Difference between revisions of "Team:Rice"

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{{Rice}}
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<h1>project description</h1>
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  <p>The photoacoustic effect describes the conversion of electromagnetic energy to mechanical energy, namely, that an object absorbing non-ionizing laser pulses experiences local thermal expansions, and vibrates with frequencies in the ultrasonic range which may be detected. Imaging based on this effect yields high contrast from the optical component, and high resolution from the acoustic component (1). For biomedical purposes, users of this technique take advantage of endogenous and exogenous contrast agents to obtain physiological information from the biological tissue, endogenous examples including oxy- and deoxy-hemoglobin to determine blood flow speed (2). The bacterial pigment Violacein (Vio) has been reported to be an effective contrast agent under this technique (3). Furthermore, previous iGEM teams have developed and optimized a biosynthesis pathway for this pigment (4, 5).
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This team seeks to build upon, and move forward from, these past investigations and develop a biosensor in E. coli to produce Violacein in the presence of significant concentrations of biomarkers for disease; naturally, the team’s search for potential biomarkers will be for those which may pass through an animal’s or human’s gastrointestinal tract. This team considers the additional design aspect of logic gates to modulate the specificity for our system. Alongside Violacein, this team will experiment with similar genetic circuits using the fluorescent protein iRFP. For the purposes of testing the resultant system(s), this team has made an arrangement with a group at MD Anderson who can introduce our bacteria into mice, and who have photoacoustic imaging equipment to image the bacteria within the gastrointestinal tracts of the mice.
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<br>
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References
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Jun X, Junjia Y, and Lihong VW. “Photoacoustic Tomography: Principles and Advances.” Progress in Electromagnetics Research 147:1-22, 2014.
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Fang H, Maslov K, and Wang LV. “Photoacoustic Doppler Effect from Flowing Small Light-Absorbing Particles.” Physical Review Letters 99:184501, 2007.
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Yuanyuan J, et al. “Violacein as a Genetically-Controlled, Enzymatically Amplified and Photobleaching-Resistance Chromophore for Optoacoustic Bacterial Imaging.” Nature.com. Nature Publishing Group. 19 June 2015. Web. 18 May 2016.
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E. Chromi. 2009. (18 May 2016; https://2009.igem.org/Team:Cambridge)
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USCF iGEM 2012. 2012. (18 May 2016; https://2012.igem.org/Team:UCSF)
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</p>
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<h2> Welcome to iGEM 2016! </h2>
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<p>Your team has been approved and you are ready to start the iGEM season! </p>
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<h5>Before you start: </h5>
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<p> Please read the following pages:</p>
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<li>  <a href="https://2016.igem.org/Requirements">Requirements page </a> </li>
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<li> <a href="https://2016.igem.org/Wiki_How-To">Wiki Requirements page</a></li>
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<li> <a href="https://2016.igem.org/Resources/Template_Documentation"> Template Documentation </a></li>
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<h5> Styling your wiki </h5>
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<p>You may style this page as you like or you can simply leave the style as it is. You can easily keep the styling and edit the content of these default wiki pages with your project information and completely fulfill the requirement to document your project.</p>
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<p>While you may not win Best Wiki with this styling, your team is still eligible for all other awards. This default wiki meets the requirements, it improves navigability and ease of use for visitors, and you should not feel it is necessary to style beyond what has been provided.</p>
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<h5> Wiki template information </h5>
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<p>We have created these wiki template pages to help you get started and to help you think about how your team will be evaluated. You can find a list of all the pages tied to awards here at the <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions">Pages for awards</a> link. You must edit these pages to be evaluated for medals and awards, but ultimately the design, layout, style and all other elements of your team wiki is up to you!</p>
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<h5> Editing your wiki </h5>
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<p>On this page you can document your project, introduce your team members, document your progress and share your iGEM experience with the rest of the world! </p>
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<p> <a href="https://2016.igem.org/wiki/index.php?title=Team:Example&action=edit"> </a>Use WikiTools - Edit in the black menu bar to edit this page</p>
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<h5>Tips</h5>
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<p>This wiki will be your team’s first interaction with the rest of the world, so here are a few tips to help you get started: </p>
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<ul>
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<li>State your accomplishments! Tell people what you have achieved from the start. </li>
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<li>Be clear about what you are doing and how you plan to do this.</li>
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<li>You have a global audience! Consider the different backgrounds that your users come from.</li>
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<li>Make sure information is easy to find; nothing should be more than 3 clicks away.  </li>
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<li>Avoid using very small fonts and low contrast colors; information should be easy to read.  </li>
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<li>Start documenting your project as early as possible; don’t leave anything to the last minute before the Wiki Freeze. For a complete list of deadlines visit the <a href="https://2016.igem.org/Calendar">iGEM 2016 calendar</a> </li>
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<li>Have lots of fun! </li>
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</ul>
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</div>
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<h5>Inspiration</h5>
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<p> You can also view other team wikis for inspiration! Here are some examples:</p>
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<ul>
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<li> <a href="https://2014.igem.org/Team:SDU-Denmark/"> 2014 SDU Denmark </a> </li>
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<li> <a href="https://2014.igem.org/Team:Aalto-Helsinki">2014 Aalto-Helsinki</a> </li>
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<li> <a href="https://2014.igem.org/Team:LMU-Munich">2014 LMU-Munich</a> </li>
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<li> <a href="https://2014.igem.org/Team:Michigan"> 2014 Michigan</a></li>
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<li> <a href="https://2014.igem.org/Team:ITESM-Guadalajara">2014 ITESM-Guadalajara </a></li>
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<li> <a href="https://2014.igem.org/Team:SCU-China"> 2014 SCU-China </a></li>
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</ul>
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</div>
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<h5> Uploading pictures and files </h5>
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<p> You can upload your pictures and files to the iGEM 2016 server. Remember to keep all your pictures and files within your team's namespace or at least include your team's name in the file name. <br />
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When you upload, set the "Destination Filename" to <br><code>T--YourOfficialTeamName--NameOfFile.jpg</code>. (If you don't do this, someone else might upload a different file with the same "Destination Filename", and your file would be erased!)</p>
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<div class="button_click"  onClick=" parent.location= 'https://2016.igem.org/Special:Upload '"> 
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UPLOAD FILES
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Revision as of 00:59, 28 July 2016

