Difference between revisions of "Team:BIT-China/Design"

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         .block-content-header{
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        .block-content-brief{
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            margin: 20px auto 10px;
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        .step-style{
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         }
 
</style>
 
</style>
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<div class="col-sm-12" style="padding: 0;padding-top:30px;background: url(https://static.igem.org/mediawiki/2016/4/45/T--BIT-China--content_bg.jpg)">
+
<div class="col-sm-12 clearfix" style="padding: 0;padding-top:30px;
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+
background: url(https://static.igem.org/mediawiki/2016/4/45/T--BIT-China--content_bg.jpg)">
 
     <div class="content-right" style="float: left;width:100%;padding: 10px;">
 
     <div class="content-right" style="float: left;width:100%;padding: 10px;">
 
         <div style="margin-left:220px;background: white;margin-top: 0.5em;margin-bottom:0.5em;padding: 1px;border-radius: 10px">
 
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                         alt="title" class="col-sm-8 col-sm-offset-2">
 
                         alt="title" class="col-sm-8 col-sm-offset-2">
 
                     <br>
 
                     <br>
−
                 </div><br>
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                 </div>
  
 
                 <!--问题描述-->
 
                 <!--问题描述-->
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                 <div class="problem-txt">
+
                 <div class="problem-txt col-sm-12">
 
                     <div class="problem-title">What is the problem?</div>
 
                     <div class="problem-title">What is the problem?</div>
 
                     <div>
 
                     <div>
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                         <img src="https://static.igem.org/mediawiki/2016/c/c1/T--BIT-China--Project--Design--ul_logo1.png"
+
                         <i class="fa fa-thumb-tack" aria-hidden="true"></i>
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                            alt="ul_logo1" width="18" height="18">
+
                        <span>Plasmid segragational instability has been the limit step for large-scale protein production and bioremediation. Antibiotic abuse or Stress Conditions for plasmid retention is not practical in this situation.</span>
−
                    <span>Plasmid segragational instability has been the limit
+
−
                        step for large-scale protein production and bioremediation.
+
−
                        Use of antibiotics for plasmid retention is not practical
+
−
                        in this situation.</span>
+
 
                     </div>
 
                     </div>
 
                     <div>
 
                     <div>
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                         <img src="https://static.igem.org/mediawiki/2016/c/c1/T--BIT-China--Project--Design--ul_logo1.png"
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                         <i class="fa fa-thumb-tack" aria-hidden="true"></i>
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                            alt="ul_logo1" width="18" height="18">
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                        <span>High copy number (hcn) plasmids are lost from population at a high rate due to the large metabolic burden and lack of nature factors for plasmid maintenance.</span>
−
                    <span>High copy number (hcn) plasmids are lost from population at a high rate due to the
+
−
                        large metabolic burden and lack of nature factors for plasmid maintenance.</span>
+
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
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                         <div class="block-content-item-block">
 
                         <div class="block-content-item-block">
 
                             <div>
 
                             <div>
−
                                 <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
+
                                 <i class="fa fa-hand-o-right" aria-hidden="true"></i>
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                                    alt="ul_logo1" width="18" height="18">
+
 
                                 <span class="block-content-header">IDEA</span>
 
                                 <span class="block-content-header">IDEA</span>
 
                             </div>
 
                             </div>
 
                             <div>
 
                             <div>
−
                                 Equip the bacteria with a plasmid-sensing logically adjustable cell killer (P-SLACKiller). Use the inhibitor protein as a signal indicating plasmid numbers,
+
                                 Equip the bacteria with a plasmid-sensing logically adjustable cell killer (P-SLACKiller), we need to select a signal which can indicate the intracellular plasmid numbers. There is a basic rule: when the plasmid numbers are above the threshold, we regard it as a normally-working bacterium and the P-SLACKiller won’t start; however, when the plasmid numbers are below the threshold, we judge it as a slacker and the P-SLACKiller will kill these slackers, so that we can achieve the goal of stabling the number of plasmid. In the end, we selected the inhibitor protein as the signal molecular and the in-promoter as a switch to start the killer gene in order to control the plasmid numbers.
−
                                when the plasmid concentration reduces to a threshold, the switch of killer gene will turn on.
+
                            </div>
 +
                        </div>
 +
 
 +
                        <!--小分块-->
 +
                        <div class="block-content-item-block">
 +
                            <div>
 +
                                <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                                <span class="block-content-header">PART DESIGN</span>
 +
                            </div>
 +
                            <div>
 +
                                The basic circuit is shown in Fig.1.
 
                             </div>
 
                             </div>
 
                             <div>
 
                             <div>
 
                                 <img src="https://static.igem.org/mediawiki/2016/a/a9/T--BIT-China--Project--Design--fig1.png"
 
                                 <img src="https://static.igem.org/mediawiki/2016/a/a9/T--BIT-China--Project--Design--fig1.png"
−
                                     alt="fig1" class="center-block" style="width: 60%;">
+
                                     alt="fig1" class="center-block" style="width: 80%;">
 +
                            </div>
 +
                            <div>
 +
                                We use the constitutive promoter to express the inhibitor protein, thus the intracellular inhibitor concentration is positively correlated with the plasmid numbers. The inhibitor can repress the in-promoter and control the expression of downstream killer gene. To avoid the unexpected influence on killer gene caused by the constitutive promoter, we designed the gene circuit with the constitutive promoter and the in-promoter which express along different directions. When the signal of plasmid losing is detected，that is, the inhibitor concentration decreases, the executor killer will play a role.
 +
                            </div>
 +
                            <div>
 +
                                The genetic locus of functional gene can be substituted on the basis of production demand in the future.
 
