Difference between revisions of "Team:TU Delft/Proof"

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        <title>iGEM TU Delft</title>
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<div class="column full_size judges-will-not-evaluate">
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        <div class="main-container project">
<h3>★  ALERT! </h3>
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<p>This page is used by the judges to evaluate your team for the <a href="https://2016.igem.org/Judging/Medals">gold medal criterion for proof of concept</a>. </p>
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<p> Delete this box in order to be evaluated for this medal. See more information at <a href="https://2016.igem.org/Judging/Pages_for_Awards/Instructions"> Instructions for Pages for awards</a>.</p>
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            <div class="container">
iGEM teams are great at making things work! We value teams not only doing an incredible job with theoretical models and experiments, but also in taking the first steps to make their project real.
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</p>
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                <div class="our-project">
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                    <span class="anchor" id="description"></span>
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                    <br><br>
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                    <h2 class="title-style-1">Functional proof of concept<span class="title-under"></span></h2>
  
<h4> What should we do for our proof of concept? </h4>
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                </div>
<p>
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You can assemble a device from BioBricks and show it works. You could build some equipment if you're competing for the hardware award. You can create a working model of your software for the software award. Please note that this not an exhaustive list of activities you can do to fulfill the gold medal criterion. As always, your aim is to impress the judges!
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</p>
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</div>
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                <div class="col-md-10 col-md-offset-1 col-sm-12">  
  
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                    <h2 class="title-style-2">Producing microlenses with bacteria</h2>
  
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                    <p>To produce biolenses we need our <i>E. coli</i> to perform two special activities: produce a glass layer and change its shape from rod to spherical. To be able to obtain biological lenses we need a coating of polysilicate, biological glass, around the cell. This glass will give optical properties for the cell. <i>E. coli</i> is intrinsically not able to coat itself in polysilicate. However, upon transformation of the silicatein-α gene, originating from sponges, it is possible to coat the bacterium in a layer of polysilicate <a href="#references">(Müller <i>et al.</i>, 2008; Müller <i>et al.</i>, 2003)</a>. Therefore, we are transforming <i>E. coli</i> with silicatein-α. We test silicatein from two different organisms expressed in three different ways. The most successful construct consists of silicatein from <i>Tethya aurantia</i> fused to the membrane protein OmpA (Part <b><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1890002" target="_blank">K1890002</a></b>) as shown by Rhodamine 123 staining of the polysilicate (Figure 1) and <a href="https://2016.igem.org/Team:TU_Delft/Project#silicatein" target="_blank"><b>other imaging experiments</b></a>.
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                    </p>
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                    <div class = "row">
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                        <div class="col-md-10 col-md-offset-1 col-sm-12">
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                            <figure>
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                                <img src="https://static.igem.org/mediawiki/2016/8/8c/T--TU_Delft--silicatein92.png" alt="Rhodamine staining">
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                                <figcaption><b>Figure 1:</b> Widefield and fluorescence images of OmpA-silicatein with silicic acid and OmpA-silicatein without silicic acid (negative control) at maximum excitation energy. Of the widefield and fluorescence images an overlay was made to show the fraction of fluorescent cells. The negative control causes overexposure of the camera, therefore the fluorescent image only gives one uniform signal. </figcaption>
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                            </figure>
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                        </div></div>
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                    <p>When making biological lenses, the shape of the lens is of crucial importance. <i>E. coli</i> is a rod-shaped organism,
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                        so it is not symmetrical along all axes. Shining light on the round parts of <i>E. coli</i> has a different effect
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                        on the focusing of light than shining light on the long sides (Figure 2). More information on this can be found
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                        on the <b><a href="https://2016.igem.org/Team:TU_Delft/Model#lenses" target="_blank">modeling</a></b> and
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                        <a href="https://2016.igem.org/Team:TU_Delft/Project#silicatein" target="_blank"><b>project</b></a> pages.
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                    <div class = "row">
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                        <div class="col-md-10 col-md-offset-1 col-sm-12">
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                            <figure>
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                                <img src="https://static.igem.org/mediawiki/2016/b/b8/T--TU_Delft--light_focussing_model.png" alt="Modeling"">
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                                <figcaption><b>Figure 2:</b> Our models show that rod shaped lenses focus light in an orientation dependent way (A, B),
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                                    but spherical lenses focus light in an orientation independent way (C).</figcaption>
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                            </figure>
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                        </div></div>   
  
