Difference between revisions of "Team:HUST-China/Description"

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<div class="column full_size judges-will-not-evaluate">
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<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the<a href="https://2016.igem.org/Judging/Medals"> improve a previous part or project gold medal criterion</a>. </p>
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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<p>Tell us about your project, describe what moves you and why this is something important for your team.</p>
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<h5>What should this page contain?</h5>
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<ul>
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<li> A clear and concise description of your project.</li>
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<li>A detailed explanation of why your team chose to work on this particular project.</li>
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<li>References and sources to document your research.</li>
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<li>Use illustrations and other visual resources to explain your project.</li>
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<h5>Advice on writing your Project Description</h5>
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We encourage you to put up a lot of information and content on your wiki, but we also encourage you to include summaries as much as possible. If you think of the sections in your project description as the sections in a publication, you should try to be consist, accurate and unambiguous in your achievements.
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Judges like to read your wiki and know exactly what you have achieved. This is how you should think about these sections; from the point of view of the judge evaluating you at the end of the year.
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<h5>References</h5>
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<p>iGEM teams are encouraged to record references you use during the course of your research. They should be posted somewhere on your wiki so that judges and other visitors can see how you thought about your project and what works inspired you.</p>
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<h5>Inspiration</h5>
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<p>See how other teams have described and presented their projects: </p>
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<ul>
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<li><a href="https://2014.igem.org/Team:Imperial/Project"> Imperial</a></li>
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<li><a href="https://2014.igem.org/Team:UC_Davis/Project_Overview"> UC Davis</a></li>
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<li><a href="https://2014.igem.org/Team:SYSU-Software/Overview">SYSU Software</a></li>
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</ul>
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                                <li><a href="https://2016.igem.org/Team:HUST-China/project/background">Background</a></li>
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                                <li><a href="https://2016.igem.org/Team:HUST-China/Description">Description</a></li>
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                                <li><a href="https://2016.igem.org/Team:HUST-China/Proof">Proof of concept</a></li>
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                                <li><a href="https://2016.igem.org/Team:HUST-China/Demonstrate">Application</a></li>
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                <h2>OVERVIEW</h2>
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                    This year, we want to offer a handy, adjustable and useful tool kit to everyone working on Synthetic Biology--Signal Filter. The core circuit is based on a positive feedback bi-stable or tri-stable system with the capacity of reducing noise and converting pulse signal into robust and persistent signal. To adapt to different experimental requirements,we also developed two versions of our Signal Filter--prokaryotic one and eukaryotic one.
 +
                </p>
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                <h2>Prokaryotic version:</h2>
 +
                <p>
 +
                    It is a tri-stable system adapted from bacteriophage λ operon. In the operon, promoter RE is activated by CII trascriptional activator. Ftsh is an ATP-dependent host metalloprotease which will normally degrade CII, while CIII serves as an inhibitor of Ftsh to free CII. And CI can function as a inhibitor to block pR, while Cro can bind pRE to stop the downstream gene’s expression. The positive feedback control under pRE is used to enhance pulse signal 1 and convert it into robust stable signal.
 +
                </p>
 +
                <!-- 图片 -->
 +
                <img src="https://static.igem.org/mediawiki/2016/8/88/T--HUST-China--Description-Fig-Eukaryote.png" alt="" class="img-responsive">
 +
                <p class="text-center">Fig*: circuit of prokaryote version serving as tri-stable signal filter</p>
 +
                <!-- <h2>Creation based on Signal Filter</h2> -->
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                <!-- 文字 -->
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                    When signal 1 comes,a double promoter structure will help induce Cro and CII downstream pRE. At the same time constitutively produced CIII will guarantee enough CII to enhance the transcription downstream the pRE. Thus,there forms a positive feedback loop to direct a fast and strong expression of cro. A quantity of Cro represses transcription under pRM by binding to Cro binding site and blocks gene of interest 2’s expression, so it turns to a stable state of expressing gene of interest 1.
 +
                </p>
 +
                <!-- <img src="" alt=""> -->
 +
                <p>When signal 2 comes, under a certain inducible promoter,CI will be expressed and then binds to cI binding site within pR promoter,blocking gene of interest 1 and cIII’s expressions. With CIII’s reduction, FtsH gradually degrades CII to interrupt the stable state. Therefore, Cro’s expression immediately drop down , allowing transcription from pRM. The system turn to another stable state of gene of interest 2‘s expression.
 +
                </p>
 +
                <p>
 +
                    If there is no signal.Both genes of interest will be expressed. And if both of the two signal exist,the expression state will depend on the intensity of the initial signal input.
 +
                </p>
 +
                <h2>Eukaryotic version:</h2>
 +
                <p>It is a bi-stable system derived from Arabidopsis thaliana stress response system. Enzyme catalysis are core of this design to increase the efficiency of state transition.
 +
                </p>
 +
                <img src="https://static.igem.org/mediawiki/2016/8/88/T--HUST-China--Description-Fig-Eukaryote.png" alt="" class="img-responsive">
 +
                <p class="text-center">Fig*: circuit of Eukaryote version serving as bii-stable signal filter</p>
 +
                <p>Clade A protein phosphatases type 2C(PP2CA) and SUCROSE NONFERMENTING1-RELATED SUBFAMILY2(SnRK2s) protein kinase are both components of Abscisic acid signaling network in Arabidopsis thaliana. ABF2 is a leucine zipper transcription factor which basically binds ABA-response element (ABRE). ABF2 can be phosphorylated by SnRK2s and be efficiently dephosphorylated by PP2CA. Also, in the absence of Abscisic acid,SnRK2 kinases can be inactivated by PP2Cs thus shut down the gene expression efficiently.
 +
                </p>
 +
                <p>When signal 1(ON) comes, promoter RD29A drives expression of SnRK2.2, which can phosphorylate ABF2 (constitutively expressed). Comparing to protein co-facter association ,enzyme catalysis can produce a large quantity of phosphorylated ABF2 in a short time, then enhances pRD29A to turn on the gene of interest’s expression. When signal 2(OFF) comes,gene PP2CA expresses, dephosphorylating ABF2 and inactivating SnRK2.2, thus turning the system into OFF state.
 +
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Revision as of 08:50, 2 October 2016

