Difference between revisions of "Team:XJTU-China/Hardware"

 
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         <div class="container row fixedBackground">
 
         <div class="container row fixedBackground">
 
             <div class="fixedBackgroundImg"
 
             <div class="fixedBackgroundImg"
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                 style="background-image: url(https://static.igem.org/mediawiki/2021/f/fd/T--XJTU-China--bg.jpg);">
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                 style="background-image: url(https://static.igem.org/mediawiki/2021/4/40/T--XJTU-China--hardware-bg.jpg);">
 
             </div>
 
             </div>
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             <div class="pageHeadline"><span>Contribution</span></div>
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             <div class="pageHeadline"><span>Hardware</span></div>
 
         </div>
 
         </div>
 
     </section>
 
     </section>
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                 <div class="side col-lg-3">
 
                 <div class="side col-lg-3">
 
                     <nav class="dr-menu">
 
                     <nav class="dr-menu">
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                         <h3>Contribution</h3>
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                         <h3>Hardware</h3>
 
                         <ul>
 
                         <ul>
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                             <li><a class="fa fa-plug" href="#nav-part">&nbsp;Part</a></li>
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                             <li><a class="fa fa-plug" href="#overview">&nbsp;1. Overview</a></li>
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                             <li><a class="fa fa-plug" href="#nav-hardware">&nbsp;Hardware</a></li>
+
                             <li><a class="fa fa-plug" href="#design">&nbsp;2. Design</a>
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                             <li><a class="fa fa-plug" href="#nav-protocol">&nbsp;Protocols</a></li>
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                                <ul>
 +
                                    <li><a class="fa fa-plug" href="#detecting-module">&nbsp;2.1 Detecting Module</a>
 +
                                    </li>
 +
                                    <li><a class="fa fa-plug" href="#controlling-module">&nbsp;2.2 Controlling
 +
                                            Module</a></li>
 +
                                    <li><a class="fa fa-plug" href="#cultivation-module">&nbsp;2.3 Cultivation
 +
                                            Module</a></li>
 +
                                </ul>
 +
                            </li>
 +
                             <li><a class="fa fa-plug" href="#program">&nbsp;3. Program</a></li>
 +
                            <li><a class="fa fa-plug" href="#showcase">&nbsp;4. Showcase</a></li>
 +
 
 
                         </ul>
 
                         </ul>
 
                     </nav>
 
                     </nav>
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                         <div class="row">
 
                         <div class="row">
 
                             <div class="col-12">
 
                             <div class="col-12">
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                                 <h1>Contribution</h1>
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                                 <!-- hardware -->
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                            </div>
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                                <a class="anchor" id="hardware"></a>
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                                <h1>Hardware</h1>
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                            <!-- part -->
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                                 <a class="anchor" id="overview"></a>
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                            <a class="anchor" id="nav-part"></a>
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                                <h2 class="ml-5">1. Overview</h2>
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                            <h2 class="mt-5 ml-5">Part</h2>
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                                <p>In order to realize the coordination of hardware circuit and gene
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                            <div class="col-12 d-flex justify-content-center">
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                                    circuit, we have made an automatic culture device. At the same time of
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                                 <div class="card card-dark" style="width: 90%;">
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                                    detecting the growth and production status of bacteria, the device can
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                                    <button class="btn btn-primary" type="button" data-toggle="collapse"
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                                    feedback and adjust the conditions of culture, thus controlling the
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                                        data-target="#part" aria-expanded="false" aria-controls="part">
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                                    toggle-switch circuit to allow cells to enter different states between
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                                        <h4>Document new published literature in existing parts</h4>
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                                    “proliferation” and “production”. Through the fitting of experimental
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                                    </button>
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                                    results and modeling prediction, we can calculate the best time to
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                                    <div class="collapse" id="part">
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                                    change the cultivation conditions, and write it into the control program
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                                        <div class="card card-body card-dark">
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                                    to realize the automatic control of the production process. </p>
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                                            <h3>Overview</h3>
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                                <a class="anchor" id="design"></a>
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                                            <p>This year, XJTU-China does the literature review about the existing part
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                                <h2 class="ml-5">2. Design</h2>
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                                                (<a href="http://parts.igem.org/Part:BBa_K3196028">BBa_K3196028</a>)
+
                                <div class="imgWrapper centerize">
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                                                held in the iGEM part repository. BBa_K3196028 is a low-pH induced
+
                                    <img src="https://static.igem.org/mediawiki/2021/3/30/T--XJTU-China--POC-Fig1-3.jpeg"
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                                                promoter, Pgas, originally registered by iGEM19_HUST-China, and
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                                        alt="design of hardware" width="80%" class="hoverLarger">
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                                                XJTU-China
+
                                    <span class="description"><strong>Fig. 2.1 The design of
−
                                                appends its functional parameters characterized by Yin et al. (2017),
+
                                             hardware</strong></span>
−
                                                to the footer of the original webpage. Below exhibits the information we
+
−
                                                add on.</p>
+
−
 
