Difference between revisions of "Team:BITSPilani-Goa India/Engineering"

 
Line 11: Line 11:
 
nav:not(.menu-open) .nav-transparent:not(.nav-colored) .menu-icon::after {
 
nav:not(.menu-open) .nav-transparent:not(.nav-colored) .menu-icon::after {
 
   background-color: #187a7a !important;
 
   background-color: #187a7a !important;
}</style><meta charset="utf-8"/><meta content="width=device-width,initial-scale=1" name="viewport"/><title>Engineering | SugarGain | iGEM BITS Goa</title><link href="https://2020.igem.org/Template:BITSPilani-Goa_India/css/engineeringCSS?action=raw&amp;ctype=text/css" rel="stylesheet"/></head><body><div id="safari-toast"><p>The Safari browser doesn't support some features of this website. Please switch to Firefox, Edge or Chrome for a better experience.</p></div><nav id="main-nav"><div class="navbar bg-none nav-transparent"><div class="row" id="navbar-row"><a class="navbar-brand" href="https://2020.igem.org/Team:BITSPilani-Goa_India"><i class="navbar-logo"></i><span> Sugar<strong>Gain</strong></span></a><div class="controls h-100 d-flex align-items-center"><div class="align-items-center" id="themeSwitchWrapper"><i class="icon-light"></i><div id="themeSwitch"><label class="switch" for="themeSwitchInput"><input id="themeSwitchInput" type="checkbox"/><span class="slider round"></span></label></div><i class="icon-dark"></i></div><button class="btn" id="menuSwitch"><div class="menu-icon"></div></button></div></div><div class="row w-100" id="progress-container-wrapper"><div id="progress-container"><div id="nav-progress-bar"></div></div></div></div><div id="fullscreenMenuWrapper"><div class="w-100 h-100" id="fullscreenMenu"><div class="container-fluid d-flex align-items-stretch pr-0 flex-column"><div class="row nav-header w-100"><div class="col-xl-3 col-lg-2"><div class="teamLogo"></div></div><div class="col-xl-6 col-lg-8"></div><div class="col-xl-3 col-lg-2"></div></div><div class="row flex-grow-1 w-100"><div class="col-xl-3 col-lg-2"></div><div class="col-xl-6 col-lg-8 d-flex justify-content-between flex-column" id="menuContent"><div class="row"><div class="col-md-6" id="nav-headings"><ul role="tablist"><li><a href="javascript:;" id="Project-tab">Project</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></li><li><a href="javascript:;" id="Human_Practices-tab">Human Practices</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></li><li><a href="javascript:;" id="Parts-tab">Parts</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></li><li><a href="javascript:;" id="Journal-tab">Journal</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></li><li><a href="javascript:;" id="Team-tab">Team</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></li><li><a href="javascript:;" id="Contribution-tab">Contribution</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></li><li><a href="javascript:;" id="Entrepreneurship-tab">Entrepreneurship</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></li><li><a href="javascript:;" id="Judging-tab">Judging</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/https:/igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></li></ul></div><div class="col-6" id="nav-items"><div class="tab-content"><div class="tab-pane" id="Project-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></div><div class="tab-pane" id="Human_Practices-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></div><div class="tab-pane" id="Parts-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></div><div class="tab-pane" id="Journal-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></div><div class="tab-pane" id="Team-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></div><div class="tab-pane" id="Contribution-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></div><div class="tab-pane" id="Entrepreneurship-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></div><div class="tab-pane" id="Judging-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li><a href="https://igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></div></div></div></div><div class="row"><div id="contact-links"><ul><li><a href="https://instagram.com/igem_bits" rel="noopener" target="_blank"><i class="insta"></i><span>Instagram</span></a></li><li><a href="https://twitter.com/igembitsgoa" rel="noopener" target="_blank"><i class="twitter"></i><span>Twitter</span></a></li><li><a href="mailto:igembitsgoa@gmail.com" rel="noopener" target="_blank"><i class="email"></i><span>Email</span></a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Sample"><i class="sample"></i><span>Sample</span></a></li></ul><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Acknowledgements">Acknowledgements</a></li></ul></div></div></div><div class="col-xl-3 col-lg-2"></div></div><div class="row nav-footer w-100"><div class="col-xl-3 col-lg-2"></div><div class="col-xl-6 col-lg-8"></div><div class="col-xl-3 col-lg-2"></div></div></div></div></div></nav><style>#header-background {
