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

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         <h1>DESIGN</h1>
 
         <h1>DESIGN</h1>
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             we introduced three promoters, two sensing the pH and one sensing the temperature of the culture media. Activation
 
             we introduced three promoters, two sensing the pH and one sensing the temperature of the culture media. Activation
 
             of one promoter leads to transcription and translation of a fluorescence protein.
 
             of one promoter leads to transcription and translation of a fluorescence protein.
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            <h3 class="section-sub-sub">"ibpA" - Heat Shock Promoter</h3>
+
        </div>
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            <div class="section-sub-text container">
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        <h3 class="section-sub-sub">"ibpA" - Heat Shock Promoter</h3>
−
                The heat shock promoter ibpA is controlled by the transcription factor σ32. In principle, the exposure to high temperatures
+
        <div class="section-sub-text container">
−
                leads to an increase of σ32, which subsequently enables heat shock promoters to be recognized by the RNA
+
            The heat shock promoter ibpA is controlled by the transcription factor σ32. In principle, the exposure to high temperatures
−
                polymerase. The promoter exhibits a high induction rate and high levels of expression. In our experiment,
+
            leads to an increase of σ32, which subsequently enables heat shock promoters to be recognized by the RNA polymerase.
−
                the ibpA promoter controls the expression of GFP.
+
            The promoter exhibits a high induction rate and high levels of expression. In our experiment, the ibpA promoter
 +
            controls the expression of GFP.
 +
        </div>
 +
        <h3 class="section-sub-sub">"asr" - Acid Inductible Promoter</h3>
 +
        <div class="row">
 +
            <div class="col section-sub-text container">
 +
                Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate
 +
                is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated by a switch
 +
                of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression an extra ribosome
 +
                binding site (RBS) was inserted between the promoter and mCardinal.
 
             </div>
 
             </div>
−
            <h3 class="section-sub-sub">"asr" - Acid Inductible Promoter</h3>
+
             <div class="col section-image border border-secondary">
−
             <div class="section-sub-text container">
+
                 <img src="" alt="[asr inductible promoter]">
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                 <div class="row">
+
−
                    <div class="col">
+
−
                        Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate
+
−
                        is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated
+
−
                        by a switch of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression
+
−
                        an extra ribosome binding site (RBS) was inserted between the promoter and mCardinal.
+
−
                    </div>
+
−
                    <div class="col">
+
−
                        <img src="" alt="[asr inductible promoter]">
+
−
                    </div>
+
−
                </div>
+
 
             </div>
 
             </div>
−
            <h3 class="section-sub-sub">"alx" - Alkaline-induced Roboswitch</h3>
+
 
−
            <div class="section-sub-text container">
+
        </div>
−
                <div class="row">
+
        <h3 class="section-sub-sub">"alx" - Alkaline-induced Roboswitch</h3>
−
                    <div class="col">
+
        <div class="row">
−
                        <img src="" alt="[alx riboswitch]">
+
            <div class="col section-image border border-secondary">
−
                    </div>
+
                <img src="" alt="[alx riboswitch]">
−
                    <div class="col">
+
            </div>
−
                        Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate
+
            <div class="col section-sub-text container">
−
                        is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated
+
                Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate
−
                        by a switch of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression
+
                is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated by a switch
−
                        an extra ribosome binding site (RBS) was inserted between the promoter and mCardinal.
+
                of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression an extra ribosome
−
                    </div>
+
                binding site (RBS) was inserted between the promoter and mCardinal.
−
                </div>
+
 
             </div>
 
             </div>
 
         </div>
 
         </div>
 +
 +
 
     </div>
 
     </div>
 
     <br>
 
     <br>
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         <h2 class="section-sub">The Bioreactor</h2>
 