Application

Description

OVERVIEW

This year, we want to offer a handy, adjustable and useful tool kit to everyone working on Synthetic Biology--Signal Filter. The core circuit is based on a positive feedback bi-stable or tri-stable system with the capacity of reducing noise and converting pulse signal into robust and persistent signal. To adapt to different experimental requirements,we also developed two versions of our Signal Filter--prokaryotic one and eukaryotic one.

Prokaryotic version:

It is a tri-stable system adapted from bacteriophage λ operon. In the operon, promoter RE is activated by CII trascriptional activator. Ftsh is an ATP-dependent host metalloprotease which will normally degrade CII, while CIII serves as an inhibitor of Ftsh to free CII. And CI can function as a inhibitor to block pR, while Cro can bind pRE to stop the downstream gene’s expression. The positive feedback control under pRE is used to enhance pulse signal 1 and convert it into robust stable signal.

Fig*: circuit of prokaryote version serving as tri-stable signal filter

When signal 1 comes,a double promoter structure will help induce Cro and CII downstream pRE. At the same time constitutively produced CIII will guarantee enough CII to enhance the transcription downstream the pRE. Thus,there forms a positive feedback loop to direct a fast and strong expression of cro. A quantity of Cro represses transcription under pRM by binding to Cro binding site and blocks gene of interest 2’s expression, so it turns to a stable state of expressing gene of interest 1.

When signal 2 comes, under a certain inducible promoter,CI will be expressed and then binds to cI binding site within pR promoter,blocking gene of interest 1 and cIII’s expressions. With CIII’s reduction, FtsH gradually degrades CII to interrupt the stable state. Therefore, Cro’s expression immediately drop down , allowing transcription from pRM. The system turn to another stable state of gene of interest 2‘s expression.

If there is no signal.Both genes of interest will be expressed. And if both of the two signal exist,the expression state will depend on the intensity of the initial signal input.

Eukaryotic version:

It is a bi-stable system derived from Arabidopsis thaliana stress response system. Enzyme catalysis are core of this design to increase the efficiency of state transition.

Fig*: circuit of Eukaryote version serving as bii-stable signal filter

Clade A protein phosphatases type 2C(PP2CA) and SUCROSE NONFERMENTING1-RELATED SUBFAMILY2(SnRK2s) protein kinase are both components of Abscisic acid signaling network in Arabidopsis thaliana. ABF2 is a leucine zipper transcription factor which basically binds ABA-response element (ABRE). ABF2 can be phosphorylated by SnRK2s and be efficiently dephosphorylated by PP2CA. Also, in the absence of Abscisic acid,SnRK2 kinases can be inactivated by PP2Cs thus shut down the gene expression efficiently.

When signal 1(ON) comes, promoter RD29A drives expression of SnRK2.2, which can phosphorylate ABF2 (constitutively expressed). Comparing to protein co-facter association ,enzyme catalysis can produce a large quantity of phosphorylated ABF2 in a short time, then enhances pRD29A to turn on the gene of interest’s expression. When signal 2(OFF) comes,gene PP2CA expresses, dephosphorylating ABF2 and inactivating SnRK2.2, thus turning the system into OFF state.