                             </div>
 
                             </div>
 
                         </div>
 
                         </div>
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                         <div class="block-content-item-block">
 
                         <div class="block-content-item-block">
 
                             <div>
 
                             <div>
−
                                 <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
+
                                 <i class="fa fa-hand-o-right" aria-hidden="true"></i>
−
                                    alt="ul_logo1" width="18" height="18">
+
                                 <span class="block-content-header">INSIDE MECHANISM</span>
−
                                 <span class="block-content-header">PART DESIGN</span>
+
 
                             </div>
 
                             </div>
 
                             <div>
 
                             <div>
−
                                 The basic circuit is shown in Fig.2, the genetic locus of functional gene can be substituted on the basis of production demand in the future. Inhibitor and in-promoter are key to control the threshold.
+
                                 Under normal circumstance, for the constitutive promoter, the plasmid numbers are above the threshold, the inhibitor concentration is high enough to completely repress the activity of in-promoter. Considering the effect of plasmids segregational stability, the concentration of plasmids will decline with time going on. When the plasmid numbers are below the threshold, the decrease of inhibitor proteins will lead to the increase of in-promoter’s activity. At this time, the killer gene will express and kill the cell. We define that, when the killer expressed is just able to kill the cell, the plasmid numbers is the threshold we’ve talked about. Based on this, we concluded that when the plasmid numbers are above the threshold, the bacteria can survive and have high working efficiency. This range is called survival range. To prevent the slackers consume a lot of nutrition, we kill it when the range comes to the dead one.
−
                                When the signal of plasmid losing is detected, the executor killer will play a role.
+
 
 +
                            </div>
 +
                            <div>
 +
                                In this way, we can optimize the general population structure through plasmid-numbers-control.
 
                             </div>
 
                             </div>
 
                             <div>
 
                             <div>
 
                                 <img src="https://static.igem.org/mediawiki/2016/0/01/T--BIT-China--Project--Design--fig2.png"
 
                                 <img src="https://static.igem.org/mediawiki/2016/0/01/T--BIT-China--Project--Design--fig2.png"
−
                                     alt="fig2" class="center-block" style="width: 60%;">
+
                                     alt="fig1" class="center-block" style="width: 80%;">
 
                             </div>
 
                             </div>
 
                         </div>
 
                         </div>
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                 </div>
 
                 </div>
  
−
                 <!--Killer device-->
+
                 <!--Threshold device-->
−
                 <div id="killer_device" class="block-title">Killer device</div>
+
                 <div id="threshold_device" class="block-title">Threshold device</div>
 
                 <div class="block-content">
 
                 <div class="block-content">
−
                    <!--Killer Device 简介-->
 
 
                     <div class="block-content-brief">
 
                     <div class="block-content-brief">
 
                         <div>
 
                         <div>
−
                             As an executor for killing the cell labeled as slackers, killer device
+
                             The most critical factor in our system is the inhibitor concentration since it controls the switch of our killer system. Thus we need to prove that the in-promoter will have different responses corresponding to different concentrations of inhibitor。
−
                            should include the detecting part like in-promoter interacting
+
−
                            with inhibitor protein as well as the killing part like toxin gene
+
−
                            mazF and hokD.
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             Ways of self-killing:
+
                             We combined the wet experiment results and the mathematical model to measure the final result.
 +
                            <a href="https://2016.igem.org/Team:BIT-China/Model" style="color: blue;"> (know more about our model)</a>
 +
                        </div>
 +
                        <div class="step-style">
 +
                            <i class="fa fa-play-circle" aria-hidden="true"></i>
 +
                            First Step
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             1) toxic protein
+
                             Since it’s hard to control the plasmid numbers, we employed the arabinose induced pBAD promoter. The plasmid numbers is stable in short time. By adding different concentration of arabinose, we can simulate the production of inhibitors with different concentration. In this way, we can see the downstream in-promoter stay in the corresponding statues。RFP is used to replace the killer gene for simplifying our wet experiment. To expand the application of our system, we choose three combinations of inhibitor and in-promoter.
 
                         </div>
 
                         </div>
 +
 +
                    </div>
 +
                    <div class="content-block-item">
 
                         <div>
 
                         <div>
−
                             2) sgRNA targeting genome of strains with no NHEJ repair system
+
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">Goal</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             3) sgRNA targeting essential genes
+
                             (1) Build three parallel circuits employing different inhibitor proteins
 +
                        </div>
 +
                        <div>
 +
                            (2) Find the relationship of the inhibitor and in-promoter
 +
                        </div>
 +
                        <div>
 +
                            (3) Find out the initial thresholds by measuring RFP intensity
 +
                        </div>
 +
                        <div>
 +
                            (4) Provide experimental data for modeling part
 +
                        </div>
 +
                    </div>
 +
                    <div class="content-block-item">
 +
                        <div>
 +
                            <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">Part Design</span>
 +
                        </div>
 +
                        <div>
 +
                            The gene circuits are shown in Fig.3.
 +
                        </div>
 +
                        <div>
 +
                            <img src="https://static.igem.org/mediawiki/2016/a/a9/T--BIT-China--Project--Design--fig3.png"
 +
                                alt="fig3" class="center-block" style="width: 80%;">
 +
                        </div>
 +
                        <div>
 +
                            (1) <b>Part:BBa_K808000 Arac-pBAD</b> is used to control the expression of inhibitor proteins, The concentration of inducer arabinose is regarded as an input signal, and the red fluorescence intensity controlled by in-promoter is the output.
 +
                        </div>
 +
                        <div>
 +
                            (2) Three combinations of inhibitor and in-promoter are selected to prove the concept of plasmid quorum sensing. Due to the limit of time, we measured 1-2 circuits.
 +
                            <a href="https://2016.igem.org/Team:BIT-China/Inhibitor"></a>[see inhibitor mechanisms]
 +
                        </div>
 +
                        <div>
 +
                            (3) RFP is used as an indicator since it’s easier to quantify compare with the killer gene.
 +
                        </div>
 +
                        <div>
 +
                            (4) The inducible promoter PBAD and the in-promoter express towards different directions, a terminator B0015 is added between the two promoters。
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
−
 
