Team:ESBS-Strasbourg/Project/Application
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<li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Results/Modelling"> | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Results/Modelling"> | ||
Modeling</a></li> | Modeling</a></li> | ||
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</ul> | </ul> | ||
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<li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Notebook/Microfluidics"> | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Notebook/Microfluidics"> | ||
Microfluidics</a></li> | Microfluidics</a></li> | ||
+ | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Results/Device">Lighting device</a></li> | ||
<li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Notebook/Labbook"> | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Notebook/Labbook"> | ||
Lab-book</a></li> | Lab-book</a></li> | ||
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<li> | <li> | ||
- | <p><br/><a> | + | <p><br/><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice"> |
HUMAN PRACTICE</a></p> | HUMAN PRACTICE</a></p> | ||
<ul> | <ul> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#organisation"> |
Organisation</a></li> | Organisation</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#survey"> |
Survey</a></li> | Survey</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#video"> |
The ClpX video</a></li> | The ClpX video</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#game"> |
The ClpX game</a></li> | The ClpX game</a></li> | ||
- | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/ | + | <li><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Humanpractice#safety"> |
Project Safety</a></li> | Project Safety</a></li> | ||
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<div class="desc"> | <div class="desc"> | ||
<ul> | <ul> | ||
- | <li><a href="#knock"> | + | <li><a href="#knock">Protein analysis</a></li> |
<li><a href="#flip">Flip Flop</a></li> | <li><a href="#flip">Flip Flop</a></li> | ||
<li><a href="#geneos">Genetic Oscillator </a></li> | <li><a href="#geneos">Genetic Oscillator </a></li> | ||
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<td width="10" rowspan=3 bgcolor="#222222"> | <td width="10" rowspan=3 bgcolor="#222222"> | ||
</div> | </div> | ||
- | + | <div id="windowbox" style="position:fixed; top:50%; left:20px; width:11%;"> | |
+ | <span style="color:ivory;"> | ||
+ | | ||
+ | <a href="https://2010.igem.org/Team:ESBS-Strasbourg/science"> | ||
+ | <img border="0" src="https://static.igem.org/mediawiki/2010/d/da/ESBS-Strasbourg-Clpx.gif" width="70" height="85" ></a> | ||
+ | <br> | ||
+ | Let me guide you</span> | ||
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<div class="desc"> | <div class="desc"> | ||
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<br> | <br> | ||
As previously described, our degradation system consists of an engineered protease which can be activated by light impulses. This allows a tight control over the catalytic activity core enabling the modulation of protein function in a general fashion with the combined characteristics of specificity, high temporal precision and rapid reversibility. | As previously described, our degradation system consists of an engineered protease which can be activated by light impulses. This allows a tight control over the catalytic activity core enabling the modulation of protein function in a general fashion with the combined characteristics of specificity, high temporal precision and rapid reversibility. | ||
- | + | The system is easily adaptable to new targets proteins, the target-labeling only requires the fusion to the specific degradation tag and PIF. This offers a very cheap, easy and applicable method for protein analysis. | |
- | The system is easily adaptable to new targets proteins, the target-labeling only requires the fusion to the specific degradation tag and PIF. This offers a very cheap easy and applicable method for protein analysis. | + | |
<br><br> | <br><br> | ||
- | One of the major advantages is the "non invasive" induction of the protein degradation. Chemical genetics enable perturbations through the introduction of cell membrane-permeable small molecules, allowing the conditional regulation of activity through non-covalent and reversible interactions which is convenient for studies at the cellular level. The use of photolabile ‘‘caged’’ chemical compounds allows to affect subcellular targets in a second-timescale. Some chemical photoswitches such as azobenzene even offer reversible photo-control when attached to macromolecules <i><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Project/Reference"> | + | One of the major advantages is the "non invasive" induction of the protein degradation. Chemical genetics enable perturbations through the introduction of cell membrane-permeable small molecules, allowing the conditional regulation of activity through non-covalent and reversible interactions which is convenient for studies at the cellular level. The use of photolabile ‘‘caged’’ chemical compounds allows to affect subcellular targets in a second-timescale. Some chemical photoswitches such as azobenzene even offer reversible photo-control when attached to macromolecules <i><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Project/Reference">[26]</a></i>. However, the requirement to introduce exogenous, chemically modified materials into cells limits the use of these methods in biological applications. |
<br><br> | <br><br> | ||
<a name="knock"></a> | <a name="knock"></a> | ||
<p><b>A universal tool for protein analysis</b></p> | <p><b>A universal tool for protein analysis</b></p> | ||
- | A complex understanding of living cells requires methods to affect and control the activities of their constituent proteins at fine spatial and temporal resolutions. Measuring responses to precise perturbations, allows the testing and improvement of predictive models of cellular networks.Instead of the induction by chemical agents, the induction of our system is achieved by light impulses. Chemical agents can interfere with host cell metabolism thereby changing their behavior and impact on complex pathways which may create the impossibility of obtaining neutral results. The induction by light enables the studies of target proteins in a natural unaffected environment. | + | A complex understanding of living cells requires methods to affect and control the activities of their constituent proteins at fine spatial and temporal resolutions. Measuring responses to precise perturbations, allows the testing and improvement of predictive models of cellular networks.<br> |
