complex with sgRNA(red) and target DNA(purple) sequence (with PAM AGAAACC). We have annotated the protein by color according to their specific functions[1]. The white REC1 domain and the grey REC2 domain form the REC (crRNA recognition) domain. The cyan RuvC domain, the blue PLL domain, the yellow WED domain and the incarnadine PI domain form the NUC(nuclease) domain. Further explanation about the functions of these region can be found at Yomada 2017.

The display is created using the free online software Jmol[1] to vistualize the 3D structure of CjCas9, with the help of PicGIF Lite to transform images into gif.

2. Estimated Number of Cas9 Encapsulation by OMVs

OMVs have diameters that vary from 20 to 250 nanometers[3], which allows it to carry great amount of substance. To provide a more statistical explanation of the Cas9 carrying ability of OMVs, we use a simulant model to calculate the amount of Cas9 proteins one OMV can carry. The approximate volume of CjCas9, approximately 700 nanometers cube(82x96x88), is determined by the bounding box volume obtained by Jmol.

In addition, as supplementary material for our choice in the type of Cas9s, we also estimated the number of SgCas9s[4] one OMV can cargo through the same method. The result shows an estimated bounding box volume of 1430 nanometers cube. The difference between the results is shown in Figure.2. As shown, CjCas9’s small size allows it to be carried in great amount during the transmission and is, therefore, more suitable to be used in OMV-mediated gene editing.

Figure.2Estimated quantity of Cas9s encapsulation by OMVs. The data is calculated assuming cuboid shape of Cas9 proteins and perfect sphere shape of OMVs.