Difference between revisions of "Team:BIT-China/InterLab"

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</head>
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 +
<body>
 +
 
 +
          <ul id="left-nav">
 +
        <li>
 +
            <a>PROJECT</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Background">Background</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Description">Description</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Design">Idea & Design</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>EXPERIMENTS</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsRegulator">Regulator</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsFeedback">Feedback</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/ExperimentsOutput">Output</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Results">Results</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>MODELING</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Model">Overview</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/FluorescentProbesModel">Fluorescent Probe Model </a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/H2O2DecompositionModel">H<sub>2</sub>O<sub>2</sub>
 +
                        Decomposition Model</a></li>
 +
 
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/roGFP2-Orp1MichaelisEquationModel">roGFP2-Orp1
 +
                        Michaelis equation Model</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>HUMAN PRACTICES</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/HPOverview">Overview</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Human_Practices">Integrated Human Practices</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Public_Engagement">Education & Public Engagement</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Collaborations">Collaborations</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>NOTEBOOK</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Notebook">Lab Book</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Protocols">Methodology / Protocols</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Equipment">Material & Equipment</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/InterLab">Measurement / InterLab</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Safety">Safety</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>ACHIEVEMENTS</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/JudgingForm">Judging Form</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Parts">Parts</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Improve">Improve</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Applied_Design">Applied Design</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Demonstrate">Demonstrate</a></li>
 +
            </ul>
 +
        </li>
 +
 
 +
        <li>
 +
            <a>TEAM</a>
 +
            <ul>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Team">Members</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Attributions">Attributions</a></li>
 +
                <li><a href="https://2018.igem.org/Team:BIT-China/Gallery">Gallery</a></li>
 +
            </ul>
 +
        </li>
 +
    </ul>
 +
    <a href="https://2018.igem.org/Team:BIT-China"><img id="imgA" class="imgA-new-pos" src="https://static.igem.org/mediawiki/2018/4/46/T--BIT-China--iGEM2018-A_img.png" /></a>
 +
    <!-- end -->
 +
 
 +
    <div class="NOT-white-head"></div>
 +
 
 +
    <div id="NOT" class="NOT-content-container" style="margin-top: calc(25vh - 30px);">
 +
        <div id="NOT0" class="cd-section">
 +
            <div class="NOT-title">
 +
                <a class="NOT-title-1" style="z-index:1;border-bottom: 3px solid #131313;text-decoration: none;font-size:30px !important;">INTERLAB</a>
 +
            </div>
 +
        </div>
 +
 
 +
        <div id="NOT1" class="cd-section">
 +
            <div class="NOT-title-2 NOT-margin-title2UP">
 +
                <a style="text-decoration: none;color:#131313;">Introduction</a>
 +
            </div>
 +
 
 +
            <div class="NOT-content-all">
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        Interlab is aimed to improve reproducibility and compare the difference between laboratories.
 +
                        To complete this job,we make three sets of unit calibration measurements: an OD600 reference
 +
                        point, a particle standard curve, and a fluorescein standard curve. Completion of the
 +
                        calibrations will ensure that we understand the measurement process and that we can take the
 +
                        cell measurements under the same conditions. For the sake of consistency and reproducibility,
 +
                        we used <i>E. coli</i> K-12 DH5-alpha like other teams. Later, we conducted the CFU experiment.
 +
                        We
 +
                        count colonies for our two Positive Control (BBa_I20270) cultures and two Negative Control
 +
                        (BBa_R0040) cultures.
 +
                    </p>
 +
                </div>
 +
            </div>
 +
 
 +
        </div>
 +
 
 +
        <div id="NOT2" class="cd-section">
 +
            <div class="NOT-title-2 NOT-margin-title2UP">
 +
                <a style="text-decoration: none;color:#131313;">Methods</a>
 +
            </div>
 +
 
 +
            <div class="NOT-content-all">
 +
                <div class="NOT-title-3 NOT-margin-title3UP">
 +
                    <a style="text-decoration: none;color:#131313;">—— OD 600 Reference point - LUDOX Protocol</a>
 +
                </div>
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        We use LUDOX CL-X (45% colloidal silica suspension) as a single point reference to obtain a
 +
                        conversion factor to transform your absorbance (Ab<sub>S600</sub>) data from our plate reader
 +
                        into a
 +
                        comparable OD<sub>600</sub> measurement.
 +
                    </p>
 +
 
 +
                    <div class="NOT-formula">
 +
                        $$ Correction\ factor=\frac{ReferenceOD_{600}}{reading_{LUDOX CL-X}-reading_{H_2 O}} $$
 +
                    </div>
 +
                </div>
 +
 
