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| − | <h2><a id="Introduction"></a>Introduction</h2>
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| − | In synthetic biology, measurement is a critical challenge that is receiving an increasing amount of attention each year. For example, one of the long-standing goals of both iGEM and synthetic biology at large, is to characterize biological parts, so that they can be more easily used for designing new systems. The aim of the iGEM Measurement Track is to get students informed and excited about these problems, and to highlight the successes that teams are able to achieve in the area of measurement. The Measurement Track also aims to find out what measurement assays teams have available and to lay groundwork for future more complex measurement activities in iGEM.</p> | + | In iGEM, as in the rest of synthetic biology, measurement is a critical challenge that is receiving an increasing amount of attention each year. For example, one of the long-standing goals of both iGEM and synthetic biology at large, is to characterize biological parts, so that they can be more easily used for designing new systems. Teams in the iGEM Measurement Track is tackle these sort of problems, whether they are about applying known techniques to parts not yet quantified or developing new or better methods for quantifying important biological phenomena.</p> |
| | | | |
| − | <h2>Measurement Challenges in Synthetic Biology</h2>
| |
| − | <p>With all the instruments in our laboratories, why isn't measurement
| |
| − | a solved problem in synthetic biology? Part of the problem is
| |
| − | knowing what to measure and in what context. One way to think
| |
| − | about the impact of measurements is in terms of four levels, each
| |
| − | building upon the last:</p>
| |
| − | <ol>
| |
| − | <li>Measurement quantifies a phenomenon that has been experimentally
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| − | observed.<br>
| |
| − | </li>
| |
| − | <li>Quantitative measurements may be used to create a model of how the
| |
| − | phenomenon was produced.<br>
| |
| − | </li>
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| − | <li>Models may be applied to predict what quantitative phenomena will be
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| − | observed in a new context.<br>
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| − | </li>
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| − | <li>Predictions may be used to inform choices about how to engineer
| |
| − | towards desired phenomena.<br>
| |
| − | </li>
| |
| − | </ol>
| |
| | <p> | | <p> |
| − | Instruments, by themselves, only address the first level. In
| + | <i><b>Please note</b></i>: All Measurement Track teams are <b>required</b> to participate in the iGEM interlab study.<br> |
| − | synthetic biology, many models are constructed, often post-facto.
| + | |
| − | Quantitative predictions, however, are still extremely difficult: an
| + | |
| − | important part of the problem is determining how measurement relates to
| + | |
| − | context, so that we can understand what sorts of things a model can be
| + | |
| − | reasonably expected to predict.<br>
| + | |
| − | <p>Even when we know what we wish to quantify, it may be impractical to | + | |
| − | obtain with our current instruments. For example, many
| + | |
| − | quantitative models describe how the concentration of chemicals in a
| + | |
| − | single cell changes over time. Behaviors often vary greatly from
| + | |
| − | cell to cell, so it is often desirable to collect data from a large
| + | |
| − | number of individual cells. Most current instruments, however,
| + | |
| − | cannot readily measure this. Instead we end up having to make
| + | |
| − | tradeoffs like these:<br>
| + | |
| | </p> | | </p> |
| − | <table style="text-align: left; width: 100%;" border="1" cellpadding="2"
| |
| − | cellspacing="2">
| |
| − | <tbody>
| |
| − | <tr>
| |
| − | <td style="vertical-align: top;">
| |
| − | <center><img src="https://static.igem.org/mediawiki/2014/a/a0/Sample-mass-spec.png" style="width: 95%"></center><br>
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| − | A mass spectrometer can measure the amount of particular chemicals
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| − | in a sample, but any cell measured is destroyed, it is difficult to
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| − | obtain measurement from individual cells, and often difficult to
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| − | interpret the massive pattern of data produced to quantify particular
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| − | chemicals of interest. <br>
