Difference between revisions of "Team:Peking/Description"

 
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            <title>Overview</title>
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        <title></title>
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            <meta name="description" content="Wiki of Peking iGEM 2016" />
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        <meta name="description" content="Wiki of Peking iGEM 2016" />
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            <meta name="author" content="Li Jiamian & Wang Yuqing">
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        <meta name="author" content="Li Jiamian & Wang Yuqing"/>
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         </div>
 
         </div>
 
         <!--/Navigation -->
 
         <!--/Navigation -->
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                 <div class="twelve columns centered text-center">
 
                 <div class="twelve columns centered text-center">
 
                     <h1>Description</h1>
 
                     <h1>Description</h1>
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                     <p class="title1" style="text-align:center">Description</p>
+
                     <p class="title1" style="text-align:center">In this section, you could find what we achieved during this summer. For detailed lab results, models or human practices, please use the navigation bar for a quick webpage-redirecting.</p>
 
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                 </div>
 
             </div>
 
             </div>
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         </div><!-- Page Title End-->
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        <!-- Page Title End-->
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                                    <h4><a href="javascript:void(0);" onclick="naver('A')">To&nbsp;A</a></h4>
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('B')">To&nbsp;B</a></h4>
 +
                                    <h4><a href="javascript:void(0);" onclick="naver('C')">To&nbsp;C</a></h4>
 +
                                </div>
 +
                            </div>
 +
                        </div>
 +
                       
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 +
                       
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                        <div class="nine columns">
 +
                           
 +
                            <a id="A"></a>
 +
                            <div class="texttitle">Project Achievements</div>
 +
                            <br/>
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">1.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Constructed a multifunctional protein of interest via molecular biological methods, and introduced the constructed plasmids into the engineered bacteria for protein expression. <a href="https://2016.igem.org/Team:Peking/Basic_Part"/>(Learn more)</a></p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">2.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Searched for methods and the best conditions for the extraction of each protein. <a href="https://2016.igem.org/Team:Peking/Notebook/Protocol:purification_of_recombinant_proteins"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">3.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Demonstrated a quick and stable crosslinking process of Triple SpyTag-SUP and Triple SpyTag-mSA with Triple SpyCatcher via covalent bonds. We also optimized this reaction concerning the relevant parameters such as temperature, pH, etc.. <a href="https://2016.igem.org/Team:Peking/Crosslinking"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">4.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Demonstrated effective adsorption of uranyl ions by monomeric Triple SpyTag-SUP or polymer network containing the SUP module under a number of conditions. The adsorption was highly efficient and fast, not only under experimental conditions but also in simulated seawater or lake water containing uranium pollution. <a href="https://2016.igem.org/Team:Peking/Uranyl-adsorption"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">5.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Attached biotin to amino-coated magnetic beads and achieved clearance of the polymer network formed via the crosslinking of Triple SpyTag-SUP and Triple SpyTag-mSA with Triple SpyCatcher with a magnet. <a href="https://2016.igem.org/Team:Peking/Clearance"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">6.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Set up a signal peptide library and screened for optimally suited signal peptides in order to efficiently secrete the proteins of interest. We found two signal peptides of high efficiency - those derived from OmpA and LtIIb. <a href="https://2016.igem.org/Team:Peking/Secretion"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">7.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Used all the above-mentioned experiments together to demonstrate that the complete Uranium Reaper system, consisting of Triple SpyTag-SUP, Triple SpyTag-mSA, Triple SpyCatcher and biotin-coated magnetic beads, could effectively handle uranium pollution under simulated real-life conditions in about 2 hours. We aimed to optimize this strategy and hoped it could be implemented as a uranyl removal kit. <a href="https://2016.igem.org/Team:Peking/Proof"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">8.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We exchanged the Triple SpyTag-SUP monomer for Triple SpyTag-LBP or Triple SpyTag-CBP, and tried using the same strategy to adsorb lead and cadmium. The results were remarkable, clearly demonstrating that the Uranium Reaper strategy has much potential to be expanded to other heavy metals. <a href="https://2016.igem.org/Team:Peking/Demonstrate"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                            <br/>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">&nbsp;</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <figure>
 +
                                        <p style="text-align:center;"><img style="width:90%;" src="https://static.igem.org/mediawiki/2016/a/af/T--Peking--image_demotable1.png" alt=""/></p>
 +
                                        <figcaption style="text-align:left;">
 +
                                           
