Difference between revisions of "Team:Cornell/DesignProcess"

 
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<html>
 
<html>
 
 
<head>
 
<head>
 
<style>
 
<style>
    /* hides "Team:Cornell" and iGEM logo */
+
        /* hides "Team:Cornell" and iGEM logo */
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+
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     /******************** ALL FONTS START ********************/
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     }
 
     }
  
     .standard-page-banner > svg > text, .standard-page-content-title, .standard-page-side-bar-wrapper, .standard-page-content-subheading {
+
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     p {
 
     p {
 
         color: #000;
 
         color: #000;
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        font-family: 'Open Sans', sans-serif;
 
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         padding-right: 100px;
 
         padding-right: 100px;
 
         background-color: #a0e0bd;
 
         background-color: #a0e0bd;
 +
        height: 98px;
 
     }
 
     }
  
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     }
 
     }
  
     .home-banner-wrapper {
+
     .nav-bar-main-menu {
         position: relative;
+
         font-family: 'Raleway', sans-serif;
        background: #a0e0bd;
+
        height: 675px;
+
        width: 100%;
+
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+
 
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    .home-banner-logo {
 
        height: 200px;
 
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     .dropbtn {
 
     .dropbtn {
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     .toolkit-dropdown-content {
 
     .toolkit-dropdown-content {
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+
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         left: -160px;
 
         left: -160px;
 
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     }
 
     }
  
    /*Start Styles for Standard Page*/
+
     .notebook-page-content-wrapper {
     .standard-page-banner {
+
         padding-bottom: 5%;
         background-color: #a0e0bd;
+
 
     }
 
     }
  
     .standard-page-side-bar-content-wrapper {
+
     .notebook-content-wrapper {
         padding: 5% 0;
+
         padding-right: 100px;
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     .standard-page-side-bar>li>a {
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+
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+
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+
        margin: 40px !important;
+
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+
 
+
    .standard-page-side-bar>li {
+
        margin-bottom: 15px;
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+
    .standard-page-content-title {
+
 
         font-size: 24px;
 
         font-size: 24px;
 
         color: #000 !important;
 
         color: #000 !important;
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     }
 
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     .standard-page-content-subheading {
+
     .notebook-text-wrapper {
         font-size: 18px;
+
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    .notebook-body-text {
 
         color: #000;
 
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        padding-top: 40px;
 
        padding-bottom: 0;
 
 
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     .standard-page-content-section {
+
     /******************** NOTEBOOK PAGE START ********************/
        margin-top: 40px;
+
  .parts-page-banner {
         margin-bottom: 40px;
+
    background-image: url(https://static.igem.org/mediawiki/2019/d/db/T--Cornell--basicparts-lucas.jpeg);
 +
    background-size: cover;
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    fill: black;    }
 +
   
 +
    .parts-page-content-wrapper {
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         padding-bottom: 5%;
 
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    .parts-text-wrapper {
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 +
    .parts-body-text {
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        color: #000;
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        margin-top: 20px;
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.pd-component-a-image {
+
.notebook-page-banner {
  height: 250px;
+
        background-image: url(https://static.igem.org/mediawiki/2019/4/44/T--Cornell--JackiePD.jpeg);
  padding-top: 35px;
+
    background-size: cover;
  padding-right: 35px;
+
    fill: black;
}
+
    }
  
.pd-fab-a-image {
+
    .notebook-page-content-wrapper {
  height: 400px;
+
        padding-bottom: 5%;
  padding-top: 45px;
+
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}
+
  
.pd-com-b-image {
+
    .notebook-header-text {
  height: 300px;
+
        font-size: 24pt;
  padding-top: 35px;
+
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}
+
        color: #000;
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.pd-fab-b-img {
+
    .notebook-text-wrapper {
  height: 300px;
+
        padding-top: 20px;
  padding-top: 35px;
+
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}
+
  
.pd-page-banner {
+
    .notebook-body-text {
    background-image: url(https://static.igem.org/mediawiki/2019/4/44/T--Cornell--JackiePD.jpeg);
+
        color: #000;
    background-size: cover;
+
        margin-top: 20px;
     fill: black;
+
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}
+
  
 +
    #safety-hyperlink {
 +
        color: #c93843;
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     /*End Style for Standard Page*/
+
.standard-page-content-title {
    /******************** STANDARD PAGE GRID START ********************/
+
        margin-top: 40px;
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        font-size: 24px;
 +
        color: #000 !important;
 +
        position: relative;
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 +
 
