Difference between revisions of "Team:Valencia UPV/InterLab"
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| + | {{Valencia_UPV/bootstrap.css}} | ||
| + | <!--{{Valencia_UPV/bootstrapMin.css}}--> | ||
| + | {{Valencia_UPV/custom.css}} | ||
| + | {{Valencia_UPV/flickity.css}} | ||
| + | {{Valencia_UPV/iconsmind.css}} | ||
| + | {{Valencia_UPV/jquery.steps.css}} | ||
| + | {{Valencia_UPV/lightbox.min.css}} | ||
| + | {{Valencia_UPV/stackinterface.css}} | ||
| + | {{Valencia_UPV/theme.css}} | ||
| + | {{Valencia_UPV/navBar}} | ||
| + | <html> | ||
| + | <style> | ||
| + | |||
| + | #home_logo, #sideMenu { display:none; } | ||
| + | #sideMenu, #top_title, .patrollink {display:none;} | ||
| + | #content { margin-left:0px; margin-top:-30px; padding:0px; width:100%;} | ||
| + | |||
| + | </style> | ||
| + | |||
| + | <head> | ||
| + | <meta charset="utf-8"> | ||
| + | <title>Stack Multipurpose HTML Template</title> | ||
| + | <meta name="viewport" content="width=device-width, initial-scale=1.0"> | ||
| + | <meta name="description" content="Site Description Here"> | ||
| + | <link href="https://fonts.googleapis.com/css?family=Open+Sans:200,300,400,400i,500,600,700%7CMerriweather:300,300i" rel="stylesheet"> | ||
| + | <link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet"> | ||
| + | <link href="https://fonts.googleapis.com/css?family=Lato:400,700,900" rel="stylesheet"> | ||
| + | <link href="https://2018.igem.org/Template:Valencia_UPV/fontAwesome?action=raw&ctype=text/css" rel="stylesheet" type="text/css"> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | </head> | ||
| + | <body class="" style="background-color:#353535;"> | ||
| + | <a class="anchorOffset" id="start"></a> | ||
| + | |||
| + | |||
| + | <!--------- NAVBAR--------------------------------------------------------------------------------------------------------------------------------------------------------------> | ||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | |||
| + | <!------------CONTENEDOR PRINCIPAL ----------------------------------------------------------------------------------------------------------------------------------> | ||
| + | |||
| + | |||
| + | <div class="main-container"> | ||
| + | |||
| + | <section style=" | ||
| + | ; ; background-size: 100%;height: 44.2em;margin-top: 0em;padding-top: 1.1em;" class="height-90 parallax"> | ||
| + | <div class="main-container" style=" | ||
| + | height: 100%;"> | ||
| + | <center style=" | ||
| + | height: 100%;"> | ||
| + | <div class="col-md-10" style=" | ||
| + | height: 100%;margin-top: 4em;"> | ||
| + | <div id="logoPrinteria" class="item" style=" | ||
| + | background-image: url(https://static.igem.org/mediawiki/2018/thumb/1/16/T--Valencia_UPV--InterlabFondoUPV2018.jpeg/1200px-T--Valencia_UPV--InterlabFondoUPV2018.jpeg); | ||
| + | height: 100%; | ||
| + | width: 100%;background-attachment: fixed;background-size: cover;"><img src="https://static.igem.org/mediawiki/2018/thumb/0/0f/T--Valencia_UPV--InterlabTextoUPV2018.jpeg/1200px-T--Valencia_UPV--InterlabTextoUPV2018.jpeg.png" style=" margin-top: 0px;"> | ||
| + | <a class="btn down inner-link active" href="#story" style="font-size: 82%;right: 50%;/* position: fixed; *//* bottom: 7%; */top: 85.2%;z-index: 99;background-color: white;position: absolute;border-radius: 80%;width: 3.8em;height: 3.8em;padding: 0;padding-top: 14px;"> | ||
| + | <i class="stack-interface stack-down-open-big"></i> | ||
| + | </a> | ||
| + | </div> | ||
| + | </div> | ||
| + | </center> | ||
| + | </div><div class="all-page-modals"></div><div class="all-page-modals"></div> | ||
| + | <div class="all-page-modals"></div> | ||
| + | </section> | ||
| + | </div> | ||
| + | <a class="anchorOffset" id="story"></a> | ||
| + | <section class="feature-large" style="padding-top: 6em; padding-bottom: 50px; outline: none;" data-scroll-id="story" tabindex="-1"> | ||
| + | <div class="container"> | ||
| + | <div class="row"> | ||
| + | <div class="col-md-3" style=" | ||
| + | margin-left: 0em; | ||
| + | padding-right: 0px; | ||
| + | padding-left: 0.2em;"> | ||
| + | <div class="tabs-container tabs--vertical page-navigator" style="position: -webkit-sticky;position: sticky;padding-bottom: 0px;margin-top: 11.4em;"> | ||
| + | <h4 style=" | ||
| + | padding-left: 1em; | ||
| + | ">Index</h4> | ||
| + | <ul class="lateral"> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#Introduction" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Introduction</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#goal" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">What is this year's goal?</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#plateReader" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Plate Reader Setup</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#usedParts" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Used Parts</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#od600" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Calibration 1: OD<sub>600</sub> Reference Point</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#particle" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Calibration 2: Particle Standard Curve</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#fluorescence" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Calibration 3: Fluorescence Standard Curve</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#experiment" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Experiment</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <li class="lateral"> | ||
| + | <div class="tab__title" style=" | ||
| + | line-height: 1.3em; | ||
| + | "> | ||
| + | <a href="#app" class="lateral inner-link" style=" | ||
| + | color: #353535; | ||
| + | opacity: 1; | ||
| + | ">Application</a> | ||
| + | </div> | ||
| + | </li> | ||
| + | <!--</ul> | ||
| + | <ul class="tabs-content">--> | ||
| + | |||
| + | <!--What is this years...--> | ||
| + | <!--Plate reader...--> | ||
| + | <!--Used parts--> | ||
| + | <!--Calibration 1, 2 y 3--> | ||
| + | <!--Experiment--> | ||
| + | |||
| + | </ul> | ||
| + | </div> | ||
| + | </div> | ||
| + | <div class="col-md-9" style=" | ||
| + | /* margin-left: 0px; */ | ||
| + | padding-left: 6em; | ||
| + | padding-right: 2em; | ||
| + | "> | ||
| + | <div style=" | ||
| + | "> | ||
| + | <!--<h1 style=" | ||
| + | color: #353535; | ||
| + | ">Lorem ipsum</h1>--> | ||
| + | <!--<h2 style=" | ||
| + | color: #353535; | ||
| + | ">Lorem ipsum</h2>--> | ||
| + | |||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> </p> | ||
| + | <a class="anchorOffset" id="Introduction"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | "> | ||
| + | Introduction | ||
| + | </h4> | ||
| + | <!--<h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Lorem ipsum</h5>--> | ||
| + | <!--<h6 style=" | ||
| + | color: #797979; | ||
| + | ">Lorem ipsum</h6>--> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Do you imagine doing an experiment that could not be repeated? What if, after performing the same experiment several times, you obtain <b>different results each time</b>? This is a <6>common problem</6> throughout almost all laboratories in the entire world. A <b>challenge</b>, not just for Synthetic Biology but for any type of science, is <b>taking reliable and repeatable measurements</b>. | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Over the past four years, the <b>iGEM Measurement Committee</b> has been developing a series of experiments to make <b>the biggest interlaboratory</b> studies ever done in synthetic biology, and, in that way, try to <b>fix all possible variables</b> within a particular protocol. | ||
