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                             <a href="https://2021.igem.org/Team:Shanghai_high_school/Experiments">Experiments</a>
 
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         <h1>Result</h1>
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         <section class="article p-t-54 p-b-54">
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        <!--ABSTRACT-->
             <section>
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         <section class="article p-t-96 p-b-30">
                <h1 class="title">Plasmid Construction</h1>
+
             <h1 class="title" style="margin: 0 0 64px !important;">ABSTRACT</h1>
 +
            <p style="font-size: 20px !important;">A new oral vaccine against rotavirus can help children get antibodies
 +
                against rotavirus in a needle-free way. It can enter the child's body in the form of oral liquid, capsule,
 +
                drink, etc. The oral form can facilitate rotavirus patients' treatment and prevent children from developing
 +
                resistance. In this project, the construction and characterization of the plasmids for oral rotavirus
 +
                vaccine production were completed in order to prepare the target vaccine. Genes for the β subunit of the
 +
                heat-labile enterotoxin (LTB) from E. coli and the immunodominant outer core protein VP7 were cloned and
 +
                expressed as a fusion protein. After being introduced into Bacillus subtilis, the plasmid could recognize
 +
                rotavirus and express antigens LTB-VP7 successfully. This work here set the stage for the future development
 +
                of the oral rotavirus vaccine.</p>
 +
        </section>
  
                <section>
+
        <!--PROMOTIONAL VIDEO-->
                    <h2 class="title2">Polymerase Chain Reaction</h2>
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        <section class="promotional article p-b-54 p-t-96">
 
+
            <h1 class="title">PROMOTIONAL VIDEO</h1>
                    <p>A PCR verification was performed to confirm whether the synthesized plasmid pET28a-VP7-LTB contains
+
            <video src="https://static.igem.org/mediawiki/2021/f/f9/T--Shanghai_high_school--video_index_1.mp4"
                        the correct gene sequences. According to Snap Gene data (Fig 1&2), gene for VP7 has 846 nucleotides
+
                  controls preload="metadata"
                        (nt) and VP7-LTB has 1242 nt. Agarose gel electrophoresis was used to assess the PCR’s result.
+
                  class="m-t-24"
                        According to the 15000 bp DNA marker, the PCR amplified DNA fragments possess the desired right
+
                  style="width: 100%; height: 100%">
                        size. This verification was critical for our subsequent experiments—if the original plasmid was
+
             </video>
                        defective, every other plasmid constructed based on its DNA would have no chance of being right.</p>
+
 
+
                    <div class="img-container m-t-18">
+
                        <img src="https://static.igem.org/mediawiki/2021/0/06/T--Shanghai_high_school--img_results_1.jpg" alt="" style="width: 55%">
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                        <span class="figure">Figure 1 The genetic information of vp7.</span>
+
                    </div>
+
 
+
                    <div class="img-container">
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                        <img src="https://static.igem.org/mediawiki/2021/5/5a/T--Shanghai_high_school--img_results_2.jpg" alt="" style="width: 75%">
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                        <span class="figure">Figure 2 The genetic information for fusion protein of Vp7 and Ltb.</span>
+
                    </div>
+
 
+
                    <div class="img-container m-t-12">
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                        <img src="https://static.igem.org/mediawiki/2021/4/42/T--Shanghai_high_school--img_results_3.jpg" alt="" style="width: 65%">
+
                        <span class="figure">Figure 3 PCR verification of pET28a-VP7-LTB.</span>
+
                    </div>
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                </section>
+
 
+
                <section class="p-t-30">
+
                    <h2 class="title2">Restriction enzyme digestion</h2>
+
 
+
                    <p>At this point we had two empty plasmid vectors (pET28a and pHT43-his) and two DNA fragments
+
                        (<i>vp7</i> and <i>Ltb</i>) awaiting to be inserted. To that end, we used 5 μL BamHI (a restriction
+
                        enzyme) to digest and linearize the plasmid, making a specific site for fragment insertion . When
+
                        BamHI was mixed with the plasmid vectors in a 10.5 μL Cusmart solution that created the chemical
+
                        environment for the enzyme to function, it targeted its unique recognition sequence 5’-GGATCC-3’,
+
                        cut this site open, and linearized the plasmid (Fig 4). </p>
+
 
