Difference between revisions of "Team:NAWI Graz/Description"

 
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         <h1>PROJECT DESCRIPTION</h1>
 
         <h1>PROJECT DESCRIPTION</h1>
 
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             The aim of our project <command class="colibot"/> was to create a robot-bacteria interface, where information processing is done by a bacterial culture
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             The aim of project <command class="colibot"/> was to create a robot-bacteria interface. Information processing is done by a bacterial culture that exhibits a feedback loop with a mobile robot. To enable communication between bacteria and robot, we decided to engineer <i>Escherichia coli</i> cells to respond to environmental changes with an increase in fluorescence in the culture. To achieve environment-dependent expression of fluorescence proteins, we used the temperature-inducible ibpA-promoter and two promoters which respond to shifts in pH, the acid-inducible asr-promoter and the alkaline-inducible alx-promoter.  
            that exhibits a feedback loop with a mobile robot. To enable communication between bacteria and robot, we decided to engineer <i>Escherichia coli</i> cells to respond to changes in pH with a change in fluorescence. To achieve pH-dependent expression of fluorescence protein, we used two different promoters: the acid-inducible asr promoter and the alkaline inducible alx promoter.
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<b>Vid. 1:</b> Video about our <command class="colibot"/> project. This video gives a short overview of project <command class="colibot"/>.
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         <h2 class="section-sub">Introduction</h2>
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         <h2 class="section-sub">Project <command class="colibot"/></h2>
 
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           An important area at the cutting edge of technology is the integration of biological systems in mechanical and automated systems. For our iGEM project we therefore chose to take a new approach on the integration of biology into technology. Our goal is the creation of a robot-bacteria interface that acts in a constant feedback loop. We create a pH-sensitive <i>E. coli</i> strain that expresses detectable proteins according to pH-level. The pH-level is determined by the position of a mobile robot in an arena with a virtual pH-gradient. The pH-level indicated by the robot's position is passed on to a bacterial culture in a bioreactor. As a response to the pH-shift, a shift in fluorescence protein expression is achieved due to the pH-sensitive promoters alx and asr. This altered expression correlates with a change in color, that is detectable with an optical system. The data from the optical signal is then sent back to the robot resulting in a response in the form of a directional change. Thus, we can control the motion of the robot through the arena with a constant feedback loop to the bioreactor.
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           An important area at the cutting edge of technology is the integration of biological systems in mechanical and automated systems. For our iGEM project we therefore chose to take a new approach on the integration of biology into technology. Our goal was the creation of a robot-bacteria interface that acts in a constant feedback loop. The first step was to make communication between bacteria and a technical system possible. Therefore, we engineered <i>E. coli</i> cells, which are sensitive to certain environmental conditions. When these conditions are met, the bacteria will express certain detectable proteins.  
 