| + | </p><p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | </p> | ||
| + | <p></p> | ||
| + | <a class="anchorOffset" id="goal"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">What is this year's goal?</h4> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | To know if there is any chance to <b>reduce lab-to-lab variability in fluorescence measurements</b> by normalizing to absolute cell count or <b>c-forming units</b> (CFUs) instead of optical density (OD). | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> In order to compute the cell count in our samples, we will use two orthogonal <b>approaches</b>: | ||
| + | </p> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Approach 1: Converting between absorbance of cells to absorbance of a known concentration of beads</h5> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | The theory under how absorbance is measured is quite simple: a <b>liquid sample of cells scatter light</b> in a way or another depending on the number of cells this sample contains. The Committee provides us a sample with <b>silica beads</b> which are almost the <b>same size and shape as a typical E. coli cell</b>. So, when mixed with water, we obtain a liquid that should scatter light in a similar way as our E. coli sample does. | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | Because we know the concentration of beads, the absorbance measurement from a particular cell sample could be converted into an “equivalent concentration of beads” measurement, so that they are <b>more universal and comparable measurements</b> between different labs. | ||
| + | </p> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Approach 2: Counting c-forming units (CFUs) from the sample</h5> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | This method relies on the idea that every colony grown in our plate <b>comes from a single cell</b>. So, if we spread a known cell culture volume over an agar plate and then we count the number of colonies, we should have an idea on how many cells our liquid sample had. We will have to <b>determine the number of CFUs in positive and negative control samples</b> in order to compute a conversion factor from absorbance to CFU. | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | </p> | ||
| + | <a class="anchorOffset" id="plateReader"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Plate reader setup</h4> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Absorbance<sub>600</sub></h5> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Absorbance Endpoint | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Full Plate | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Wavelengths: 600 nm | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;">Read Speed: Normal, Delay: 100 msec, Measurements/Data Point: 8 | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | </p> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Fluorescence</h5> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Excitation: 485, Emission: 528 | ||
| + | </p><p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Optics: Top, Gain: 50 | ||
| + | </p><p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Light Source: Xenon Flash, Lamp Energy: High | ||
| + | </p><p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Read Speed: Normal, Delay: 100 msec, Measurements/Data Point: 10 | ||
| + | </p><p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Read Height: 7 mm | ||
| + | </p> | ||
| + | <a class="anchorOffset" id="usedParts"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Used Parts</h4> | ||
| + | <div> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Device</th> | ||
| + | <th class="thHec">Part number</th> | ||
| + | <th class="thHec">Plate</th> | ||
| + | <th class="thHec">Location</th> | ||
| + | </tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">Negative control</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_R0040">BBa_R0040</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2D</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">Positive control</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_I20270">BBa_I20270</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2B</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 1</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364000">BBa_J364000</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2F</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 2</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364001">BBa_J364001</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2H</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 3</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364002">BBa_J364002</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2J</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 4</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364007">BBa_J364007</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2L</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 5</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364008">BBa_J364008</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2N</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Test Device 6</td> | ||
| + | <td class="tdHec"><a href="http://parts.igem.org/Part:BBa_J364009">BBa_J364009</a></td> | ||
| + | <td class="tdHec">Kit Plate 7</td> | ||
| + | <td class="tdHec">Well 2P</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 1. Used parts, links, and well information.</h6> | ||
| + | <a class="anchorOffset" id="od600"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Calibration 1: OD<sub>600</sub> Reference Point</h4> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Using <b>LUDOX CL-X </b> as a point reference to obtain a conversion factor to transform our absorbance (Abs<sub>600</sub>) data from our plate reader into a comparable OD<sub>600</sub> measurement as would be obtained in a spectrophotometer. | ||
| + | </p> | ||
| + | <div> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec"></th> | ||
| + | <th class="thHec">LUDOX CL-X</th> | ||
| + | <th class="thHec">H2O</th> | ||
| + | </tr></thead><tbody><tr> | ||
| + | <td class="tdHec">R1</td> | ||
| + | <td class="tdHec">0.061</td> | ||
| + | <td class="tdHec">0.051</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">R2</td> | ||
| + | <td class="tdHec">0.060</td> | ||
| + | <td class="tdHec">0.049</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">R3</td> | ||
| + | <td class="tdHec">0.061</td> | ||
| + | <td class="tdHec">0.043</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">R4</td> | ||
| + | <td class="tdHec">0.062</td> | ||
| + | <td class="tdHec">0.049</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Arithmetic Mean</td> | ||
| + | <td class="tdHec">0.061</td> | ||
| + | <td class="tdHec">0.048</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Corrected Abs<sub>600</sub></td> | ||
| + | <td class="tdHec">0.013</td> | ||
| + | </tr> | ||
| + | <tr><td class="tdHec">Reference OD<sub>600</sub></td> | ||
| + | <td class="tdHec">0.063 | ||
| + | </td></tr> | ||
| + | <tr><td class="tdHec">OD<sub>600</sub>/Abs<sub>600</sub></td> | ||
| + | <td class="tdHec">4.846</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 2. OD<sub>600</sub> reference point.</h6> | ||
| + | <a class="anchorOffset" id="particle"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Calibration 2: Particle Standard Curve</h4> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> This allows us to construct a standard curve of particle concentration which can be used <b>to convert Abs<sub>600</sub> measurements to an estimated number of cells</b>. | ||