         <h2 class="section-sub">The Bioreactor</h2>
 
         <div class="section-text container">
 
         <div class="section-text container">
−
             <div class="section-link">([[Parts#Bioreactor|‘’full description’’]])</div>  
+
             <div class="section-link">([[Parts#Bioreactor|‘’full description’’]])</div>
−
             <h3 class="section-sub-sub">subsubsection</h3>
+
             Our system consist of several modules, we differentiate them in 3 layers seen in figure XXX. The layer on top is the INPUT
−
             <div class="section-sub-text container">
+
            layer, it is a steady source of medium or variable liquid, which can be changed and is a key component for its
 +
            variability. The ANALYSE and MAINTAIN layer consists of two elements and the reactor important to maintain our
 +
            culture and two separate measuring units, one of which is the OD600 measure unit and the other one can be changed
 +
            is a variable component (see [[Design#Interaction Modules (IMs)|IMs]] and [[Design#Fluorescence Measurement Chamber
 +
            (FMC)|FMC]] below). Both the variable liquid and the variable measure unit gives us the freedom to change our
 +
            system for different projects. In the OUTPUT layer we collect the waste from our measure units. Further to obtain
 +
            a steady OD600 value the OD600 measure unit also transports medium containing cell mass to the waste to regulate
 +
            the OD600 value if it is too high.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
             <img src="" alt="[Bioreactor]">
 +
        </div>
 +
    </div>
 +
    <br>
  
−
            </div>
+
    <div class="section container">
−
            <h3 class="section-sub-sub">"subsubsection</h3>
+
        <h2 class="section-sub">Interaction Modules (IMs)</h2>
−
            <div class="section-sub-text container">
+
        <div class="section-text container">
−
                <div class="row">
+
            <div class="section-link">([[Parts#InteractionModules|‘’full description’’]])</div>
−
                    <div class="col">
+
            Our system consist of several modules, we differentiate them in 3 layers seen in figure XXX. The layer on top is the INPUT
−
                        texttexttext
+
            layer, it is a steady source of medium or variable liquid, which can be changed and is a key component for its
−
                    </div>
+
            variability. The ANALYSE and MAINTAIN layer consists of two elements and the reactor important to maintain our
−
                    <div class="col">
+
            culture and two separate measuring units, one of which is the OD600 measure unit and the other one can be changed
−
                        <img src="" alt="[image]">
+
            is a variable component (see [[Design#Interaction Modules (IMs)|IMs]] and [[Design#Fluorescence Measurement Chamber
−
                    </div>
+
            (FMC)|FMC]] below). Both the variable liquid and the variable measure unit gives us the freedom to change our
−
                </div>
+
            system for different projects. In the OUTPUT layer we collect the waste from our measure units. Further to obtain
−
             </div>
+
            a steady OD600 value the OD600 measure unit also transports medium containing cell mass to the waste to regulate
 +
            the OD600 value if it is too high.
 +
        </div>
 +
        <h3 class="section-sub-sub">Temperature IM</h3>
 +
        <div class="section-sub-text container">
 +
            In this module, tubes carrying the bacterial suspension are coiled between a Peltier-element and a styrofoam block allowing
 +
            for quick heating of the suspension.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[Temperature IM]">
 +
        </div>
 +
        <h3 class="section-sub-sub">pH IM</h3>
 +
        <div class="section-sub-text container">
 +
             This module consists of two lab bottles, containing acid and base solution. Two peristaltic pumps are controlled according
 +
            to the sensor values of the robot, to specifically set the pH value of the reactor medium.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[pH IM]">
 
         </div>
 
         </div>
 
     </div>
 
     </div>
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     <div class="section container">
 
     <div class="section container">
−
         <h2 class="section-sub">TITLE</h2>
+
         <h2 class="section-sub">Fluorescence Measurement Chamber (FMC)</h2>
 
         <div class="section-text container">
 
         <div class="section-text container">
 +
            <div class="section-link">([[Parts#Fluorescence Measurement Chamber|‘’full description’’]])</div>
 +
            A 3D printed case housing a cuvette (with in- and outflow tubes), LEDs to excite the fluorescent proteins, optical filters
 +
            and a camera-module. We look into the raw RGB data in a region of interest to detect bacterial fluorescence.
 +
            The camera is connected to and controlled by the server ([[Design#Server|see below]]).
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[FMC]">
 +
        </div>
 +
    </div>
 +
    <br>
  