+
}</style><meta charset="utf-8"/><meta content="width=device-width,initial-scale=1" name="viewport"/><title>Engineering | SugarGain | iGEM BITS Goa</title><link href="https://2020.igem.org/Template:BITSPilani-Goa_India/css/engineeringCSS?action=raw&amp;ctype=text/css" rel="stylesheet"/></head><body><div id="safari-toast"><p>The Safari browser doesn't support some features of this website. Please switch to Firefox, Edge or Chrome for a better experience.</p></div><nav id="main-nav"><div class="navbar bg-none nav-transparent"><div class="row" id="navbar-row"><a class="navbar-brand" href="https://2020.igem.org/Team:BITSPilani-Goa_India"><i class="navbar-logo"></i><span> Sugar<strong>Gain</strong></span></a><div class="controls h-100 d-flex align-items-center"><div class="align-items-center" id="themeSwitchWrapper"><i class="icon-light"></i><div id="themeSwitch"><label class="switch" for="themeSwitchInput"><input id="themeSwitchInput" type="checkbox"/><span class="slider round"></span></label></div><i class="icon-dark"></i></div><button class="btn" id="menuSwitch"><div class="menu-icon"></div></button></div></div><div class="row w-100" id="progress-container-wrapper"><div id="progress-container"><div id="nav-progress-bar"></div></div></div></div><div id="fullscreenMenuWrapper"><div class="w-100 h-100" id="fullscreenMenu"><div class="container-fluid d-flex align-items-stretch pr-0 flex-column"><div class="row nav-header w-100"><div class="col-xl-3 col-lg-2"><div class="teamLogo"></div></div><div class="col-xl-6 col-lg-8"></div><div class="col-xl-3 col-lg-2"></div></div><div class="row flex-grow-1 w-100"><div class="col-xl-3 col-lg-2"></div><div class="col-xl-6 col-lg-8 d-flex justify-content-between flex-column" id="menuContent"><div class="row"><div class="col-md-6" id="nav-headings"><ul role="tablist"><li><a href="javascript:;" id="Project-tab">Project</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></li><li><a href="javascript:;" id="Human_Practices-tab">Human Practices</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></li><li><a href="javascript:;" id="Parts-tab">Parts</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></li><li><a href="javascript:;" id="Journal-tab">Journal</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></li><li><a href="javascript:;" id="Team-tab">Team</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></li><li><a href="javascript:;" id="Contribution-tab">Contribution</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></li><li><a href="javascript:;" id="Entrepreneurship-tab">Entrepreneurship</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></li><li><a href="javascript:;" id="Judging-tab">Judging</a><ul class="mobile-nav-items"><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Awards">Awards</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/https:/igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></li></ul></div><div class="col-6" id="nav-items"><div class="tab-content"><div class="tab-pane" id="Project-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></div><div class="tab-pane" id="Human_Practices-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></div><div class="tab-pane" id="Parts-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></div><div class="tab-pane" id="Journal-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></div><div class="tab-pane" id="Team-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></div><div class="tab-pane" id="Contribution-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></div><div class="tab-pane" id="Entrepreneurship-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></div><div class="tab-pane" id="Judging-pane"><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Awards">Awards</a></li><li><a href="https://igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></div></div></div></div><div class="row"><div id="contact-links"><ul><li><a href="https://instagram.com/igem_bits" rel="noopener" target="_blank"><i class="insta"></i><span>Instagram</span></a></li><li><a href="https://twitter.com/igembitsgoa" rel="noopener" target="_blank"><i class="twitter"></i><span>Twitter</span></a></li><li><a href="mailto:igembitsgoa@gmail.com" rel="noopener" target="_blank"><i class="email"></i><span>Email</span></a></li><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Sample"><i class="sample"></i><span>Sample</span></a></li></ul><ul><li><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Acknowledgements">Acknowledgements</a></li></ul></div></div></div><div class="col-xl-3 col-lg-2"></div></div><div class="row nav-footer w-100"><div class="col-xl-3 col-lg-2"></div><div class="col-xl-6 col-lg-8"></div><div class="col-xl-3 col-lg-2"></div></div></div></div></div></nav><style>#header-background {
 