| + | </p> | ||
| + | <div style="padding-bottom: 0.8em;text-align: right;"> | ||
| + | <div class="row" style=" | ||
| + | margin: 0; | ||
| + | "> | ||
| + | <div class="col-md-6" style=" | ||
| + | padding: 0; | ||
| + | padding-right: 0.3em; | ||
| + | "> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/3/3f/T--Valencia_UPV--im1UPV2018.jpeg" alt="" style=" | ||
| + | margin-top: 1.8em; | ||
| + | margin-bottom: 0.8em; | ||
| + | border-radius: 0.3em; | ||
| + | "> | ||
| + | </div> | ||
| + | <div class="col-md-6" style=" | ||
| + | padding: 0; | ||
| + | padding-left: 0.3em; | ||
| + | "> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/2/28/T--Valencia_UPV--im2UPV2018.jpeg" alt="" style=" | ||
| + | margin-top: 1.8em; | ||
| + | margin-bottom: 0.8em; | ||
| + | border-radius: 0.3em; | ||
| + | "> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
| + | <h6> Figure 1. Particle standard curve and particle standard curve in logarithmic scale.</h6> | ||
| + | <a class="anchorOffset" id="fluorescence"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Calibration 3: Fuorescence Standard Curve</h4> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> Absolute fluorescence values cannot be directly compared from one instrument to another. In order <b>to compare fluorescence output of test devices</b> between teams, it is necessary for each team to create a standard fluorescence curve. | ||
| + | </p> | ||
| + | <div style=" | ||
| + | padding-bottom: 0.8em; | ||
| + | text-align: right; | ||
| + | " class="col-md-12"> | ||
| + | <div class="row" style=" | ||
| + | margin: 0; | ||
| + | "> | ||
| + | <div class="col-md-6" style=" | ||
| + | padding: 0; | ||
| + | padding-right: 0.3em; | ||
| + | "> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/2/2e/T--Valencia_UPV--im3UPV2018.jpeg" alt="" style=" | ||
| + | margin-top: 1.8em; | ||
| + | margin-bottom: 0.8em; | ||
| + | border-radius: 0.3em; | ||
| + | "> | ||
| + | </div> | ||
| + | <div class="col-md-6" style=" | ||
| + | padding: 0; | ||
| + | padding-left: 0.3em; | ||
| + | "> | ||
| + | <img src="https://static.igem.org/mediawiki/2018/2/23/T--Valencia_UPV--im4UPV2018.jpeg" alt="" style=" | ||
| + | margin-top: 1.8em; | ||
| + | margin-bottom: 0.8em; | ||
| + | border-radius: 0.3em; | ||
| + | "> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
| + | <h6>Figure 2. Fluorescein standard curve and fluorescein standard curve in logarithmic scale.</h6> | ||
| + | <a class="anchorOffset" id="experiment"></a> | ||
| + | <h4 style=" | ||
| + | color: #353535; | ||
| + | font-weight: 700; | ||
| + | font-size: 21px; | ||
| + | margin-bottom: 0.8em; | ||
| + | ">Experiment</h4> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Fluorescence Raw Readings:</h5> | ||
| + | <div style=" | ||
| + | padding-left: 0px; padding-bottom: 0.8em; text-align: right;" class="col-md-12"> | ||
| + | <table class=" border--round table--alternate-row tableHec" style=" | ||
| + | width: 100%;"> | ||
| + | <thead><tr style=" | ||
| + | ;"> | ||
| + | <th class="thHec" style=" | ||
| + | ;">Hour 0:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | <th class="thHec">LB+Chlor (blank)</th></tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">3618</td> | ||
| + | <td class="tdHec">3087</td> | ||
| + | <td class="tdHec">5355</td> | ||
| + | <td class="tdHec">2950</td> | ||
| + | <td class="tdHec">3402</td> | ||
| + | <td class="tdHec">4799</td> | ||
| + | <td class="tdHec">4112</td> | ||
| + | <td class="tdHec">3901</td> | ||
| + | <td class="tdHec">3350</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">3648</td> | ||
| + | <td class="tdHec">3414</td> | ||
| + | <td class="tdHec">5158</td> | ||
| + | <td class="tdHec">2887</td> | ||
| + | <td class="tdHec">3260</td> | ||
| + | <td class="tdHec">4647</td> | ||
| + | <td class="tdHec">4159</td> | ||
| + | <td class="tdHec">3758</td> | ||
| + | <td class="tdHec">3193</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">3273</td> | ||
| + | <td class="tdHec">3442</td> | ||
| + | <td class="tdHec">5077</td> | ||
| + | <td class="tdHec">1611</td> | ||
| + | <td class="tdHec">3331</td> | ||
| + | <td class="tdHec">4607</td> | ||
| + | <td class="tdHec">3972</td> | ||
| + | <td class="tdHec">3793</td> | ||
| + | <td class="tdHec">3234</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">3301</td> | ||
| + | <td class="tdHec">1381</td> | ||
| + | <td class="tdHec">5307</td> | ||
| + | <td class="tdHec">1074</td> | ||
| + | <td class="tdHec">3446</td> | ||
| + | <td class="tdHec">4519</td> | ||
| + | <td class="tdHec">4416</td> | ||
| + | <td class="tdHec">3804</td> | ||
| + | <td class="tdHec">3221</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">3350</td> | ||
| + | <td class="tdHec">3537</td> | ||
| + | <td class="tdHec">5091</td> | ||
| + | <td class="tdHec">3702</td> | ||
| + | <td class="tdHec">3976</td> | ||
| + | <td class="tdHec">4621</td> | ||
| + | <td class="tdHec">4517</td> | ||
| + | <td class="tdHec">3969</td> | ||
| + | <td class="tdHec">3256</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">3262</td> | ||
| + | <td class="tdHec">3409</td> | ||
| + | <td class="tdHec">4758</td> | ||
| + | <td class="tdHec">3623</td> | ||
| + | <td class="tdHec">3660</td> | ||
| + | <td class="tdHec">4208</td> | ||
| + | <td class="tdHec">4679</td> | ||
| + | <td class="tdHec">3867</td> | ||
| + | <td class="tdHec">3265</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">3255</td> | ||
| + | <td class="tdHec">3401</td> | ||
| + | <td class="tdHec">4784</td> | ||
| + | <td class="tdHec">3620</td> | ||
| + | <td class="tdHec">3662</td> | ||
| + | <td class="tdHec">4248</td> | ||
| + | <td class="tdHec">4481</td> | ||
| + | <td class="tdHec">3951</td> | ||
| + | <td class="tdHec">3231</td> | ||
| + | </tr> <tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">3225</td> | ||
| + | <td class="tdHec">3020</td> | ||
| + | <td class="tdHec">4855</td> | ||
| + | <td class="tdHec">3518</td> | ||
| + | <td class="tdHec">3672</td> | ||
| + | <td class="tdHec">4451</td> | ||
| + | <td class="tdHec">4281</td> | ||
| + | <td class="tdHec">4183</td> | ||
| + | <td class="tdHec">4070</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 3. Fluorescence raw readings, 0 hours.</h6> | ||
| + | |||
| + | <div class="col-md-12" style=" | ||
| + | padding-left: 0px;"> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 6:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | <th class="thHec">LB+Chlor (blank)</th></tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">4087</td> | ||
| + | <td class="tdHec">23103</td> | ||
| + | <td class="tdHec">44980</td> | ||
| + | <td class="tdHec">7751</td> | ||
| + | <td class="tdHec">4312</td> | ||
| + | <td class="tdHec">29208</td> | ||
| + | <td class="tdHec">6183</td> | ||
| + | <td class="tdHec">10720</td> | ||
| + | <td class="tdHec">3306</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">4238</td> | ||
| + | <td class="tdHec">23435</td> | ||
| + | <td class="tdHec">46319</td> | ||
| + | <td class="tdHec">7594</td> | ||
| + | <td class="tdHec">4341</td> | ||
| + | <td class="tdHec">28505</td> | ||
| + | <td class="tdHec">6522</td> | ||
| + | <td class="tdHec">10895</td> | ||
| + | <td class="tdHec">3177</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">4194</td> | ||
| + | <td class="tdHec">23871</td> | ||
| + | <td class="tdHec">45601</td> | ||
| + | <td class="tdHec">7757</td> | ||
| + | <td class="tdHec">4371</td> | ||
| + | <td class="tdHec">28765</td> | ||
| + | <td class="tdHec">6359</td> | ||