+
                    <div class="half m-t-18">
+
                        <div class="left">
+
                            <img src="https://static.igem.org/mediawiki/2021/f/f7/T--Shanghai_high_school--img_results_4.jpg" alt="" style="width: 90%">
+
                        </div>
+
                        <div class="right">
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                            <img src="https://static.igem.org/mediawiki/2021/1/1e/T--Shanghai_high_school--img_results_5.jpg" alt="" style="width: 90%">
+
                        </div>
+
                    </div>
+
                    <span class="figure">Figure 4 Restriction enzyme digestion sites of BamHI for cloning.</span>
+
 
+
                    <ul class="normal m-t-18">
+
                        <li>
+
                            <p>pET28a</p>
+
                            <p>Once digestion completed, we set up gel electrophoresis again to assess the result. According
+
                                to the gel (Fig 5), the first three lanes was DNA marker ladder, pET28a after digestion, and
+
                                the control, respectively. The control was the uncut plasmid pET28a and showed two DNA bands
+
                                in nicked DNA and supercoiled DNA confirmation, respectively. Super coiled was the native
+
                                conformation of a plasmid extracted from a bacterium that is highly compacted and is able to
+
                                migrate faster through a gel. Therefore, it presented smaller band than that of the
+
                                equivalently sized within the ladder. Nicked DNA was also commonly found in uncut plasmid,
+
                                which migrates even slower than linear DNA. Now, on the second lane was our linear pET28a
+
                                with 5639 nt. The place of band in the gel was consistent with its real size. </p>
+
 
+
                            <div class="img-container">
+
                                <img src="https://static.igem.org/mediawiki/2021/a/a6/T--Shanghai_high_school--img_results_27.jpg" alt="" style="width: 80%">
+
 
+
                                <span class="figure">Figure 5 The digestion of pET28a.</span>
+
                            </div>
+
                        </li>
+
                        <li>
+
                            <p>pHT43-His</p>
+
                            <p>We did the same digestion of pHT43-His. On the following image (Fig 6), lanes 2 to 7 were the
+
                                linearized plasmids and the last was the original supercoiled and nicked DNA. It can be
+
                                identified that the DNA was around 8000 bp, which was consistent to pHT43-His’s standard
+
                                size-8101 bp. Unlike the one clear band of linear DNA shown in figure 5, many additional
+
                                vague but distinguishable smaller bands can be found in figure 6. One probable explanation
+
                                to this might be the plasmid in each sample were digested incompletely, leading to
+
                                additional bands. Those stayed in supercoiled or circular conformation and had a larger
+
                                migration speed. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/c/c8/T--Shanghai_high_school--img_results_8.jpg" alt="" style="width: 80%">
+
 
+
                                <span class="figure">Figure 6 The digestion of pHT43-His.</span>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </section>
+
 
+
                <section>
+
                    <h2 class="title2">Conclusion</h2>
+
 
+
                    <p>The two gel images demonstrated that we had successfully digested the plasmid vectors pET28a and
+
                        pHT43-his. According to the standard ladder, linearized DNAs are consistent with their size and
+
                        distinctively different to the controls. </p>
+
                </section>
+
 
+
                <section class="p-t-30">
+
                    <h2 class="title2">NEBuider HiFi DNA Assembly Reaction</h2>
+
 