 +
 
 +
     /******************** NOTEBOOK PAGE END ********************/
 +
 
 +
  /******************** NOTEBOOK PAGE GRID START ********************/
 +
    .home-page-wrapper {
 +
        display: grid;
 +
        grid-template-columns: auto;
 +
        grid-template-rows: 100px auto auto 100px auto 100px 100px;
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        grid-template-areas: 'navbar' 'banner' 'homedescription' '.' 'tiles' '.' 'footer';
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 +
 
 +
    .home-banner-wrapper {
 +
        display: grid;
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        grid-area: banner;
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 +
 
 
     nav {
 
     nav {
 
         grid-area: navbar;
 
         grid-area: navbar;
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     }
 
     }
  
     .standard-page-wrapper {
+
     .notebook-page-wrapper {
 
         display: grid;
 
         display: grid;
 
         grid-template-columns: auto;
 
         grid-template-columns: auto;
 
         grid-template-rows: 100px 550px auto 100px;
 
         grid-template-rows: 100px 550px auto 100px;
         grid-template-areas: 'navbar' 'standardpagebanner' 'standardpagesidebarcontent' 'footer';
+
         grid-template-areas: "navbar" "notebookpagebanner" "notebookpagecontent" "footer";
 
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     .standard-page-banner {
+
     .notebook-page-content-wrapper {
        grid-area: standardpagebanner;
+
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+
 
+
    .standard-page-side-bar-content-wrapper {
+
 
         display: inline-grid;
 
         display: inline-grid;
         grid-area: standardpagesidebarcontent;
+
         grid-area: notebookpagecontent;
        grid-template-columns: 7.5% 20% 65% 7.5%;
+
        grid-template-areas: '. standardpagesidebar standardpagecontent .';
+
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+
 
+
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+
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+
 
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+
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         grid-area: standardpagecontent;
+
         grid-area: notebookpagebanner;
 
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         padding: 0 !important;
 
         padding: 0 !important;
 
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     }
    /******************** STANDARD PAGE GRID END ********************/
 
  </style>
 
    <title>Team:Cornell - 2019.igem.org</title>
 
 
  
 +
  .grey-background {
 +
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 +
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 +
  /******************** NOTEBOOK PAGE GRID END ********************/
 +
    </style>
 +
    <title>Team:Cornell - 2019.igem.org</title>
 +
    <!-- CSS -->
 +
    <link rel="stylesheet" type="text/css" href="styles/styles.css">
 +
    <link rel="stylesheet" type="text/css" href="styles/grids.css">
 
     <!-- JS -->
 
     <!-- JS -->
 
     <script src="https://2019.igem.org/Team:Cornell/jquerymin?action=raw&ctype=text/javascript"></script>
 
     <script src="https://2019.igem.org/Team:Cornell/jquerymin?action=raw&ctype=text/javascript"></script>
 
</head>
 
</head>
<!--NOTE: REMEMBER TO CHANCE active-page CLASS TO CORRECT DROPDOWN-->
 
<body>
 
    <div class ="standard-page-wrapper">
 
  
 +
<body>
 +
    <div class ="notebook-page-wrapper">
 
         <!------------------------ NAV BAR START ------------------------>
 
         <!------------------------ NAV BAR START ------------------------>
 
         <nav>
 
         <nav>
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                         <button class="dropbtn">OUTREACH</button>
 
                         <button class="dropbtn">OUTREACH</button>
 
                         <div class="dropdown-content outreach-dropdown-content">
 
                         <div class="dropdown-content outreach-dropdown-content">
                             <a href="https://2019.igem.org/Team:Cornell/EducationAndEngagement">EDUCATION & ENGAGEMENT</a>
+
                             <a href="https://2019.igem.org/Team:Cornell/Public_Engagement">EDUCATION & ENGAGEMENT</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Collaborations">COLLABORATIONS</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Collaborations">COLLABORATIONS</a>
 
                         </div>
 
                         </div>
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                         <button class="dropbtn">HUMAN PRACTICES</button>
 
                         <button class="dropbtn">HUMAN PRACTICES</button>
 
                         <div class="dropdown-content human-dropdown-content">
 
                         <div class="dropdown-content human-dropdown-content">
                             <a href="https://2019.igem.org/Team:Cornell/IntegratedPractices">INTEGRATED PRACTICES</a>
+
                             <a href="https://2019.igem.org/Team:Cornell/Human_Practices">INTEGRATED PRACTICES</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Policies">POLICIES</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Policies">POLICIES</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Entrepreneurship">ENTREPRENEURSHIP</a>
 
                             <a href="https://2019.igem.org/Team:Cornell/Entrepreneurship">ENTREPRENEURSHIP</a>
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                     </div>
 