 +
                <div class="NOT-title-3 NOT-margin-title3UP">
 +
                    <a style="text-decoration: none;color:#131313;">—— Particle Standard Curve - Microsphere Protocol</a>
 +
                </div>
 +
 
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        We prepare a dilution series of monodisperse silica microspheres and measure the Ab<sub>S600</sub>
 +
                        in our
 +
                        plate reader. This measurement allow us to construct a standard curve of particle concentration
 +
                        which can be used to convert Abs600 measurements to an estimated number of cells.
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Prepare the Microsphere Stock Solution
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Prepare the serial dilution of Microspheres
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Measure Ab<sub>S600</sub> of all samples in instrument
 +
                    </p>
 +
                </div>
 +
 
 +
                <div class="NOT-title-3 NOT-margin-title3UP">
 +
                    <a style="text-decoration: none;color:#131313;">——Fluorescence standard curve - Fluorescein
 +
                        Protocol</a>
 +
                </div>
 +
 
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        We will prepare a dilution series of fluorescein in four replicates and measure the
 +
                        fluorescence in a 96 well plate in our plate reader. By measuring these in our plate reader,we
 +
                        generate a
 +
                        standard curve of fluorescence for fluorescein concentration. Thus we are able to use this to
 +
                        convert our cell based readings to an equivalent fluorescein concentration.
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Prepare the fluorescein stock solution
 +
                    </p>
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Prepare the serial dilutions of fluorescein
 +
                    </p>
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Measure fluorescence of all samples in instrument
 +
                    </p>
 +
 
 +
                    <figure class="NOT-Fig NOT-margin-toContentP">
 +
                        <img src="https://static.igem.org/mediawiki/2018/2/21/T--BIT-China--iGEM2018-NOT-InterLab-1.png">
 +
                        <figcaption></figcaption>
 +
                    </figure>
 +
 
 +
                    <figure class="NOT-Fig NOT-margin-toContentP">
 +
                        <img src="https://static.igem.org/mediawiki/2018/8/82/T--BIT-China--iGEM2018-NOT-InterLab-2.png">
 +
                        <figcaption></figcaption>
 +
                    </figure>
 +
                </div>
 +
 
 +
                <div class="NOT-title-3 NOT-margin-title3UP">
 +
                    <a style="text-decoration: none;color:#131313;">—— Cell measurement protocol</a>
 +
                </div>
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        For all of these cell measurements, we use the same plates and volumes that we used in our
 +
                        calibration protocol. For the first time,we have measurements that are off scale (“OVERFLOW”),
 +
                        so we adjust our settings to make the data in range. Finally, we get the right data.
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Transform <i>Escherichia coli</i> DH5α with these following plasmids
 +
                    </p>
 +
 
 +
                    <div class="table-body" style="width:80%;">
 +
                        <table>
 +
                            <colgroup>
 +
                                <col />
 +
                                <col />
 +
                                <col />
 +
                            </colgroup>
 +
                            <tbody style="font-size:16px;">
 +
                                <tr>
 +
                                    <td>Negative control</td>
 +
                                    <td>BBa_R0040</td>
 +
                                    <td>Kit Plate 7 Well 2D</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Positive control</td>
 +
                                    <td>BBa_I20270</td>
 +
                                    <td>Kit Plate 7 Well 2B</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 1</td>
 +
                                    <td> BBa_J364000</td>
 +
                                    <td>Kit Plate 7 Well 2F</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 2 </td>
 +
                                    <td>BBa_J364001</td>
 +
                                    <td>Kit Plate 7 Well 2H</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 3</td>
 +
                                    <td> BBa_J364002</td>
 +
                                    <td>Kit Plate 7 Well 2J</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 4 </td>
 +
                                    <td>BBa_J364007</td>
 +
                                    <td>Kit Plate 7 Well 2L</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 5</td>
 +
                                    <td>BBa_J364008</td>
 +
                                    <td>Kit Plate 7 Well 2N</td>
 +
                                </tr>
 +
                                <tr>
 +
                                    <td>Test Device 6</td>
 +
                                    <td>BBa_J364009</td>
 +
                                    <td>Kit Plate 7 Well 2P</td>
 +
                                </tr>
 +
                            </tbody>
 +
                        </table>
 +
                    </div>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Pick 2 colonies from each of the transformation plates and inoculate in 5-10 mL LB
 +
                        medium
 +
                        +Chloramphenicol. Grow the cells overnight (16-18 hours) at 37°C and 220 rpm
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Cell growth, sampling, and measurement
 +
                    </p>
 +
                </div>
 +
 