     background-image: url(https://static.igem.org/mediawiki/2020/1/11/T--BITSPilani-Goa_India--img--Engineering--header.svg);
 
     background-image: url(https://static.igem.org/mediawiki/2020/1/11/T--BITSPilani-Goa_India--img--Engineering--header.svg);
 
}
 
}
 
header {
 
header {
 
     background-color: #c5fffd;
 
     background-color: #c5fffd;
}</style><header class="d-flex justify-content-center"><div class="custom-container"><div id="header-background"></div><div id="heading"><h1>Engineering</h1></div><a href="https://freepik.com" rel="noopener" target="_blank"><span data-placement="top" id="bg-attribution" title="Photo from Freepik"></span></a></div></header><main class="theme-journal"><div class="custom-container"><div class="row"><div class="sidebar"><div class="nav" id="contents"><ul></ul></div></div><div class="content"><article><div class="intro"><p>While designing SugarGain, we had to keep various considerations in mind. The initial idea was broken down into a set of problem statements and these formed the major pillars of our project. The following diagrams illustrate the flow of our thought as we tried to solve these problems to the best of our ability. We also illustrate how we modelled our project and its interconnectedness with the experiments we designed to complement the modelled data. Furthermore, we have taken into consideration the different outcomes that these experiments might lead to and planned accordingly. Due to unavailability of lab access this year, we plan to finish these experiments in phase 2.</p><p>For more details about these experiments, please see our <a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a> page.</p></div><br/><br/><h1>pFruB-Cra System</h1><div class="chart-wrapper"><section id="biosensor"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Our project aims to reduce the activity of invertase, an enzyme that converts useful sucrose into profitless glucose and fructose. Since this process was important to the life cycle of the plant, it wasn’t practical to genetically re-engineer sugarcane cells itself. The most harm this enzyme causes is post-harvest and hence, that seemed like the most logical time period for us to target.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>After surveying publications on invertases, we came across a group of proteins called anti-invertases/invertase inhibitor which regulate invertase and control sugar hydrolysis.</p></div><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>We also discovered that anti-invertase has quite a small half-life. This meant that the invertase would have to be secreted at the site of action (i.e., inside the sugarcane).</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>To decrease the nutrient load on our bacterial chassis and have a controlled release of our protein, we decided on a biosensor mechanism.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>Since the concentration of fructose was a more or less direct result of invertase activity, we wanted to calibrate a self-regulatory mechanism that modulated the secretion of the anti-invertase in tandem with the concentration of fructose in the medium. We were able to achieve that by using a pFruB-Cra system.</p></div></div><div class="col-5"><div class="rounded-rectangle mt-5"><div class="number"><p>5</p></div><p>Using these parts, we constructed our fructose regulated anti invertase.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">Biosensor will simulate output of invertase inhibitor for particular levels of fructose in the environment and will also link the promoter activity to a measurable output.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="biosensor-mod1"><strong>Homology Modelling and Docking</strong><p>We tried to get an insight into the protein-protein interaction through modelling of anti-invertase with invertase.</p></div><div class="rounded-rectangle" id="biosensor-mod2"><strong>Homology Modelling</strong><p>We tried to get an insight into the protein-DNA interaction through homology modelling of FruR.</p></div><div class="rounded-rectangle" id="biosensor-mod3"><strong>Docking studies of FruR with F-1-P</strong><p>Since FruR and its interactions are not extensively characterised, we had to conduct molecular docking studies in order to elucidate the interactions between FruR and fructose.</p></div><div class="rounded-rectangle" id="biosensor-mod4"><p>Identify the optimum Kd value for the system to work</p></div><div class="rounded-rectangle" id="biosensor-mod5"><p>In phase 2, prediction of overall efficiency of the pFruB-Cra system and the amount of inoculant required per sugarcane using information from experiments.</p></div></div><div class="col-4"><div class="oval" id="biosensor-exp1"><p>Anti-Invertase Assay to characterise the functioning of anti-invertase.</p></div><div class="oval" id="biosensor-exp2"><p>FruR Specificity Experiment</p></div><div class="oval" id="biosensor-exp3"><p>pFruB-FruR Characterisation</p></div><div class="oval" id="biosensor-exp4"><p>Gel shift assay to experimentally determine K<sub>d</sub> value of pFruB.</p></div><div class="oval" id="biosensor-exp5"><p>Site-directed mutagenesis of the pFruB to bring the K<sub>d</sub> value to the one established through the model</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#biosensor-mod1" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp1"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-exp1" data-offset-x1="20" data-offset-x2="-5" data-offset-y1="35" data-offset-y2="-75" data-to="#biosensor-mod5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-exp1_#biosensor-mod5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-exp1_#biosensor-mod5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod3" data-offset-x1="8" data-offset-x2="-10" data-offset-y1="-75" data-offset-y2="10" data-to="#biosensor-exp2"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod3" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp3"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod4" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp4"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod4" data-label-offset-x="0" data-label-offset-y="0" data-offset-x1="0" data-offset-x2="0" data-offset-y1="30" data-offset-y2="-40" data-to="#biosensor-exp5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-mod4_#biosensor-exp5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-mod4_#biosensor-exp5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if inadequate</p></div><div class="arrow-container" data-from="#biosensor-exp4" data-offset-x1="5" data-offset-x2="13" data-offset-y1="20" data-offset-y2="-30" data-to="#biosensor-mod5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-exp4_#biosensor-mod5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-exp4_#biosensor-mod5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div></div></section></div><h1>Atmosphere Regulated Killswitch</h1><div class="chart-wrapper"><section id="killswitch"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Given the consumable nature of our product, we had to come up with a robust killswitch that was capable of effectively terminating the bacteria taking into account the toxicity of killswitch with respect to the humans.