                     </div>
 
                     <div class="dropdown">
 
                     <div class="dropdown">
                         <button class="dropbtn">TOOLKIT</button>
+
                         <button class="dropbtn active-page">TOOLKIT</button>
 
                         <div class="dropdown-content toolkit-dropdown-content">
 
                         <div class="dropdown-content toolkit-dropdown-content">
 
                             <ul>
 
                             <ul>
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                                 </div>
 
                                 </div>
 
                                 <div class="nav-second-col">
 
                                 <div class="nav-second-col">
                                     <li class="pd-list-title"><b>DESIGN</b></li>
+
                                     <li class="pd-list-title"><b>PRODUCT DEVELOPMENT</b></li>
 
                                     <li><a href="https://2019.igem.org/Team:Cornell/DesignProcess">DESIGN PROCESS</a></li>
 
                                     <li><a href="https://2019.igem.org/Team:Cornell/DesignProcess">DESIGN PROCESS</a></li>
 +
                                    <li><a href="https://2019.igem.org/Team:Cornell/Hardware">HARDWARE</a></li>
 
                                 </div>
 
                                 </div>
 
                                 <div class="nav-third-col">
 
                                 <div class="nav-third-col">
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                     </div>
 
                     </div>
 
                     <div class="dropdown">
 
                     <div class="dropdown">
                         <button class="dropbtn active-page"
+
                         <button class="dropbtn"
 
                             onclick="location.href='https://2019.igem.org/Team:Cornell'">HOME</button>
 
                             onclick="location.href='https://2019.igem.org/Team:Cornell'">HOME</button>
 
                     </div>
 
                     </div>
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         <!------------------------ NAV BAR END ------------------------>
 
         <!------------------------ NAV BAR END ------------------------>
 
         <!------------------------ STANDARD PAGE BANNER START ------------------------>
 
         <!------------------------ STANDARD PAGE BANNER START ------------------------>
         <header class="pd-page-banner">
+
         <header class="notebook-page-banner">
 
             <svg viewBox="0 0 100 100" width=100% height=100%>
 
             <svg viewBox="0 0 100 100" width=100% height=100%>
 
                 <text text-anchor="middle" alignment-baseline="middle" x=50% y=50%>Design Process</text>
 
                 <text text-anchor="middle" alignment-baseline="middle" x=50% y=50%>Design Process</text>
             </svg>  
+
             </svg>
 
         </header>
 
         </header>
 
         <!------------------------ STANDARD PAGE BANNER END ------------------------>
 
         <!------------------------ STANDARD PAGE BANNER END ------------------------>
         <!------------------------ STANDARD PAGE SIDE BAR + CONTENT START ------------------------>
+
         <!------------------------ NOTEBOOK PAGE CONTENT START ------------------------>
        <div class="standard-page-side-bar-content-wrapper">
+
<div class="parts-page-content-wrapper">
            <!------------------------ STANDARD PAGE SIDE BAR START ------------------------>
+
<div class="parts-content-wrapper">
            <div class="standard-page-side-bar-wrapper">
+
<div class="standard-page-content-title">Design Process</div>
                <ul class="standard-page-side-bar">
+
                      <hr class="green-accent-line-left">
                    <li><a href="#pageheading1">Overview</a></li>
+
<div class="parts-text-wrapper">
                    <li><a href="#pageheading2">Sampler</a></li>
+
                        <p style="margin-top: 40px; width=70%">    
                    <li><a href="#pageheading3">Fabrication of Sampler</a></li>
+
 
