Difference between revisions of "Team:Tuebingen/Description"

 
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<h2> Part Documentation</h2>
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<p>Each team will make new parts during iGEM and will submit them to the Registry of Standard Biological Parts. The iGEM software provides an easy way to present the parts your team has created. The <code>&lt;groupparts&gt;</code> tag (see below) will generate a table with all of the parts that your team adds to your team sandbox.</p>
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<script type="text/javascript">
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<p>Remember that the goal of proper part documentation is to describe and define a part, so that it can be used without needing to refer to the primary literature. Registry users in future years should be able to read your documentation and be able to use the part successfully. Also, you should provide proper references to acknowledge previous authors and to provide for users who wish to know more.</p>
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<h4>Note</h4>
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<p>Note that parts must be documented on the <a href="http://parts.igem.org/Main_Page"> Registry</a>. This page serves to <i>showcase</i> the parts you have made. Future teams and other users and are much more likely to find parts by looking in the Registry than by looking at your team wiki.</p>
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    <image width="1920" height="1080" xlink:href="https://static.igem.org/mediawiki/2015/f/f3/Graphical-abstract.png"></image>
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<h4>Adding parts to the registry</h4>
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<p>You can add parts to the Registry at our <a href="http://parts.igem.org/Add_a_Part_to_the_Registry">Add a Part to the Registry</a> link.</p>
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<p>We encourage teams to start completing documentation for their parts on the Registry as soon as you have it available. The sooner you put up your parts, the better you will remember all the details about your parts. Remember, you don't need to send us the DNA sample before you create an entry for a part on the Registry. (However, you <b>do</b> need to send us the DNA sample before the Jamboree. If you don't send us a DNA sample of a part, that part will not be eligible for awards and medal criteria.)</p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:46px;font-weight:bold;color:black;">The expression of the Dronpa-Cre-Dronpa construct is under control of a promotor, that is influenced by a sensor.
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Any biosensor that is able to positively regulate a promotor can be used in our setting.</p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:52px;font-weight:bold;color:black;">After expression the Dronpa-Cre-Dronpa construct is constituted of fluorescent Dronpa domains that attach to each other and thereby inhibit the Cre domain sterically.</p>
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<h4>What information do I need to start putting my parts on the Registry?</h4>
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<p>The information needed to initially create a part on the Registry is:</p>
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<foreignObject x="200" y="780" width="1100" height="300" >
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<li>Part Name</li>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:52px;font-weight:bold;color:black;">Illumination with violet light (400nm) re-activates Dronpa fluorescence and also leads to the closed conformation of the construct.</p>
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<li>Part type</li>
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<li>Creator</li>
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<li>Sequence</li>
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<li>Short Description (60 characters on what the DNA does)</li>
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<li>Long Description (Longer description of what the DNA does)</li>
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<li>Design considerations</li>
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</ul>
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We encourage you to put up <em>much more</em> information as you gather it over the summer. If you have images, plots, characterization data and other information, please also put it up on the part page. </p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:47px;font-weight:bold;color:black;">Illumination with blue light (500nm) deactivates Dronpa fluorescence and thereby also multimerisation of the Dronpa domains.</p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:52px;font-weight:bold;color:black;">In the induced open conformation of the construct, the Dronpa domains are only losely connected to the Cre, which thereby becomes active.</p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:46px;font-weight:bold;color:black;">The RFP-luciferase reporter switch leads to expression of RFP if the memory system has not been activated by CREllumination.</p>
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<p xmlns="http://www.w3.org/1999/xhtml" style="font-size:52px;font-weight:bold;color:black;">After activation of the Cre protein it removes the loxp-RFP-loxp part of the reporter switch. This leads to expression of luciferase, which serves as the final reporter of the system.</p>
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<h4>Inspiration</h4>
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<p>We have a created  a <a href="http://parts.igem.org/Well_Documented_Parts">collection of well documented parts</a> that can help you get started.</p>
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      <a xlink:href="https://2015.igem.org/Team:Tuebingen/Design?slide=3">
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<p> You can also take a look at how other teams have documented their parts in their wiki:</p>
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      <a xlink:href="https://2015.igem.org/Team:Tuebingen/Design?slide=1">
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<li><a href="https://2014.igem.org/Team:MIT/Parts"> 2014 MIT </a></li>
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<li><a href="https://2014.igem.org/Team:Heidelberg/Parts"> 2014 Heidelberg</a></li>
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<li><a href="https://2014.igem.org/Team:Tokyo_Tech/Parts">2014 Tokyo Tech</a></li>
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      <a xlink:href="https://2015.igem.org/Team:Tuebingen/Design?slide=2">
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<h2> Project Description</h2>
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<h4> A Biosensor Memory Module: Cre Sensor</h4>
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<p><Analysis and imaging methods are an indispensable element of every scientific study - in a wider sense the results are only as good as their measurement methods.<br/>
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Photostimulation is one of the most important non-invasive analysis methods allowing researchers to examine the relationship between metabolic processes, e.g. through activating a molecule via light treatment. We want to create a module which makes it possible to take a snapshot of the activity of a sensor at any time.
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Our designed system should be capable of capturing such a ‘snapshot’ of the activity of a sensor. Therefore our aim is to create a Cre recombinase whose activity can be reversibly controlled by light. By activating this construct only for a short period of time, we can use a Cre to switch on expression of Luciferase in only a limited amount of the sensor cells. Through coupling the Cre expression to the sensor we can thereby permanently write the sensor state of a given time point into the DNA of a system. </p>
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<p>
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To achieve the construction of a reversibly activatable Cre recombinase we want to apply the caging mechanism described by Zhou et al <a href="https://2015.igem.org/Team:Tuebingen/References">[Zhou 2012]</a>. This caging is performed by fusing a copy of a variant of the fluorescent protein Dronpa to both the C- and N-terminus of the Cre recombinase. Since this Dronpa variant is able to form monomers or dimers depending on illumination with light of different wavelengths, we hope that the dimerized form inhibits the activity of the Cre recombinase. </p>
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<p>
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Because our system only needs the expression of the caged Cre construct to be dependent on a sensor, it can be combined with almost all Biosensors that include a means of transcriptional control. This gives the system a wide variety of possible applications, especially in the context of the work of other iGEM teams.</p>
  