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>First, we ascertained the trigger to be the swift and abrupt change in atmospheric conditions (anaerobic inside the sugarcane stem and aerobic outside)</p></div><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>Second, we found a toxin-antitoxin pair that was quite fatal to bacteria but did not affect human cells.</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>After an extensive search of the registry, we found the FNR promoter that was only activated in anaerobic conditions.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>Using these parts, we designed our killswitch genetic circuit.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">We focussed on modelling the behaviour of the circuit to the change in concentration of oxygen in the atmosphere. We further predicted the response time for the same.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="killswitch-mod1"><p>Create a persister cell model in phase 2</p></div><div class="rounded-rectangle" id="killswitch-mod2"><p>Differential expression of the antitoxin in the presence and absence of oxygen</p></div><div class="rounded-rectangle" id="killswitch-mod3"><p>Time required for the buildup of toxin concentration sufficient to restrict bacterial growth</p></div><div class="rounded-rectangle" id="killswitch-mod4"><p>Identify the optimum Kd value for the system to work</p></div></div><div class="col-4"><div class="oval" id="killswitch-exp1"><p>Assay to check if the killswitch functions as intended</p></div><div class="oval" id="killswitch-exp2"><p>Killswitch response time assay to ascertain the time required after exposure for the cell to succumb</p></div><div class="oval" id="killswitch-exp3"><p>Gel shift assay to experimentally determine Kd value of the FNR promoter</p></div><div class="oval" id="killswitch-exp4"><p>Site-directed mutagenesis of the FNR promoter to bring the Kd value to the one established through the model</p></div><div class="oval" id="killswitch-exp5"><p>pH dependency of the FNR promoter (due to the fluctuation in pH in the sugar extraction process)</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#killswitch-exp1" data-offset-x1="0" data-offset-x2="10" data-offset-y1="0" data-offset-y2="0" data-to="#killswitch-mod1"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-exp1_#killswitch-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-exp1_#killswitch-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod1" data-label-offset-x="-30" data-label-offset-y="-30" data-offset-x1="0" data-offset-x2="10" data-offset-y1="15" data-offset-y2="-40" data-to="#killswitch-exp2"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod1_#killswitch-exp2" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod1_#killswitch-exp2)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if high cell viability</p></div><div class="arrow-container" data-from="#killswitch-exp2" data-offset-x1="-10" data-offset-x2="10" data-offset-y1="15" data-offset-y2="0" data-to="#killswitch-mod3"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod4" data-offset-x1="0" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#killswitch-exp3"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod4_#killswitch-exp3" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod4_#killswitch-exp3)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod3" data-label-offset-x="-75" data-label-offset-y="-40" data-offset-x1="0" data-offset-x2="10" data-offset-y1="10" data-offset-y2="-40" data-to="#killswitch-exp4"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod3_#killswitch-exp4" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod3_#killswitch-exp4)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if not quick enough</p></div><div class="arrow-container" data-from="#killswitch-exp3" data-label-offset-x="20" data-label-offset-y="-30" data-offset-x1="0" data-offset-x2="0" data-offset-y1="0" data-offset-y2="-10" data-to="#killswitch-exp4"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-exp3_#killswitch-exp4" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-exp3_#killswitch-exp4)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if inadequate Kd value</p></div></div></section></div><h1>Polymer Inoculant</h1><div class="chart-wrapper"><section id="inoculant"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Since our product includes live bacteria, we wanted to ensure that the product had a long shelf life. After consulting farmers in various belts across India, we also came across the need for the product to be organic, non-toxic and cheap.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>We started researching polymer-based inoculants that had longevity and were organic in nature.</p></div><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>We determined the optimal inoculant composition of a Carboxymethylcellulose-based polymer with bentonite suspending agent and sorbic acid preservative.</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>We optimized the viscosity to minimize the inoculant's toxicity, and ensured that it is close to that of water for efficient transport.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>This inoculant would be supplied to the farmer and can be used through an injector mechanism. In this manner the sugarcane's inherent transport mechanism due to transpirational pull is leveraged for the uniform distribution of the bacteria through the plant.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">Keeping in mind the concerns of the sugarcane farmers across major Indian belts,we devised ways to optimise the features of the polymer inoculant.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="inoculant-mod1"><p>Kinematic Viscosity model and Toxicity model</p></div><div class="rounded-rectangle" id="inoculant-mod2"><p>Proposed implementation and economic scalability model</p></div></div><div class="col-4"><div class="oval" id="inoculant-exp1"><p>Removal of chemical residues of polymer inoculant during processing of sugarcane juice</p></div><div class="oval" id="inoculant-exp2"><p>Validating toxicity model</p></div><div class="oval" id="inoculant-exp3"><p>Capillary action experiment will help with delivery mechanism model in proposed implementation</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#inoculant-exp1" data-offset-x1="0" data-offset-x2="10" data-offset-y1="0" data-offset-y2="15" data-to="#inoculant-mod1"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp1_#inoculant-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp1_#inoculant-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#inoculant-exp2" data-offset-x1="0" data-offset-x2="0" data-offset-y1="0" data-offset-y2="40" data-to="#inoculant-mod1"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp2_#inoculant-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp2_#inoculant-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#inoculant-exp3" data-offset-x1="0" data-offset-x2="4" data-offset-y1="0" data-offset-y2="45" data-to="#inoculant-mod2"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp3_#inoculant-mod2" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp3_#inoculant-mod2)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div></div></section></div></article><div