| |
| − | </td>
| |
| − | <td style="vertical-align: top;">
| |
| − | <center><img src="https://static.igem.org/mediawiki/2014/3/34/Flow_cytometry_sample.png" style="width: 95%"></center><br>
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| − | A flow cytometer can take vast numbers of individual cell
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| − | measuremements, but the measurements are of a proxy fluorescent protein
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| − | rather than the actual chemical of interest and the cells may still be
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| − | disrupted by running them through the instrument. Unless
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| − | calibration controls are run with an experiment, the measurements are
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| − | relative and non-reproducible.<br>
| |
| − | </td>
| |
| − | </tr>
| |
| − | <tr>
| |
| − | <td style="vertical-align: top;">
| |
| − | <center><img src="https://static.igem.org/mediawiki/2014/6/67/Microplate_reader.jpg" style="width: 95%"></center><br>
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| − | A fluorimeter is less invasive than a flow cytometer and can measure
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| − | changing fluorescence over time with little impact on the cells, but
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| − | still uses a fluorescent proxy. Its measurements are also of the whole sample
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| − | rather than individual cells, and also relative to the number of cells
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| − | in the sample.<br>
| |
| − | </td>
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| − | <td style="vertical-align: top;">
| |
| − | <center><img src="https://static.igem.org/mediawiki/2014/a/a6/Microscopy_sample.jpg" style="width: 95%"></center><br>
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| − | A microscope can track and quantify fluorescence from individual cells,
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| − | but not very many of them, and often needs human help on tracking.<br>
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| − | </td>
| |
| − | </tr>
| |
| − | </tbody>
| |
| − | </table>
| |
| − | <blockquote><b>Figure 1:</b> No generally available instrument can measure chemical concentrations in large number of single cells over time.</blockquote>
| |
| | | | |
| − | <p>Relative measurements are a major problem, because they cannot be | + | <p> |
| − | compared. If you build models of biological devices using
| + | The Measurement track is a new track, introduced in 2014. You will find images and abstracts of winning Measurement teams in the page below. Also, follow the links below to see projects from all the Measurement track teams. |
| − | different relative measurements, then you cannot combine the models to
| + | |
| − | predict what will happen when you combine the devices. If units
| + | |
| − | are relative to a batch of samples or to a laboratory, then you cannot
| + | |
| − | reproduce experimental results: even if two experiments produce the
| + | |
| − | same numbers in a new experiment, if the units are relative you cannot
| + | |
| − | tell whether the results are actually the same or whether they have
| + | |
| − | been uniformly shifted (which might be very important!).<br>
| + | |
| | </p> | | </p> |
| − | </p>
| |
| − | <center><img src="https://static.igem.org/mediawiki/2014/3/38/Unit_mismatch.png" style="width: 80%"></center>
| |
| | | | |
| | + | <ul> |
| | + | <li><a href ="https://igem.org/Team_Tracks?year=2015"> iGEM 2015 Measurement team list</a></li> |
| | + | <li><a href ="https://igem.org/Team_Tracks?year=2014"> iGEM 2014 Measurement team list</a></li> |
| | + | </ul> |
| | | | |
| − | <blockquote>
| |
| − | <b>Figure 2:</b> Models using different relative units cannot be
| |
| − | compared or connected. How many "Blue" in the output characterized for
| |
| − | Repressor #1 are equal to a "Red" in the input characterized for
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| − | Repressor #2?<br>
| |
| − | </blockquote>
| |
| − | <p>Beyond these core scientific concerns, there are pragmatic problems
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| − | as well. Instruments are also often very expensive to buy and to
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| − | operate. This is an especially big problem for DIY groups and
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| − | researchers in smaller institutions or developing nations.