 
                     <div class="block-content-item">
 
                     <div class="block-content-item">
−
                         <!--Killer device小分块-->
+
                         <div>
−
                        <div class="block-content-item-block">
+
                            <i class="fa fa-hand-o-right" aria-hidden="true"></i>
−
                            <div>
+
                            <span class="block-content-header">We assume that:</span>
−
                                <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
+
                        </div>
−
                                    alt="ul_logo1" width="18" height="18">
+
                        <div>
−
                                <span class="block-content-header">PART DESIGN</span>
+
                            Different concentrations of arabinose will induce inhibitor with different concentrations.
−
                            </div>
+
                        </div>
−
                            <div>
+
                        <div>
−
                                At the first stage, we need to verify the function of two toxin proteins
+
                            The high concentration of inducers can simulate high concentration of plasmids due to the same effect of producing more inhibitor proteins.
−
                                and make sure the bacteria can be killed after arabinose induction.
+
                        </div>
−
                                To control the expression of killer gene, instead of J23119,
+
                        <div>
−
                                arabinose inducible regulatory promoter/repressor unit [part number] is employed in our circuit.
+
                            By adding different concentration of arabinose, we can measure the fluorescence intensity of RFP and find out the relationship of the arabinose and RFP intensity and the initial thresholds under control of certain inhibitor proteins.
−
                            </div>
+
−
                            <div>
+
−
                                <img src="https://static.igem.org/mediawiki/2016/a/a9/T--BIT-China--Project--Design--fig3.png"
+
−
                                    alt="fig3" class="center-block" style="width: 60%;">
+
−
                            </div>
+
−
                            <div>
+
−
                                After measuring the growth curve, we observed the obvious
+
−
                                difference between the testing group and control group. [see results page for killer]
+
−
                            </div>
+
−
                            <div>
+
−
                                To facilitate the measurement of plasmid threshold, we combined the inhibitor circuit with
+
−
                                the killer circuit and replace the RFP for killer gene. [see design for threshold]
+
−
                            </div>
+
−
                            <div>
+
−
                                <img src="https://static.igem.org/mediawiki/2016/b/b4/T--BIT-China--Project--Design--fig4.png"
+
−
                                    alt="fig4" class="center-block" style="width: 60%;">
+
−
                            </div>
+
−
                            <div>
+
−
                                For the toxic protein,
+
−
                                MazF and HokD were chosen as candidates. [see more about the killing mechanisms]
+
−
                            </div>
+
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
−
                </div>
 
  
−
                <!--Threshold device-->
+
                    <!--second-->
−
                <div id="threshold_device" class="block-title">Threshold device</div>
+
−
                <div class="block-content">
+
 
                     <div class="block-content-brief">
 
                     <div class="block-content-brief">
−
                         Inhibitor and in-promoter are used to measure and adjust
+
                         <div class="step-style">
−
                         the threshold. Before apply the threshold value into our
+
                            <i class="fa fa-play-circle" aria-hidden="true"></i>
−
                         model, we need to use RFP as a reporter
+
                            Second step
−
                        gene since the expression of toxin protein is hard to quantify. (know more about our model)
+
                         </div>
 +
                         <div>
 +
                            In order to find out the concentrations of inhibitor under different concentrations of arabinose and use the results to derive the threshold of plasmids number in the constitutive circuit. Inhibitor is replaced by RFP and induced based on the same condition. The concentration of inhibitor can represented by measuring the fluorescence intensity of RFP.
 +
                        </div>
 
                     </div>
 
                     </div>
 
                     <div class="content-block-item">
 
                     <div class="content-block-item">
 
                         <div>
 
                         <div>
−
                             <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
+
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
−
                                alt="ul_logo1" width="18" height="18">
+
 
                             <span class="block-content-header">Goal</span>
 
                             <span class="block-content-header">Goal</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             (1) Build three parallel circuits employing different inhibitor proteins
+
                             (1)Represent the concentration of inhibitor by measuring the fluorescence intensity of RFP.
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             (2) Find out the initial thresholds by measuring RFP intensity
+
                             (2) Derive the threshold of plasmids number in the constitutive circuit
 
                         </div>
 
                         </div>
 +
                    </div>
 +
                    <div class="content-block-item">
 
                         <div>
 
                         <div>
−
                             (3) Provide experimental data for modeling part
+
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">Part Design</span>
 +
                        </div>
 +
                        <div>
 +
                            The gene circuits are shown in Fig.4.
 +
                        </div>
 +
                        <div>
 +
                            <img src="https://static.igem.org/mediawiki/2016/b/b4/T--BIT-China--Project--Design--fig4.png"
 +
                                alt="fig4" class="center-block" style="width: 80%;">
 +
                        </div>
 +
                    </div>
 +
                    <div class="block-content-item">
 +
                        <div>
 +
                            <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">We assume that:</span>
 +
                        </div>
 +
                        <div>
 +
                            More arabinose added, more RFP expressed which can stand for the concentration of inhibitor, and vice versa.
 +
                        </div>
 +
                        <div>
 +
                            <img src="https://static.igem.org/mediawiki/2016/7/7e/T--BIT-China--Project--Design--fig5.png"
 +
                                alt="fig5" style="width: 80%;">
 +
                        </div>
 +
                        <div>
 +
                            Thus we could find out the relationship between the concentration of arabinose and inhibitor.
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
  