class="d-flex justify-content-between my-5"><a class="button prev" href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model"><span class="button-background"><span aria-hidden="" class="circle"><span class="icon arrow"></span></span></span><span class="button-text">Model</span></a><a class="button next" href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety"><span class="button-background"><span aria-hidden="" class="circle"><span class="icon arrow"></span></span></span><span class="button-text">Safety</span></a></div></div></div></div></main><footer><div id="footerNav"><div class="container"><div class="row justify-content-between"><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Project</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Human Practices</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Parts</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Journal</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Team</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Contribution</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Entrepreneurship</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Judging</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/https:/igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></div></div></div></div><div id="footerBrand"><div class="container"><div class="row justify-content-center"><div id="footerTeamLogo"></div><div id="BITSLogo"></div></div><p>iGEM BITS Goa</p><p>Birla Institute of Technology and Science, Pilani</p><p>K K Birla Goa Campus</p><p>NH-17B, Sancoale, Goa, India</p><div class="row justify-content-center" id="footerIcons"><a class="gmail" href="mailto:igembitsgoa@gmail.com"></a><a class="insta" href="https://instagram.com/igem_bits" rel="noopener" target="_blank"></a><a class="twitter" href="https://twitter.com/igembitsgoa" rel="noopener" target="_blank"></a></div></div></div></footer><script src="https://2020.igem.org/Template:BITSPilani-Goa_India/engineering-bundleJS?action=raw&amp;ctype=text/javascript"></script></body></html>
+
}</style><header class="d-flex justify-content-center"><div class="custom-container"><div id="header-background"></div><div id="heading"><h1>Engineering</h1></div><a href="https://freepik.com" rel="noopener" target="_blank"><span data-placement="top" id="bg-attribution" title="Photo from Freepik"></span></a></div></header><main class="theme-journal"><div class="custom-container"><div class="row"><div class="sidebar"><div class="nav" id="contents"><ul></ul></div></div><div class="content"><article><div class="intro"><p>While designing SugarGain, we had to keep various considerations in mind. The initial idea was broken down into a set of problem statements and these formed the major pillars of our project. The following diagrams illustrate the flow of our thought as we tried to solve these problems to the best of our ability. We also illustrate how we modelled our project and its interconnectedness with the experiments we designed to complement the modelled data. Furthermore, we have taken into consideration the different outcomes that these experiments might lead to and planned accordingly. Due to unavailability of lab access this year, we plan to finish these experiments in phase 2.</p><p>For more details about these experiments, please see our <a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a> page.</p></div><br/><br/><h1>pFruB-Cra System</h1><div class="chart-wrapper"><section id="biosensor"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Our project aims to reduce the activity of invertase, an enzyme that converts useful sucrose into profitless glucose and fructose. Since this process was important to the life cycle of the plant, it wasn’t practical to genetically re-engineer sugarcane cells itself. The most harm this enzyme causes is post-harvest and hence, that seemed like the most logical time period for us to target.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>After surveying publications on invertases, we came across a group of proteins called anti-invertases/invertase inhibitor which regulate invertase and control sugar hydrolysis.</p></div><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>We also discovered that anti-invertase has quite a small half-life. This meant that the invertase would have to be secreted at the site of action (i.e., inside the sugarcane).</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>To decrease the nutrient load on our bacterial chassis and have a controlled release of our protein, we decided on a biosensor mechanism.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>Since the concentration of fructose was a more or less direct result of invertase activity, we wanted to calibrate a self-regulatory mechanism that modulated the secretion of the anti-invertase in tandem with the concentration of fructose in the medium. We were able to achieve that by using a pFruB-Cra system.</p></div></div><div class="col-5"><div class="rounded-rectangle mt-5"><div class="number"><p>5</p></div><p>Using these parts, we constructed our fructose regulated anti invertase.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">Biosensor will simulate output of invertase inhibitor for particular levels of fructose in the environment and will also link the promoter activity to a measurable output.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="biosensor-mod1"><strong>Homology Modelling and Docking</strong><p>We tried to get an insight into the protein-protein interaction through modelling of anti-invertase with invertase.</p></div><div class="rounded-rectangle" id="biosensor-mod2"><strong>Homology Modelling</strong><p>We tried to get an insight into the protein-DNA interaction through homology modelling of FruR.</p></div><div class="rounded-rectangle" id="biosensor-mod3"><strong>Docking studies of FruR with F-1-P</strong><p>Since FruR and its interactions are not extensively characterised, we had to conduct molecular docking studies in order to elucidate the interactions between FruR and fructose.</p></div><div class="rounded-rectangle" id="biosensor-mod4"><p>Identify the optimum Kd value for the system to work</p></div><div class="rounded-rectangle" id="biosensor-mod5"><p>In phase 2, prediction of overall efficiency of the pFruB-Cra system and the amount of inoculant required per sugarcane using information from experiments.</p></div></div><div class="col-4"><div class="oval" id="biosensor-exp1"><p>Anti-Invertase Assay to characterise the functioning of anti-invertase.</p></div><div class="oval" id="biosensor-exp2"><p>FruR Specificity Experiment</p></div><div class="oval" id="biosensor-exp3"><p>pFruB-FruR Characterisation</p></div><div class="oval" id="biosensor-exp4"><p>Gel shift assay to experimentally determine K<sub>d</sub> value of pFruB.