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| − | Cheaper instruments are sometimes available, but usually produce much
| |
| − | less accurate or precise data. Once you've got the data, you also
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| − | need to be able to share it effectively, so that everybody can benefit
| |
| − | from the information that is being learned. The community will
| |
| − | thus likely also need new tools and data exchange standards to allow
| |
| − | for simpler and more effective sharing of measurements and models.<br>
| |
| − | </p>
| |
| − | The challenges of measurement in synthetic biology are large and
| |
| − | broad. They cover everything from fundamental biological
| |
| − | questions to the need for better cheaper instruments and community data
| |
| − | sharing. But because measurement affects so many things,
| |
| − | improvements in any of these areas are likely to have a big impact.<br>
| |
| | | | |
| | | | |
| − | <h3>Additional Reading on Measurement and Synthetic Biology</h3> | + | <div class="clear"></div> <div class="clear"></div> |
| − | <p>Here are some additional resources that may be interesting and can
| + | |
| − | help you learn more about the lay of the land for measurement in
| + | |
| − | synthetic biology:<br>
| + | |
| − | </p>
| + | |
| − | <table style="text-align: left; width: 100%;" border="0" cellpadding="2"
| + | |
| − | cellspacing="2">
| + | |
| − | <tbody>
| + | |
| − | <tr>
| + | |
| − | <td style="vertical-align: top;"><span style="font-weight: bold;">Readings
| + | |
| − | on
| + | |
| − | Metrology & Calibration</span><br>
| + | |
| − | </td>
| + | |
| − | <td style="vertical-align: top;"><span style="font-weight: bold;">Readings
| + | |
| − | on
| + | |
| − | Device
| + | |
| − | Characterization</span><br>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td style="vertical-align: top;"><a href="https://static.igem.org/mediawiki/2014/9/9a/MarcSalit_InterlabNotes.pdf">Notes on design of interlab
| + | |
| − | studies</a><br>
| + | |
| − | </td>
| + | |
| − | <td style="vertical-align: top;"><a
| + | |
| − | href="http://www.jbioleng.org/content/3/1/4">Relative Promoter Units</a><br>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td style="vertical-align: top;"><a
| + | |
| − | href="http://www.agilent.com/labs/features/2011_101_bio.html">Agilent
| + | |
| − | 101: An Introduction to Bio-Analytical Measurement</a> </td>
| + | |
| − | <td style="vertical-align: top;"><a
| + | |
| − | href="http://journal.frontiersin.org/article/10.3389/fbioe.2014.00087/full">Model-driven design and device characterization with calibrated flow cytometry</a><br>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td style="vertical-align: top;"><a href="http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22086/pdf">NIST/ISAC interlab study on flow
| + | |
| − | cytometer calibration</a><br>
| + | |
| − | </td>
| + | |
| − | <td style="vertical-align: top;"><a href="https://openwetware.org/images/9/99/Nbt1413.pdf">A BioBrick "datasheet" proposal<a/><br>
| + | |
| − | (<a href="http://parts.igem.org/Part:BBa_F2620">Current datasheet for BBa_F2620 in the registry</a>)<br>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | <tr>
| + | |
| − | <td style="vertical-align: top;"><a href="http://www.spherotech.com/Rainbow%20Calibration%20Particles%20catalog%202010-2011%20rev%20a.pdf">SpheroTech Calibration Particles</a><br>
| + | |
| − | </td>
| + | |
| − | <td style="vertical-align: top;"><a href="http://jakebeal.com/Publications/ACSSynBio14-CircuitPrediction.pdf">High-precision prediction of repressor cascades from
| + | |
| − | device characterization</a><br>
| + | |
| − | </td>
| + | |
| − | </tr>
| + | |
| − | </tbody>
| + | |
| − | </table>
| + | |
| − | <br>
| + | |
| | | | |
| − | <!--
| |
| | | | |
| − | <h2>Plans for the Measurement Track in 2015</h2> | + | <h2>Recent Winning Measurement projects</h2> |
| − | <p>The 2015 event expands on iGEM's long-running inclusion of
| + | |
| − | measurement as a focus area (a measurement award has been given since
| + | |
| − | 2006), and on the great success of teams in the 2014 Measurement Track.</p>
| + | |
| − | <p>Teams participating in the Measurement Track in 2015 can also earn a
| + | |
| − | Measurement Prize by taking part in a group measurement project (the <a href="https://2015.igem.org/Tracks/Measurement/Interlab_study">Interlab Study</a>), in which each team
| + | |
| − | measures the same properties of several known samples. We will