                    <li><a href="#pageheading4">Bioreactor</a></li>
+
            Our team began tackling the issue of harmful algae by proposing a boat that physically cleans up the algae. We thought that it could essentially skim the algae off the top of the water and we would have a bioreactor that breaks down the toxins in the surface level water. We had this idea in mind because we knew that the majority of microcystin will be located within the first 1.6 meters of water. Past that depth, the concentration of microcystin drastically decreases, hence the remediation of lake water below this depth is not as important (González-Piana, pp. 614). We would use an Electro-coagulation-flotation(ECF) process to remove algae by designing a ECF reactor and attaching it to the bottom side of the boat. <br><br>
                    <li><a href="#pageheading5">Fabrication of Bioreactor</a></li>
+
            Although this was a good starting point, there were 2 issues we discovered with this design:speed and battery capacity. To break down algae using the ECF process, we would have to slow down the boat drastically. At that rate, using a small remote controlled boat would take hundreds if not thousands of years to clean Cayuga lake. With the size of our battery, we would only be able to run the ECF reactor for 30 minutes at a time.<br><br>
                </ul>
+
            From this point, we began to brainstorm other ways we could accomplish our end goal of sampling and remediation. An autonomous way to sample water is not well developed in the scientific community and we opted to remove the microcystin, a greater danger than the algae itself. We decided as a team that having a boat to take samples quickly and having a separate bioreactor for water treatment plants where water could be pumped through at the correct speed would be more effective. With this two-part idea, we could detect the toxin as quickly as possible and then completely treat water (not just the surface) that is being distributed to the public. <br><br>
            </div>
+
            After deciding on a separate boat and bioreactor, we had a complete plan for the boat, but needed new designs for the bioreactor. Weighing the pros and cons of various types of bioreactors for our specific project, we decided that a design resembling Gautier’s artificial liver reactor (Gautier 2011) would be ideal. We chose this idea because we needed a way for all of the water to interact with the bacteria while the bacteria remain enclosed for environmental safety. Pumping water through a tube of alginate beads would ensure both of these things. In addition, by manipulating how many beads, the nozzle, and speed of the pump, we would be able to ensure effective reactions, which gave us a lot more control than alternative designs such as a closed bioreactor where the water is held inside and mixed. <br><br>
            <!------------------------ STANDARD PAGE SIDE BAR END ------------------------>
+
            <!------------------------ STANDARD PAGE CONTENT START ------------------------>
+
            <div class="standard-page-content-wrapper">
+
                <div class="standard-page-content-section">
+
                    <div class="standard-page-content-title"><div id="pageheading1">Overview</div></div>
+
                    <hr class="green-accent-line-left">
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                      The hardware component of this interdisciplinary project uses various engineering principles. We started by consulting researchers and research papers to find issues that we can solve in relation to harmful algae blooms. We found many issues, but after weeks of feedback from people around the community, we locked into something that can be applied to not only our project, but also to other researchers. Our team started with a rigorous prototyping process and moved to an iterative design process until we got to the complete product. All the while, we had one major goal in mind—to create an integrated system that can be inexpensive and usable by anyone and everyone.
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Cornell iGEM’s reHAB simplifies data collection and provides a way to use data insightfully. Our system is composed of hardware components and biological components. Our integrated system begins with HabCab. It is an automated inexpensive sampler which will collect samples in water along with storing the GPS location of the sample collected. Next, once we find out that the water contains microcystin toxins, we can  utilize the HabLab, a bioreactor that utilizes a flow dispersion nozzle to optimize the flow of water through a microcystin-removing array of alginate beads. Our wet lab team designed the bacteria responsible for the breaking down of microcystins which are locked safely inside each alginate bead.
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                    <div class="standard-page-content-title"><div id="pageheading2">Sampler</div></div>
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                      Our sampling system consists of one vacuum pump connected to a solenoid valve array which regulate water inflow of each sample through plastic tubing. This apparatus can be placed on any aquatic vehicle, and in our case we built a small boat. The gps module on top of the boat coordinates the movement of the boat, the vacuum pump, and solenoid. Once we arrive at each location, an unused tube’s solenoid valve opens. An arduino controls the entire process.The vacuum pump transfers the water through the open valve into the test tube to complete a sample collection. After 8 seconds, the pump turns off and the valve closes. This specific valve remains closed for the duration of the trip. The number of seconds that we keep the pump on for and valve open for was determined through trial and error to determine how long it would take the test tube to fill up without overflowing.
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By using one pump for all of the samples, we sped up the design process and made it much cheaper to build. However, contamination became a much bigger problem. Because of this, in order to use different tubes all connected to the same pump and only have one fill with water at a time, we incorporated the solenoid valves into our design.
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                    <img class="pd-component-a-image" src="https://static.igem.org/mediawiki/2019/0/06/T--Cornell--component-sampler.jpeg" alt="sampler">
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            González-Piana, M., Piccardo, A., Ferrer, C., Brena, B., Pírez, M., Fabián, D., & Chalar, G. (2018). Effects of Wind Mixing in a Stratified Water Column on Toxic Cyanobacteria and Microcystin-LR Distribution in a Subtropical Reservoir. Bulletin of Environmental Contamination and Toxicology, 101(5), 611–616. doi: 10.1007/s00128-018-2446-x<br><br>
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            Gautier, A., Carpentier, B., Dufresne, M., Vu Dinh, Q., Paullier, P., & Legallais, C. (2011)Impact of alginate type and bead diameter on mass transfers and the metabolic activities of encapsulated C3A cells in bioartificial liver applications. European Cells & Materials, 21,  94– 106.<br><br>
                    <div class="standard-page-content-title"><div id="pageheading3">Fabrication of Sampler</div></div>
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                      We modeled a prototype of the sampler vessel in Fusion 360 before fabrication. We then constructed the vessel by laser-cutting acrylic sheets and connecting the pieces with a solvent weld. We chose the method of laser-cutting because it is precise and can cut the acrylic sheet material with ease. The solvent welding method was extremely effective in creating strong, waterproof joints in the boat, which are necessary to prevent leaking. We also 3D modeled and printed a holder for the sample collection device using ABS plastic. We chose this additive manufacturing technique over a subtractive technique due to its accessibility and low cost of materials. Since the holder is not under considerable stress, the ABS plastic material is sufficiently strong.
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                      The bioreactor consists of two sizes of inert tubing ¼ inch radius and ½ inch radius, flow distribution nozzles, 2 filters and a syringe. The water sample to be cleaned starts in the syringe and is pressed through the ¼ inch into the main compartment of the bioreactor. The main compartment consists of the ½ inch tubing filled with our alginate bead encapsulated bacteria. The water continues moving through, interacting with the bacteria so that the toxin breaks down, and then exits the system fully cleaned on the other side. Inert tubing was chosen in order to prevent chemical reactions with the microcystins or any other molecules in the waterFilters were included on both ends of the bioreactor in order to ensure that bacteria did not travel outside of the reaction vessel, even if they somehow escaped the alginate beadsNozzles were included in order to evenly spread out the flow from the small tube coming from the syringe to the large reaction vessel tube. We designed the nozzles using Autodesk Inventor and then 3D printed them in our lab.
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                      We used a MakerBot Pro to 3D print the bioreactor nozzles out of ABS plastic. This method was the simplest way to produce the small and intricate parts. A subtractive manufacturing method wouldn’t have been able to accurately produce the interior chambers necessary in the design of the nozzle. The tight 3D printer tolerances resulted in fully watertight pieces.
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Latest revision as of 01:40, 22 October 2019

