Difference between revisions of "Team:NCKU Tainan/Software"

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                 <h2 class="mb-3">Modeling</h2>
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                 <h2 class="mb-3">Software in Modeling</h2>
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                <h4 class="mb-3">Description</h4>
 
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                         <p>    Literature research stated that the increase in patients’ IOP will result in the deformation of cornea, further leading to a structural change in contact lens<sup>[<a href="#ref2" class="linklink">2</a>]</sup>. We utilized this phenomenon to design a pair of contact lenses that structurally change in response to fluctuations in intraocular pressure.</p>
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                         <p>    For every iGEM team, modeling is a necessary part to link wet team experimental results and dry team theories together. In most of the cases, we need to simulate the behavior of chemicals or bacteria, such as distribution or concentration of them. Scientists often utilize partial differentiation equations (PDEs) to describe those target substances’ behavior. However, PDEs usually don’t have solutions due to the lack of strategies to deal with them since the governing equation, say the heat equation, is usually involved in the distance and the time passed by, which implies it to be a function that has 2 variables. Here, we introduce a method that might help future iGEM teams to deal with PDEs—<b>double Laplace transform</b>.</p>
 
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                 <h4 class="mb-3">Definition</h4>
 
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                         <p>   Our contact lens will be fitted with a tubular semipermeable chamber that is filled with our engineered bacteria, IPTG, NO precursor - L-arginine, and DAP. The volume change of the chamber will cause water to flow out thus increasing the IPTG concentration inside the chamber. The increase in IPTG will induce the bacteria to produce more Nitric Oxide Synthase, which can then convert L-arginine into nitric oxide to lower the intraocular pressure (IOP). This structural change is then able to induce dynamic drug delivery.</p>
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                         <p>   The definition of the single-variable Laplace transform, which is what we normally adopted, is listed below:</p>
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                 <h3 class="mb-0" style="margin-top: 1rem;">IOP simulation experiment</h3>
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                        <p>  The definition of the double-variable Laplace transform (or, double Laplace transform) has a similar form, listed below:</p>
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                        <p>  Notice that for single variable Laplace transform, the x domain is defined: { x | x > 0 }, so analogously, the domain of double Laplace transform, (x, y), is defined to be in the first quadrant, namely { (x, y) | x, y > 0 }.</p>
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                 <h4 class="mb-3">Properties</h4>
 
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                        <p>   To prove the concept of our contact lens and our device, we designed an IOP simulation experiment with porcine eye.By changing the drip bag’s height, water pressure will directly increase IOP in the porcine eye, enabling precise control of IOP for experiments<sup>[<a href="#ref3" class="linklink">3</a>]</sup><sup>[<a href="#ref4" class="linklink">4</a>]</sup>.</p>
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                        <p>   The general properties of double Laplace transform are listed below [1]:</p>
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              <h4 class="mb-3">Solving Partial Differential Equations</h4>
 
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                        <p>   For more details, please visit <a href="https://2020.igem.org/Team:NCKU_Tainan/Proof_Of_Concept" class="linkinthetext">proof of concept</a> and <a href="https://2020.igem.org/Team:NCKU_Tainan/Hardware" class="linkinthetext">hardware.</a></p>
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                        <p>   We performed a solution to one example of a partial differential equation using double Laplace transform.</p>
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                      <p><b>Problem :</b></p>
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                <a href="https://static.igem.org/mediawiki/2020/4/4e/T--NCKU_Tainan--design_contact_lens.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/4/4e/T--NCKU_Tainan--design_contact_lens.png" alt="" title="" style="width:100%"></a>
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                <figcaption class="caption-design">Fig. 1. The structure and design of contact lens.</figcaption>
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                      <p>Solve the equation</p>
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                      <p>with</p>
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                      <p><b>Solution :</b></p>
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                      <p>Taking the double Laplace transform of both side of the equation.</p>
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                      <p>with</p>
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                      <p>taking the inverse Laplace transform with respect to q gives</p>
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                      <p>taking the inverse Laplace transform with respect to p gives the solution</p>
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                      <p>from the property of convolution, we obtained the solution.</p>
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         <section class="resume-section" >
 