</p></div><div class="oval" id="biosensor-exp5"><p>Site-directed mutagenesis of the pFruB to bring the K<sub>d</sub> value to the one established through the model</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#biosensor-mod1" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp1"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-exp1" data-offset-x1="20" data-offset-x2="-5" data-offset-y1="35" data-offset-y2="-75" data-to="#biosensor-mod5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-exp1_#biosensor-mod5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-exp1_#biosensor-mod5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod3" data-offset-x1="8" data-offset-x2="-10" data-offset-y1="-75" data-offset-y2="10" data-to="#biosensor-exp2"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod3" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp3"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod4" data-offset-x1="10" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#biosensor-exp4"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#biosensor-mod4" data-label-offset-x="0" data-label-offset-y="0" data-offset-x1="0" data-offset-x2="0" data-offset-y1="30" data-offset-y2="-40" data-to="#biosensor-exp5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-mod4_#biosensor-exp5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-mod4_#biosensor-exp5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if inadequate</p></div><div class="arrow-container" data-from="#biosensor-exp4" data-offset-x1="5" data-offset-x2="13" data-offset-y1="20" data-offset-y2="-30" data-to="#biosensor-mod5"><svg height="100" width="100"><defs><marker id="arrow_#biosensor-exp4_#biosensor-mod5" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#biosensor-exp4_#biosensor-mod5)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div></div></section></div><h1>Atmosphere Regulated Killswitch</h1><div class="chart-wrapper"><section id="killswitch"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Given the consumable nature of our product, we had to come up with a robust killswitch that was capable of effectively terminating the bacteria taking into account the toxicity of killswitch with respect to the humans.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>First, we ascertained the trigger to be the swift and abrupt change in atmospheric conditions (anaerobic inside the sugarcane stem and aerobic outside)</p></div><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>Second, we found a toxin-antitoxin pair that was quite fatal to bacteria but did not affect human cells.</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>After an extensive search of the registry, we found the FNR promoter that was only activated in anaerobic conditions.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>Using these parts, we designed our killswitch genetic circuit.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">We focussed on modelling the behaviour of the circuit to the change in concentration of oxygen in the atmosphere. We further predicted the response time for the same.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="killswitch-mod1"><p>Create a persister cell model in phase 2</p></div><div class="rounded-rectangle" id="killswitch-mod2"><p>Differential expression of the antitoxin in the presence and absence of oxygen</p></div><div class="rounded-rectangle" id="killswitch-mod3"><p>Time required for the buildup of toxin concentration sufficient to restrict bacterial growth</p></div><div class="rounded-rectangle" id="killswitch-mod4"><p>Identify the optimum Kd value for the system to work</p></div></div><div class="col-4"><div class="oval" id="killswitch-exp1"><p>Assay to check if the killswitch functions as intended</p></div><div class="oval" id="killswitch-exp2"><p>Killswitch response time assay to ascertain the time required after exposure for the cell to succumb</p></div><div class="oval" id="killswitch-exp3"><p>Gel shift assay to experimentally determine Kd value of the FNR promoter</p></div><div class="oval" id="killswitch-exp4"><p>Site-directed mutagenesis of the FNR promoter to bring the Kd value to the one established through the model</p></div><div class="oval" id="killswitch-exp5"><p>pH dependency of the FNR promoter (due to the fluctuation in pH in the sugar extraction process)</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#killswitch-exp1" data-offset-x1="0" data-offset-x2="10" data-offset-y1="0" data-offset-y2="0" data-to="#killswitch-mod1"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-exp1_#killswitch-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-exp1_#killswitch-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod1" data-label-offset-x="-30" data-label-offset-y="-30" data-offset-x1="0" data-offset-x2="10" data-offset-y1="15" data-offset-y2="-40" data-to="#killswitch-exp2"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod1_#killswitch-exp2" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod1_#killswitch-exp2)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if high cell viability</p></div><div class="arrow-container" data-from="#killswitch-exp2" data-offset-x1="-10" data-offset-x2="10" data-offset-y1="15" data-offset-y2="0" data-to="#killswitch-mod3"><svg height="100" width="100"><defs><marker id="startarrow" markerHeight="7" markerWidth="6" orient="auto" refX="6" refY="3.5"><polygon fill="#ea526f" points="6 0, 6 7, 0 3.5"></polygon></marker><marker id="endarrow" markerHeight="7" markerUnits="strokeWidth" markerWidth="6" orient="auto" refX="0" refY="3.5"><polygon fill="#ea526f" points="0 0, 6 3.5, 0 7"></polygon></marker></defs><line class="arrow" marker-end="url(#endarrow)" marker-start="url(#startarrow)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod4" data-offset-x1="0" data-offset-x2="-10" data-offset-y1="0" data-offset-y2="0" data-to="#killswitch-exp3"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod4_#killswitch-exp3" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod4_#killswitch-exp3)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#killswitch-mod3" data-label-offset-x="-75" data-label-offset-y="-40" data-offset-x1="0" data-offset-x2="10" data-offset-y1="10" data-offset-y2="-40" data-to="#killswitch-exp4"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-mod3_#killswitch-exp4" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-mod3_#killswitch-exp4)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if not quick enough</p></div><div class="arrow-container" data-from="#killswitch-exp3" data-label-offset-x="20" data-label-offset-y="-30" data-offset-x1="0" data-offset-x2="0" data-offset-y1="0" data-offset-y2="-10" data-to="#killswitch-exp4"><svg height="100" width="100"><defs><marker id="arrow_#killswitch-exp3_#killswitch-exp4" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#killswitch-exp3_#killswitch-exp4)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg><p class="label">if inadequate Kd value</p></div></div></section></div><h1>Polymer Inoculant</h1><div class="chart-wrapper"><section id="inoculant"><div class="row problem"><div class="col-6"><h2>Problem Statement</h2><div class="rounded-rectangle"><p>Since our product includes live bacteria, we wanted to ensure that the product had a long shelf life. After consulting farmers in various belts across India, we also came across the need for the product to be organic, non-toxic and cheap.