Team:Cornell - 2019.igem.org

Design Process
Design Process

Our team began tackling the issue of harmful algae by proposing a boat that physically cleans up the algae. We thought that it could essentially skim the algae off the top of the water and we would have a bioreactor that breaks down the toxins in the surface level water. We had this idea in mind because we knew that the majority of microcystin will be located within the first 1.6 meters of water. Past that depth, the concentration of microcystin drastically decreases, hence the remediation of lake water below this depth is not as important (González-Piana, pp. 614). We would use an Electro-coagulation-flotation(ECF) process to remove algae by designing a ECF reactor and attaching it to the bottom side of the boat.

Although this was a good starting point, there were 2 issues we discovered with this design:speed and battery capacity. To break down algae using the ECF process, we would have to slow down the boat drastically. At that rate, using a small remote controlled boat would take hundreds if not thousands of years to clean Cayuga lake. With the size of our battery, we would only be able to run the ECF reactor for 30 minutes at a time.

From this point, we began to brainstorm other ways we could accomplish our end goal of sampling and remediation. An autonomous way to sample water is not well developed in the scientific community and we opted to remove the microcystin, a greater danger than the algae itself. We decided as a team that having a boat to take samples quickly and having a separate bioreactor for water treatment plants where water could be pumped through at the correct speed would be more effective. With this two-part idea, we could detect the toxin as quickly as possible and then completely treat water (not just the surface) that is being distributed to the public.

After deciding on a separate boat and bioreactor, we had a complete plan for the boat, but needed new designs for the bioreactor. Weighing the pros and cons of various types of bioreactors for our specific project, we decided that a design resembling Gautier’s artificial liver reactor (Gautier 2011) would be ideal. We chose this idea because we needed a way for all of the water to interact with the bacteria while the bacteria remain enclosed for environmental safety. Pumping water through a tube of alginate beads would ensure both of these things. In addition, by manipulating how many beads, the nozzle, and speed of the pump, we would be able to ensure effective reactions, which gave us a lot more control than alternative designs such as a closed bioreactor where the water is held inside and mixed.

González-Piana, M., Piccardo, A., Ferrer, C., Brena, B., Pírez, M., Fabián, D., & Chalar, G. (2018). Effects of Wind Mixing in a Stratified Water Column on Toxic Cyanobacteria and Microcystin-LR Distribution in a Subtropical Reservoir. Bulletin of Environmental Contamination and Toxicology, 101(5), 611–616. doi: 10.1007/s00128-018-2446-x

Gautier, A., Carpentier, B., Dufresne, M., Vu Dinh, Q., Paullier, P., & Legallais, C. (2011). Impact of alginate type and bead diameter on mass transfers and the metabolic activities of encapsulated C3A cells in bioartificial liver applications. European Cells & Materials, 21, 94– 106.