         <section class="resume-section" >
 
             <div class="resume-section-content" id="app">
 
             <div class="resume-section-content" id="app">
                 <h2 class="mb-3">APP</h2>
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                 <h2 class="mb-3">Software in APP</h2>
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                <h4 class="mb-3">Description</h4>
 
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                         <p>    In order for our bacteria to reduce intraocular pressure, we planned to engineer our bacteria to have the ability to produce Nitric Oxide Synthase (NOS)<sup>[<a href="#ref5" class="linklink">5</a>]</sup>, an enzyme that can convert L-arginine into NO.</p>
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                         <p>    In order to create a personalized IOP tracking system, we designed an app - Eye Cloud that works with Eye Screen. Eye Cloud not only displays the IOP value on the phone through the Bluetooth connection but also upload each measurement value to ThingSpeak’s personal account that is convenient for long-term tracking and observation. In addition, it can also be used as a tool for large-scale data collection to assist the development of Eye kNOw or other research related to intraocular pressure.</p>
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                        <p>    For biosafety, we engineered our bacteria to overexpress <i>csgD</i> and <i>csgA</i> for securing bacteria onto the contact lens by increasing binding affinity between bacteria and lens.</p>
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              <h3 class="mb-0" style="margin-top: 1rem;"><i>Nitric Oxide Synthases</i> (<i>NOS</i>)</h3>
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                        <p>    During literature research, we found out that Bacillus subtilis carries <i>Nitric Oxide Synthases</i>(<i>NOS</i>) and has the ability to produce NO, which is responsive to oxidative stress. So we cloned this gene from Bacillus subtilis' genome and designed a new biobrick which we then incorporated into our chassis, WM3064, allowing it to produce NO.</p>
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                        <p>    In order to dynamically express NOS as patients’ IOP fluctuate, we put <i>NOS</i> under the control of <i>T7</i> promoter and a <i>lacO</i> binding site, which can be controlled by IPTG-inducible <i>T7</i> RNA polymerase provided by another plasmid PDT7 (Plasmid Drive <i>T7</i> RNA polymerase). As previously mentioned, the IPTG concentration inside the ring-like compartment will fluctuate according to the patients’ IOP, leading to dynamic expression of <i>NOS</i>.</p>
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                <h4 class="mb-3">App Design</h4> 
 
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                 <a href="https://static.igem.org/mediawiki/2020/3/3b/T--NCKU_Tainan--design_NOS.gif" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/3/3b/T--NCKU_Tainan--design_NOS.gif" alt="" title="" style="width:100%"></a>
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                 <a href="https://static.igem.org/mediawiki/2020/5/51/T--NCKU_Tainan--soft_app.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/5/51/T--NCKU_Tainan--soft_app.png" alt="" title="" style="width:100%"></a>
                 <figcaption class="caption-design">Fig. 2. Plasmid design for <i>NOS</i>.</figcaption>
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                 <figcaption class="caption-design">Fig. 1. App OverviewThingSpeak</figcaption>
 
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                <h4 class="mb-0">Functional Test</h4>
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                         <p>    We tested the kinetics of the enzyme using a NOS assay kit, which utilizes Griess reagents to react with NO and generate colorimetric readouts by measuring O.D.540 value. For the purpose of controlling the production of NOS, we induced bacteria with different concentrations of IPTG and cultured them for different period times.</p>
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                         <p>    <a href="https://thingspeak.com/" alt="" target="_blank">ThingSpeak</a> is an IoT analytics platform service that allows us to aggregate, visualize, and analyze live data streams in the cloud. We can easily send data to ThingSpeak from Eye Screen, allowing users to upload and record IOP value through a URL (your personal API Keys)</p>
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                <a href="https://static.igem.org/mediawiki/2020/5/56/T--NCKU_Tainan--Soft_think.png " target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/5/56/T--NCKU_Tainan--Soft_think.png " alt="" title="" style="width:100%"></a>
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                <figcaption class="caption-design">Fig. 2. ThingSpeak Homepage</figcaption>
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                <h3 class="mb-0" style="margin-top: 1rem;">Biosafety</h3>
 