| + | <td class="tdHec">10515</td> | ||
| + | <td class="tdHec">3260</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">4195</td> | ||
| + | <td class="tdHec">24568</td> | ||
| + | <td class="tdHec">45744</td> | ||
| + | <td class="tdHec">7709</td> | ||
| + | <td class="tdHec">4546</td> | ||
| + | <td class="tdHec">29372</td> | ||
| + | <td class="tdHec">6156</td> | ||
| + | <td class="tdHec">11334</td> | ||
| + | <td class="tdHec">3205</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">4398</td> | ||
| + | <td class="tdHec">11707</td> | ||
| + | <td class="tdHec">43194</td> | ||
| + | <td class="tdHec">17428</td> | ||
| + | <td class="tdHec">4756</td> | ||
| + | <td class="tdHec">28009</td> | ||
| + | <td class="tdHec">11866</td> | ||
| + | <td class="tdHec">10612</td> | ||
| + | <td class="tdHec">3269</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">4351</td> | ||
| + | <td class="tdHec">12443</td> | ||
| + | <td class="tdHec">43496</td> | ||
| + | <td class="tdHec">17570</td> | ||
| + | <td class="tdHec">4804</td> | ||
| + | <td class="tdHec">28545</td> | ||
| + | <td class="tdHec">11928</td> | ||
| + | <td class="tdHec">10545</td> | ||
| + | <td class="tdHec">3250</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">4291</td> | ||
| + | <td class="tdHec">11451</td> | ||
| + | <td class="tdHec">43156</td> | ||
| + | <td class="tdHec">17421</td> | ||
| + | <td class="tdHec">4796</td> | ||
| + | <td class="tdHec">28475</td> | ||
| + | <td class="tdHec">11726</td> | ||
| + | <td class="tdHec">10544</td> | ||
| + | <td class="tdHec">3295</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">4292</td> | ||
| + | <td class="tdHec">12396</td> | ||
| + | <td class="tdHec">42704</td> | ||
| + | <td class="tdHec">17353</td> | ||
| + | <td class="tdHec">4938</td> | ||
| + | <td class="tdHec">28869</td> | ||
| + | <td class="tdHec">11517</td> | ||
| + | <td class="tdHec">10546</td> | ||
| + | <td class="tdHec">3231</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 4. Fluorescence raw readings, 6 hours.</h6> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">Abs<sub>600</sub> Raw Readings:</h5> | ||
| + | <div class="col-md-12" style="padding-left: 0px;"> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 0:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | <th class="thHec">LB+Chlor (blank)</th></tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">0.067</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.060</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.047</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">0.061</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.054</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.046</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.047</td> | ||
| + | <td class="tdHec">0.065</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.045</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">0.062</td> | ||
| + | <td class="tdHec">0.047</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.048</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.045</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.046</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.054</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.054</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.047</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">0.071</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.071</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">0.046</td> | ||
| + | </tr> <tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">0.055</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.056</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | <td class="tdHec">0.049</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 5. Abs<sub>600</sub> Raw Readings, 0 hours.</h6> | ||
| + | <div class="col-md-12" style="padding-left: 0px;"> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 6:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | <th class="thHec">LB+Chlor (blank)</th></tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">0.595</td> | ||
| + | <td class="tdHec">0.513</td> | ||
| + | <td class="tdHec">0.471</td> | ||
| + | <td class="tdHec">0.391</td> | ||
| + | <td class="tdHec">0.554</td> | ||
| + | <td class="tdHec">0.518</td> | ||
| + | <td class="tdHec">0.083</td> | ||
| + | <td class="tdHec">0.487</td> | ||
| + | <td class="tdHec">0.066</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">0.567</td> | ||
| + | <td class="tdHec">0.527</td> | ||
| + | <td class="tdHec">0.508</td> | ||
| + | <td class="tdHec">0.363</td> | ||
| + | <td class="tdHec">0.556</td> | ||
| + | <td class="tdHec">0.519</td> | ||
| + | <td class="tdHec">0.084</td> | ||
| + | <td class="tdHec">0.501</td> | ||
| + | <td class="tdHec">0.053</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">0.566</td> | ||
| + | <td class="tdHec">0.524</td> | ||
| + | <td class="tdHec">0.479</td> | ||
| + | <td class="tdHec">0.381</td> | ||
| + | <td class="tdHec">0.566</td> | ||
| + | <td class="tdHec">0.501</td> | ||
| + | <td class="tdHec">0.083</td> | ||
| + | <td class="tdHec">0.490</td> | ||
| + | <td class="tdHec">0.059</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">0.580</td> | ||
| + | <td class="tdHec">0.570</td> | ||
| + | <td class="tdHec">0.530</td> | ||
| + | <td class="tdHec">0.373</td> | ||
| + | <td class="tdHec">0.549</td> | ||
| + | <td class="tdHec">0.559</td> | ||
| + | <td class="tdHec">0.088</td> | ||
| + | <td class="tdHec">0.551</td> | ||
| + | <td class="tdHec">0.051</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">0.611</td> | ||
| + | <td class="tdHec">0.513</td> | ||
| + | <td class="tdHec">0.519</td> | ||
| + | <td class="tdHec">0.531</td> | ||
| + | <td class="tdHec">0.515</td> | ||
| + | <td class="tdHec">0.530</td> | ||
| + | <td class="tdHec">0.117</td> | ||
| + | <td class="tdHec">0.520</td> | ||
| + | <td class="tdHec">0.053</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">0.562</td> | ||
| + | <td class="tdHec">0.538</td> | ||
| + | <td class="tdHec">0.523</td> | ||
| + | <td class="tdHec">0.536</td> | ||
| + | <td class="tdHec">0.522</td> | ||
| + | <td class="tdHec">0.543</td> | ||
| + | <td class="tdHec">0.116</td> | ||
| + | <td class="tdHec">0.517</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">0.561</td> | ||
| + | <td class="tdHec">0.493</td> | ||
| + | <td class="tdHec">0.517</td> | ||
| + | <td class="tdHec">0.507</td> | ||
| + | <td class="tdHec">0.518</td> | ||
| + | <td class="tdHec">0.502</td> | ||
| + | <td class="tdHec">0.106</td> | ||
| + | <td class="tdHec">0.488</td> | ||
| + | <td class="tdHec">0.054</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">0.555</td> | ||
| + | <td class="tdHec">0.537</td> | ||
| + | <td class="tdHec">0.498</td> | ||
| + | <td class="tdHec">0.512</td> | ||
| + | <td class="tdHec">0.533</td> | ||
| + | <td class="tdHec">0.508</td> | ||
| + | <td class="tdHec">0.101</td> | ||
| + | <td class="tdHec">0.491</td> | ||
| + | <td class="tdHec">0.06</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 6. Abs<sub>600</sub> Raw Readings, 6 hours. </h6> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | "><meta charset="utf-8">μM Fluorescein/OD:</h5> | ||
| + | <div> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 0:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | </tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">0.415</td> | ||
| + | <td class="tdHec">-1.019</td> | ||
| + | <td class="tdHec">4.780</td> | ||
| + | <td class="tdHec">-1.377</td> | ||
| + | <td class="tdHec">0.134</td> | ||