 +
                <div class="NOT-title-3 NOT-margin-title3UP">
 +
                    <a style="text-decoration: none;color:#131313;">——Protocol: Colony Forming Units per 0.1 OD600 <i>E.
 +
                            coli</i> cultures</a>
 +
                </div>
 +
 
 +
                <div class="NOT-content">
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        This procedure is used to calibrate OD600 to colony forming unit (CFU) counts, which are
 +
                        directly relatable to the cell concentration of the culture. For the CFU protocol, we count
 +
                        colonies for our two Positive Control (BBa_I20270) cultures and two Negative Control
 +
                        (BBa_R0040) cultures.
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Starting Sample Preparation
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Dilution Series Instructions
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        $\surd$ Calculation
 +
                    </p>
 +
 
 +
                    <p class="NOT-content-p NOT-margin-pUP">
 +
                        <a href="https://static.igem.org/mediawiki/2018/5/55/T--BIT-China--iGEM2018-NOT-excel.xlsx" target="_Blank"
 +
                            style="text-decoration: none;color:#131313;"><b>Check
 +
                            here for more details.</b></a>
 +
                    </p>
 +
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            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">Institute of
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                Biotransformation and synthetic biosystem School of life science
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            <p style="font-size:15px;margin: 0;padding: 0;margin-top: 4px;">
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                Beijing Institute of Technology
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                Email:lichun@bit.edu.cn
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Latest revision as of 01:12, 18 October 2018

Interlab is aimed to improve reproducibility and compare the difference between laboratories. To complete this job,we make three sets of unit calibration measurements: an OD600 reference point, a particle standard curve, and a fluorescein standard curve. Completion of the calibrations will ensure that we understand the measurement process and that we can take the cell measurements under the same conditions. For the sake of consistency and reproducibility, we used E. coli K-12 DH5-alpha like other teams. Later, we conducted the CFU experiment. We count colonies for our two Positive Control (BBa_I20270) cultures and two Negative Control (BBa_R0040) cultures.

We use LUDOX CL-X (45% colloidal silica suspension) as a single point reference to obtain a conversion factor to transform your absorbance (AbS600) data from our plate reader into a comparable OD600 measurement.

$$ Correction\ factor=\frac{ReferenceOD_{600}}{reading_{LUDOX CL-X}-reading_{H_2 O}} $$

We prepare a dilution series of monodisperse silica microspheres and measure the AbS600 in our plate reader. This measurement allow us to construct a standard curve of particle concentration which can be used to convert Abs600 measurements to an estimated number of cells.

$\surd$ Prepare the Microsphere Stock Solution

$\surd$ Prepare the serial dilution of Microspheres

$\surd$ Measure AbS600 of all samples in instrument

We will prepare a dilution series of fluorescein in four replicates and measure the fluorescence in a 96 well plate in our plate reader. By measuring these in our plate reader,we generate a standard curve of fluorescence for fluorescein concentration. Thus we are able to use this to convert our cell based readings to an equivalent fluorescein concentration.

$\surd$ Prepare the fluorescein stock solution

$\surd$ Prepare the serial dilutions of fluorescein

$\surd$ Measure fluorescence of all samples in instrument

For all of these cell measurements, we use the same plates and volumes that we used in our calibration protocol. For the first time,we have measurements that are off scale (“OVERFLOW”), so we adjust our settings to make the data in range. Finally, we get the right data.

$\surd$ Transform Escherichia coli DH5α with these following plasmids

Negative control BBa_R0040 Kit Plate 7 Well 2D
Positive control BBa_I20270 Kit Plate 7 Well 2B
Test Device 1 BBa_J364000 Kit Plate 7 Well 2F
Test Device 2 BBa_J364001 Kit Plate 7 Well 2H
Test Device 3 BBa_J364002 Kit Plate 7 Well 2J
Test Device 4 BBa_J364007 Kit Plate 7 Well 2L
Test Device 5 BBa_J364008 Kit Plate 7 Well 2N
Test Device 6 BBa_J364009 Kit Plate 7 Well 2P

$\surd$ Pick 2 colonies from each of the transformation plates and inoculate in 5-10 mL LB medium +Chloramphenicol. Grow the cells overnight (16-18 hours) at 37°C and 220 rpm

$\surd$ Cell growth, sampling, and measurement

This procedure is used to calibrate OD600 to colony forming unit (CFU) counts, which are directly relatable to the cell concentration of the culture. For the CFU protocol, we count colonies for our two Positive Control (BBa_I20270) cultures and two Negative Control (BBa_R0040) cultures.

$\surd$ Starting Sample Preparation

$\surd$ Dilution Series Instructions

$\surd$ Calculation

Check here for more details.