                <h4 class="mb-0">DAP-deficient strain</h4>
 
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                        <p>    We chose <i>E. coli</i> WM3064 as our chassis, which lacks the essential gene <i>dapA</i>. This gene encodes for 4-hydroxy-tetrahydrodipicolinate synthase that is critical to the production of lysine through the DAP pathway<sup>[<a href="#ref6" class="linklink">6</a>]</sup>. Lysine is an essential amino acid in animals, including humans, but can be synthesised de novo in bacteria, lower eukaryotes and plants for utilisation in protein and peptidoglycan cell wall synthesis<sup>[<a href="#ref1" class="linklink">7</a>]</sup>. Without this gene, the bacteria will have to depend on exogenous diaminopimelate (DAP) to survive.</p>
 
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                    <ol class="mb-4">
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                        <li><p>Sign up for ThingSpeak.</p></li>
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                      <li><p>Click <b>Channels > My Channels</b>. Create a new channel.</p></li>
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                        <li><p>Check the boxes next to Fields 1–3. Enter these channel setting values:</p></li>
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                      <p style="position: relative;left: 2rem;">Name: Eye Screen</p>
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                      <p style="position: relative;left: 2rem;">Field 1: IOP (mV)</p>
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                      <li><p>Click <b>Save Channel</b> at the bottom of the settings.</p></li>
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                      <li><p>Click API Keys tab and copy the <b>write URL</b>.</p></li>
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                 <figcaption class="caption-design">Fig. 3. Design of biosafety chassis.</figcaption>
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                 <figcaption class="caption-design">Fig. 3. ThingSpeak Setting ( API Keys > Write URL )</figcaption>
 
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              <h4 class="mb-3">User manual of Eye Cloud</h4>
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                <a href="https://static.igem.org/mediawiki/2020/d/dd/T--NCKU_Tainan--soft_all.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/d/dd/T--NCKU_Tainan--soft_all.png" alt="" title="" style="width:100%"></a>
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                <figcaption class="caption-design">Fig. 4. Eye Cloud </figcaption>
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                </figure>
 
                 </div>
 
                 </div>
                <h4 class="mb-0">Functional Test</h4>
 
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                    <div class="flex-grow-1">                     
 
                        <p>    To test whether the bacteria will survive without exogenous DAP, we made plates with and without DAP. After streaking our engineered bacteria onto these plates, we can demonstrate the result by checking its phenotype. Furthermore, we ran a SDS-PAGE to confirm the function of the <i>T7</i> expression system in our engineered WM3064.</p>
 
                    </div>
 
 
                 </div>
 
                 </div>
                 <h4 class="mb-0">Overexpression <i>csgD</i> and <i>csgA</i></h4>
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                 </div>
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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              <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 +
                    <div class="flex-grow-1">
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                    <ol class="mb-4">
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                        <li><p>This is the homepage of Eye Cloud, with our lovely logo. Click the “START” button to start.</p></li>
 +
                        <li><p>Then the next screen will ask if you have applied for a ThingSpeak account.</p></li>
 +
                      <p style="position: relative;left: 2rem;">Click “Yes! Ready to start” button to next page and wait for your IOP receiving.</p>
 +
                            <p style="position: relative;left: 2rem;">Click “No, click to apply” button to link to ThingSpeak homepage.</p>
 +
                            <p style="position: relative;left: 2rem;">Click “No,thanks” button to start directly</p>
 +
                        <li><p>Click “Bluetooth ” button to connect with Eye Screen when reaching this page.</p></li>
 +
                      <li><p>Bluetooth connection screen.</p></li>
 +
                    </ol>
 +
                    </div>   
 +
                  </div>
 +
              <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
 