| + | <td class="tdHec">3.742</td> | ||
| + | <td class="tdHec">2.362</td> | ||
| + | <td class="tdHec">1.423</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">0.940</td> | ||
| + | <td class="tdHec">0.685</td> | ||
| + | <td class="tdHec">5.075</td> | ||
| + | <td class="tdHec">-1.185</td> | ||
| + | <td class="tdHec">0.160</td> | ||
| + | <td class="tdHec">4.506</td> | ||
| + | <td class="tdHec">2.495</td> | ||
| + | <td class="tdHec">1.459</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">0.101</td> | ||
| + | <td class="tdHec">0.496</td> | ||
| + | <td class="tdHec">4.760</td> | ||
| + | <td class="tdHec">-25.149</td> | ||
| + | <td class="tdHec">0.150</td> | ||
| + | <td class="tdHec">3.273</td> | ||
| + | <td class="tdHec">2.079</td> | ||
| + | <td class="tdHec">1.237</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">0.155</td> | ||
| + | <td class="tdHec">-28.512</td> | ||
| + | <td class="tdHec">4.973</td> | ||
| + | <td class="tdHec">-22.179</td> | ||
| + | <td class="tdHec">0.536</td> | ||
| + | <td class="tdHec">3.352</td> | ||
| + | <td class="tdHec">3.086</td> | ||
| + | <td class="tdHec">1.291</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">0.324</td> | ||
| + | <td class="tdHec">0.968</td> | ||
| + | <td class="tdHec">4.739</td> | ||
| + | <td class="tdHec">1.536</td> | ||
| + | <td class="tdHec">1.716</td> | ||
| + | <td class="tdHec">4.700</td> | ||
| + | <td class="tdHec">3.908</td> | ||
| + | <td class="tdHec">2.210</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">-0.012</td> | ||
| + | <td class="tdHec">0.372</td> | ||
| + | <td class="tdHec">6.610</td> | ||
| + | <td class="tdHec">1.233</td> | ||
| + | <td class="tdHec">1.224</td> | ||
| + | <td class="tdHec">4.175</td> | ||
| + | <td class="tdHec">3.652</td> | ||
| + | <td class="tdHec">1.696</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">0.030</td> | ||
| + | <td class="tdHec">0.585</td> | ||
| + | <td class="tdHec">4.813</td> | ||
| + | <td class="tdHec">0.482</td> | ||
| + | <td class="tdHec">1.336</td> | ||
| + | <td class="tdHec">2.865</td> | ||
| + | <td class="tdHec">3.522</td> | ||
| + | <td class="tdHec">1.859</td> | ||
| + | </tr> <tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">-3.741</td> | ||
| + | <td class="tdHec">-3.254</td> | ||
| + | <td class="tdHec">4.055</td> | ||
| + | <td class="tdHec">-2.138</td> | ||
| + | <td class="tdHec">-2.056</td> | ||
| + | <td class="tdHec">1.581</td> | ||
| + | <td class="tdHec">0.934</td> | ||
| + | <td class="tdHec">0.350</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <div> | ||
| + | <h6>Table 7. <meta charset="utf-8">μM Fluorescein/OD, 0 hours. </h6> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 6:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | </tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdHec">C1, R1</td> | ||
| + | <td class="tdHec">0.046</td> | ||
| + | <td class="tdHec">1.373</td> | ||
| + | <td class="tdHec">3.189</td> | ||
| + | <td class="tdHec">0.424</td> | ||
| + | <td class="tdHec">0.064</td> | ||
| + | <td class="tdHec">1.776</td> | ||
| + | <td class="tdHec">5.245</td> | ||
| + | <td class="tdHec">0.546</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdHec">C1, R2</td> | ||
| + | <td class="tdHec">0.064</td> | ||
| + | <td class="tdHec">1.325</td> | ||
| + | <td class="tdHec">2.939</td> | ||
| + | <td class="tdHec">0.442</td> | ||
| + | <td class="tdHec">0.072</td> | ||
| + | <td class="tdHec">1.684</td> | ||
| + | <td class="tdHec">3.344</td> | ||
| + | <td class="tdHec">0.534</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R3</td> | ||
| + | <td class="tdHec">0.057</td> | ||
| + | <td class="tdHec">1.374</td> | ||
| + | <td class="tdHec">3.124</td> | ||
| + | <td class="tdHec">0.433</td> | ||
| + | <td class="tdHec">0.068</td> | ||
| + | <td class="tdHec">1.788</td> | ||
| + | <td class="tdHec">4.002</td> | ||
| + | <td class="tdHec">0.522</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C1, R4</td> | ||
| + | <td class="tdHec">0.058</td> | ||
| + | <td class="tdHec">1.276</td> | ||
| + | <td class="tdHec">2.752</td> | ||
| + | <td class="tdHec">0.433</td> | ||
| + | <td class="tdHec">0.083</td> | ||
| + | <td class="tdHec">1.596</td> | ||
| + | <td class="tdHec">2.472</td> | ||
| + | <td class="tdHec">0.504</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R1</td> | ||
| + | <td class="tdHec">0.063</td> | ||
| + | <td class="tdHec">0.568</td> | ||
| + | <td class="tdHec">2.655</td> | ||
| + | <td class="tdHec">0.918</td> | ||
| + | <td class="tdHec">0.100</td> | ||
| + | <td class="tdHec">1.607</td> | ||
| + | <td class="tdHec">4.163</td> | ||
| + | <td class="tdHec">0.487</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R2</td> | ||
| + | <td class="tdHec">0.068</td> | ||
| + | <td class="tdHec">0.592</td> | ||
| + | <td class="tdHec">2.677</td> | ||
| + | <td class="tdHec">0.927</td> | ||
| + | <td class="tdHec">0.104</td> | ||
| + | <td class="tdHec">1.613</td> | ||
| + | <td class="tdHec">4.558</td> | ||
| + | <td class="tdHec">0.491</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R3</td> | ||
| + | <td class="tdHec">0.061</td> | ||
| + | <td class="tdHec">0.576</td> | ||
| + | <td class="tdHec">2.668</td> | ||
| + | <td class="tdHec">0.966</td> | ||
| + | <td class="tdHec">0.100</td> | ||
| + | <td class="tdHec">1.742</td> | ||
| + | <td class="tdHec">5.025</td> | ||
| + | <td class="tdHec">0.518</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdHec">C2, R4</td> | ||
| + | <td class="tdHec">0.066</td> | ||
| + | <td class="tdHec">0.595</td> | ||
| + | <td class="tdHec">2.793</td> | ||
| + | <td class="tdHec">0.968</td> | ||
| + | <td class="tdHec">0.112</td> | ||
| + | <td class="tdHec">1.764</td> | ||
| + | <td class="tdHec">6.263</td> | ||
| + | <td class="tdHec">0.526</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6>Table 8. <meta charset="utf-8">μM Fluorescein/OD, 6 hours. </h6> | ||
| + | <h5 style=" | ||
| + | color: #353535; | ||
| + | font-size: 16px; | ||
| + | font-weight: 750; | ||
| + | ">MEFL/particle:</h5> | ||
| + | <div> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 0:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | </tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdAlb">C1, R1</td> | ||
| + | <td class="tdAlb">1.31E+05</td> | ||
| + | <td class="tdAlb">-3.22E+05</td> | ||
| + | <td class="tdAlb">1.51E+06</td> | ||
| + | <td class="tdAlb">-4.35E+05</td> | ||
| + | <td class="tdAlb">4.24E+04</td> | ||
| + | <td class="tdAlb">1.18E+06</td> | ||
| + | <td class="tdAlb">7.46E+05</td> | ||
| + | <td class="tdAlb">4.50E+05</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdAlb">C1, R2</td> | ||
| + | <td class="tdAlb">2.97E+05</td> | ||
| + | <td class="tdAlb">2.16E+05</td> | ||
| + | <td class="tdAlb">1.60E+06</td> | ||
| + | <td class="tdAlb">-3.75E+05</td> | ||
| + | <td class="tdAlb">5.05E+04</td> | ||
| + | <td class="tdAlb">1.42E+06</td> | ||
| + | <td class="tdAlb">7.89E+05</td> | ||
| + | <td class="tdAlb">4.61E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C1, R3</td> | ||
| + | <td class="tdAlb">3.18E+04</td> | ||
| + | <td class="tdAlb">1.57E+05</td> | ||
| + | <td class="tdAlb">1.50E+06</td> | ||
| + | <td class="tdAlb">-7.95E+06</td> | ||
| + | <td class="tdAlb">4.75E+04</td> | ||
| + | <td class="tdAlb">1.03E+06</td> | ||
| + | <td class="tdAlb">6.57E+05</td> | ||
| + | <td class="tdAlb">3.91E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C1, R4</td> | ||
| + | <td class="tdAlb">4.90E+04</td> | ||
| + | <td class="tdAlb">-9011826</td> | ||
| + | <td class="tdAlb">1.57E+06</td> | ||
| + | <td class="tdAlb">-7.01E+06</td> | ||