</p></div></div></div><div class="row design"><div class="col-12"><h2>Designing Process</h2></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>1</p></div><p>We started researching polymer-based inoculants that had longevity and were organic in nature.</p></div><div class="rounded-rectangle"><div class="number"><p>2</p></div><p>We determined the optimal inoculant composition of a Carboxymethylcellulose-based polymer with bentonite suspending agent and sorbic acid preservative.</p></div></div><div class="col-5"><div class="rounded-rectangle"><div class="number"><p>3</p></div><p>We optimized the viscosity to minimize the inoculant's toxicity, and ensured that it is close to that of water for efficient transport.</p></div><div class="rounded-rectangle"><div class="number"><p>4</p></div><p>This inoculant would be supplied to the farmer and can be used through an injector mechanism. In this manner the sugarcane's inherent transport mechanism due to transpirational pull is leveraged for the uniform distribution of the bacteria through the plant.</p></div></div></div><div class="row brief"><div class="col-5"><h2>Modelling</h2><p class="text-center">Keeping in mind the concerns of the sugarcane farmers across major Indian belts,we devised ways to optimise the features of the polymer inoculant.</p></div><div class="col-5"><h2>Experimental Design</h2><p class="text-center">Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.</p></div></div><div class="row graph"><div class="col-5"><div class="rounded-rectangle" id="inoculant-mod1"><p>Kinematic Viscosity model and Toxicity model</p></div><div class="rounded-rectangle" id="inoculant-mod2"><p>Proposed implementation and economic scalability model</p></div></div><div class="col-4"><div class="oval" id="inoculant-exp1"><p>Removal of chemical residues of polymer inoculant during processing of sugarcane juice</p></div><div class="oval" id="inoculant-exp2"><p>Validating toxicity model</p></div><div class="oval" id="inoculant-exp3"><p>Capillary action experiment will help with delivery mechanism model in proposed implementation</p></div></div></div><div class="arrows"><div class="arrow-container" data-from="#inoculant-exp1" data-offset-x1="0" data-offset-x2="10" data-offset-y1="0" data-offset-y2="15" data-to="#inoculant-mod1"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp1_#inoculant-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp1_#inoculant-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#inoculant-exp2" data-offset-x1="0" data-offset-x2="0" data-offset-y1="0" data-offset-y2="40" data-to="#inoculant-mod1"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp2_#inoculant-mod1" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp2_#inoculant-mod1)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div><div class="arrow-container" data-from="#inoculant-exp3" data-offset-x1="0" data-offset-x2="4" data-offset-y1="0" data-offset-y2="45" data-to="#inoculant-mod2"><svg height="100" width="100"><defs><marker id="arrow_#inoculant-exp3_#inoculant-mod2" markerHeight="7" markerWidth="10" orient="auto" refX="0" refY="3.5"><polygon points="0 0, 6 3.5, 0 7" style="fill: #ea526f;"></polygon></marker></defs><line class="arrow" marker-end="url(#arrow_#inoculant-exp3_#inoculant-mod2)" stroke="#ea526f" x1="0" x2="87" y1="0" y2="87"></line></svg></div></div></section></div></article><div class="d-flex justify-content-between my-5"><a class="button prev" href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model"><span class="button-background"><span aria-hidden="" class="circle"><span class="icon arrow"></span></span></span><span class="button-text">Model</span></a><a class="button next" href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety"><span class="button-background"><span aria-hidden="" class="circle"><span class="icon arrow"></span></span></span><span class="button-text">Safety</span></a></div></div></div></div></main><footer><div id="footerNav"><div class="container"><div class="row justify-content-between"><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Project</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Description">Description</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Design">Design</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Model">Model</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Engineering">Engineering</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Safety">Safety</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Implementation">Implementation</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Human Practices</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Human_Practices">Human-Centered Design</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Education">Science Communication</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Parts</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Parts">Parts</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Journal</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Notebook">Notebook</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Experiments">Experiments</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Appendix">Appendix</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Team</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Team">Team</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Attributions">Attributions</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Collaborations">Collaborations</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Contribution</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Contribution">Overview</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Software">Software</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Entrepreneurship</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Entrepreneurship">Entrepreneurship</a></li></ul></div><div class="col-sm-6 col-md-4 col-lg-3 py-2"><a class="footer-heading">Judging</a><ul><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Judging">Judging</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/Awards">Awards</a></li><li class="py-1"><a href="https://2020.igem.org/Team:BITSPilani-Goa_India/https:/igem.org/2020_Judging_Form?id=3512">Judging Form</a></li></ul></div></div></div></div><div id="footerBrand"><div class="container"><div class="row justify-content-center"><div id="footerTeamLogo"></div><div id="BITSLogo"></div></div><p>iGEM BITS Goa</p><p>Birla Institute of Technology and Science, Pilani</p><p>K K Birla Goa Campus</p><p>NH-17B, Sancoale, Goa, India</p><div class="row justify-content-center" id="footerIcons"><a class="gmail" href="mailto:igembitsgoa@gmail.com"></a><a class="insta" href="https://instagram.com/igem_bits" rel="noopener" target="_blank"></a><a class="twitter" href="https://twitter.com/igembitsgoa" rel="noopener" target="_blank"></a></div></div></div></footer><script src="https://2020.igem.org/Template:BITSPilani-Goa_India/engineering-bundleJS?action=raw&amp;ctype=text/javascript"></script></body></html>