</div>
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                    <p>  Biolenses with a spherical phenotype have an advantage over biolenses with the rod-shaped <i>E. coli</i> phenotype, as for the round lenses, orientation does not matter. In order to create spherical <i>E. coli</i>, we overexpress the <i>BolA</i> gene. <i>BolA</i> is a gene that controls the morphology of <i>E. coli</i> in the stress response <a href="#references">(Santos <i>et al.</i>, 1999)</a>. By overexpressing this gene, the rod-shaped <i>E. coli</i> cells will become spherical <a href="#references">(Aldea <i>et al.</i>, 1988)</a>. We express this gene both under a constitutive promoter (Part <b><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1890031" target="_blank">K1890031</a></b>), as well as an inducible promoter (Part <b><a href="http://parts.igem.org/wiki/index.php?title=Part:BBa_K1890030" target="_blank">K1890030</a></b>), the latter being our favorite due to the better result obtained (Figure 3).</p>
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                    <div class = "row">
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                        <div class="col-md-10 col-md-offset-1 col-sm-12">
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                            <center><figure>
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                                    <img src="https://static.igem.org/mediawiki/2016/e/e7/T--TU_Delft--BolA_ind_widefield.png" alt="BolA widefield">
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                                    </center>
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                                    <figcaption><b>Figure 3:</b> Widefield images of <i>E. coli</i> BL21 transformed the OmpA-silicatein construct not altering the cell shape (A). When the cells are also transformed with the BolA under an inducible promoter the cells become spherical (B).</figcaption>
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                                </figure>
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                        </div></div>
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                    <p>
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                        The spherical cells we produced had an increased volume compared to wildtype <i>E. coli</i>. The diameter of 1 µm that we observed matches the size of a photovoltaic cell (the smallest unit of a solar panel)<a href="#references">(Yang, Shtein, & Forrest, 2005)</a>, and this size is hard to produce using conventional techniques. Conventional microlenses are usually bigger. Therefore, <strong>our method of producing microlenses has an advantage over the conventional production</strong>, since we are able to produce far smaller lenses. Using smaller lenses also means we are able to put more lenses on a surface, which increases the focusing effect. When we express both the <i>BolA</i> gene as well as silicatein gene, we are able to construct round cells, coated in glass (Figure 4).
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                    </p>
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                    <div class = "row">
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                        <div class="col-md-10 col-md-offset-1 col-sm-12">
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                            <figure>
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                                <img src="https://static.igem.org/mediawiki/2016/c/c2/T--TU_Delft--BolA_SEM.png" alt="BolA">
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                                <figcaption><b> Figure 4: </b> SEM images of <i>E. coli</i> BL21 without the <i>BolA</i> gene covered in polysilicate (A) and <i>E. coli</i> BL21 transformed with the <i>BolA</i> gene covered in polysilicate (B). </figcaption>
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                            </figure>
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                        </div></div>
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        <span class="anchor" id="references"></span>
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        <div class="references container">
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            <h4 class="footer-title">References</h4>
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            <ol>
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                <li>Aldea, M., Hernandez-Chico, C., De La Campa, A., Kushner, S., & Vicente, M. (1988). Identification, cloning, and expression of bolA, an ftsZ-dependent morphogene of Escherichia coli. Journal of bacteriology, 170(11), 5169-5176. </li>
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                <li>Müller, W. E. G. (2003). Silicon biomineralization.</li>
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                <li>Müller, W. E., Engel, S., Wang, X., Wolf, S. E., Tremel, W., Thakur, N. L., Schröder, H. C. (2008). Bioencapsulation of living bacteria (Escherichia coli) with poly (silicate) after transformation with silicatein-α gene. Biomaterials, 29(7), 771-779. </li>
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                <li>Santos, J. M., Freire, P., Vicente, M., & Arraiano, C. M. (1999). The stationary‐phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth. Molecular microbiology, 32(4), 789-798. </li>
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                <li>Yang, F., Shtein, M., & Forrest, S. R. (2005). Controlled growth of a molecular bulk heterojunction photovoltaic cell. Nature materials, 4(1), 37-41. </li> 
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Latest revision as of 23:38, 19 October 2016