| + | <td class="tdAlb">1.70E+05</td> | ||
| + | <td class="tdAlb">1.06E+06</td> | ||
| + | <td class="tdAlb">9.75E+05</td> | ||
| + | <td class="tdAlb">4.08E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R1</td> | ||
| + | <td class="tdAlb">1.02E+05</td> | ||
| + | <td class="tdAlb">3.06E+05</td> | ||
| + | <td class="tdAlb">1.50E+06</td> | ||
| + | <td class="tdAlb">4.85E+05</td> | ||
| + | <td class="tdAlb">5.43E+05</td> | ||
| + | <td class="tdAlb">1.49E+06</td> | ||
| + | <td class="tdAlb">1.24E+06</td> | ||
| + | <td class="tdAlb">6.98E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R2</td> | ||
| + | <td class="tdAlb">-3.67E+03</td> | ||
| + | <td class="tdAlb">1.18E+05</td> | ||
| + | <td class="tdAlb">2.09E+06</td> | ||
| + | <td class="tdAlb">3.90E+05</td> | ||
| + | <td class="tdAlb">3.87E+05</td> | ||
| + | <td class="tdAlb">1.32E+06</td> | ||
| + | <td class="tdAlb">1.15E+06</td> | ||
| + | <td class="tdAlb">5.36E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R3</td> | ||
| + | <td class="tdAlb">9.40E+03</td> | ||
| + | <td class="tdAlb">1.85E+05</td> | ||
| + | <td class="tdAlb">2.09E+06</td> | ||
| + | <td class="tdAlb">1.52E+05</td> | ||
| + | <td class="tdAlb">4.22E+05</td> | ||
| + | <td class="tdAlb">9.06E+05</td> | ||
| + | <td class="tdAlb">1.11E+06</td> | ||
| + | <td class="tdAlb">5.88E+05</td> | ||
| + | </tr> <tr> | ||
| + | <td class="tdAlb">C2, R4</td> | ||
| + | <td class="tdAlb">-1.18E+06</td> | ||
| + | <td class="tdAlb">-1.03E+06</td> | ||
| + | <td class="tdAlb">1.28E+06</td> | ||
| + | <td class="tdAlb">-6.76E+05</td> | ||
| + | <td class="tdAlb">-6.50E+05</td> | ||
| + | <td class="tdAlb">3.73E+05</td> | ||
| + | <td class="tdAlb">2.95E+05</td> | ||
| + | <td class="tdAlb">1.11E+05</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <div> | ||
| + | <h6>Table 9. MEFL/particle, 0 hours. </h6> | ||
| + | <table class="border--round table--alternate-row tableHec" style="width:100%"> | ||
| + | <thead><tr> | ||
| + | <th class="thHec">Hour 6:</th> | ||
| + | <th class="thHec">Neg. Control</th> | ||
| + | <th class="thHec">Pos. Control</th> | ||
| + | <th class="thHec">Device 1</th> | ||
| + | <th class="thHec">Device 2</th> | ||
| + | <th class="thHec">Device 3</th> | ||
| + | <th class="thHec">Device 4</th> | ||
| + | <th class="thHec">Device 5</th> | ||
| + | <th class="thHec">Device 6</th> | ||
| + | </tr> | ||
| + | </thead><tbody><tr> | ||
| + | <td class="tdAlb">C1, R1</td> | ||
| + | <td class="tdAlb">1.45E+04</td> | ||
| + | <td class="tdAlb">4.34E+05</td> | ||
| + | <td class="tdAlb">1.01E+06</td> | ||
| + | <td class="tdAlb">1.34E+05</td> | ||
| + | <td class="tdAlb">2.02E+04</td> | ||
| + | <td class="tdAlb">5.61E+05</td> | ||
| + | <td class="tdAlb">1.66E+06</td> | ||
| + | <td class="tdAlb">1.73E+05</td> | ||
| + | </tr> | ||
| + | <tr> | ||
| + | <td class="tdAlb">C1, R2</td> | ||
| + | <td class="tdAlb">2.02E+04</td> | ||
| + | <td class="tdAlb">4.19E+05</td> | ||
| + | <td class="tdAlb">9.29E+05</td> | ||
| + | <td class="tdAlb">1.40E+05</td> | ||
| + | <td class="tdAlb">2.27E+04</td> | ||
| + | <td class="tdAlb">5.32E+05</td> | ||
| + | <td class="tdAlb">1.06E+06</td> | ||
| + | <td class="tdAlb">1.69E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C1, R3</td> | ||
| + | <td class="tdAlb">1.80E+04</td> | ||
| + | <td class="tdAlb">4.34E+05</td> | ||
| + | <td class="tdAlb">9.87E+05</td> | ||
| + | <td class="tdAlb">1.37E+05</td> | ||
| + | <td class="tdAlb">2.15E+04</td> | ||
| + | <td class="tdAlb">5.65E+05</td> | ||
| + | <td class="tdAlb">1.26E+06</td> | ||
| + | <td class="tdAlb">1.65E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C1, R4</td> | ||
| + | <td class="tdAlb">1.83E+04</td> | ||
| + | <td class="tdAlb">4.03E+05</td> | ||
| + | <td class="tdAlb">8.70E+05</td> | ||
| + | <td class="tdAlb">1.37E+05</td> | ||
| + | <td class="tdAlb">2.64E+04</td> | ||
| + | <td class="tdAlb">5.05E+05</td> | ||
| + | <td class="tdAlb">7.81E+05</td> | ||
| + | <td class="tdAlb">1.59E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R1</td> | ||
| + | <td class="tdAlb">1.98E+04</td> | ||
| + | <td class="tdAlb">1.80E+05</td> | ||
| + | <td class="tdAlb">8.39E+05</td> | ||
| + | <td class="tdAlb">2.90E+05</td> | ||
| + | <td class="tdAlb">3.15E+04</td> | ||
| + | <td class="tdAlb">5.08E+05</td> | ||
| + | <td class="tdAlb">1.32E+06</td> | ||
| + | <td class="tdAlb">1.54E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R2</td> | ||
| + | <td class="tdAlb">2.14E+04</td> | ||
| + | <td class="tdAlb">1.87E+05</td> | ||
| + | <td class="tdAlb">8.46E+05</td> | ||
| + | <td class="tdAlb">2.93E+05</td> | ||
| + | <td class="tdAlb">3.27E+04</td> | ||
| + | <td class="tdAlb">5.10E+05</td> | ||
| + | <td class="tdAlb">1.44E+06</td> | ||
| + | <td class="tdAlb">1.55E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R3</td> | ||
| + | <td class="tdAlb">1.92E+04</td> | ||
| + | <td class="tdAlb">1.82E+05</td> | ||
| + | <td class="tdAlb">8.43E+0.5</td> | ||
| + | <td class="tdAlb">3.05E+05</td> | ||
| + | <td class="tdAlb">3.17E+04</td> | ||
| + | <td class="tdAlb">5.51E+05</td> | ||
| + | <td class="tdAlb">1.59E+06</td> | ||
| + | <td class="tdAlb">1.64E+05</td> | ||
| + | </tr><tr> | ||
| + | <td class="tdAlb">C2, R4</td> | ||
| + | <td class="tdAlb">2.10E+04</td> | ||
| + | <td class="tdAlb">1.88E+05</td> | ||
| + | <td class="tdAlb">8.83E+05</td> | ||
| + | <td class="tdAlb">3.06E+05</td> | ||
| + | <td class="tdAlb">3.54E+04</td> | ||
| + | <td class="tdAlb">5.61E+05</td> | ||
| + | <td class="tdAlb">1.98E+06</td> | ||
| + | <td class="tdAlb">1.66E+05</td> | ||
| + | </tr> | ||
| + | </tbody></table> | ||
| + | </div> | ||
| + | <h6> Table 10. MEFL/particle, 6 hours.</h6> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
| + | </div> | ||
| + | |||
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| + | color: #353535; | ||
| + | font-weight: 700; | ||
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| + | margin-bottom: 0.8em; | ||
| + | "> | ||
| + | Application | ||
| + | </h4> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | Thanks to the InterLab Study initiative, the Valencia UPV iGEM team has decided to go one step further in this competition. From Interlab experimental data, we know that <b>we can obtain equivalence factors between arbitrary fluorescence units and equivalent molecules of fluorophore (MEFL)</b>, such as fluorescein. However, <b>for what reason is this conversion useful?</b> | ||
| + | </p> | ||
| + | <p style=" | ||
| + | line-height: 1.7; | ||
| + | margin-bottom: 0; | ||
| + | color: #353535;"> | ||
| + | In Printeria, one of the most important tools for characterization has been modeling. We have developed mathematical models of genetic constructions and we have characterized the parts through parameter optimization. Thanks to the conversion of experimental fluorescence data to MEFL, we have been able to obtain <b>more realistic parameters values</b> and, therefore, closer to reality. If you want to discover our results, visit our Modeling section.<a href="https://2018.igem.org/Team:Valencia_UPV/Model" target="_blank"></a> | ||
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Latest revision as of 03:59, 18 October 2018
Introduction
Do you imagine doing an experiment that could not be repeated? What if, after performing the same experiment several times, you obtain different results each time? This is a <6>common problem throughout almost all laboratories in the entire world. A challenge, not just for Synthetic Biology but for any type of science, is taking reliable and repeatable measurements.