| + | |
| − | provide some recommendations for experimental and measurement
| + | |
| − | protocols, but teams are encouraged to use whatever approach will
| + | |
| − | provide the most reliable and accurate measurements with the resources
| + | |
| − | available to them. All of the results will be collected together
| + | |
| − | and later shared, which will allow people to see the
| + | |
| − | tradeoffs between different approaches.</p>
| + | |
| | | | |
| − | </li> | + | <a href="https://2015.igem.org/Team:William_and_Mary">William & Mary</a> |
| − | </ul> | + | |
| | | | |
| − | -->
| + | <img src="https://static.igem.org/mediawiki/2016/c/c7/William_and_mary2015.png" width="920px"> |
| | | | |
| − | <h2><a id="Details"></a>Details</h2>
| |
| − |
| |
| − | <p>The measurement track offers two separate opportunities for teams:</p>
| |
| − | <ol>
| |
| − | <li>Earning a Measurement Prize: any team may do this, including teams that compete in other tracks</li>
| |
| − | <li>Competing for awards within the Measurement Track</li>
| |
| − | </ol>
| |
| − |
| |
| − | <!--
| |
| − |
| |
| − | <h3>Earning a Measurement Prize:</h3>
| |
| − |
| |
| − | <p>Last year, the Measurement Track ran <a href="https://2014.igem.org/Tracks/Measurement/Interlab_study">the biggest ever synthetic biology interlab study</a>, with 85 teams around the world signing up to participate, and collectively produce highly valuable information on the reproducibility of fluorescent expression from BioBricks. Can you help us make it even bigger and more successful this year?</p>
| |
| − |
| |
| − | <p>In iGEM 2015, the Measurement Track will once again feature an <a href="https://2015.igem.org/Tracks/Measurement/Interlab_study">Interlab Study</a>, in which teams around the world will measure the same genetic devices in order to determine the amount of variation and reliability of various properties and approaches to measurement. This is not restricted to the Measurement Track teams - any team from any track that participates in the interlab study will earn a Measurement Prize!
| |
| − | </p>
| |
| − | <p>
| |
| − | Your team does not have to compete in the Measurement Track to participate: <b>teams in any track can participate in the interlab study and earn a Measurement Prize</b>. All teams that compete in the Measurement Track, however, are <b>required</b> to participate in the interlab study.
| |
| − | </p>
| |
| | <p> | | <p> |
| − | <i>Any team that participates in the interlab study will receive a Measurement Prize!</i></p> | + | <strong>Project abstract:</strong> |
| − | <br>
| + | As synthetic biologists continue to construct increasingly complex gene regulatory networks, the need for accurate quantitative characterization of their regulatory components becomes more pressing. Despite the BioBrick registry's thorough characterization of the average strength of promoters, there is insufficient description of the variability in their expression. iGEM William & Mary's project aims to characterize this variability, or noise, for the most commonly used promoters in synthetic biology and provide additional tools for the regulation of these promoters. |
| | | | |
| − | -->
| + | <h3>Undergraduate Grand Prize Winner, Winner of Best Measurement project 2015, Best Education & Public Engagement, Nominated for Best Mathematical Model</h3> |
| | | | |
| − | <h3>Competing in the Measurement Track:</h3> | + | <div class="clear"></div> <div class="clear"></div> |
| | | | |
| − | <p>To compete for an award in the measurement track, your team must:</p> | + | <a href="https://2014.igem.org/Team:Aachen">Aachen</a> |
| | | | |
| − | <ol> | + | <img src="https://static.igem.org/mediawiki/2016/c/c7/Aachen2014_banner.png" width="920px"> |
| − | <li>Meet the general <a href="https://2016.igem.org/Requirements">iGEM 2016 requirements</a></li>
| + | |
| − | <li>For medals, Measurement Track follow the <a href="https://2016.igem.org/Judging/Medals">Special Track Medal Criteria</a></li>
| + | |
| − | </ol>
| + | |
| − | | + | |
| − | <p>All Measurement teams are encouraged (but not required) to participate in the <a href="https://2016.igem.org/Tracks/Measurement/Interlab_study">InterLab Study</a>
| + | |
| − | | + | |
| − | | + | |
| − | | + | |
| − | <!--
| + | |
| − | <h2><a id="Requirements"></a>Requirements</h2>
| + | |
| | | | |
| | <p> | | <p> |
| − | Measurement teams must meet the general <a href="https://2016.igem.org/Requirements">iGEM 2016 requirements</a>.