+
                    <p>NEBuider HiFi DNA Assembly is an effective method for the high-fidelity assembly of multiple DNA
+
                        fragments. In our project, we used this technique to insert VP7 and VP&-LTB’s DNA to the linearized
+
                        plasmid vectors through assembling both 5’ and 3’ restriction enzyme mismatches. In the first step
+
                        (Fig 7), a 5’ to 3’ exonuclease activity created single stranded 3’ overhangs. These complementary
+
                        sequences then annealed, creating the double stranded DNA of interest. A high-fidelity DNA
+
                        polymerase then extended the 3’ ends, filling in the gaps, and a DNA ligase sealed the remining
+
                        nicks. The end products were four complete circular plasmids-pET28a-VP7, pET28a-VP7-LTB,
+
                        pHT43-His-VP7 and pHT43-His-VP7-LTB—that could be used for direct transformation. </p>
+
 
+
                    <div class="img-container m-t-18">
+
                        <img src="https://static.igem.org/mediawiki/2021/f/f6/T--Shanghai_high_school--img_results_9.jpg" alt="" style="width: 70%">
+
 
+
                        <span class="figure">Figure 7 The depiction of NEBuider HiFi DNA Assembly Reaction.</span>
+
                    </div>
+
                </section>
+
 
+
                <section class="p-t-30">
+
                    <h2 class="title2">Colony PCR</h2>
+
 
+
                    <p>After completing restriction enzyme digestion and ligation, we had transformed the new plasmids into
+
                        different cultures of <i>E. coli</i> BL21 for cloning. Additionally, we also transformed the empty
+
                        plasmid vector pHT43-HIS into WB800N through electroporation instead of normal processes. We then
+
                        performed a colony PCR to verify if the two types of bacteria contain the target plasmids. </p>
+
 
+
                    <ul class="normal m-t-18">
+
                        <li>
+
                            <p>pET28a-VP7 & pET28a-VP7-LTB</p>
+
                            <p>To verify plasmid transformation, we extracted 1 μL of DNA template from both the BL21
+
                                culture containing pET28a-VP7 and the other containingpET28a-VP7-LTB, and mixed the solution
+
                                with primers, DNA polymerase, and ddH<sub>2</sub>O. According to the agarose gel
+
                                electrophoresis image
+
                                (Fig 8), using with a 2000bp DNA ladder, we were able to identify that the target genes of
+
                                the correct sizes have been successfully amplified. Sequence VP7 had 846 nt, which was
+
                                parallel to the data, and same was for VP7-LTB that had 1242 nt. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/4/49/T--Shanghai_high_school--img_results_10.jpg" alt="" style="width: 35%">
+
 
+
                                <span class="figure">Figure 8 PCR verification of <i>E. coli</i> BL21 containing pET28a-VP7 and pET28a-VP7-LTB.</span>
+
                            </div>
+
                        </li>
+
                        <li>
+
                            <p>pHT43-His-VP7 & pHT43-His-VP7-LTB</p>
+
                            <p>We expected these two plasmids to be inserted into WB800N at the end of the project. However,
+
                                considering that WB800N is Gram-positive, we suspect whether they are able to be entered at
+
                                all. For this reason, we first transformed the plasmids into <i>E. coli</i> BL21, a
+
                                Gram-negative
+
                                bacterium with substantially thinner cell wall, to test the feasibility, and performed a
+
                                colony PCR using 1 μL of the solution containing the cell as DNA template. As a result, the
+
                                gel image (Fig 9&10) clearly demonstrates that our target genes with correct size have been
+
                                amplified from the cell’s DNA. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/a/aa/T--Shanghai_high_school--img_results_11.jpg" alt="" style="width: 35%">
+
 
+
                                <span class="figure">Figure 9 PCR verification of <i>E. coli</i> BL21 containing pHT43-His-VP7.</span>
+
                            </div>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/6/6c/T--Shanghai_high_school--img_results_12.jpg" alt="" style="width: 35%">
+
 