+
−
                                            <h3>Functional Parameters of Pgas</h3>
+
−
                                            <p>As is shown in figure below (Yin et al., 2017), the strength of Pgas is
+
−
                                                mainly
+
−
                                                dependent on the pH, while limited influenced by the types of acids.</p>
+
−
                                            <div class="imgWrapper centerize">
+
−
                                                <img src="https://static.igem.org/mediawiki/2021/8/89/T--XJTU-China--Pgas-ref.png"
+
−
                                                    alt="Pgas Reference">
+
−
                                                <span class="description"><strong>Fig. 1 Factors affecting
+
−
                                                        relative Pgas-inducing capacity.</strong> (A) Influence of acid
+
−
                                                    type on
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−
                                                    Pgas-inducing capacity. (B) Influence of citrate concentration on
+
−
                                                    Pgas-inducing capacity. (C) Fold changes in CAD expression at
+
−
                                                    different pHs. Error bars represent the standard errors of the means
+
−
                                                    of results for three biological replicates.</span>
+
−
                                            </div>
+
−
                                            <p>The author gives an equation with linear regression analysis to describe
+
−
                                                the relationship between the relative expression level and pH:</p>
+
−
                                            <p class="text-center">log(E)=[(6.042/pH)-0.9059]</p>
+
−
                                            <p>in which, E represents the relative expression level compared with
+
−
                                                expression at pH 7.0. The correlation coefficient factor R<span
+
−
                                                    class="sup">2</span> is 0.9962.
+
−
                                             </p>
+
−
                                        </div>
+
−
                                    </div>
+
 
                                 </div>
 
                                 </div>
−
                            </div>
+
                                <a class="anchor" id="detecting-module"></a>
−
 