 +
                    <!--third-->
 +
                    <div class="block-content-brief">
 +
                        <div class="step-style">
 +
                            <i class="fa fa-play-circle" aria-hidden="true"></i>
 +
                            Third step
 +
                        </div>
 +
                        <div>
 +
                            We use plasmids with different copy numbers to simulate the concentration of plasmids losing on different levels. Three kinds of plasmids, pSB1k3(100~200 copies), pSB3k3（20~30 copies）, pSB4k5（5~10 copies, are chosen and constructed with target fragment. By observing our system’s working conditions, we can finally prove its function of controlling plasmids number.
 +
                        </div>
 +
                    </div>
 
                     <div class="content-block-item">
 
                     <div class="content-block-item">
 
                         <div>
 
                         <div>
−
                             <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
+
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
−
                                alt="ul_logo1" width="18" height="18">
+
                            <span class="block-content-header">Goal</span>
 +
                        </div>
 +
                        <div>
 +
                            (1) Simulate the plasmids losing on different levels
 +
                        </div>
 +
                        <div>
 +
                            (2) Prove that our system is functional
 +
                        </div>
 +
                    </div>
 +
                    <div class="content-block-item">
 +
                        <div>
 +
                            <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 
                             <span class="block-content-header">Part Design</span>
 
                             <span class="block-content-header">Part Design</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             The gene circuits are shown in Fig.5.
+
                             The gene circuits are shown in Fig.6.
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             <img src="https://static.igem.org/mediawiki/2016/7/7e/T--BIT-China--Project--Design--fig5.png"
+
                             <img src="https://static.igem.org/mediawiki/2016/5/5c/T--BIT-China--Project--Design--fig6.png"
−
                                 alt="fig5" class="center-block" style="width: 60%;">
+
                                 alt="fig6" class="center-block" style="width: 80%;">
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             (1) The concentration of inducer arabinose is regarded as an input signal,
+
                             (1) We constructed the circuit on different plasmids with different copy numbers.
−
                            thus Part:BBa_K808000 Arac-pBAD is used to control the expression of inhibitor proteins
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             (2) Three combinations of inhibitor and in-promoter are selected to prove
+
                             (2) The locus of constitutive promoter will be replaced by another constitutive promoter which has the similar strength as pBAD promoter.
−
                            the concept of plasmid quorum sensing [see inhibitor mechanisms]
+
 
                         </div>
 
                         </div>
 +
                    </div>
 +
                    <div class="block-content-item">
 
                         <div>
 
                         <div>
−
                             (3) RFP is used as an indicator
+
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">We assume that:</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             We assume that:
+
                             When the number of plasmids is less than N, inhibitor is not strong enough to inhibit the in-promoter totally, so the killer gene will express triggering the death of bacteria. On the contrary, if the number of plasmids is higher than N, the bacteria won’t die.
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             The high concentration of inducers can simulate high concentration
+
                             We expect that in the high copy number plasmid circuit, fluorescence gene will express, and in the low copy number plasmid circuit, there will no fluorescence.
−
                            of plasmids due to the same effect of producing more inhibitor proteins.
+
                        </div>
 +
                    </div>
 +
 
 +
                    <!--fourth-->
 +
                    <div class="block-content-brief">
 +
                        <div class="step-style">
 +
                            <i class="fa fa-play-circle" aria-hidden="true"></i>
 +
                            Forth step
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             By adding different concentration of arabinose, we can measure the fluorescence intensity
+
                             The threshold of plasmid number is decided by the relationship between inhibitor and in-promoter. To achievement the goal of build a controllable system, we decide to use different RBS (B0034 B0032) and promoters (J23119 J23116 J23109) with different strengths to change their concentrations. Thus we can finally change the threshold of plasmid as we hope.
−
                             of RFP and find out the initial thresholds under control of certain inhibitor proteins.
+
                        </div>
 +
                    </div>
 +
                    <div class="content-block-item">
 +
                        <div>
 +
                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">Goal</span>
 +
                        </div>
 +
                        <div>
 +
                            (1) Adjust the threshold of plasmids by substituting different biobricks.
 +
                        </div>
 +
                    </div>
 +
                    <div class="content-block-item">
 +
                        <div>
 +
                            <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                            <span class="block-content-header">Part Design</span>
 +
                        </div>
 +
                        <div>
 +
                            The gene circuits are shown in Fig.7.
 +
                        </div>
 +
                        <div>
 +
                            <img src="https://static.igem.org/mediawiki/2016/c/cd/T--BIT-China--Project--Design--fig7.png"
 +
                                alt="fig7" class="center-block" style="width: 80%;">
 +
                        </div>
 +
                        <div>
 +
                            (1) Simulate the plasmids losing on different levels.
 +
                        </div>
 +
                        <div>
 +
                            (2) The locus of B0034 and J23119 will be replaced by B0032 and J23109 J23116.
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
  