 +
                                        </figcaption>
 +
                                    </figure>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">&nbsp;</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Even though the efficiency of the Uranium Reaper system may be somewhat lower than current methods, it could certainly be optimized through further development work. Importantly, Uranium Reaper is much better in other aspects. In the future, we plan to optimize the entire Uranium Reaper strategy in order to enhance the adsorption efficiency.</p>
 +
                                </div>
 +
                            </div>
  
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">&nbsp;</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>For an overall view of our project, please redirect to <a href="https://2016.igem.org/Team:Peking/Description"/>Overview Page</a> or <a href="https://2016.igem.org/Team:Peking/Design"/>Design Page</a>. Links to detailed lab results could also be found on these pages.</p>
 +
                                </div>
 +
                            </div>
  
  
−
Description
+
                           
−
Ever since the beginning of life, compartment has been playing a crucial rule in biological systems. The famous Miller-Urey experiment shows that inorganic molecules can transform into organic substances under extreme conditions, for example lightening. However, homogeneously distributed organic matters are not enough for life to emerge. It is almost impossible that all conditions are proper in the entire primordial soup.
+
                           
−
 
+
                            <p>&nbsp;</p>
−
That (pause) is where the compartment comes in.
+
                           
−
 
+
                           
−
Only after coacervate droplet forms and organic molecules condense inside, a completely different environment can be attained within, thus enabling the emergence of bio-macromolecules, or in other word, making life possible.
+
                           
−
 
+
                           
−
In cells, compartmentalization is mainly achieved be all sorts of organelles, for instance, mitochondrion, chloroplast, lysosome etc. They take up three major roles: A, B, C
+
                           
−
 
+
                            <a id="B"></a>
−
Intuitively, for a organelle to sustain a stable compartment, it seems necessary to require a material boundary, more precisely, a membrane. Membrane-bound organelles are indeed common and stable, but from the perspective of synthesis, it is way too complicated. However, there are also non-membrane-bound organelles, for instance, stress granule, P granule and nucleolus. More importantly, their formation is guided by simple physical principals.
+
                           
−
 
+
                            <div class="texttitle">Beyond Experiment</div>
−
Then came the question that how can we synthase membraneless organelles. The process where material self-assemble into organelles is described as ‘phase separation’ according to physical chemistry, which is the conversion of a single-phase system into a multiphase system, much like how oil and water will demix from each other. In general, materials flow to regions with low chemical potential instead of low concentration. Finally, the components no longer distribute uniformly but form granules locally which are organelles in the cell.
+
                            <br/>
−
(图片2)
+
                            <div class="coll">
−
(动图3)
+
                                <div class="info">
−
That is to say, the main work to synthase an organelle is to fulfill phase separation in a cell. We take our inspiration from existing life systems. For example, stress granules and P bodies are formed by the interaction between mRNA and proteins. RNA and protein play a significant part in the phase separation in cells. IDR(Intrinsic Disordered Regions) are the symbol of massive phase separation in the cell. IDR interact with each other through the van der Waals force, electrostatic effect and hydrophobic effect between the residues of amino acids, while RNA get together with proteins through massive bases and ribose. Previous work has been done to reproduce natural phase separation by connecting interaction modules like SUMO/SIM, SH3/PRM, constructing granules in the cell.
+
                                    <div class="ordi">1.</div>
−
(图片4)
+
                                </div>
−
Summarizing these examples and according to physical principles, interaction between modules and multivalence are essential for phase separation. In general, interaction binds the parts together and multivalence makes larger assemblies, which are two guidance of our design.
+
                                <div class="content">
−
(图片5)
+
                                    <p>We submitted 53 high-quality and well-characterized Standard BioBricks, including a set of derivatives of Triple SpyTag and Triple SpyCatcher, such as the Triple SpyTag-SUP and Triple SpyTag-mSA. <a href="https://2016.igem.org/Team:Peking/Basic_Part"/>(Learn more)</a></p>
−
 
+
                                </div>
−
 
+
                            </div>
−
 
+
                           
−
 
+
                            <div class="coll">
−
 
+
                                <div class="info">
−
            </div> <!-- page-content End-->
+
                                    <div class="ordi">2.</div>
−
        </div> <!-- Content End-->
+
                                </div>
−
       