+
                                <h3 class="ml-5">2.1 Detecting Module</h3>
−
 
+
                                <p>We use a simple spectroscopic device to monitor the cell density and the
−
                            <!-- hardware -->
+
                                    concentration of tryptophan in the medium. Our detecting module includes
−
                            <a class="anchor" id="nav-hardware"></a>
+
                                    two sets of tungsten light sources, filters of the corresponding
−
                            <h2 class="mt-5 ml-5">Hardware</h2>
+
                                    wavelength and CCDs. By measuring the absorbance of light filtered to
−
                            <div class="col-12 d-flex justify-content-center">
+
                                    600nm wavelength, the cell density can be represented. While with the
−
                                <div class="card card-dark" style="width: 90%;">
+
                                    presence of tryptophan detection circuit, the light passing through the
−
                                    <button class="btn btn-primary" type="button" data-toggle="collapse"
+
                                    485nm optical filter can excite GFP and its emission light will be
−
                                        data-target="#hardware" aria-expanded="false" aria-controls="part">
+
                                    detected by the CCD after a 510nm filter. After receiving by CCDs, all
−
                                        <h4>Design and construct the prototype of our machine</h4>
+
                                    optical signals of this module are converted into corresponding circuit
−
                                    </button>
+
                                    signals and transmitted to the control module for processing.</p>
−
                                    <div class="collapse" id="hardware">
+
                                <a class="anchor" id="controlling-module"></a>
−
                                        <div class="card card-body card-dark">
+
                                <h3 class="ml-5">2.2 Controlling Module</h3>
−
                                            <h3>1. Overview</h3>
+
                                <p>This module contains a single chip microcomputer (SCM) with its
−
                                            <p>In order to realize the coordination of hardware circuit and gene
+
                                    controlling program, controlling the parts in cultivation module by
−
                                                circuit, we have made an automatic culture device. At the same time of
+
                                    receiving and analyzing the signals from detecting module. After
−
                                                detecting the growth and production status of bacteria, the device can
+
                                    receiving the signal, according to the program written into the SCM, it
−
                                                feedback and adjust the conditions of culture, thus controlling the
+
                                    can calculate the state of the cell density and product concentration in
−
                                                toggle-switch circuit to allow cells to enter different states between
+
                                    the culture medium. When certain conditions are met, corresponding
−
                                                “proliferation” and “production”. Through the fitting of experimental
+
                                    instructions are issued to control the temperature of culture medium and
−
                                                results and modeling prediction, we can calculate the best time to
+
                                    the pumping of inducer, with the information fed back to users in real
−
                                                change the cultivation conditions, and write it into the control program
+
                                    time.</p>
−
                                                to realize the automatic control of the production process. </p>
+
                                <a class="anchor" id="cultivation-module"></a>
−
                                            <h3>2. Design</h3>
+
                                <h3 class="ml-5">2.3 Cultivation Module</h3>
−
                                            <div class="imgWrapper centerize">
+
                                <p>All fermentation and culture conditions are provided by this module. The
−
                                                <img src="https://static.igem.org/mediawiki/2021/3/30/T--XJTU-China--POC-Fig1-3.jpeg"
+
                                    electric heater and ventilator maintain the temperature of the incubator
−
                                                    alt="design of hardware" width="80%" class="hoverLarger">
+
                                    and are controlled by the SCM to switch the temperature between 37 and
−
                                                <span class="description"><strong>Fig. 2.1 The design of
+
                                    42 degrees Celsius. A ration pump can be used to add IPTG to the medium
−
                                                        hardware</strong></span>
+
                                    upon receiving the SCM signal. The main part is a sterile tank made of
−
                                            </div>
+
                                    plexiglass, including a transparent and equal thickness area for
−
                                            <h4>2.1 Detecting Module</h4>
+
                                    spectrophotometry and fluorescence detection. Plus, magnetic stirrer,
−
                                            <p>We use a simple spectroscopic device to monitor the cell density and the
+
                                    ventilation device and other devices for cultivation are also contained
−
                                                concentration of tryptophan in the medium. Our detecting module includes
+
                                    in this module.</p>
−
                                                two sets of tungsten light sources, filters of the corresponding
+
                                <a class="anchor" id="program"></a>
−
                                                wavelength and CCDs. By measuring the absorbance of light filtered to
+
                                <h2 class="ml-5">3. Program</h2>
−
                                                600nm wavelength, the cell density can be represented. While with the
+
                                <p>The core function of this module is realized by STM32 single chip
−
                                                presence of tryptophan detection circuit, the light passing through the
+
                                    microcomputer. The logic control program is designed as follows: the
−
                                                485nm optical filter can excite GFP and its emission light will be
+
                                    digital temperature controller continuously monitors the temperature
−
                                                detected by the CCD after a 510nm filter. After receiving by CCDs, all
+
                                    changes in the container, and keeps communicating with the micro
−
                                                optical signals of this module are converted into corresponding circuit
+
                                    controller. Micro controller controls the relay to turn on the light
−
                                                signals and transmitted to the control module for processing.</p>
+
                                    source and photocell briefly every minute to detect the growth of
−
 