  
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<h4>Part Table </h4>
 
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<groupparts>iGEM015 Example</groupparts>
 
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Latest revision as of 14:57, 9 November 2015

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Project Description

A Biosensor Memory Module: Cre Sensor

Photostimulation is one of the most important non-invasive analysis methods allowing researchers to examine the relationship between metabolic processes, e.g. through activating a molecule via light treatment. We want to create a module which makes it possible to take a snapshot of the activity of a sensor at any time. Our designed system should be capable of capturing such a ‘snapshot’ of the activity of a sensor. Therefore our aim is to create a Cre recombinase whose activity can be reversibly controlled by light. By activating this construct only for a short period of time, we can use a Cre to switch on expression of Luciferase in only a limited amount of the sensor cells. Through coupling the Cre expression to the sensor we can thereby permanently write the sensor state of a given time point into the DNA of a system.

To achieve the construction of a reversibly activatable Cre recombinase we want to apply the caging mechanism described by Zhou et al [Zhou 2012]. This caging is performed by fusing a copy of a variant of the fluorescent protein Dronpa to both the C- and N-terminus of the Cre recombinase. Since this Dronpa variant is able to form monomers or dimers depending on illumination with light of different wavelengths, we hope that the dimerized form inhibits the activity of the Cre recombinase.

Because our system only needs the expression of the caged Cre construct to be dependent on a sensor, it can be combined with almost all Biosensors that include a means of transcriptional control. This gives the system a wide variety of possible applications, especially in the context of the work of other iGEM teams.