<p>We were honored to host the other two Israeli iGEM teams, <b>Ben Gurion University</b> and <b>Tel Aviv University</b> at our campus for what
<p>We were honored to host the other two Israeli iGEM teams, <ahref="https://2022.igem.wiki/bgu-israel/"><b>iGEM BGU-Israel</b></a> and <ahref="https://2022.igem.wiki/tau-israel/"><b>iGEM TAU-Israel</b></a> at our campus for what
we call <b>the “mini jamboree”</b>. This event was meant to resemble the grand jamboree on a smaller scale. Each of the groups presented
their projects, along with a fifteen-minute question session. In addition, we invited two guest lecturers: The first is Anna Shreder, a debate coach who gave us a lecture about the art of presenting in front of an audience, preparing us for the grand jamboree. The second is Dr. Michael Levy from the faculty of Biotechnology and Food engineering that gave us a lecture about his field of research in synthetic biology - engineering ribosomes.
This event was a fantastic opportunity to become more comfortable in presenting the projects
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<hr>
<p>We reached out to other teams to hear about their projects, ideas and experiences. After hearing from a few teams, we realized
that we may not be the only people interested in these projects. This led us to the idea of creating an <b>educational podcast</b>
centered around synthetic biology and iGEM groups specifically. We invited three groups from around the world: <b>Latvia, Athens and
United Arab Emirates</b>; each group told us about their project and some of the challenges they faced. You can read more about our
centered around synthetic biology and iGEM groups specifically. We invited three groups from around the world: <b><ahref="https://2022.igem.wiki/latvia-riga/">iGEM Latvia-Riga</a>, <ahref="https://2022.igem.wiki/athens/">iGEM Athens</a> and
<ahref="https://2022.igem.wiki/nyu-abu-dhabi/">iGEM NYU-Abu-Dhabi</a></b>; each group told us about their project and some of the challenges they faced. You can read more about our
podcast in the <ahref="{{ url_for('pages', page='communication') }}">Education & Communication</a> page.<br> You can listen to our podcast, just click on the advertisement post photo.</p>
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<h2>OraCell</h2>
<h2>Lavtia-Riga: OraCell</h2>
<hr>
<p>As explained on previous pages, we lacked a satisfactory solution for detecting and quantifying
<p>
As explained on previous pages, we lacked a satisfactory solution for detecting and quantifying
decursin, which is how <b>OraCell</b> was born. More information on this can be found on the <ahref="{{ url_for('pages', page='measurement') }}">measurement</a> page.
We realized that quantification
of metabolites is a problem not unique to our project. Therefore, we began to search for fellow iGEM teams in the biomanufacturing track,
whose molecules could potentially affect the Hippo pathway as well. We reached out to the <b>Latvian iGEM 2022 team</b>, who are producing a molecule
known as crocin, which recent studies have shown impacts the Hippo pathway in a similar manner to decursin. After explaning the mechanism of our assay to them, we offered to establish a calibration
curve using a sample sent by them, for possible future detection and measurment of crocin. They have sent us a sample for setting up the first experiment. This is also the first time that
a Latvian group has participated in iGEM, which made our collaboration with their team even more impactful and significant.</p>
whose molecules could potentially affect the Hippo pathway as well. We reached out to the <ahref="https://2022.igem.wiki/latvia-riga/"<b>Latvian iGEM 2022 team</b></a> who are producing a molecule
known as crocin, which recent studies have shown impacts the Hippo pathway in a similar manner to decursin<sup>[<ahref="#ref1">1</a>]</sup>. After explaining the mechanism of our assay to them, we offered to establish a calibration
curve using a sample sent by them, for possible future detection and measurement of crocin. They have sent us a sample for setting up the first experiment.
Furthermore, this is also the first time that a Latvian group has participated in iGEM, which made our collaboration with their team even more impactful and significant.
As a fellow group in the biomanufacturing track, we were able to discuss our work and models and learn from each other. </p>
<h2>iGEM Challenge</h2>
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set at a challenging level and therefore, prior to the escape room, a lesson in synthetic biology was given to high school students.