| + | <strong>Project abstract:</strong> |
| | + | Cellock Holmes is a 2D biosensing technology with which can detect bacteria on solid surfaces, devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method. iGEM Aachen demonstrated the proof-of-concept for Cellock Holmes by detecting Pseudomonas aeruginosa, a gram-negative prokaryote that infects patients with open wounds and burns as well as immunodeficient people. P. aeruginosa cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, they engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of P. aeruginosa and elicit a distinct fluorescence signal. Wwith a modular composition of a genetic device or an alternative approach using Galectin-3, it is also possible to engineer Cellocks to detect other bacteria. |
| | + | Hand in hand with the biological side of our project, the team built the WatsOn measurement device able to read and analyze the fluorescent signal emitted by the 2D biosensor, and an OD/F Device designed to measure optical density and fluorescence of a liquid sample in cuvettes, both designed in accordance with the Open Source principle and with all technical details as well as construction manuals published online. |
| | </p> | | </p> |
| | | | |
| | + | <h3> Winner of Best Measurement project 2014, Best Supporting Software, Safety Commendation</h3> |
| | | | |
| − | <ul> | + | <div class="clear"></div> <div class="clear"></div> |
| − | <li><strong>Interlab Measurement Study:</strong>
| + | |
| − | Details for the interlab study can be found <a href="https://2015.igem.org/Tracks/Measurement/Interlab_study">here</a>.
| + | |
| − | <br>
| + | |
| − | All iGEM teams are invited and encouraged to participate in the first international inter-lab measurement study in synthetic biology. We’re hoping this study will get you excited for iGEM and help prepare you for the summer!<br>
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | <i><b>Please note</b></i>: All Measurement Track teams are <b>required</b> to participate in the inter-lab study.<br>
| + | |
| − | </p>
| + | |
| − | <p>
| + | |
| − | <i>All teams who participate in the inter-lab study will be acknowledged at the Giant Jamboree with a Measurement Prize!</i><br>
| + | |
| − | </p> | + | |
| | | | |
| − | --> | + | <a href="https://2015.igem.org/Team:UGA-Georgia">UGA Georgia</a> |
| | | | |
| − | <p> | + | <img src="https://static.igem.org/mediawiki/2016/f/f6/UGA-GeorgiaBanner-2015.jpg" width="920px"> |
| − | For any questions, email measurement (at) igem (dot) org.
