Difference between revisions of "Team:IISc Bangalore/Description"

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           <li class="active"><a href="#">Home</a></li>
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          <li><a href="#">Team</a></li>
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           <li><a href="#">Project</a></li>
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          <li><a href="#">Parts</a></li>
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            <li>Project
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      <h1>IISc Bangalore</h1>
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      <p>We are a group of undergraduates interested in synthetic biology.</p>
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                  Description
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      <div class="col-sm-4"> Hello bootstrap.
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                Cellfifuge
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                An auto-pelleting system
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                  <a href="#description">Description</a>  
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                  <a href="#protein">Protein production module</a><br><br>
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          <a href="#overview">Overview</a>
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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          Briefly about us
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      <h2>How we came up with the idea</h2>
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<p>We had been thinking about an idea for iGEM 2016 since one year. We held intense brainstorming sessions and killed off many of the ideas. One of the common problem which most of our ideas had was that most of them had a very insignificant application. Having realised this, we decided to address problems which could have a bigger impact on the society. We had several ideas related to several industries which come under the umbrella of Biotechnology. If our project had to reach out to more number of industries, it was only logical to work on something which was common to most if not all sectors of biotechnology industry.Thus, we took common elements of our previous ideas and cooked up a new idea out of it.</p>
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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        <div id="overview" class="sub">
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            Overview
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            <p>Since the advent of rDNA technology in the late 1970s, the use of recombinant protein has been on the rise, starting from insulin and hormones all the way through to monoclonal antibodies and one hundred and fifty-one FDA approved protein based recombinant pharmaceuticals by the year 2009[1]. Despite being in high demand, recombinant proteins have heavy price tags, thanks to the significant manufacturing costs. One of the important steps in the manufacturing process is Centrifugation but on an industrial scale, it is an economic nightmare. [2] Further, existing industrial setups use complex sensors to monitor cell density to determine the point at which to begin separation of the cells from the cell culture. One can immediately see the humongous relief that would be associated with finding a way to deal with the above problems. Hence, we came up with the idea of our project, the Cellfifuge.</p>
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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        <div id="design" class="sub">
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          Our Bioreactor Design
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            <p>We realized that manufacturing units use expensive and energy expensive machinery [3]. Hence, we engineered our bacteria in such a way that it could do most of the work done by these monstrous machines so that we no longer have to buy them and pay their bills.
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To increase the yield of the product, we came up with the idea of separating cell growth and target protein production so that when the cells have grown up to a high enough cell density, they shuttle all their energy towards the required protein production.[4] Based on the above ideas, we came up with the design of our bioreactor. (Figure 1)</p>
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<p>We realized that we would not be able to work on the whole idea this summer so, we focussed on two modules of our design: the Protein production module and the auto-aggregation module leaving the arresting of cell growth for future iGEM teams as a seed for their ideas.</p>
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            Figure 1: The bioreactor design of Cellfifuge
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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        <div id="protein" class="sub">
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          Protein Production Module
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            <p>Induction synthesis of protein of interest is another important step. Microorganisms in bioreactors are induced at the OD, at which the protein production is maximum. [5] Because of this, factories install sophisticated machinery to keep track of the OD value of the culture so as to know when to induce the production. We wanted our bacteria to know when to start protein production and start it by itself. Hence, we used the lux quorum sensing system to sense this cell density. [6] We have expressed the gene for our protein of interest under the luxI gene so that protein of interest is produced in significant quantities only when the quorum is achieved.(Figure 2) We also wish to tune the quorum sensing system by tweaking with the strength of the promoters involved in quorum sensing.
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[[File:Lux_iisc.jpg]]
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          Figure 2 : The lux quorum sensing system. Note the gene of interest "geneX*" downstream of the luxI gene. Image Courtesy: ETH Zurich 2013, iGEM team.
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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          Auto-aggregation Module
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To achieve cellular aggregation, we use the famous auto-transporter protein, Antigen43 (Ag43). [7] It has shown to cause auto-aggregation of cells when overexpressed. (Figure 3) We plan to exploit this property of Ag43 to substitute centrifugation. We acknowledge previous iGEM teams who have worked on Ag43 (Hokkaido University, 2012; Aberdeen Scotland, 2014 and some more) as we got the BioBricks for Ag43 readily available.  We intend to express Ag43 only when the cells have made the product of interest. Hence, we use the diauxic shift in the media to act as a switch for the expression of Ag43.
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[[File:Tube_iisc.jpg]]
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Figure 3: a) Cell culture without expression of Ag43 b) Cell culture overexpressing Ag43
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Source: MarjanW. van derWoude et al, 2008
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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          References
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          <li> Ferrer-Miralles N, Domingo-Espin J, Corchero JL, Vazquez E, Villaverde A. Microbial factories for recombinant pharmaceuticals, Microbial Cell Factories, 2009:8:17. </li>
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          <li> Medipally S.R., Yusoff F. Md., Banerjee S., Shariff M. Microalgae as sustainable renewable energy Feedstock for Biofuel Production, BioMed Research International, 2015. </li>
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          <li> Felo M., Christensen B., Higgins J., Process cost and facility considerations in the selection of primary cell culture clarification technology, AIChE, 2013. </li>
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          <li> Motoo Suzuki, Rohini Roy, Haiyan Zheng, Nancy Woychik, Masayori Inouye, Bacterial Bioreactors for High Yield Production of Recombinant Protein. The Journal of Biological Chemistry, 2006.</li>
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          <li> Rosano G.L., Ceccarelli E. A., Recombinant protein expression in Escherichia coli: advances and challenges, Frontiers in Microbiology, 2014.</li>
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          <li> Miller M.B., Bassler B.L., Quorum Sensing in Bacteria, Annual Review of Microbiology, 2001.</li>
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          <li> Marjan W. van der Woude, Ian R. Henderson, Regulation and Function of Ag43 (Flu), Annu. Rev. Microbiol., 2008.
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<svg class="panel" onclick="openBar()" enable-background="new 0 0 128 128" height="40px" id="Layer_1" version="1.1" viewBox="0 0 128 128" width="40px" xml:space="preserve" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"><g><g><path d="M64,0C28.656,0,0,28.656,0,64s28.656,64,64,64s64-28.656,64-64S99.344,0,64,0z M64,120    C33.125,120,8,94.875,8,64S33.125,8,64,8s56,25.125,56,56S94.875,120,64,120z" fill="#B0BEC5"/></g></g><g><g><path d="M96,56H72V32c0-4.414-3.586-8-8-8s-8,3.586-8,8v24H32c-4.414,0-8,3.586-8,8s3.586,8,8,8h24v24    c0,4.414,3.586,8,8,8s8-3.586,8-8V72h24c4.414,0,8-3.586,8-8S100.414,56,96,56z" fill="#8BC34A"/></g></g></svg>
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          Work till now
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<h2>Work done till now</h2>
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<p>For most parts till now, we have been trying to get everything set on paper. Some preliminary experiments have been tried out and labs have been primed with stock solutions and other consumables. We have done some preliminary experiments related to both the modules – Product Synthesis Module as well as Auto-aggregation modules individually with the parts from the DNA kit. We have to think over better
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We have the design for our new parts ready on paper. Our primers have arrived and soon we will start making our new parts.
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The mathematical modelling of the project has started and we are ready with a naïve model. We are in talks with other teams for collaboration.
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We have done some work, although we still have a long way to go.</p>
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Revision as of 16:12, 14 August 2016

IISc Bangalore

We are a group of undergraduates interested in synthetic biology.

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