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In our setup a mobile robot moves through an arena and uses its proximity sensors to measure whether there is a wall in front of it. If the robot detects a wall, a signal will be transferred to a bacterial culture in the form of an environmental change. To provide them with stable conditions, the bacteria are cultivated in a <a href="https://2017.igem.org/Team:NAWI_Graz/Bioreactor">bioreactor</a>. In the bacteria, promoters sensitive to the these environmental changes will be activated and promote the expression of a fluorescent protein.  The resulting fluorescence signal can be detected by an optical system and relayed back to the robot resulting in a response in form of a directional change.  
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For the realization of this concept we created a <a href="https://2017.igem.org/Team:NAWI_Graz/TemperaturePlasmid">temperature-sensitive construct</a> first. The heat shock promoter ibpA controls the expression of one fluorescent protein, which allows a simple yes/no decision. We used it for preliminary experiments to move a robot through a maze. To expand the possibilities of communication we created <a href="https://2017.igem.org/Team:NAWI_Graz/pHPlasmid">constructs sensitive to acidic and alkaline pH</a>. The acid-inducible asr-promoter and the alkaline-inducible alx-promoter are used to control the expression of two different fluorescent proteins. A shift in pH-value will lead to a change of fluorescence and allow navigation of the robot in a more sophisticed way.  
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        <h2 class="section-sub">Detailed Project Description</h2>
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        We designed two different pH-sensitive plasmids, which are transformed in an <i>E. coli</i> strain. Each of the plasmids contains a pH-sensitive promoter. The promoters are induced by different pH-levels. An acidic pH leads to the expression of a red fluorescent protein, mCardinal and an alkaline pH to a green fluorescent protein, mNeonGreen.  
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Both fluorescent proteins contain a N-terminal TEV-site followed by a F-degron. The TEV-site allows the degradation by the TEV-protease. Once the TEV-site is cleaved off, the F-degron can be recognized by the endogenous ClpAP-machinery. This ClpAP-machinery induces the degradation of the fluorescent proteins and enables a faster change in fluorescence, when a pH-shift occurs. This addition could be beneficial in the future to avoid accumulation of fluorescence protein, if you plan to use the same bacterial culture for an extended amount of time. Therefore, the TEV-protease will be integrated into the genome by CRISPR/Cas9, a novel method for gene-editing.
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The fluorescence signals are detected by a camera, leading to maneuvering the robot through an arena. Depending on the fluorescent color of the media, the robot turns either left or right.
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        <h2 class="section-sub">Applications and Implications</h2>
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    One of the possible applications could be a bioreactor with bacteria that control their environment via active feedback. This enables the bacteria to give a signal, if they are in need of a different media composition. For example, if more nutrients or a correction of the pH-level become necessary, bacteria will indicate it and a robot automatically adapts the medium to the circumstances. The technology also holds potential in the creation of reusable biosensors or a controlled bioremediation effort, where bacteria are mobile due to the connection to a robot host.
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Latest revision as of 01:51, 2 November 2017

PROJECT DESCRIPTION

The aim of project was to create a robot-bacteria interface. Information processing is done by a bacterial culture that exhibits a feedback loop with a mobile robot. To enable communication between bacteria and robot, we decided to engineer Escherichia coli cells to respond to environmental changes with an increase in fluorescence in the culture. To achieve environment-dependent expression of fluorescence proteins, we used the temperature-inducible ibpA-promoter and two promoters which respond to shifts in pH, the acid-inducible asr-promoter and the alkaline-inducible alx-promoter.

Vid. 1: Video about our project. This video gives a short overview of project .

Project

An important area at the cutting edge of technology is the integration of biological systems in mechanical and automated systems. For our iGEM project we therefore chose to take a new approach on the integration of biology into technology. Our goal was the creation of a robot-bacteria interface that acts in a constant feedback loop. The first step was to make communication between bacteria and a technical system possible. Therefore, we engineered E. coli cells, which are sensitive to certain environmental conditions. When these conditions are met, the bacteria will express certain detectable proteins. In our setup a mobile robot moves through an arena and uses its proximity sensors to measure whether there is a wall in front of it. If the robot detects a wall, a signal will be transferred to a bacterial culture in the form of an environmental change. To provide them with stable conditions, the bacteria are cultivated in a bioreactor. In the bacteria, promoters sensitive to the these environmental changes will be activated and promote the expression of a fluorescent protein. The resulting fluorescence signal can be detected by an optical system and relayed back to the robot resulting in a response in form of a directional change. For the realization of this concept we created a temperature-sensitive construct first. The heat shock promoter ibpA controls the expression of one fluorescent protein, which allows a simple yes/no decision. We used it for preliminary experiments to move a robot through a maze. To expand the possibilities of communication we created constructs sensitive to acidic and alkaline pH. The acid-inducible asr-promoter and the alkaline-inducible alx-promoter are used to control the expression of two different fluorescent proteins. A shift in pH-value will lead to a change of fluorescence and allow navigation of the robot in a more sophisticed way.