+
                                    biological community in the container. If the electromagnetic wave of
−
                                            <h4>2.2 Controlling Module</h4>
+
                                    600 nanometer wavelength reaches a certain threshold, the micro
−
                                            <p>This module contains a single chip microcomputer (SCM) with its
+
                                    controller opens the relay of the electric heating rod through the
−
                                                controlling program, controlling the parts in cultivation module by
+
                                    digital temperature controller; If the wavelength of 485 nanometer to
−
                                                receiving and analyzing the signals from detecting module. After
+
                                    510 nanometer, the micro controller through the digital temperature
−
                                                receiving the signal, according to the program written into the SCM, it
+
                                    controller to disconnect the relay of the electric heating rod, and
−
                                                can calculate the state of the cell density and product concentration in
+
                                    prompt to replace the solution.</p>
−
                                                the culture medium. When certain conditions are met, corresponding
+
−
                                                instructions are issued to control the temperature of culture medium and
+
−
                                                the pumping of inducer, with the information fed back to users in real
+
−
                                                time.</p>
+
−
                                            <h4>2.3 Cultivation Module</h4>
+
−
                                            <p>All fermentation and culture conditions are provided by this module. The
+
−
                                                electric heater and ventilator maintain the temperature of the incubator
+
−
                                                and are controlled by the SCM to switch the temperature between 37 and
+
−
                                                42 degrees Celsius. A ration pump can be used to add IPTG to the medium
+
−
                                                upon receiving the SCM signal. The main part is a sterile tank made of
+
−
                                                plexiglass, including a transparent and equal thickness area for
+
−
                                                spectrophotometry and fluorescence detection. Plus, magnetic stirrer,
+
−
                                                ventilation device and other devices for cultivation are also contained
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                                                in this module.</p>
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                                            <h3>3. Program</h3>
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                                            <p>The core function of this module is realized by STM32 single chip
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                                                microcomputer. The logic control program is designed as follows: the
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                                                digital temperature controller continuously monitors the temperature
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                                                changes in the container, and keeps communicating with the micro
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                                                controller. Micro controller controls the relay to turn on the light
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                                                source and photocell briefly every minute to detect the growth of
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                                                biological community in the container. If the electromagnetic wave of
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                                                600 nanometer wavelength reaches a certain threshold, the micro
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                                                controller opens the relay of the electric heating rod through the
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                                                digital temperature controller; If the wavelength of 485 nanometer to
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                                                510 nanometer, the micro controller through the digital temperature
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                                                controller to disconnect the relay of the electric heating rod, and
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                                                prompt to replace the solution.</p>
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                                            <h3>4. Showcase</h3>
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                                <a class="anchor" id="showcase"></a>
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                                            <p>Worked by our skillful teammates in hardware group, the prototype of our
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                                <h2 class="ml-5">4. Showcase</h2>
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                                                hardware is
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                                <p>Worked by our skillful teammates in hardware group, the prototype of our hardware is
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                                                built and tested. We record and document a clip of video of this
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                                    built and tested. We record and document a clip of video of this machine, upload it
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                                                machine, upload it to
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                                    to
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                                                iGEM repository, and append it below. </p>
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                                    iGEM repository, and append it below.</p>
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                                            <video
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                                <div class="row">
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                                                src="https://static.igem.org/mediawiki/2021/e/ef/T--XJTU-China--Hardware.mp4"
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                                    <div class="col-12 d-flex justify-content-center">
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                                                class="mt-5 ml-5" width="70%"></video>
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                                        <video src="https://static.igem.org/mediawiki/2021/e/ef/T--XJTU-China--Hardware.mp4"
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                                        </div>
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                                            width="70%" controls preload="metadata"></video>
 