Over the past four years, the iGEM Measurement Committee has been developing a series of experiments to make the biggest interlaboratory studies ever done in synthetic biology, and, in that way, try to fix all possible variables within a particular protocol.
What is this year's goal?
To know if there is any chance to reduce lab-to-lab variability in fluorescence measurements by normalizing to absolute cell count or c-forming units (CFUs) instead of optical density (OD).
In order to compute the cell count in our samples, we will use two orthogonal approaches:
Approach 1: Converting between absorbance of cells to absorbance of a known concentration of beads
The theory under how absorbance is measured is quite simple: a liquid sample of cells scatter light in a way or another depending on the number of cells this sample contains. The Committee provides us a sample with silica beads which are almost the same size and shape as a typical E. coli cell. So, when mixed with water, we obtain a liquid that should scatter light in a similar way as our E. coli sample does.
Because we know the concentration of beads, the absorbance measurement from a particular cell sample could be converted into an “equivalent concentration of beads” measurement, so that they are more universal and comparable measurements between different labs.
Approach 2: Counting c-forming units (CFUs) from the sample
This method relies on the idea that every colony grown in our plate comes from a single cell. So, if we spread a known cell culture volume over an agar plate and then we count the number of colonies, we should have an idea on how many cells our liquid sample had. We will have to determine the number of CFUs in positive and negative control samples in order to compute a conversion factor from absorbance to CFU.
Plate reader setup
Absorbance600
Absorbance Endpoint
Full Plate
Wavelengths: 600 nm
Read Speed: Normal, Delay: 100 msec, Measurements/Data Point: 8
Fluorescence
Excitation: 485, Emission: 528
Optics: Top, Gain: 50
Light Source: Xenon Flash, Lamp Energy: High
Read Speed: Normal, Delay: 100 msec, Measurements/Data Point: 10
Read Height: 7 mm
Used Parts
| Device | Part number | Plate | Location |
|---|---|---|---|
| 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 |
Table 1. Used parts, links, and well information.
Calibration 1: OD600 Reference Point
Using LUDOX CL-X as a point reference to obtain a conversion factor to transform our absorbance (Abs600) data from our plate reader into a comparable OD600 measurement as would be obtained in a spectrophotometer.
| LUDOX CL-X | H2O | |
|---|---|---|
| R1 | 0.061 | 0.051 |
| R2 | 0.060 | 0.049 |
| R3 | 0.061 | 0.043 |
| R4 | 0.062 | 0.049 |
| Arithmetic Mean | 0.061 | 0.048 |
| Corrected Abs600 | 0.013 | |
| Reference OD600 | 0.063 | |
| OD600/Abs600 | 4.846 |
Table 2. OD600 reference point.
Calibration 2: Particle Standard Curve
This allows us to construct a standard curve of particle concentration which can be used to convert Abs600 measurements to an estimated number of cells.
Figure 1. Particle standard curve and particle standard curve in logarithmic scale.
Calibration 3: Fuorescence Standard Curve
Absolute fluorescence values cannot be directly compared from one instrument to another. In order to compare fluorescence output of test devices between teams, it is necessary for each team to create a standard fluorescence curve.
Figure 2. Fluorescein standard curve and fluorescein standard curve in logarithmic scale.
Experiment
Fluorescence Raw Readings:
| Hour 0: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 | LB+Chlor (blank) |
|---|---|---|---|---|---|---|---|---|---|
| C1, R1 | 3618 | 3087 | 5355 | 2950 | 3402 | 4799 | 4112 | 3901 | 3350 |
| C1, R2 | 3648 | 3414 | 5158 | 2887 | 3260 | 4647 | 4159 | 3758 | 3193 |
| C1, R3 | 3273 | 3442 | 5077 | 1611 | 3331 | 4607 | 3972 | 3793 | 3234 |
| C1, R4 | 3301 | 1381 | 5307 | 1074 | 3446 | 4519 | 4416 | 3804 | 3221 |
| C2, R1 | 3350 | 3537 | 5091 | 3702 | 3976 | 4621 | 4517 | 3969 | 3256 |
| C2, R2 | 3262 | 3409 | 4758 | 3623 | 3660 | 4208 | 4679 | 3867 | 3265 |
| C2, R3 | 3255 | 3401 | 4784 | 3620 | 3662 | 4248 | 4481 | 3951 | 3231 |
| C2, R4 | 3225 | 3020 | 4855 | 3518 | 3672 | 4451 | 4281 | 4183 | 4070 |
Table 3. Fluorescence raw readings, 0 hours.
| Hour 6: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 | LB+Chlor (blank) |
|---|---|---|---|---|---|---|---|---|---|
| C1, R1 | 4087 | 23103 | 44980 | 7751 | 4312 | 29208 | 6183 | 10720 | 3306 |
| C1, R2 | 4238 | 23435 | 46319 | 7594 | 4341 | 28505 | 6522 | 10895 | 3177 |
| C1, R3 | 4194 | 23871 | 45601 | 7757 | 4371 | 28765 | 6359 | 10515 | 3260 |
| C1, R4 | 4195 | 24568 | 45744 | 7709 | 4546 | 29372 | 6156 | 11334 | 3205 |
| C2, R1 | 4398 | 11707 | 43194 | 17428 | 4756 | 28009 | 11866 | 10612 | 3269 |
| C2, R2 | 4351 | 12443 | 43496 | 17570 | 4804 | 28545 | 11928 | 10545 | 3250 |
| C2, R3 | 4291 | 11451 | 43156 | 17421 | 4796 | 28475 | 11726 | 10544 | 3295 |
| C2, R4 | 4292 | 12396 | 42704 | 17353 | 4938 | 28869 | 11517 | 10546 | 3231 |
Table 4. Fluorescence raw readings, 6 hours.
Abs600 Raw Readings:
| Hour 0: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 | LB+Chlor (blank) |
|---|---|---|---|---|---|---|---|---|---|
| C1, R1 | 0.067 | 0.055 | 0.060 | 0.056 | 0.059 | 0.059 | 0.057 | 0.059 | 0.047 |
| C1, R2 | 0.061 | 0.056 | 0.058 | 0.054 | 0.059 | 0.056 | 0.058 | 0.058 | 0.046 |
| C1, R3 | 0.057 | 0.058 | 0.057 | 0.047 | 0.065 | 0.058 | 0.056 | 0.059 | 0.045 |
| C1, R4 | 0.062 | 0.047 | 0.058 | 0.048 | 0.058 | 0.057 | 0.057 | 0.059 | 0.045 |
| C2, R1 | 0.055 | 0.055 | 0.058 | 0.055 | 0.059 | 0.055 | 0.056 | 0.056 | 0.046 |
| C2, R2 | 0.055 | 0.059 | 0.054 | 0.056 | 0.057 | 0.054 | 0.059 | 0.058 | 0.047 |
| C2, R3 | 0.071 | 0.055 | 0.056 | 0.071 | 0.056 | 0.057 | 0.057 | 0.058 | 0.046 |
| C2, R4 | 0.056 | 0.059 | 0.055 | 0.057 | 0.055 | 0.059 | 0.056 | 0.059 | 0.049 |
Table 5. Abs600 Raw Readings, 0 hours.
| Hour 6: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 | LB+Chlor (blank) |
|---|---|---|---|---|---|---|---|---|---|
| C1, R1 | 0.595 | 0.513 | 0.471 | 0.391 | 0.554 | 0.518 | 0.083 | 0.487 | 0.066 |
| C1, R2 | 0.567 | 0.527 | 0.508 | 0.363 | 0.556 | 0.519 | 0.084 | 0.501 | 0.053 |
| C1, R3 | 0.566 | 0.524 | 0.479 | 0.381 | 0.566 | 0.501 | 0.083 | 0.490 | 0.059 |
| C1, R4 | 0.580 | 0.570 | 0.530 | 0.373 | 0.549 | 0.559 | 0.088 | 0.551 | 0.051 |
| C2, R1 | 0.611 | 0.513 | 0.519 | 0.531 | 0.515 | 0.530 | 0.117 | 0.520 | 0.053 |
| C2, R2 | 0.562 | 0.538 | 0.523 | 0.536 | 0.522 | 0.543 | 0.116 | 0.517 | 0.057 |
| C2, R3 | 0.561 | 0.493 | 0.517 | 0.507 | 0.518 | 0.502 | 0.106 | 0.488 | 0.054 |
| C2, R4 | 0.555 | 0.537 | 0.498 | 0.512 | 0.533 | 0.508 | 0.101 | 0.491 | 0.06 |
Table 6. Abs600 Raw Readings, 6 hours.