+
                                <div class="content">
−
       
+
                                    <p>We developed a special software which could be used to calculate the molecular weight distribution of protein polymers using Flory’s theory. The results of testing have demonstrated that the software is accurate and useful. <a href="https://2016.igem.org/Team:Peking/Software"/>(Learn more)</a> </p>
−
       
+
                                </div>
−
          
+
                            </div>
−
          
+
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">3.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We visited experts from the College of Chemistry and Molecular Engineering and School of Physics of Peking University, respectively, to learn about the current situation surrounding uranium pollution in the real world and how people could control the situation. After finishing the main work, we presented them with the achievements of the project and got their feedback. <a href="https://2016.igem.org/Team:Peking/HP/consulting"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">4.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We did an interview with the Hunan Nuclear Geology 311 Brigade and gained thorough insights into the treatment of uranyl pollution used by the people on the firing line. This way we could compare the methods they were using with the Uranium Reaper strategy. <a href="https://2016.igem.org/Team:Peking/HP/Gold/311"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">5.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We helped and collaborated with other iGEM teams by guiding a new team (BHU_China), as well as discussing about project design and technical skills and sharing DNA materials (OUC-China, BIT-China, Tianjin, UCAS, Jinlin_China and BNU-China). <a href="https://2016.igem.org/Team:Peking/Collaborations"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">6.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We attended the CCiC (Central China iGEM Consortium), which is a large-scale competition-free jamboree of about 50 teams, providing participants with an opportunity for meaningful exchanges of ideas and problem solving. <a href="https://2016.igem.org/Team:Peking/Collaborations"/>(Learn more)</a> </p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                           
 +
                            <p>&nbsp;</p>
 +
                           
 +
                           
 +
                           
 +
                            <a id="C"></a>
 +
                            <div class="texttitle">Our future plan</div>
 +
                            <br/>
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">1.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We should reproduce all of the experiments that we have done this summer to make sure the results are credible.</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">2.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We will optimize the whole strategy to enhance the adsorption efficiency by changing pH, temperature, reaction time of crosslinking and clearance. (The efficiency is only about 60% without further optimization)</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">3.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>According to the results for the adsorption of 13nM uranyl, the polymer network exhibited a good ability in a simulated seawater environment. We could thus also look into other usage scenarios of Uranium Reaper, such as bio-mining and uranium enrichment.</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">4.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>Exchange of the SUP module for other functional proteins. For example, we could integrate proteins which could bind other heavy metals such as mercury so that the polymer network could be used to treat other kinds of pollution as well.</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">5.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>We could assemble enzyme systems behind the SpyTag backbone to create a production plant in vitro. In the protein polymeric network, the concentration of enzymes could be increased and the efficiency of biocatalysis may consequently also be enhanced.</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                            <div class="coll">
 +
                                <div class="info">
 +
                                    <div class="ordi">6.</div>
 +
                                </div>
 +
                                <div class="content">
 +
                                    <p>If we optimize the number of SpyTag or SpyCatcher modules per protein monomer, as well as the working concentrations of proteins, we may make protein-3D printing using the Spy Crosslinking Network come true.</p>
 +
                                </div>
 +
                            </div>
 +
                           
 +
                           
 +
                           
 +
                        </div><!--9 columns end-->
 +
                       
 +
                    </div>
 +
                   
 +
                   
 +
                   
 +
                   
 +
                    </div><!--row end-->
 +
            </section>
 +
         </div><!--12 columes end-->
 +
         </div><!--page-content end-->
 
          
 
          
 
          
 
          
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                     <ul class="copyright">
 
                     <ul class="copyright">
 
                         <!--<li>&copy; 2014 Sparrow</li> -->
 
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Latest revision as of 07:22, 14 October 2018

Description

In this section, you could find what we achieved during this summer. For detailed lab results, models or human practices, please use the navigation bar for a quick webpage-redirecting.

Project Achievements

1.

Constructed a multifunctional protein of interest via molecular biological methods, and introduced the constructed plasmids into the engineered bacteria for protein expression. (Learn more)

2.

Searched for methods and the best conditions for the extraction of each protein. (Learn more)

3.

Demonstrated a quick and stable crosslinking process of Triple SpyTag-SUP and Triple SpyTag-mSA with Triple SpyCatcher via covalent bonds. We also optimized this reaction concerning the relevant parameters such as temperature, pH, etc.. (Learn more)

4.