                     <div class="flex-grow-1">                       
 
                     <div class="flex-grow-1">                       
                         <p>    Bacteria biofilm has been shown to exhibit extraordinary ability to help bacteria bind to biotic and abiotic surfaces[measurement reference]. We exploited this property to design one of the biosafety measures.</p>
+
                         <p>    After the IOP value shows on the screen, click the “Record” button to upload data to your ThingSpeak’s personal account, monitoring daily or monthly measurement records.</p>
                    </div>
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                </div>
                </div>
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                </div>
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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              <div class="container-fluid p-0">
                    <div class="flex-grow-1">                     
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                      <p>    We engineered our bacteria to overexpress <i>CsgD</i>, a master transcription regulator of biofilm formation, and <i>CsgA</i>, the major subunit of curli fibers. Overexpression of these two proteins have been reported to increase biofilm formation[measurement reference], which we anticipated to help the bacteria bind to the contact lenses more securely, thus preventing the leakage of bacteria if the contact lens encounters any damage.</p>
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                    </div>
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                </div>
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                <h4 class="mb-0">Functional Test</h4>
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                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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                    <div class="flex-grow-1">                     
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                        <p>    We first characterized the biofilm formation using conventional congo red staining, then we developed a simple method to assess the binding ability of our engineered bacteria. For more information, please visit our <a href="https://2020.igem.org/Team:NCKU_Tainan/Measurement" class="linkinthetext">measurement page</a>.</p>
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                    </div>
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                </div>
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                <h3 class="mb-0" style="margin-top: 1rem;">Growth switch</h3>
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                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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                    <div class="flex-grow-1">                     
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                        <p>    There are several things that need to be considered before selling Eye kNOw as a product. Since Eye kNOw won’t be used by the patient immediately after being manufactured, we designed a growth switch in order to control bacteria growth in different stages of our product lifetime. We were inspired by the work of <a href="https://2019.igem.org/Team:NUS_Singapore" class="linkinthetext">iGEM NUS 2019</a> who used a toxin-antitoxin system, <i>hicA</i>-<i>hicB</i>, to control the growth of bacteria. By manipulating the toxin-antitoxin ratio in a bacteria, we can determine when the bacteria should hibernate or grow.</p>
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                    </div>
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                </div>
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                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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                    <div class="flex-grow-1">                     
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                        <p>    In our design, the <i>hicB</i> antitoxin is constitutively expressed at a basal level, while the <i>hicA</i> toxin is controlled by arabinose inducible promoter. The entire <i>hicA</i> cassette is flanked with <i>FRT</i> sites, which can later be deleted by the FLP recombinase. We also added a heat-activated <i>FRT</i>-FLP recombinase system from pCP20 as an inducible switch. This design enables us to control the bacteria growth in three stages - production, storage and medication.</p>
+
                    </div>
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                </div>
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                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
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                    <div class="flex-grow-1">                     
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                        <p>    The production stage is when we are culturing our bacteria, so we need the bacteria to be able to grow normally. After the production process, the bacteria needs to be stored in the contact lens until it can be used. During the storage stage, <i>hicA</i> will be induced to hibernate the bacteria. The last stage is the medication stage, during which the contact lens will be used. When the contact lens is placed on the patient’s eye, the body temperature will activate the recombinase system and delete the hicA cassette, which will cause the bacteria to resuscitate and start producing the therapeutic agent.</p>
+
                    </div>
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                </div>
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                <div class="container-fluid p-0">
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                 <div class="row no-gutters">
 