 +
    <div class="section container">
 +
        <h2 class="section-sub">Server</h2>
 +
        <div class="section-text container">
 +
            <div class="section-link">([[Parts#Server|‘’full description’’]])</div>
 +
            A Raspberry Pi [explain? footnote?] that coordinates the behavior of all the components of the system as well as offering
 +
            an interface to users. It maintains a steady-state in the bioreactor, pumps bacterial suspension from the reactor
 +
            into the other modules (the [[Design#Interaction Modules (IMs)|IM]] and [[Design#Fluorescence Measurement Chamber
 +
            (FMC)|FMC]]), controls the behavior of those and communicates with the robot by receiving sensor readings and
 +
            sending commands.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[Server image]">
 
         </div>
 
         </div>
 
     </div>
 
     </div>
−
 
+
    <br>
−
 
+
−
 
+
−
 
+
−
 
+
  
 +
    <div class="section container">
 +
        <h2 class="section-sub">Robot</h2>
 +
        <div class="section-text container">
 +
            <div class="section-link">([[Parts#Robot|‘’full description’’]])</div>
 +
            We hooked up a Raspberry Pi [explain? footnote?] to a Thymio II educational robot [explain? footnote?] in order to enable
 +
            it to communicate with a server on the internet. The robot moves around in a maze and streams its various sensor
 +
            readings to the server, while in return receiving commands from the server (according to bacterial fluorescence)
 +
            to change its behavior.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[Robot image]">
 +
        </div>
 +
    </div>
 +
    <br>
  
 +
    <div class="section container">
 +
        <h2 class="section-sub">Arena</h2>
 +
        <div class="section-text container">
 +
            <div class="section-link">([[Parts#Arena|‘’full description’’]])</div>
 +
            A collection of wooden boards and obstacles that can be used to set up a great variety of environments for the robot, some
 +
            simple, others more challenging.
 +
        </div>
 +
        <div class="section-image border border-secondary">
 +
            <img src="" alt="[Arena image]">
 +
        </div>
 +
    </div>
 +
    <br>
  
  

Revision as of 13:51, 28 October 2017

DESIGN


The bacteria-robot interface is realized as a highly modular feedback system.

A mobile robot’s sensor values alter the environment of ‘’’E. coli’’’ strains that were designed to respond to these changes with increased expression of fluorescent proteins. In turn, this fluorescence is measured and its quantities are translated into robot behaviour.

For how it all played out, see [[Results]], but let’s first have a glimpse at the modules comprising the feedback loop (for a full description see [[Parts]]):


The Bacteria

([[Parts#Bacteria|‘’full description’’]])
Our cultures have one goal: they should react to changes in their environment by expressing fluorescent proteins.  Therefore, we introduced three promoters, two sensing the pH and one sensing the temperature of the culture media. Activation of one promoter leads to transcription and translation of a fluorescence protein.

"ibpA" - Heat Shock Promoter

The heat shock promoter ibpA is controlled by the transcription factor σ32. In principle, the exposure to high temperatures leads to an increase of σ32, which subsequently enables heat shock promoters to be recognized by the RNA polymerase. The promoter exhibits a high induction rate and high levels of expression. In our experiment, the ibpA promoter controls the expression of GFP.

"asr" - Acid Inductible Promoter

Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated by a switch of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression an extra ribosome binding site (RBS) was inserted between the promoter and mCardinal.
[asr inductible promoter]

"alx" - Alkaline-induced Roboswitch

[alx riboswitch]
Promoter activity is controlled by the RstAB System detecting the pH and the PhoRB System activated when inorganic phosphate is rare. Thus, expression only works in low phosphate media (LPM). When grown in LPM and activated by a switch of pH to 5,5 the promoter becomes active and mCardinal is expressed. To enhance expression an extra ribosome binding site (RBS) was inserted between the promoter and mCardinal.