Demonstrated effective adsorption of uranyl ions by monomeric Triple SpyTag-SUP or polymer network containing the SUP module under a number of conditions. The adsorption was highly efficient and fast, not only under experimental conditions but also in simulated seawater or lake water containing uranium pollution. (Learn more)

5.

Attached biotin to amino-coated magnetic beads and achieved clearance of the polymer network formed via the crosslinking of Triple SpyTag-SUP and Triple SpyTag-mSA with Triple SpyCatcher with a magnet. (Learn more)

6.

Set up a signal peptide library and screened for optimally suited signal peptides in order to efficiently secrete the proteins of interest. We found two signal peptides of high efficiency - those derived from OmpA and LtIIb. (Learn more)

7.

Used all the above-mentioned experiments together to demonstrate that the complete Uranium Reaper system, consisting of Triple SpyTag-SUP, Triple SpyTag-mSA, Triple SpyCatcher and biotin-coated magnetic beads, could effectively handle uranium pollution under simulated real-life conditions in about 2 hours. We aimed to optimize this strategy and hoped it could be implemented as a uranyl removal kit. (Learn more)

8.

We exchanged the Triple SpyTag-SUP monomer for Triple SpyTag-LBP or Triple SpyTag-CBP, and tried using the same strategy to adsorb lead and cadmium. The results were remarkable, clearly demonstrating that the Uranium Reaper strategy has much potential to be expanded to other heavy metals. (Learn more)


 

 

Even though the efficiency of the Uranium Reaper system may be somewhat lower than current methods, it could certainly be optimized through further development work. Importantly, Uranium Reaper is much better in other aspects. In the future, we plan to optimize the entire Uranium Reaper strategy in order to enhance the adsorption efficiency.

 

For an overall view of our project, please redirect to Overview Page or Design Page. Links to detailed lab results could also be found on these pages.

 

Beyond Experiment

1.

We submitted 53 high-quality and well-characterized Standard BioBricks, including a set of derivatives of Triple SpyTag and Triple SpyCatcher, such as the Triple SpyTag-SUP and Triple SpyTag-mSA. (Learn more)

2.

We developed a special software which could be used to calculate the molecular weight distribution of protein polymers using Flory’s theory. The results of testing have demonstrated that the software is accurate and useful. (Learn more)

3.

We visited experts from the College of Chemistry and Molecular Engineering and School of Physics of Peking University, respectively, to learn about the current situation surrounding uranium pollution in the real world and how people could control the situation. After finishing the main work, we presented them with the achievements of the project and got their feedback. (Learn more)

4.

We did an interview with the Hunan Nuclear Geology 311 Brigade and gained thorough insights into the treatment of uranyl pollution used by the people on the firing line. This way we could compare the methods they were using with the Uranium Reaper strategy. (Learn more)

5.

We helped and collaborated with other iGEM teams by guiding a new team (BHU_China), as well as discussing about project design and technical skills and sharing DNA materials (OUC-China, BIT-China, Tianjin, UCAS, Jinlin_China and BNU-China). (Learn more)

6.

We attended the CCiC (Central China iGEM Consortium), which is a large-scale competition-free jamboree of about 50 teams, providing participants with an opportunity for meaningful exchanges of ideas and problem solving. (Learn more)

 

Our future plan

1.

We should reproduce all of the experiments that we have done this summer to make sure the results are credible.

2.

We will optimize the whole strategy to enhance the adsorption efficiency by changing pH, temperature, reaction time of crosslinking and clearance. (The efficiency is only about 60% without further optimization)

3.

According to the results for the adsorption of 13nM uranyl, the polymer network exhibited a good ability in a simulated seawater environment. We could thus also look into other usage scenarios of Uranium Reaper, such as bio-mining and uranium enrichment.

4.

Exchange of the SUP module for other functional proteins. For example, we could integrate proteins which could bind other heavy metals such as mercury so that the polymer network could be used to treat other kinds of pollution as well.

5.

We could assemble enzyme systems behind the SpyTag backbone to create a production plant in vitro. In the protein polymeric network, the concentration of enzymes could be increased and the efficiency of biocatalysis may consequently also be enhanced.

6.

If we optimize the number of SpyTag or SpyCatcher modules per protein monomer, as well as the working concentrations of proteins, we may make protein-3D printing using the Spy Crosslinking Network come true.