+ | Instead of the induction by chemical agents, the induction of our system is achieved by light impulses. Chemical agents can interfere with host cell metabolism thereby changing their behavior and impact on complex pathways which may create the impossibility of obtaining neutral results. The induction by light enables the studies of target proteins in a natural unaffected environment. | ||
<br> | <br> | ||
Another alternative in protein function studies is the use of gene-knockout techniques. These approaches can provide information about incompletely known gene functions, for instance the role of the corresponding protein in interactions with other proteins. But they do not provide any possibility to study kinetic characteristics or the dynamic of protein interactions. | Another alternative in protein function studies is the use of gene-knockout techniques. These approaches can provide information about incompletely known gene functions, for instance the role of the corresponding protein in interactions with other proteins. But they do not provide any possibility to study kinetic characteristics or the dynamic of protein interactions. | ||
<br> | <br> | ||
- | Our system provides a very effective alternative to this approach. Due to the possibility to regulate protein degradation by light-guided on/off switching of the protease activity, it is a tool to control the level of target protein concentration. The common gene knock out methods do not provide any insight to the impact of varying protein concentration. | + | Our system provides a very effective alternative to this approach. Due to the possibility to regulate protein degradation by light-guided on/off switching of the protease activity, it is a tool to control the level of target protein concentration. The common gene knock out methods do not provide any insight to the impact of varying protein concentration. |
+ | <br><br> | ||
+ | This new system allows through its high turnover rate for proteins <i><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Project/Reference">[13]</a></i> a complete degradation of the protein, simulating a gene knockdown. After light induction with 660nm the system should rest in its active state until a light impulse of 730nm changes its back on its inactive state. So a permanent on switch simulates a gene knockdown as every protein is immediately degraded and a permanent off switch favors the native gene expression. | ||
<br><br> | <br><br> | ||
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With alternating light impulses it should be also possible to adjust certain protein levels by switching the system on and off. This allows the control of complex protein dynamics in vivo as all protein levels can be adjusted to simulate the desired condition. | With alternating light impulses it should be also possible to adjust certain protein levels by switching the system on and off. This allows the control of complex protein dynamics in vivo as all protein levels can be adjusted to simulate the desired condition. | ||
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<a name="flip"></a> | <a name="flip"></a> | ||
<p><b>Flip Flop</b></p> | <p><b>Flip Flop</b></p> | ||
- | The system further allows the control of transcriptional regulation. Another application of this system is the creating of a flip flop mechanism which can be induced by light. This can allow the expression of two different genes sequentially. In the beginning just the gene in gene cassette one is expressed. In the example this is the GPF protein. After a light induction the gene expression is switched to gene cassette two, which is RFP in this example. Figure 2 gives a more detailed description of this mechanism. This allows the tight control of two genes in one host organism. The tight control and sequentially nature of this flip flop mechanism allows a light-controlled multistep synthesis which a huge potential for industrial | + | The system further allows the control of transcriptional regulation. Another application of this system is the creating of a flip flop mechanism which can be induced by light. This can allow the expression of two different genes sequentially. In the beginning just the gene in gene cassette one is expressed. In the example this is the GPF protein. After a light induction the gene expression is switched to gene cassette two, which is RFP in this example. Figure 2 gives a more detailed description of this mechanism. This allows the tight control of two genes in one host organism. The tight control and sequentially nature of this flip flop mechanism allows a light-controlled multistep synthesis which a huge potential for industrial applications. |
<br> | <br> | ||
Moreover several enzymatic steps can be conducted sequentially in one single organism, so even complex biomolecules can be produced in a single bioreactor. This is an enormous gain of time and money. | Moreover several enzymatic steps can be conducted sequentially in one single organism, so even complex biomolecules can be produced in a single bioreactor. This is an enormous gain of time and money. | ||
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<a name="geneos"></a> | <a name="geneos"></a> | ||
<p><b>Genetic Oscillator</b></p> | <p><b>Genetic Oscillator</b></p> | ||
- | The idea of the flip flop mechanism can be extended to a genetic oscillator with three, four or even more sequential steps | + | The idea of the flip flop mechanism can be extended to a genetic oscillator with three, four or even more sequential steps. Such an implementation would present a genetically encoded device to store multiple bits of information within a living cell.<br> |
- | <br>< | + | Natural oscillator circuits are autonomous orchestrating periodic inductions of specific target genes and are found in central and peripheral circadian clocks <i><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Project/Reference">[38]</a></i>. Many physiological activities are coordinated by circadian pacemakers <i><a href="https://2010.igem.org/Team:ESBS-Strasbourg/Project/Reference">[43],[44]</a></i>, making them particular interesting. Synthetic oscillator circuits which mediate protein expression dynamics could provide new insights into protein networks of by simulating natural conditions. <br> |
- | + | <br> | |
+ | Figure 3 shows an example of a three step oscillator. This oscillator is tightly controlled by light and allows the sequentially expression of three different genes. | ||
<br><br> | <br><br> | ||
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</center> | </center> | ||
<br><br><br> | <br><br><br> | ||
- | + | The light-dependent protease with its specific degradation tags is a versatile approach for transcriptional regulation and protein analysis. It gives the synthetic biology community a basic device with a broad range of applications in fundamental research. The only limits are imagination and motivation. | |
+ | <br><br> | ||
</div> | </div> |
Latest revision as of 00:15, 28 October 2010
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