                 <div class="row no-gutters">
 
                 <div class="col-lg ">
 
                 <div class="col-lg ">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
 
                 <figure class="d-flex flex-column justify-content-center align-items-center px-lg-3">
                 <a href="https://static.igem.org/mediawiki/2020/9/9a/T--NCKU_Tainan--design_HicAB.gif" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/9/9a/T--NCKU_Tainan--design_HicAB.gif" alt="" title="" style="width:100%"></a>
+
                 <a href="https://static.igem.org/mediawiki/2020/5/5a/T--NCKU_Tainan--soft_data.png" target="_blank" style="width:60%"><img src="https://static.igem.org/mediawiki/2020/5/5a/T--NCKU_Tainan--soft_data.png" alt="" title="" style="width:100%"></a>
                 <figcaption class="caption-design">Fig. 4. Plasmid design for grow switch</figcaption>
+
                 <figcaption class="caption-design">Fig. 5. Daily Measurement Records</figcaption>
 
                 </figure>
 
                 </figure>
 
                 </div>
 
                 </div>
 
                 </div>
 
                 </div>
                 </div>
+
                 </div>  
                <h4 class="mb-0">Functional Test</h4>
+
                <div class="d-flex flex-column flex-md-row justify-content-between mb-2">
+
                    <div class="flex-grow-1">                     
+
                        <p>    To verify the function of the FLP-<i>FRT</i> system, we will culture the bacteria with three plasmids, containing <i>hicA</i>, <i>hicB</i>, and <i>CI857</i> and <i>FLP</i> genes respectively. As the temperature rises to 42<sup>o</sup>C, <i>CI857</i> gene will be degraded, activating the <i>FLP</i> gene and deleting the <i>hicA</i> gene. If the <i>hicA</i> gene is present, the O.D.600 value will not increase since HicA protein represses the growth of bacteria. Hence, we can verify the function of the growth switch by measuring O.D. 600 value.</p>
+
                    </div>
+
                </div>             
+
            </div>
+
        </section>   
+
   
+
 
         <hr class="hrmar" />
 
         <hr class="hrmar" />
 
         <section class="resume-section" >
 
         <section class="resume-section" >
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             <h2>References</h2>
 
             <h2>References</h2>
 
               <ol>
 
               <ol>
                 <li id="ref1">Muenster S, Lieb WS, Fabry G, et al. The Ability of Nitric Oxide to Lower Intraocular Pressure Is Dependent on Guanylyl Cyclase. <i>Investigative Opthalmology & Visual Science.</i> 2017;58(11):4826.</li>
+
                 <li id="ref1">Debnath L. The Double Laplace Transforms and Their Properties with Applications to Functional, Integral and Partial Differential Equations. International Journal of Applied and Computational Mathematics. 2015;2(2):223-241.</li>
                <li id="ref2">Lam A. The effect of an artificially elevated intraocular pressure on the central corneal curvature. <i>Ophthalmic and Physiological Optics.</i> 1997;17(1):18-24.</li>
+
                <li id="ref3">Chen G-Z, Chan I-S, Leung LKK, Lam DCC. Soft wearable contact lens sensor for continuous intraocular pressure monitoring. <i>Medical Engineering & Physics.</i> 2014;36(9):1134-1139.</li>
+
                <li id="ref4">Zhang J, Zhang Y, Li Y, et al. Correlation of IOP with Corneal Acoustic Impedance in Porcine Eye Model. <i>BioMed Research International.</i> 2017;2017:1-6.</li>
+
                <li id="ref5">BRENDA - Information on EC 1.14.13.39 - nitric-oxide synthase (NADPH). Brenda-enzymes.org. <a href="https://www.brenda-enzymes.org/enzyme.php?ecno=1.14.13.39#pH%20OPTIMUM." target="_blank" class="linklink">https://www.brenda-enzymes.org/enzyme.php?ecno=1.14.13.39#pH%20OPTIMUM.</a> Published 2020. Accessed September 9, 2020.</li>
+
                <li id="ref6">Dante RA, Neto GC, Leite A, Yunes JA, Arruda P. Plant <i>Molecular Biology.</i> 1999;41(4):551-561.</li>
+
                <li id="ref7">McLennan N, Masters M. GroE is vital for cell-wall synthesis. <i>Nature.</i> 1998;392(6672):139-139.</li>
+
 