| + | |
| − | </p>
| + | |
| − | </li>
| + | |
| − | </ul>
| + | |
| − | | + | |
| − | <!--
| + | |
| − | Remove medal criteria until medal model confirmed by HQ
| + | |
| − | | + | |
| − | <h2><a id="Medal Criteria"></a>Medal Criteria</h2>
| + | |
| | | | |
| | <p> | | <p> |
| − | <b>Bronze. </b>The following 5 goals must be achieved:<br> | + | <strong>Project abstract:</strong> |
| − | <ol id="criterialist">
| + | Methanococcus maripaludis is a model organism for Archaea, which affords researchers the beneficial qualities such as (1) producing methane used as biogas and (2) manufacturing isoprenoids as precursors for high-value biochemicals. However, there are few genetic tools available for metabolic engineering Archaea. iGEM UGA-Georgia's goal was to develop useful tools for synthetic biology of Archaea, targeting this organism. Building on past M. maripaludis projects, which created and characterized a mCherry reporter system and a recombinant mutant making geraniol, the team worked to (1) create, characterize and model a ribosome-binding site (RBS) library using the mCherry reporter system and (2) model geraniol production of the recombinant M. maripaludis using flux balance analyses. Results showed varying levels of expression in the RBS library, and increased geraniol yield from some growth substrates. Additionally, the team initiated an Archaeal InterLab Study to further characterize the reproducibility of the mCherry reporter system. |
| − | <li>Team registration.</li>
| + | |
| − | <li>Complete Judging form.</li>
| + | |
| − | <li>Team Wiki.</li>
| + | |
| − | <li>Present a poster and a talk at the iGEM Jamboree.</li>
| + | |
| − | <li>Participate in the<a href="https://2015.igem.org/Tracks/Measurement/Interlab_study"> Measurement Interlab Study</a></li>
| + | |
| − | <li>Document at least one new standard BioBrick Part or Device used in your project/central to your project and submit this part to the iGEM Registry (submissions must adhere to the iGEM Registry guidelines). A new application of and outstanding documentation (quantitative data showing the Part’s/ Device’s function) of a previously existing BioBrick part in the “Experience” section of that BioBrick’s Registry entry also counts. Please note you must submit this new part to the iGEM Parts Registry</li></ol>
| + | |
| | </p> | | </p> |
| | | | |
| − | <p> | + | <h3> Nominated for Best Measurement project 2015</h3> |
| − | <b>Silver</b>: In addition to the Bronze Medal requirements, the following 4 goals must be achieved:<br>
| + | |
| − | <ol id="criterialist">
| + | |
| − | <li>Experimentally validate that at least one new BioBrick Part or Device of your own design and construction works as expected.</li>
| + | |
| − | <li>Document the characterization of this part in the “Main Page” section of that Part’s/Device’s Registry entry.</li>
| + | |
| − | <li>Submit this new part to the iGEM Parts Registry (submissions must adhere to the iGEM Registry guidelines).</li>
| + | |
| − | <li>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. Articulate at least one question encountered by your team, and describe how your team considered the(se) question(s) within your project. Include attributions to all experts and stakeholders consulted.</li>
| + | |
| − | </ol>
| + | |
| − | </p> | + | |
| | | | |
| − | <p>
| |
| − | <b>Gold</b>: In addition to the Bronze and Silver Medal requirements, any one or more of the following: <br>
| |
| − | <ol id="criterialist">
| |
| − | <li>Demonstrate a substantial improvement over the state of the art in cost, efficiency, precision, resolution, and/or other relevant capabilities of your measurement technique.</li>
| |
| − | <li>Increase the ease of accessibility and portability of methods to other laboratories of a new measurement technique of your choosing.</li>
| |
| − | <li>Help any registered iGEM team from another school or institution by, for example, characterizing a part, debugging a construct, or modeling or simulating their system.</li>
| |
| − | <li>iGEM projects involve important questions beyond the bench, for example relating to (but not limited to) ethics, sustainability, social justice, safety, security, or intellectual property rights. <b>Describe</b> an approach that your team used to address at least one of these questions. <b>Evaluate</b> your approach, including whether it allowed you to answer your question(s), how it influenced the team’s scientific project, and how it might be adapted for others to use (within and beyond iGEM). We encourage thoughtful and creative approaches, and those that draw on past Policy & Practice (formerly Human Practices) activities.</li>
| |
| − | </ol>
| |
| − | </p>
| |
| − | -->
| |
| − |
| |
| − | <h2>Medal Criteria</h2>
| |
| − |
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Precise measurements lie at the foundation of every scientific discipline, including synthetic biology. The limits of our knowledge are set by how well we can connect observations to reproducible quantities that give insight. Measurement is also an act of communication, allowing researchers to make meaningful comparisons between their observations. The science and technology of measurement are easily overlooked, because measuring devices are so familiar to us, but behind even the simplest devices lies an elaborate infrastructure. Consider a laboratory pipette. How accurate are the volumes it dispenses? How similar is it to other pipettes? How do you know? The answers to these questions are a complex story involving everything from the speed to light in vacuum to the atomic properties of cesium.