 
                 </div>
 
                 </div>
 +
 +
                <!--Killer device-->
 +
                <div id="killer_device" class="block-title">Killer device</div>
 +
                <div class="block-content">
 +
                    <!--Killer Device 简介-->
 +
                    <div class="block-content-brief">
 +
                        <div>
 +
                            As an executor for killing the cell labeled as slackers, killer device should include the detecting part like in-promoter interacting with inhibitor protein as well as the killing part like toxin gene mazF and hokD.
 +
                        </div>
 +
                    </div>
 +
 +
                    <div class="block-content-item">
 +
                        <div class="block-content-item-block">
 +
                            <div>
 +
                                <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                                <span class="block-content-header">Ways of self-killing:</span>
 +
                            </div>
 +
                            <div>
 +
                                1) toxic protein <i class="fa fa-check" aria-hidden="true" style="color: red;"></i>
 +
                            </div>
 +
                            <div>
 +
                                2) sgRNA targeting genome of strains with no NHEJ repair system
 +
                            </div>
 +
                            <div>
 +
                                3) sgRNA targeting essential genes
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                    <div class="block-content-item">
 +
                        <!--Killer device小分块-->
 +
                        <div class="block-content-item-block">
 +
                            <div>
 +
                                <i class="fa fa-hand-o-right" aria-hidden="true"></i>
 +
                                <span class="block-content-header">PART DESIGN</span>
 +
                            </div>
 +
                            <div>
 +
                                At the first stage, we need to verify the function of two toxin proteins and make sure the bacteria can be killed after the expression of toxin proteins. To control the expression of killer gene, instead of J23119, arabinose inducible regulatory promoter/repressor unit [part number] is employed in our circuit.
 +
                            </div>
 +
                            <div>
 +
                                <img src="https://static.igem.org/mediawiki/2016/2/2a/T--BIT-China--Project--Design--fig8.png"
 +
                                    alt="fig8" class="center-block" style="width: 80%;">
 +
                            </div>
 +
                            <div>
 +
                                After measuring the growth curve, we observed the obvious difference between the testing group and control group.
 +
                                <a href="https://2016.igem.org/Team:BIT-China/Results">[see results page for killer]</a>
 +
                            </div>
 +
                            <div>
 +
                                To facilitate the measurement of plasmid threshold, we combined the inhibitor circuit with the killer circuit and replace the RFP for killer gene.
 +
                                <a href="#threshold_device">[see design for threshold]</a>
 +
                            </div>
 +
                            <div>
 +
                                <img src="https://static.igem.org/mediawiki/2016/0/08/T--BIT-China--Project--Design--fig9.png"
 +
                                    alt="fig9" class="center-block" style="width: 80%;">
 +
                            </div>
 +
                            <div>
 +
                                For the toxic protein, MazF and HokD were chosen as candidates.
 +
                                <a href="https://2016.igem.org/Team:BIT-China/Killing_Mechanisms">[see more about the killing mechanisms]</a>
 +
                            </div>
 +
                        </div>
 +
                    </div>
 +
                </div>
 +
  
 
                 <!--Upgraded P-SLACKiller-->
 
                 <!--Upgraded P-SLACKiller-->
Line 298: Line 479:
 
                     <div class="problem-title">Why do we need to optimize our project?</div>
 
                     <div class="problem-title">Why do we need to optimize our project?</div>
 
                     <div>
 
                     <div>
−
                         <img src="https://static.igem.org/mediawiki/2016/c/c1/T--BIT-China--Project--Design--ul_logo1.png"
+
                         <!--<img src="https://static.igem.org/mediawiki/2016/c/c1/T&#45;&#45;BIT-China&#45;&#45;Project&#45;&#45;Design&#45;&#45;ul_logo1.png"-->
−
                             alt="ul_logo1" width="18" height="18">
+
                             <!--alt="ul_logo1" width="18" height="18">-->
−
                     <span>It’s possible to produce generation of plasmid-free cells.
+
                     <span>
−
                        Thus, the killer device should be integrated into the genome. [see reombination]</span>
+
                        It’s possible to produce generation of plasmid-free cells, even if all plasmids were losen. Thus, we decided to integrate the killer device into genome to solve this problem.
 +
                        <a href="https://2016.igem.org/Team:BIT-China/Recombination">[see reombination]</a>
 +
                    </span>
 
                     </div>
 
                     </div>
 
                     <div>
 
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                    <span> To meet various needs with different plasmid numbers,
+
                        <span>
−
                        we need to adjust the initial threshold
+
                            To control the plasmid number above different thresholds, we need to adjust the initial threshold through replacement of RBS as well as in-promoter mutation.
−
                        through replacement of RBS as well as in-promoter mutation. [see mutation]</span>
+
                            <a href="">[see mutation]</a>
 +
                        </span>
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
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                 <div class="block-content">
 
                 <div class="block-content">
 
                     <div class="block-content-brief">
 
                     <div class="block-content-brief">
−
                    Recombineering (recombination-mediated genetic engineering) is
+
                        <div>
−
                    an efficient molecular engineering technique used for gene
+
                            Recombineering (
−
                    replacement, deletion and insertion.
+
                            <b>recombi</b>nation-mediated genetic engi<b>neering</b>) is an efficient molecular
 +
                            engineering technique used for gene replacement, deletion and insertion.
 +
                        </div>
 +
 
 
                     </div>
 
                     </div>
 +
  
 
                     <div class="content-block-item">
 
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                             <span class="block-content-header">Ways: a linear plus circular reaction</span>
 
                             <span class="block-content-header">Ways: a linear plus circular reaction</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             A：Employment of traditional λ-Red recombination
+
                             A：Employment of traditional λ-Red recombination <i class="fa fa-check" aria-hidden="true" style="color: red;"></i>
 
                         </div>
 
                         </div>
 +
                    </div>
 +
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                             <span class="block-content-header">PART DESIGN</span>
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                             <span>PART DESIGN</span>
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             The basic circuit of upgraded P-SLACKiller is shown in Fig.6.
+
                             The basic circuit of upgraded P-SLACKiller is shown in Fig.10.
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
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                             <img src="https://static.igem.org/mediawiki/2016/5/5c/T--BIT-China--Project--Design--fig6.png"
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                             <img src="https://static.igem.org/mediawiki/2016/9/96/T--BIT-China--Project--Design--fig10.png"
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                                 alt="fig6" class="center-block" style="width: 60%;">
+
                                 alt="fig10" style="width: 80%;">
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             Compared with the original one, two homologous arms (50bp) are added.
+
                             Compared with the original one, two homologous arms (50bp) are added. With the help of lambda Red recombination system, the killer part can be integrated into genome, preventing the whole system from being invalid. The final gene circuit is shown in Fig.11.
−
                            With the help of lambda Red recombination system, the killer part can be integrated into genome,
+
−
                            preventing the whole system from being invalid. The final gene circuit is shown in Fig.7.
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
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                             <img src="https://static.igem.org/mediawiki/2016/c/cd/T--BIT-China--Project--Design--fig7.png"
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                             <img src="https://static.igem.org/mediawiki/2016/d/de/T--BIT-China--Project--Design--fig11.png"
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                                 alt="fig7" class="center-block" style="width: 60%;">
+
                                 alt="fig11" style="width: 80%;">
 