+
                                <span class="figure">Figure 10 PCR verification of <i>E. coli</i> BL21 containing pHT43-His-VP7-LTB.</span>
+
                            </div>
+
                        </li>
+
                        <li>
+
                            <p>pHT43-His</p>
+
                            <p>In the previous experiments, pHT43-His had been transferred into WB800N by electroporation,
+
                                which opened up temporary pores on host’s membrane to facilitate the entry of the plasmid.
+
                                Again, a colony PCR was used to verify the transformation using 1 μL of DNA template from
+
                                the host. The gel image with a 2000 bp DNA ladder (Fig 11) identified that our pHT43-His
+
                                sequence had been successfully amplified from the solution. Unlike BL21’s plasmid
+
                                transformation gel results, WB800N’s showed additional vague gene bands whose bp values
+
                                deviate from the standard. This was because, during PCR, not all DNA from the template was
+
                                paired with the primers; the remaining DNA may paired with random gene sequences, which lead
+
                                to various sizes. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/e/e8/T--Shanghai_high_school--img_results_13.jpg" alt="" style="width: 35%">
+
 
+
                                <span class="figure">Figure 11 PCR verification of WB800N containing pHT43.</span>
+
                            </div>
+
                        </li>
+
                        <li>
+
                            <p>PHT43-His-VP7 & PHT43-His-VP7-LTB (WB800N)</p>
+
                            <p>A colony PCR was conducted to verity the plasmid transformation of PHT43-His-VP7 &
+
                                PHT43-His-VP7-LTB into bacteria WB800N. According to the gel electrophoresis image, we
+
                                collected 2 samples of WB800N containing PHT43-His-VP7 and 1 sample of WB800N containing
+
                                PHT43-His-VP7-LTB. Again, the band of VP7 is at 846 bp and that of VP7-LTB presents at 1242
+
                                bp. Therefore, the location of each gene bands on the following image is consistent with the
+
                                values, which demonstrates successful transformations. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/e/e4/T--Shanghai_high_school--img_results_14.jpg" alt="" style="width: 45%">
+
 
+
                                <span class="figure">Figure 12 PCR verification of WB800N containing PHT43-His-VP7 & PHT43-His-VP7-LTB</span>
+
                            </div>
+
                        </li>
+
                    </ul>
+
                </section>
+
 
+
                <section>
+
                    <h2 class="title2">Conclusion</h2>
+
 
+
                    <p>All gel images are the proofs that our target plasmids have been amplified from the DNA template,
+
                        which indicates that they have been successfully connected to the cell’s DNA. Furthermore, It can be
+
                        identified that some lanes have gene bands substantially thicker than the others. This tells us that
+
                        the amount of DNA amplified in each sample is different. This is caused by the difference between
+
                        cell cultures from which the DNA template is extracted from. Whether the template is exactly 1 μL
+
                        can also influence the result.</p>
+
                </section>
+
 
+
                <section class="p-t-30">
+
                    <h2 class="title2">Inducible expression</h2>
+
 
+
                    <ul class="normal">
+
                        <li>
+
                            <h3 class="title3">OD<sub>600</sub> growth curve</h3>
+
                            <img src="https://static.igem.org/mediawiki/2021/f/f1/T--Shanghai_high_school--img_results_15.jpg" alt="" style="width: 70%">
+
                        </li>
+
                        <li class="m-t-18">
+
                            <h3 class="title3">The Curve of OD<sub>600</sub> Concentration</h3>
+
                            <img src="https://static.igem.org/mediawiki/2021/6/66/T--Shanghai_high_school--img_results_28.jpg" alt="" style="width: 90%">
+
 
+
                            <p>In general, our experiments went very orderly. At the beginning of the experiment, we
+
                                prepared the IPTG. Then, after adding the IPTG into the PET28a-VP7-LTB sample, we started to
+
                                wait for the strain to grow. The strain grew well and the experiment was very successful.
+
                                You can see that here is a picture of the OD<sub>600</sub> growth curve, in which the
+
                                bacteria firstly
+
                                slow growth, ushered in rapid growth after reaching about 3, growth again becomes slow.
+
                                Thus, bacterial culture is very successful.</p>
+
                        </li>
+
                        <li class="m-t-18">
+
                            <h3 class="title3">SDS PAGE</h3>
+
                            <p>Figure 13 shows the protein expression of <i>E. coli</i> with SDS-PAGE. SDS-PAGE is a gel
+
                                electrophoresis technique used for protein separation based on their molecular weight. Our
+
                                purpose was to identify the presence of new proteins and confirm whether they are our
+
                                proteins of interest --- VP7 and VP7-LTB. </p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/9/9b/T--Shanghai_high_school--img_results_21.jpg" alt="" style="width: 80%">
+
 