In iGEM, as in the rest of synthetic biology, measurement is a critical challenge that is receiving an increasing amount of attention each year. For example, one of the long-standing goals of both iGEM and synthetic biology at large, is to characterize biological parts, so that they can be more easily used for designing new systems. Teams in the iGEM Measurement Track is tackle these sort of problems, whether they are about applying known techniques to parts not yet quantified or developing new or better methods for quantifying important biological phenomena.
Please note: All Measurement Track teams are required to participate in the iGEM interlab study.
The Measurement track is a new track, introduced in 2014. You will find images and abstracts of winning Measurement teams in the page below. Also, follow the links below to see projects from all the Measurement track teams.
Recent Winning Measurement projects
William & Mary
Project abstract:
As synthetic biologists continue to construct increasingly complex gene regulatory networks, the need for accurate quantitative characterization of their regulatory components becomes more pressing. Despite the BioBrick registry's thorough characterization of the average strength of promoters, there is insufficient description of the variability in their expression. iGEM William & Mary's project aims to characterize this variability, or noise, for the most commonly used promoters in synthetic biology and provide additional tools for the regulation of these promoters.
Undergraduate Grand Prize Winner, Winner of Best Measurement project 2015, Best Education & Public Engagement, Nominated for Best Mathematical Model
Aachen
Project abstract:
Cellock Holmes is a 2D biosensing technology with which can detect bacteria on solid surfaces, devised to overcome the drawbacks of existing techniques and aims for a faster, inexpensive, open source, mobile and an easy to handle detection method. iGEM Aachen demonstrated the proof-of-concept for Cellock Holmes by detecting Pseudomonas aeruginosa, a gram-negative prokaryote that infects patients with open wounds and burns as well as immunodeficient people. P. aeruginosa cells use quorum sensing to communicate with each other by secreting autoinducers into their environment. Using a Synthetic Biology (SynBio) approach, they engineered sensor cells, so-called Cellocks, that are able to detect the native autoinducer of P. aeruginosa and elicit a distinct fluorescence signal. Wwith a modular composition of a genetic device or an alternative approach using Galectin-3, it is also possible to engineer Cellocks to detect other bacteria.
Hand in hand with the biological side of our project, the team built the WatsOn measurement device able to read and analyze the fluorescent signal emitted by the 2D biosensor, and an OD/F Device designed to measure optical density and fluorescence of a liquid sample in cuvettes, both designed in accordance with the Open Source principle and with all technical details as well as construction manuals published online.
Winner of Best Measurement project 2014, Best Supporting Software, Safety Commendation
UGA Georgia
Project abstract:
Methanococcus maripaludis is a model organism for Archaea, which affords researchers the beneficial qualities such as (1) producing methane used as biogas and (2) manufacturing isoprenoids as precursors for high-value biochemicals. However, there are few genetic tools available for metabolic engineering Archaea. iGEM UGA-Georgia's goal was to develop useful tools for synthetic biology of Archaea, targeting this organism. Building on past M. maripaludis projects, which created and characterized a mCherry reporter system and a recombinant mutant making geraniol, the team worked to (1) create, characterize and model a ribosome-binding site (RBS) library using the mCherry reporter system and (2) model geraniol production of the recombinant M. maripaludis using flux balance analyses. Results showed varying levels of expression in the RBS library, and increased geraniol yield from some growth substrates. Additionally, the team initiated an Archaeal InterLab Study to further characterize the reproducibility of the mCherry reporter system.
Nominated for Best Measurement project 2015