                                     </div>
 
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                            <!-- protocol -->
 
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                            <a class="anchor" id="nav-protocol"></a>
 
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                            <h2 class="mt-5 ml-5">Protocols</h2>
 
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                            <div class="col-12 d-flex justify-content-center">
 
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                                <div class="card card-dark" style="width: 90%;">
 
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                                        data-target="#protocol" aria-expanded="false" aria-controls="protocol">
 
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                                        <h4>Arrange our lab protocols</h4>
 
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                                    </button>
 
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                                    <div class="collapse" id="protocol">
 
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                                            <embed
 
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                                                src="https://static.igem.org/mediawiki/2021/9/93/T--XJTU-China--protocol.pdf"
 
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                                                style="width: 90%; height: 650px;">
 
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                                        </div>
 
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                                    </div>
 
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Latest revision as of 17:07, 21 October 2021

Team:XJTU-China/Contributions

Hardware

Hardware

1. Overview

In order to realize the coordination of hardware circuit and gene circuit, we have made an automatic culture device. At the same time of detecting the growth and production status of bacteria, the device can feedback and adjust the conditions of culture, thus controlling the toggle-switch circuit to allow cells to enter different states between “proliferation” and “production”. Through the fitting of experimental results and modeling prediction, we can calculate the best time to change the cultivation conditions, and write it into the control program to realize the automatic control of the production process.

2. Design

design of hardware Fig. 2.1 The design of hardware

2.1 Detecting Module

We use a simple spectroscopic device to monitor the cell density and the concentration of tryptophan in the medium. Our detecting module includes two sets of tungsten light sources, filters of the corresponding wavelength and CCDs. By measuring the absorbance of light filtered to 600nm wavelength, the cell density can be represented. While with the presence of tryptophan detection circuit, the light passing through the 485nm optical filter can excite GFP and its emission light will be detected by the CCD after a 510nm filter. After receiving by CCDs, all optical signals of this module are converted into corresponding circuit signals and transmitted to the control module for processing.

2.2 Controlling Module

This module contains a single chip microcomputer (SCM) with its controlling program, controlling the parts in cultivation module by receiving and analyzing the signals from detecting module. After receiving the signal, according to the program written into the SCM, it can calculate the state of the cell density and product concentration in the culture medium. When certain conditions are met, corresponding instructions are issued to control the temperature of culture medium and the pumping of inducer, with the information fed back to users in real time.

2.3 Cultivation Module

All fermentation and culture conditions are provided by this module. The electric heater and ventilator maintain the temperature of the incubator and are controlled by the SCM to switch the temperature between 37 and 42 degrees Celsius. A ration pump can be used to add IPTG to the medium upon receiving the SCM signal. The main part is a sterile tank made of plexiglass, including a transparent and equal thickness area for spectrophotometry and fluorescence detection. Plus, magnetic stirrer, ventilation device and other devices for cultivation are also contained in this module.

3. Program

The core function of this module is realized by STM32 single chip microcomputer. The logic control program is designed as follows: the digital temperature controller continuously monitors the temperature changes in the container, and keeps communicating with the micro controller. Micro controller controls the relay to turn on the light source and photocell briefly every minute to detect the growth of biological community in the container. If the electromagnetic wave of 600 nanometer wavelength reaches a certain threshold, the micro controller opens the relay of the electric heating rod through the digital temperature controller; If the wavelength of 485 nanometer to 510 nanometer, the micro controller through the digital temperature controller to disconnect the relay of the electric heating rod, and prompt to replace the solution.

4. Showcase

Worked by our skillful teammates in hardware group, the prototype of our hardware is built and tested. We record and document a clip of video of this machine, upload it to iGEM repository, and append it below.

contact us

Xi'an Jiaotong University
28 Xianning West Road
Xi'an, Shaanxi, China, 710049
xjtu_igem@xjtu.edu.cn
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XJTU-iGEMers