+
                                <span class="figure">Figure 13(a), SDS-PAGE of BL21 protein expression</span>
+
                            </div>
+
 
+
                            <p>There are supernatants and precipitates. The precipitates are usually debris of the cell such
+
                                as organelle. The supernatants are usually protein, carbohydrates, nucleic acids of the
+
                                bacteria. Usually, the soluble protein should appear in the supernatant. However, it
+
                                appeared in the precipitates. We suggest that the virus-induced proteins existed in the form
+
                                of insoluble inclusion body. </p>
+
 
+
                            <p>Compared the samples of the precipitates and the supernatants at 0 h and other times of the
+
                                figure on the left, we could see an extra band that located below 50 kD. If there are extra
+
                                bands, it is highly possible that they are our target proteins. Due to the presence of IPTG,
+
                                the amount of proteins could be limited. We should see thinner bands in the samples, which
+
                                are collected after adding IPTG. However, the extra bands are thicker than the parallel
+
                                bands which are at the 0 h. This phenomenon demonstrates that the thicker bands could be our
+
                                target proteins. The masses of the bands match pretty well with the theoretical molecular
+
                                weight of VP7-LTB. </p>
+
 
+
                            <p>Compared the left figure and the middle one, we could find that VP7-LTB induced by 1nM of
+
                                IPTG expressed better than that induced by 2nM of IPTG. Because IPTG may make the bacteria
+
                                less active, 1nM is a suitable concentration. </p>
+
 
+
                            <p>Compared the right figure with the other one, we could find that the adding of LTB stimulates
+
                                the expression of VP7.</p>
+
 
+
                            <div class="img-container m-t-18">
+
                                <img src="https://static.igem.org/mediawiki/2021/a/a4/T--Shanghai_high_school--img_results_22.jpg" alt="" style="width: 80%">
+
 
+
                                <span class="figure">Figure 13(b), SDS-PAGE of WB800n protein expression</span>
+
                            </div>
+
 
+
                            <p>Unfortunately, after IPTG induced expression, WB800n did not find the target protein from
+
                                SDS-PAGE, and there were many hetero-proteins. In conclusion, the protein expression of <i>Bacillus
+
                                    subtilis</i> failed. The picture above is the SDS-PAGE of WB800n.</p>
+
                        </li>
+
                        <li class="m-t-18">
+
                            <h3 class="title3">Western Blot</h3>
+
 
+
                            <section>
+
                                <h4 class="title4">BL21</h4>
+
                                <p>These graphs show the relationship between time and protein expression of BL21. The
+
                                    horizontal axis represents to the duration time of induced protein expression, and the
+
                                    vertical axis represents to the Gray value which means the amount of protein expression.
+
                                    The
+
                                    higher the gray value is, the higher the protein expressed.</p>
+
                                <p>The gray value are calculated by “ImageJ” which is a software used to show protein
+
                                    expression
+
                                    the by calculating the amounts of black pixels in the pictures.</p>
+
 
+
                                <br>
+
                                <p>Figure 14 VP7-LTB expression with1mM IPTG.</p>
+
                                <img src="https://static.igem.org/mediawiki/2021/0/0e/T--Shanghai_high_school--img_results_23.jpg" alt="" style="width: 80%">
+
                                <p>Conclusion: VP7 LTB was successfully induced to express and was present as inclusion
+
                                    bodies,
+
                                    which increased gradually with increasing induction time.</p>
+
 