μM Fluorescein/OD:
| Hour 0: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 |
|---|---|---|---|---|---|---|---|---|
| C1, R1 | 0.415 | -1.019 | 4.780 | -1.377 | 0.134 | 3.742 | 2.362 | 1.423 |
| C1, R2 | 0.940 | 0.685 | 5.075 | -1.185 | 0.160 | 4.506 | 2.495 | 1.459 |
| C1, R3 | 0.101 | 0.496 | 4.760 | -25.149 | 0.150 | 3.273 | 2.079 | 1.237 |
| C1, R4 | 0.155 | -28.512 | 4.973 | -22.179 | 0.536 | 3.352 | 3.086 | 1.291 |
| C2, R1 | 0.324 | 0.968 | 4.739 | 1.536 | 1.716 | 4.700 | 3.908 | 2.210 |
| C2, R2 | -0.012 | 0.372 | 6.610 | 1.233 | 1.224 | 4.175 | 3.652 | 1.696 |
| C2, R3 | 0.030 | 0.585 | 4.813 | 0.482 | 1.336 | 2.865 | 3.522 | 1.859 |
| C2, R4 | -3.741 | -3.254 | 4.055 | -2.138 | -2.056 | 1.581 | 0.934 | 0.350 |
Table 7. μM Fluorescein/OD, 0 hours.
| Hour 6: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 |
|---|---|---|---|---|---|---|---|---|
| C1, R1 | 0.046 | 1.373 | 3.189 | 0.424 | 0.064 | 1.776 | 5.245 | 0.546 |
| C1, R2 | 0.064 | 1.325 | 2.939 | 0.442 | 0.072 | 1.684 | 3.344 | 0.534 |
| C1, R3 | 0.057 | 1.374 | 3.124 | 0.433 | 0.068 | 1.788 | 4.002 | 0.522 |
| C1, R4 | 0.058 | 1.276 | 2.752 | 0.433 | 0.083 | 1.596 | 2.472 | 0.504 |
| C2, R1 | 0.063 | 0.568 | 2.655 | 0.918 | 0.100 | 1.607 | 4.163 | 0.487 |
| C2, R2 | 0.068 | 0.592 | 2.677 | 0.927 | 0.104 | 1.613 | 4.558 | 0.491 |
| C2, R3 | 0.061 | 0.576 | 2.668 | 0.966 | 0.100 | 1.742 | 5.025 | 0.518 |
| C2, R4 | 0.066 | 0.595 | 2.793 | 0.968 | 0.112 | 1.764 | 6.263 | 0.526 |
Table 8. μM Fluorescein/OD, 6 hours.
MEFL/particle:
| Hour 0: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 |
|---|---|---|---|---|---|---|---|---|
| C1, R1 | 1.31E+05 | -3.22E+05 | 1.51E+06 | -4.35E+05 | 4.24E+04 | 1.18E+06 | 7.46E+05 | 4.50E+05 |
| C1, R2 | 2.97E+05 | 2.16E+05 | 1.60E+06 | -3.75E+05 | 5.05E+04 | 1.42E+06 | 7.89E+05 | 4.61E+05 |
| C1, R3 | 3.18E+04 | 1.57E+05 | 1.50E+06 | -7.95E+06 | 4.75E+04 | 1.03E+06 | 6.57E+05 | 3.91E+05 |
| C1, R4 | 4.90E+04 | -9011826 | 1.57E+06 | -7.01E+06 | 1.70E+05 | 1.06E+06 | 9.75E+05 | 4.08E+05 |
| C2, R1 | 1.02E+05 | 3.06E+05 | 1.50E+06 | 4.85E+05 | 5.43E+05 | 1.49E+06 | 1.24E+06 | 6.98E+05 |
| C2, R2 | -3.67E+03 | 1.18E+05 | 2.09E+06 | 3.90E+05 | 3.87E+05 | 1.32E+06 | 1.15E+06 | 5.36E+05 |
| C2, R3 | 9.40E+03 | 1.85E+05 | 2.09E+06 | 1.52E+05 | 4.22E+05 | 9.06E+05 | 1.11E+06 | 5.88E+05 |
| C2, R4 | -1.18E+06 | -1.03E+06 | 1.28E+06 | -6.76E+05 | -6.50E+05 | 3.73E+05 | 2.95E+05 | 1.11E+05 |
Table 9. MEFL/particle, 0 hours.
| Hour 6: | Neg. Control | Pos. Control | Device 1 | Device 2 | Device 3 | Device 4 | Device 5 | Device 6 |
|---|---|---|---|---|---|---|---|---|
| C1, R1 | 1.45E+04 | 4.34E+05 | 1.01E+06 | 1.34E+05 | 2.02E+04 | 5.61E+05 | 1.66E+06 | 1.73E+05 |
| C1, R2 | 2.02E+04 | 4.19E+05 | 9.29E+05 | 1.40E+05 | 2.27E+04 | 5.32E+05 | 1.06E+06 | 1.69E+05 |
| C1, R3 | 1.80E+04 | 4.34E+05 | 9.87E+05 | 1.37E+05 | 2.15E+04 | 5.65E+05 | 1.26E+06 | 1.65E+05 |
| C1, R4 | 1.83E+04 | 4.03E+05 | 8.70E+05 | 1.37E+05 | 2.64E+04 | 5.05E+05 | 7.81E+05 | 1.59E+05 |
| C2, R1 | 1.98E+04 | 1.80E+05 | 8.39E+05 | 2.90E+05 | 3.15E+04 | 5.08E+05 | 1.32E+06 | 1.54E+05 |
| C2, R2 | 2.14E+04 | 1.87E+05 | 8.46E+05 | 2.93E+05 | 3.27E+04 | 5.10E+05 | 1.44E+06 | 1.55E+05 |
| C2, R3 | 1.92E+04 | 1.82E+05 | 8.43E+0.5 | 3.05E+05 | 3.17E+04 | 5.51E+05 | 1.59E+06 | 1.64E+05 |
| C2, R4 | 2.10E+04 | 1.88E+05 | 8.83E+05 | 3.06E+05 | 3.54E+04 | 5.61E+05 | 1.98E+06 | 1.66E+05 |
Table 10. MEFL/particle, 6 hours.
Application
Thanks to the InterLab Study initiative, the Valencia UPV iGEM team has decided to go one step further in this competition. From Interlab experimental data, we know that we can obtain equivalence factors between arbitrary fluorescence units and equivalent molecules of fluorophore (MEFL), such as fluorescein. However, for what reason is this conversion useful?
In Printeria, one of the most important tools for characterization has been modeling. We have developed mathematical models of genetic constructions and we have characterized the parts through parameter optimization. Thanks to the conversion of experimental fluorescence data to MEFL, we have been able to obtain more realistic parameters values and, therefore, closer to reality. If you want to discover our results, visit our Modeling section.