                         </div>
 
                         </div>
 +
                    </div>
  
−
                        <!--B 部分-->
+
                    <div class="content-block-item">
 
                         <div>
 
                         <div>
−
                             B:：CRISPR-Cas9 coupling λ-Red recombineering
+
                             B: CRISPR-Cas9 coupling λ-Red recombineering
 
                         </div>
 
                         </div>
 +
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 +
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                             <span class="block-content-header">PART DESIGN</span>
−
                             <span>PART DESIGN</span>
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             <img src="https://static.igem.org/mediawiki/2016/2/2a/T--BIT-China--Project--Design--fig8.png"
+
                             <img src="https://static.igem.org/mediawiki/2016/7/74/T--BIT-China--Project--Design--fig12.png"
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                                 alt="fig8" class="center-block" style="width: 60%;">
+
                                 alt="fig12" style="width: 80%;">
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             Difference between the two methods above: Traditional way use the resistance
+
                             Difference between the two methods above: Traditional way use the resistance gene as a selection marker, while the CRISPR coupled way introduce a double-strand break (DSB) into the strain with no recombination occurred.
−
                            gene as a selection marker, while the CRISPR coupled way
+
−
                            introduce a double-strand break (DSB) into the strain with no recombination occurred.
+
 
                         </div>
 
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                     </div>
 
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                             <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
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                             <i class="fa fa-hand-o-right" aria-hidden="true"></i>
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                                alt="ul_logo1" width="18" height="18">
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                             <span class="block-content-header">Application:</span>
 
                             <span class="block-content-header">Application:</span>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             In our project, we tried both the two ways to test the integration
+
                             In our project, we tried both the two ways to test the integration efficiency. However, the CRISPR coupled way are deleted from our plan list due to the failure of cas9 and λ-Red plasmid construction.
−
                            efficiency. However, the CRISPR coupled
+
−
                            way are deleted from our plan list due to the failure of cas9 and λ-Red plasmid construction.
+
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             We tried the traditional way with the pKD46 plasmid
+
                             We tried the traditional way with the pKD46 plasmid provided by Chun Li’s lab and got the positive results.
−
                            provided by Chun Li’s lab and got the positive results. [results for recombination]
+
                            <a href="https://2016.igem.org/Team:BIT-China/Results" style="color: blue;">[results for recombination]</a>
 
                         </div>
 
                         </div>
 
                         <div>
 
                         <div>
−
                             Two main factors will influence the recombination efficiency: the target site on genome
+
                             Two main factors will influence the recombination efficiency: the target site on genome and the length of homologous arms between donor fragment.
−
                            and the length of homologous arms between donor fragment. [recombination protocol]
+
                            <a href="https://2016.igem.org/Team:BIT-China/Protocol">[recombination protocol]</a>
 
                         </div>
 
                         </div>
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
 +
 
                 <div id="promoter_mutation" class="block-title">Promoter mutation</div>
 
                 <div id="promoter_mutation" class="block-title">Promoter mutation</div>
 
                 <div class="block-content">
 
                 <div class="block-content">
 
                     <div class="block-content-brief">
 
                     <div class="block-content-brief">
−
                         For inductive promoters, two kinds of region are significant
+
                         For inductive promoters, two kinds of region are significant to its transcription strength. One is common -10 and -35 region which can firmly bind to RNA polymerase, the other is operon region binding with regulatory factors like inhibitor proteins.
−
                        to its transcription strength. One is common -10 and -35 region
+
                        <a href="" style="color: blue;">[see mutation mechanisms]</a>
−
                        which can firmly bind to RNA polymerase, the other is
+
−
                        operon region binding with regulatory factors like
+
−
                        inhibitor proteins. [see mutation mechanisms]
+
 
                     </div>
 
                     </div>
  
 
                     <div>
 
                     <div>
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                         <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
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                         <i class="fa fa-hand-o-right" aria-hidden="true"></i>
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                         <span class="block-content-header"> Aim:</span>
 
                         <span class="block-content-header"> Aim:</span>
 
                     </div>
 
                     </div>
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                     </div>
 
                     <div>
 
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                         <img src="https://static.igem.org/mediawiki/2016/2/21/T--BIT-China--Project--Design--ul_logo2.png"
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                         <i class="fa fa-hand-o-right" aria-hidden="true"></i>
−
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+
 
                         <span class="block-content-header">Part Design</span>
 
                         <span class="block-content-header">Part Design</span>
 
                     </div>
 
                     </div>
 
                     <div>
 
                     <div>
−
                         <img src="https://static.igem.org/mediawiki/2016/0/08/T--BIT-China--Project--Design--fig9.png"
+
                         <img src="https://static.igem.org/mediawiki/2016/d/d2/T--BIT-China--Project--Design--fig13.png"
 
                             alt="fig9" class="center-block" style="width: 60%;">
 
                             alt="fig9" class="center-block" style="width: 60%;">
 
                     </div>
 
                     </div>
 
                     <div>
 
                     <div>
−
                         After analyzing the promoter region of pTet, we designed
+
                         After analyzing the promoter region of pTet, we designed random primers to mutate its -35 region. RFP intensity is measured to indicate the strength of mutated promoters.
−
                        random primers to mutate its -35 region.
+
                        <a href="" style="color: blue;">[see mutation results]</a>
−
                        RFP intensity is measured to indicate the strength of
+
−
                        mutated promoters. [see mutation results]
+
 