project description

The photoacoustic effect describes the conversion of electromagnetic energy to mechanical energy, namely, that an object absorbing non-ionizing laser pulses experiences local thermal expansions, and vibrates with frequencies in the ultrasonic range which may be detected. Imaging based on this effect yields high contrast from the optical component, and high resolution from the acoustic component (1). For biomedical purposes, users of this technique take advantage of endogenous and exogenous contrast agents to obtain physiological information from the biological tissue, endogenous examples including oxy- and deoxy-hemoglobin to determine blood flow speed (2). The bacterial pigment Violacein (Vio) has been reported to be an effective contrast agent under this technique (3). Furthermore, previous iGEM teams have developed and optimized a biosynthesis pathway for this pigment (4, 5). This team seeks to build upon, and move forward from, these past investigations and develop a biosensor in E. coli to produce Violacein in the presence of significant concentrations of biomarkers for disease; naturally, the team’s search for potential biomarkers will be for those which may pass through an animal’s or human’s gastrointestinal tract. This team considers the additional design aspect of logic gates to modulate the specificity for our system. Alongside Violacein, this team will experiment with similar genetic circuits using the fluorescent protein iRFP. For the purposes of testing the resultant system(s), this team has made an arrangement with a group at MD Anderson who can introduce our bacteria into mice, and who have photoacoustic imaging equipment to image the bacteria within the gastrointestinal tracts of the mice.
References Jun X, Junjia Y, and Lihong VW. “Photoacoustic Tomography: Principles and Advances.” Progress in Electromagnetics Research 147:1-22, 2014. Fang H, Maslov K, and Wang LV. “Photoacoustic Doppler Effect from Flowing Small Light-Absorbing Particles.” Physical Review Letters 99:184501, 2007. Yuanyuan J, et al. “Violacein as a Genetically-Controlled, Enzymatically Amplified and Photobleaching-Resistance Chromophore for Optoacoustic Bacterial Imaging.” Nature.com. Nature Publishing Group. 19 June 2015. Web. 18 May 2016. E. Chromi. 2009. (18 May 2016; https://2009.igem.org/Team:Cambridge) USCF iGEM 2012. 2012. (18 May 2016; https://2012.igem.org/Team:UCSF)