               </ol>
 
               </ol>
 
           </div>   
 
           </div>   

Revision as of 13:08, 26 October 2020


Software

Cloud service connecting you and me

Software in Modeling

Description

For every iGEM team, modeling is a necessary part to link wet team experimental results and dry team theories together. In most of the cases, we need to simulate the behavior of chemicals or bacteria, such as distribution or concentration of them. Scientists often utilize partial differentiation equations (PDEs) to describe those target substances’ behavior. However, PDEs usually don’t have solutions due to the lack of strategies to deal with them since the governing equation, say the heat equation, is usually involved in the distance and the time passed by, which implies it to be a function that has 2 variables. Here, we introduce a method that might help future iGEM teams to deal with PDEs—double Laplace transform.

Definition

The definition of the single-variable Laplace transform, which is what we normally adopted, is listed below:

The definition of the double-variable Laplace transform (or, double Laplace transform) has a similar form, listed below:

Notice that for single variable Laplace transform, the x domain is defined: { x | x > 0 }, so analogously, the domain of double Laplace transform, (x, y), is defined to be in the first quadrant, namely { (x, y) | x, y > 0 }.

Properties

The general properties of double Laplace transform are listed below [1]:

Solving Partial Differential Equations

We performed a solution to one example of a partial differential equation using double Laplace transform.

Problem :

Solve the equation

with

Solution :

Taking the double Laplace transform of both side of the equation.

with

taking the inverse Laplace transform with respect to q gives

taking the inverse Laplace transform with respect to p gives the solution

from the property of convolution, we obtained the solution.


Software in APP

Description

In order to create a personalized IOP tracking system, we designed an app - Eye Cloud that works with Eye Screen. Eye Cloud not only displays the IOP value on the phone through the Bluetooth connection but also upload each measurement value to ThingSpeak’s personal account that is convenient for long-term tracking and observation. In addition, it can also be used as a tool for large-scale data collection to assist the development of Eye kNOw or other research related to intraocular pressure.

App Design

Fig. 1. App OverviewThingSpeak

ThingSpeak is an IoT analytics platform service that allows us to aggregate, visualize, and analyze live data streams in the cloud. We can easily send data to ThingSpeak from Eye Screen, allowing users to upload and record IOP value through a URL (your personal API Keys)

Fig. 2. ThingSpeak Homepage
  1. Sign up for ThingSpeak.

  2. Click Channels > My Channels. Create a new channel.

  3. Check the boxes next to Fields 1–3. Enter these channel setting values:

  4. Name: Eye Screen

    Field 1: IOP (mV)

  5. Click Save Channel at the bottom of the settings.

  6. Click API Keys tab and copy the write URL.

Fig. 3. ThingSpeak Setting ( API Keys > Write URL )

User manual of Eye Cloud

Fig. 4. Eye Cloud
  1. This is the homepage of Eye Cloud, with our lovely logo. Click the “START” button to start.

  2. Then the next screen will ask if you have applied for a ThingSpeak account.

  3. Click “Yes! Ready to start” button to next page and wait for your IOP receiving.

    Click “No, click to apply” button to link to ThingSpeak homepage.

    Click “No,thanks” button to start directly

  4. Click “Bluetooth ” button to connect with Eye Screen when reaching this page.

  5. Bluetooth connection screen.

After the IOP value shows on the screen, click the “Record” button to upload data to your ThingSpeak’s personal account, monitoring daily or monthly measurement records.

Fig. 5. Daily Measurement Records

References

  1. Debnath L. The Double Laplace Transforms and Their Properties with Applications to Functional, Integral and Partial Differential Equations. International Journal of Applied and Computational Mathematics. 2015;2(2):223-241.