                     </div>
 
                     </div>
 
                 </div>
 
                 </div>
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             <img src="https://static.igem.org/mediawiki/2016/4/43/T--BIT-China--img--nav_left_top.png" alt="nav_left_top" style="width: 100%;">
 
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                     alt="c1" style="width: 100%;height: 70px;">
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                 <a href="#killer_device" class="nav_point">
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                 <a href="#threshold_device" class="nav_point">
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                     <span class="nav_left_txt">Killer device</span></a>
+
                     <span class="nav_left_txt">Threshold device</span></a>
 
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             <li>
 
             <li>
 
                 <img src="https://static.igem.org/mediawiki/2016/a/a1/T--BIT-China--img--nav_left_c2.png"
 
                 <img src="https://static.igem.org/mediawiki/2016/a/a1/T--BIT-China--img--nav_left_c2.png"
 
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                     alt="c1" style="width: 100%;height: 70px;">
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                 <a href="#threshold_device" class="nav_point">
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                 <a href="#killer_device" class="nav_point">
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                     <span class="nav_left_txt">Threshold device</span></a>
+
                     <span class="nav_left_txt">Killer device</span></a>
 
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Revision as of 06:06, 15 October 2016

backtop
title
What is the problem?
Plasmid segragational instability has been the limit step for large-scale protein production and bioremediation. Antibiotic abuse or Stress Conditions for plasmid retention is not practical in this situation.
High copy number (hcn) plasmids are lost from population at a high rate due to the large metabolic burden and lack of nature factors for plasmid maintenance.
Our P-SLACKiller
IDEA
Equip the bacteria with a plasmid-sensing logically adjustable cell killer (P-SLACKiller), we need to select a signal which can indicate the intracellular plasmid numbers. There is a basic rule: when the plasmid numbers are above the threshold, we regard it as a normally-working bacterium and the P-SLACKiller won’t start; however, when the plasmid numbers are below the threshold, we judge it as a slacker and the P-SLACKiller will kill these slackers, so that we can achieve the goal of stabling the number of plasmid. In the end, we selected the inhibitor protein as the signal molecular and the in-promoter as a switch to start the killer gene in order to control the plasmid numbers.
PART DESIGN
The basic circuit is shown in Fig.1.
fig1
We use the constitutive promoter to express the inhibitor protein, thus the intracellular inhibitor concentration is positively correlated with the plasmid numbers. The inhibitor can repress the in-promoter and control the expression of downstream killer gene. To avoid the unexpected influence on killer gene caused by the constitutive promoter, we designed the gene circuit with the constitutive promoter and the in-promoter which express along different directions. When the signal of plasmid losing is detected，that is, the inhibitor concentration decreases, the executor killer will play a role.
The genetic locus of functional gene can be substituted on the basis of production demand in the future.
INSIDE MECHANISM
Under normal circumstance, for the constitutive promoter, the plasmid numbers are above the threshold, the inhibitor concentration is high enough to completely repress the activity of in-promoter. Considering the effect of plasmids segregational stability, the concentration of plasmids will decline with time going on. When the plasmid numbers are below the threshold, the decrease of inhibitor proteins will lead to the increase of in-promoter’s activity. At this time, the killer gene will express and kill the cell. We define that, when the killer expressed is just able to kill the cell, the plasmid numbers is the threshold we’ve talked about. Based on this, we concluded that when the plasmid numbers are above the threshold, the bacteria can survive and have high working efficiency. This range is called survival range. To prevent the slackers consume a lot of nutrition, we kill it when the range comes to the dead one.
In this way, we can optimize the general population structure through plasmid-numbers-control.
fig1
Threshold device
The most critical factor in our system is the inhibitor concentration since it controls the switch of our killer system. Thus we need to prove that the in-promoter will have different responses corresponding to different concentrations of inhibitor。
We combined the wet experiment results and the mathematical model to measure the final result. (know more about our model)
First Step
Since it’s hard to control the plasmid numbers, we employed the arabinose induced pBAD promoter. The plasmid numbers is stable in short time. By adding different concentration of arabinose, we can simulate the production of inhibitors with different concentration. In this way, we can see the downstream in-promoter stay in the corresponding statues。RFP is used to replace the killer gene for simplifying our wet experiment. To expand the application of our system, we choose three combinations of inhibitor and in-promoter.
Goal
(1) Build three parallel circuits employing different inhibitor proteins
(2) Find the relationship of the inhibitor and in-promoter
(3) Find out the initial thresholds by measuring RFP intensity
(4) Provide experimental data for modeling part
Part Design
The gene circuits are shown in Fig.3.
fig3
(1) Part:BBa_K808000 Arac-pBAD is used to control the expression of inhibitor proteins, The concentration of inducer arabinose is regarded as an input signal, and the red fluorescence intensity controlled by in-promoter is the output.
(2) Three combinations of inhibitor and in-promoter are selected to prove the concept of plasmid quorum sensing. Due to the limit of time, we measured 1-2 circuits. [see inhibitor mechanisms]
(3) RFP is used as an indicator since it’s easier to quantify compare with the killer gene.
(4) The inducible promoter PBAD and the in-promoter express towards different directions, a terminator B0015 is added between the two promoters。
We assume that:
Different concentrations of arabinose will induce inhibitor with different concentrations.