The Bioreactor

([[Parts#Bioreactor|‘’full description’’]])
Our system consist of several modules, we differentiate them in 3 layers seen in figure XXX. The layer on top is the INPUT layer, it is a steady source of medium or variable liquid, which can be changed and is a key component for its variability. The ANALYSE and MAINTAIN layer consists of two elements and the reactor important to maintain our culture and two separate measuring units, one of which is the OD600 measure unit and the other one can be changed is a variable component (see [[Design#Interaction Modules (IMs)|IMs]] and [[Design#Fluorescence Measurement Chamber (FMC)|FMC]] below). Both the variable liquid and the variable measure unit gives us the freedom to change our system for different projects. In the OUTPUT layer we collect the waste from our measure units. Further to obtain a steady OD600 value the OD600 measure unit also transports medium containing cell mass to the waste to regulate the OD600 value if it is too high.
[Bioreactor]

Interaction Modules (IMs)

([[Parts#InteractionModules|‘’full description’’]])
Our system consist of several modules, we differentiate them in 3 layers seen in figure XXX. The layer on top is the INPUT layer, it is a steady source of medium or variable liquid, which can be changed and is a key component for its variability. The ANALYSE and MAINTAIN layer consists of two elements and the reactor important to maintain our culture and two separate measuring units, one of which is the OD600 measure unit and the other one can be changed is a variable component (see [[Design#Interaction Modules (IMs)|IMs]] and [[Design#Fluorescence Measurement Chamber (FMC)|FMC]] below). Both the variable liquid and the variable measure unit gives us the freedom to change our system for different projects. In the OUTPUT layer we collect the waste from our measure units. Further to obtain a steady OD600 value the OD600 measure unit also transports medium containing cell mass to the waste to regulate the OD600 value if it is too high.

Temperature IM

In this module, tubes carrying the bacterial suspension are coiled between a Peltier-element and a styrofoam block allowing for quick heating of the suspension.
[Temperature IM]

pH IM

This module consists of two lab bottles, containing acid and base solution. Two peristaltic pumps are controlled according to the sensor values of the robot, to specifically set the pH value of the reactor medium.
[pH IM]

Fluorescence Measurement Chamber (FMC)

([[Parts#Fluorescence Measurement Chamber|‘’full description’’]])
A 3D printed case housing a cuvette (with in- and outflow tubes), LEDs to excite the fluorescent proteins, optical filters and a camera-module. We look into the raw RGB data in a region of interest to detect bacterial fluorescence. The camera is connected to and controlled by the server ([[Design#Server|see below]]).
[FMC]

Server

([[Parts#Server|‘’full description’’]])
A Raspberry Pi [explain? footnote?] that coordinates the behavior of all the components of the system as well as offering an interface to users. It maintains a steady-state in the bioreactor, pumps bacterial suspension from the reactor into the other modules (the [[Design#Interaction Modules (IMs)|IM]] and [[Design#Fluorescence Measurement Chamber (FMC)|FMC]]), controls the behavior of those and communicates with the robot by receiving sensor readings and sending commands.
[Server image]

Robot

([[Parts#Robot|‘’full description’’]])
We hooked up a Raspberry Pi [explain? footnote?] to a Thymio II educational robot [explain? footnote?] in order to enable it to communicate with a server on the internet. The robot moves around in a maze and streams its various sensor readings to the server, while in return receiving commands from the server (according to bacterial fluorescence) to change its behavior.
[Robot image]

Arena

([[Parts#Arena|‘’full description’’]])
A collection of wooden boards and obstacles that can be used to set up a great variety of environments for the robot, some simple, others more challenging.
[Arena image]

Design

Design is the first step in the design-build-test cycle in engineering and synthetic biology. Use this page to describe the process that you used in the design of your parts. You should clearly explain the engineering principles used to design your project.

This page is different to the "Applied Design Award" page. Please see the Applied Design page for more information on how to compete for that award.

What should this page contain?
  • Explanation of the engineering principles your team used in your design
  • Discussion of the design iterations your team went through
  • Experimental plan to test your designs
Inspiration