Since the escape room was set at such a high level, we were able to share it with fellow iGEM groups as a friendly competition.
We sent out the link to the escape room on the iGEM Slack group as well as on our Instagram with the top three groups being awarded a prize
to be handed out at the grand jamboree in Paris.</p>
to be handed out at the grand jamboree in Paris.</p>
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<divclass="figure-text"><p>iGem Challenge advertisement post </p></div>
<h2>Mock Jamboree</h2>
<hr>
<p>In addition to our in-person meetup, we will also host a <b>virtual meetup</b> with the various groups we interacted with throughout our project: Athens,
Latvia and United Arab Emirates. The meetup will take place following the wiki freeze. That way, the projects and presentations are expected
to be in the final stages. This allows the mock jamboree to act as a dry run for the grand jamboree and make the teams more comfortable in
presenting their final projects. We are excited for this meeting and hope it will be beneficial for all of the groups involved.</p><br>
{% endblock %}
<hr>
<p>In addition to our in-person meetup, we will plan to host a <b>virtual meetup</b> with the various groups we interacted with throughout our project: Athens,
Latvia and United Arab Emirates. The meetup will take place following the wiki freeze. That way, the projects and presentations are expected
to be in the final stages. This allows the mock jamboree to act as a dry run for the grand jamboree and make the teams more comfortable in
presenting their final projects. We are excited for this meeting and hope it will be beneficial for all of the groups involved.</p><br>
{% endblock %}
{% block references %}
<olclass="reftext">
<liid="ref1"><ahref="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7807260/">Wu, Z., & Hui, J. (2020).</a> Crocin reverses 1-methyl-3-nitroso-1-nitroguanidine (MNNG)-induced malignant transformation in GES-1 cells through the Nrf2/Hippo signaling pathway. Journal of Gastrointestinal Oncology, 11(6), 1242.</li>
<p>First, we found the 3D structure and amino-acid sequence of XimE in the Protein Data Bank (PDB) and manually performed point mutations in desired positions to build the stock of mutant sequences destined for structural predictions. While accessing AlphaFold2 from ChimeraX <sup>[<ahref="#ref16">16</a>]</sup>, we retrieved the predicted structures of mutant proteins of the same type (XimE). AlphaFold<sup>[<ahref="#ref17">17</a>]</sup> is a computational approach capable of predicting protein structures to near experimental accuracy, whereas ChimeraX<sup>[<ahref="#ref16">16</a>]</sup> runs its script automatically on Google Colab servers. During our trials with docking between target ligand and XimE we noticed great differences in scores between WT protein retrieved from PDB, aka crystallographic structure, and WT protein predicted with AlphaFold, although both have the same amino acid sequence. Therefore, we decided to use the predicted wild-type (WT) protein from AlphaFold for comparison with predicted mutant proteins for our further investigations. </p>
<p>The next step was protein-ligand docking. It is a method in structural molecular biology, whose goal is to predict the optimal binding mode of a ligand with a protein of known three-dimensional structure. There are various programs that can be used for protein-ligand docking, however, more comfortable the fastest and the most dependable for us appeared to be CB-Dock2 used for blind docking because the protein of interest lacked the verified position of the active site. The program first automatically detects binding sites and customizes the docking box and then employs the latest version (1.2.0) of AutoDock Vina for the docking itself.<sup>[<ahref="#ref18">18</a>]</sup><sup>[<ahref="#ref19">19</a>]</sup> As a result, the software draws out the list of ranked binding sites of the ligand according to the Vina score, predicted binding affinity calculated in kcal/mol, which in turn can be translated into binding free energy ∆G. </p>
<p>Finally, we analyzed and compared all the scores and visualized the following interaction between mutant protein and target ligand using PyMol, a molecular visualization system on an open-source foundation. </p>
<p>You can find all of our files, and artifacts here: <ahref="https://gitlab.igem.org/2022/software-tools/technion-israel/-/tree/main/Mutation%20Modeling%20Supplements">Supplements</a></p>