Latest revision as of 17:08, 16 December 2020

Engineering | SugarGain | iGEM BITS Goa

The Safari browser doesn't support some features of this website. Please switch to Firefox, Edge or Chrome for a better experience.

Engineering

While designing SugarGain, we had to keep various considerations in mind. The initial idea was broken down into a set of problem statements and these formed the major pillars of our project. The following diagrams illustrate the flow of our thought as we tried to solve these problems to the best of our ability. We also illustrate how we modelled our project and its interconnectedness with the experiments we designed to complement the modelled data. Furthermore, we have taken into consideration the different outcomes that these experiments might lead to and planned accordingly. Due to unavailability of lab access this year, we plan to finish these experiments in phase 2.

For more details about these experiments, please see our Experiments page.



pFruB-Cra System

Problem Statement

Our project aims to reduce the activity of invertase, an enzyme that converts useful sucrose into profitless glucose and fructose. Since this process was important to the life cycle of the plant, it wasn’t practical to genetically re-engineer sugarcane cells itself. The most harm this enzyme causes is post-harvest and hence, that seemed like the most logical time period for us to target.

Designing Process

1

After surveying publications on invertases, we came across a group of proteins called anti-invertases/invertase inhibitor which regulate invertase and control sugar hydrolysis.

3

We also discovered that anti-invertase has quite a small half-life. This meant that the invertase would have to be secreted at the site of action (i.e., inside the sugarcane).

2

To decrease the nutrient load on our bacterial chassis and have a controlled release of our protein, we decided on a biosensor mechanism.

4

Since the concentration of fructose was a more or less direct result of invertase activity, we wanted to calibrate a self-regulatory mechanism that modulated the secretion of the anti-invertase in tandem with the concentration of fructose in the medium. We were able to achieve that by using a pFruB-Cra system.

5

Using these parts, we constructed our fructose regulated anti invertase.

Modelling

Biosensor will simulate output of invertase inhibitor for particular levels of fructose in the environment and will also link the promoter activity to a measurable output.

Experimental Design

Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.

Homology Modelling and Docking

We tried to get an insight into the protein-protein interaction through modelling of anti-invertase with invertase.

Homology Modelling

We tried to get an insight into the protein-DNA interaction through homology modelling of FruR.

Docking studies of FruR with F-1-P

Since FruR and its interactions are not extensively characterised, we had to conduct molecular docking studies in order to elucidate the interactions between FruR and fructose.

Identify the optimum Kd value for the system to work

In phase 2, prediction of overall efficiency of the pFruB-Cra system and the amount of inoculant required per sugarcane using information from experiments.

Anti-Invertase Assay to characterise the functioning of anti-invertase.

FruR Specificity Experiment

pFruB-FruR Characterisation

Gel shift assay to experimentally determine Kd value of pFruB.

Site-directed mutagenesis of the pFruB to bring the Kd value to the one established through the model

if inadequate

Atmosphere Regulated Killswitch

Problem Statement

Given the consumable nature of our product, we had to come up with a robust killswitch that was capable of effectively terminating the bacteria taking into account the toxicity of killswitch with respect to the humans.

Designing Process

1

First, we ascertained the trigger to be the swift and abrupt change in atmospheric conditions (anaerobic inside the sugarcane stem and aerobic outside)

2

Second, we found a toxin-antitoxin pair that was quite fatal to bacteria but did not affect human cells.

3

After an extensive search of the registry, we found the FNR promoter that was only activated in anaerobic conditions.

4

Using these parts, we designed our killswitch genetic circuit.

Modelling

We focussed on modelling the behaviour of the circuit to the change in concentration of oxygen in the atmosphere. We further predicted the response time for the same.

Experimental Design

Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.

Create a persister cell model in phase 2

Differential expression of the antitoxin in the presence and absence of oxygen

Time required for the buildup of toxin concentration sufficient to restrict bacterial growth

Identify the optimum Kd value for the system to work

Assay to check if the killswitch functions as intended

Killswitch response time assay to ascertain the time required after exposure for the cell to succumb

Gel shift assay to experimentally determine Kd value of the FNR promoter

Site-directed mutagenesis of the FNR promoter to bring the Kd value to the one established through the model

pH dependency of the FNR promoter (due to the fluctuation in pH in the sugar extraction process)

if high cell viability

if not quick enough

if inadequate Kd value

Polymer Inoculant

Problem Statement

Since our product includes live bacteria, we wanted to ensure that the product had a long shelf life. After consulting farmers in various belts across India, we also came across the need for the product to be organic, non-toxic and cheap.

Designing Process

1

We started researching polymer-based inoculants that had longevity and were organic in nature.

2

We determined the optimal inoculant composition of a Carboxymethylcellulose-based polymer with bentonite suspending agent and sorbic acid preservative.

3

We optimized the viscosity to minimize the inoculant's toxicity, and ensured that it is close to that of water for efficient transport.

4

This inoculant would be supplied to the farmer and can be used through an injector mechanism. In this manner the sugarcane's inherent transport mechanism due to transpirational pull is leveraged for the uniform distribution of the bacteria through the plant.

Modelling

Keeping in mind the concerns of the sugarcane farmers across major Indian belts,we devised ways to optimise the features of the polymer inoculant.

Experimental Design

Due to the global pandemic, we were unable to complement our modelling with experimental results. However, we prepared and planned for these experiments to strengthen our project design and help the next team carry out our project to completion.

Kinematic Viscosity model and Toxicity model

Proposed implementation and economic scalability model

Removal of chemical residues of polymer inoculant during processing of sugarcane juice

Validating toxicity model

Capillary action experiment will help with delivery mechanism model in proposed implementation