+
                                <br>
+
                                <p>Figure 15 VP7-LTB expression with 2mM IPTG.</p>
+
                                <img src="https://static.igem.org/mediawiki/2021/5/59/T--Shanghai_high_school--img_results_24.jpg" alt="" style="width: 80%">
+
                                <p>Conclusion: VP7 LTB was successfully induced to express and was present as inclusion
+
                                    bodies,
+
                                    which gradually increased in expression with increasing induction time, but the
+
                                    heteroprotein appeared so the optimal induction conditions were: 1 m mole IPTG for 6 h
+
                                    induction.</p>
+
 
+
                                <br>
+
                                <p>Figure 16 VP7 1mM</p>
+
                                <img src="https://static.igem.org/mediawiki/2021/f/fd/T--Shanghai_high_school--img_results_25.jpg" alt="" style="width: 80%">
+
 
+
                                <br>
+
                                <p>Figure 17 VP7 expression with 2 mM IPTG. </p>
+
                                <img src="https://static.igem.org/mediawiki/2021/a/a9/T--Shanghai_high_school--img_results_26.jpg" alt="" style="width: 80%">
+
                                <p>Conclusion: VP7 was present in both the supernatant and sediment, but predominantly as
+
                                    inclusion bodies in the sediment.</p>
+
 
+
                                <br>
+
                                <p>The researchers believed that the two phenomena on the above tables could be explained as
+
                                    bellow.</p>
+
                                <ol>
+
                                    <li>
+
                                        <p>The appearance of heteroprotein</p>
+
                                        <p>For the presence of a hybrid protein, we believe that there are two factors.
+
                                            First,
+
                                            the nonspecific binding of the His amino acid tag leads to the presence of some
+
                                            non-target proteins. Second, there may be some enzymes that degrade a portion of
+
                                            the
+
                                            protein, leading to the appearance of some target protein fragments of lower
+
                                            mass.</p>
+
                                    </li>
+
                                    <li>
+
                                        <p>The production of the target protein without IPTG induction in the 0 h sample</p>
+
                                        <p>The reason for this is the background expression of VP7. It means that BL21, the
+
                                            bacteria itself, have the possibility to express target protein spontaneously
+
                                            even
+
                                            without IPTG induction.</p>
+
                                    </li>
+
                                </ol>
+
                            </section>
+
 
+
                            <section class="m-t-18">
+
                                <h4 class="title4">WB800n</h4>
+
                                <p>The protein expression of WB800n failed. SDS-PAGE did not find the target protein.
+
                                    Western blot was performed, and there was no target protein. Besides, a large number of
+
                                    hetero-proteins appeared in the Western blot of wb800n.</p>
+
                            </section>
+
 
+
                            <section class="m-t-18">
+
                                <h4 class="title4">Future plan</h4>
+
 
+
                                <p>For BL21, in order to increase the expression of target proteins, we plan to optimize
+
                                    their expression conditions, such as temperature, time, pH value, IPTG concentration and
+
                                    so on.</p>
+
 
+
                                <p>For WB800n, we needed to analyze why it failed to express. After a successful protein
+
                                    expression, perhaps we would try to make it as through secretory protein expression.</p>
+
                            </section>
+
                        </li>
+
                    </ul>
+
                </section>
+
             </section>
+
 
         </section>
 
         </section>
 
     </div>
 
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Latest revision as of 13:57, 11 October 2021

ABSTRACT

A new oral vaccine against rotavirus can help children get antibodies against rotavirus in a needle-free way. It can enter the child's body in the form of oral liquid, capsule, drink, etc. The oral form can facilitate rotavirus patients' treatment and prevent children from developing resistance. In this project, the construction and characterization of the plasmids for oral rotavirus vaccine production were completed in order to prepare the target vaccine. Genes for the β subunit of the heat-labile enterotoxin (LTB) from E. coli and the immunodominant outer core protein VP7 were cloned and expressed as a fusion protein. After being introduced into Bacillus subtilis, the plasmid could recognize rotavirus and express antigens LTB-VP7 successfully. This work here set the stage for the future development of the oral rotavirus vaccine.

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