The high concentration of inducers can simulate high concentration of plasmids due to the same effect of producing more inhibitor proteins.
By adding different concentration of arabinose, we can measure the fluorescence intensity of RFP and find out the relationship of the arabinose and RFP intensity and the initial thresholds under control of certain inhibitor proteins.
Second step
In order to find out the concentrations of inhibitor under different concentrations of arabinose and use the results to derive the threshold of plasmids number in the constitutive circuit. Inhibitor is replaced by RFP and induced based on the same condition. The concentration of inhibitor can represented by measuring the fluorescence intensity of RFP.
Goal
(1)Represent the concentration of inhibitor by measuring the fluorescence intensity of RFP.
(2) Derive the threshold of plasmids number in the constitutive circuit
Part Design
The gene circuits are shown in Fig.4.
fig4
We assume that:
More arabinose added, more RFP expressed which can stand for the concentration of inhibitor, and vice versa.
fig5
Thus we could find out the relationship between the concentration of arabinose and inhibitor.
Third step
We use plasmids with different copy numbers to simulate the concentration of plasmids losing on different levels. Three kinds of plasmids, pSB1k3(100~200 copies), pSB3k3（20~30 copies）, pSB4k5（5~10 copies, are chosen and constructed with target fragment. By observing our system’s working conditions, we can finally prove its function of controlling plasmids number.
Goal
(1) Simulate the plasmids losing on different levels
(2) Prove that our system is functional
Part Design
The gene circuits are shown in Fig.6.
fig6
(1) We constructed the circuit on different plasmids with different copy numbers.
(2) The locus of constitutive promoter will be replaced by another constitutive promoter which has the similar strength as pBAD promoter.
We assume that:
When the number of plasmids is less than N, inhibitor is not strong enough to inhibit the in-promoter totally, so the killer gene will express triggering the death of bacteria. On the contrary, if the number of plasmids is higher than N, the bacteria won’t die.
We expect that in the high copy number plasmid circuit, fluorescence gene will express, and in the low copy number plasmid circuit, there will no fluorescence.
Forth step
The threshold of plasmid number is decided by the relationship between inhibitor and in-promoter. To achievement the goal of build a controllable system, we decide to use different RBS (B0034 B0032) and promoters (J23119 J23116 J23109) with different strengths to change their concentrations. Thus we can finally change the threshold of plasmid as we hope.
Goal
(1) Adjust the threshold of plasmids by substituting different biobricks.
Part Design
The gene circuits are shown in Fig.7.
fig7
(1) Simulate the plasmids losing on different levels.
(2) The locus of B0034 and J23119 will be replaced by B0032 and J23109 J23116.
Killer device
As an executor for killing the cell labeled as slackers, killer device should include the detecting part like in-promoter interacting with inhibitor protein as well as the killing part like toxin gene mazF and hokD.
Ways of self-killing:
1) toxic protein
2) sgRNA targeting genome of strains with no NHEJ repair system
3) sgRNA targeting essential genes
PART DESIGN
At the first stage, we need to verify the function of two toxin proteins and make sure the bacteria can be killed after the expression of toxin proteins. To control the expression of killer gene, instead of J23119, arabinose inducible regulatory promoter/repressor unit [part number] is employed in our circuit.
fig8
After measuring the growth curve, we observed the obvious difference between the testing group and control group. [see results page for killer]
To facilitate the measurement of plasmid threshold, we combined the inhibitor circuit with the killer circuit and replace the RFP for killer gene. [see design for threshold]
fig9
For the toxic protein, MazF and HokD were chosen as candidates. [see more about the killing mechanisms]
Upgraded P-SLACKiller
Why do we need to optimize our project?
It’s possible to produce generation of plasmid-free cells, even if all plasmids were losen. Thus, we decided to integrate the killer device into genome to solve this problem. [see reombination]
To control the plasmid number above different thresholds, we need to adjust the initial threshold through replacement of RBS as well as in-promoter mutation. [see mutation]
Recombination
Recombineering ( recombination-mediated genetic engineering) is an efficient molecular engineering technique used for gene replacement, deletion and insertion.
Ways: a linear plus circular reaction
A：Employment of traditional λ-Red recombination
PART DESIGN
The basic circuit of upgraded P-SLACKiller is shown in Fig.10.
fig10
Compared with the original one, two homologous arms (50bp) are added. With the help of lambda Red recombination system, the killer part can be integrated into genome, preventing the whole system from being invalid. The final gene circuit is shown in Fig.11.
fig11
B: CRISPR-Cas9 coupling λ-Red recombineering
PART DESIGN
fig12
Difference between the two methods above: Traditional way use the resistance gene as a selection marker, while the CRISPR coupled way introduce a double-strand break (DSB) into the strain with no recombination occurred.
Application:
In our project, we tried both the two ways to test the integration efficiency. However, the CRISPR coupled way are deleted from our plan list due to the failure of cas9 and λ-Red plasmid construction.
We tried the traditional way with the pKD46 plasmid provided by Chun Li’s lab and got the positive results. [results for recombination]
Two main factors will influence the recombination efficiency: the target site on genome and the length of homologous arms between donor fragment. [recombination protocol]
Promoter mutation
For inductive promoters, two kinds of region are significant to its transcription strength. One is common -10 and -35 region which can firmly bind to RNA polymerase, the other is operon region binding with regulatory factors like inhibitor proteins. [see mutation mechanisms]
Aim:
(1) To adjust threshold through changing in-promoter’s strength
(2) Tied to specific promoter like pTet, build a mutants library and improve the existing part by measuring the strength through RFP
Part Design
fig9
After analyzing the promoter region of pTet, we designed random primers to mutate its -35 region. RFP intensity is measured to indicate the strength of mutated promoters. [see mutation results]

P-SLACKiller

· Work or Die
· Monitor Plasmid Numbers
· Kill the Slacker
· Maintain the Better Biosystem

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