iGEM TU Delft


Functional proof of concept

Producing microlenses with bacteria

To produce biolenses we need our E. coli to perform two special activities: produce a glass layer and change its shape from rod to spherical. To be able to obtain biological lenses we need a coating of polysilicate, biological glass, around the cell. This glass will give optical properties for the cell. E. coli is intrinsically not able to coat itself in polysilicate. However, upon transformation of the silicatein-α gene, originating from sponges, it is possible to coat the bacterium in a layer of polysilicate (Müller et al., 2008; Müller et al., 2003). Therefore, we are transforming E. coli with silicatein-α. We test silicatein from two different organisms expressed in three different ways. The most successful construct consists of silicatein from Tethya aurantia fused to the membrane protein OmpA (Part K1890002) as shown by Rhodamine 123 staining of the polysilicate (Figure 1) and other imaging experiments.

Rhodamine staining
Figure 1: Widefield and fluorescence images of OmpA-silicatein with silicic acid and OmpA-silicatein without silicic acid (negative control) at maximum excitation energy. Of the widefield and fluorescence images an overlay was made to show the fraction of fluorescent cells. The negative control causes overexposure of the camera, therefore the fluorescent image only gives one uniform signal.

When making biological lenses, the shape of the lens is of crucial importance. E. coli is a rod-shaped organism, so it is not symmetrical along all axes. Shining light on the round parts of E. coli has a different effect on the focusing of light than shining light on the long sides (Figure 2). More information on this can be found on the modeling and project pages.

Modeling
Figure 2: Our models show that rod shaped lenses focus light in an orientation dependent way (A, B), but spherical lenses focus light in an orientation independent way (C).

Biolenses with a spherical phenotype have an advantage over biolenses with the rod-shaped E. coli phenotype, as for the round lenses, orientation does not matter. In order to create spherical E. coli, we overexpress the BolA gene. BolA is a gene that controls the morphology of E. coli in the stress response (Santos et al., 1999). By overexpressing this gene, the rod-shaped E. coli cells will become spherical (Aldea et al., 1988). We express this gene both under a constitutive promoter (Part K1890031), as well as an inducible promoter (Part K1890030), the latter being our favorite due to the better result obtained (Figure 3).

BolA widefield
Figure 3: Widefield images of E. coli BL21 transformed the OmpA-silicatein construct not altering the cell shape (A). When the cells are also transformed with the BolA under an inducible promoter the cells become spherical (B).

The spherical cells we produced had an increased volume compared to wildtype E. coli. The diameter of 1 µm that we observed matches the size of a photovoltaic cell (the smallest unit of a solar panel)(Yang, Shtein, & Forrest, 2005), and this size is hard to produce using conventional techniques. Conventional microlenses are usually bigger. Therefore, our method of producing microlenses has an advantage over the conventional production, since we are able to produce far smaller lenses. Using smaller lenses also means we are able to put more lenses on a surface, which increases the focusing effect. When we express both the BolA gene as well as silicatein gene, we are able to construct round cells, coated in glass (Figure 4).

BolA
Figure 4: SEM images of E. coli BL21 without the BolA gene covered in polysilicate (A) and E. coli BL21 transformed with the BolA gene covered in polysilicate (B).
  1. Aldea, M., Hernandez-Chico, C., De La Campa, A., Kushner, S., & Vicente, M. (1988). Identification, cloning, and expression of bolA, an ftsZ-dependent morphogene of Escherichia coli. Journal of bacteriology, 170(11), 5169-5176.
  2. Müller, W. E. G. (2003). Silicon biomineralization.
  3. Müller, W. E., Engel, S., Wang, X., Wolf, S. E., Tremel, W., Thakur, N. L., Schröder, H. C. (2008). Bioencapsulation of living bacteria (Escherichia coli) with poly (silicate) after transformation with silicatein-α gene. Biomaterials, 29(7), 771-779.
  4. Santos, J. M., Freire, P., Vicente, M., & Arraiano, C. M. (1999). The stationary‐phase morphogene bolA from Escherichia coli is induced by stress during early stages of growth. Molecular microbiology, 32(4), 789-798.
  5. Yang, F., Shtein, M., & Forrest, S. R. (2005). Controlled growth of a molecular bulk heterojunction photovoltaic cell. Nature materials, 4(1), 37-41.