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       <img src="https://static.igem.org/mediawiki/2020/8/8f/T--AUC-EGYPT--partner.png" style="width:100%; height: 100%;">
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<a href="#BG"><i class="fas fa-info-circle"></i><label>Partnership</label></a>
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<a href="#PL"><i class="fas fa-info-circle"></i><label>Partnership: leveraging resources in a resource-limited setting</label></a>
 
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                 <div class="col-lg-3 col-md-3 col-sm-3 subnav requ">
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<a href="#WF"><i class="far fa-newspaper"></i><label>Mission Luciferin</label></a>
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<a href="#ML"><i class="far fa-newspaper"></i><label>Mission Luciferin: an interactive twist on the AFCM-SynFair</label></a>
 
                 </div>
 
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<a href="#Ipt"><i class="fas fa-user-tie"></i><label>Modeling</label></a>
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<a href="#model"><i class="fas fa-user-tie"></i><label>Modeling</label></a>
 
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<a href="#instl"><i class="fas fa-user-tie"></i><label>Entrepreneurship</label></a>
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<a href="#entr"><i class="fas fa-user-tie"></i><label>Entrepreneurship</label></a>
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<h2 >Partnership: leveraging resources in a resource-limited setting</h2><br></br>
 +
<p style="font-size:medium;">Early in the season when we started to prepare for the competition, we realized that there were so many aspects that we needed help in navigating. Our team is a multidisciplinary one with members from Computer Science, Engineering, Actuarial Sciences and of course biology. However, the nature of the competition was so unique that we needed guidance navigating it. <br></br>
 +
We knew that AFCM has been Africa’s longest standing team in the competition, yet we also knew that they are a medical college and thus may also need help in navigating non-biology components of iGEM. The fact that both of our teams are based in Egypt gave us a boost to pursue a partnership with them. <br></br>
 +
Throughout the season, we held many meetings where both teams helped each other in navigating various challenges in the competition starting from modeling, entrepreneurship and education all the way to networking and hosting mutual feedback sessions. In our feedback sessions, we would each present our current progress and identify strengths and weaknesses as well as next steps. Two of AFCM's instructors actually dedicated their time with us as advisors following us along each step of the way.
 +
</p>
  
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<div class = "container">
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<h2 >Background</h2>
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    <br></br>
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<section id="ML">
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<p>Coronavirus disease 2019 (COVID-19) is an illness caused by a novel severe acute
+
<br></br>
−
respiratory syndrome coronavirus 2 (SARS-CoV-2), which was first discovered amid an
+
<br></br>
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outbreak of respiratory illness cases in Wuhan City, China. Currently, COVID-19 is classified as
+
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a world health crisis and a fast-growing global pandemic. The number of confirmed cases
+
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worldwide has exceeded 34 million, and it killed over 1 million individuals [1] . COVID-19 also
+
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affects our everyday life and is associated with a tremendous economic burden due to
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lockdowns, Medicare expenditures, and the slowing of manufacturing. The average economic
+
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loss, only in the first 4 months of the pandemic, has significantly affected several countries with
+
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high, middle, and low income by 18%, 24%, and 22%, respectively [2] . <br></br>
+
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The virus is known for its rapid cell entry and replication. First, the coronavirus spike (S)
+
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protein attaches to angiotensin-converting enzyme 2 (ACE2) receptors that are located on the
+
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surface of many human cells, including those in the lungs permitting the virus entry. This will
+
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then activate virus fusion into the host cell and allow the viral genetic material (ssRNA) to be
+
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fully released into the cytoplasm, where the replication and transcription processes occur, relying
+
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on the host machinery. Following the virus RNA translation, replicase proteins will be generated
+
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from open reading frame 1a/b (ORF 1a/b). These proteins use the genome as a template to
+
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produce more RNAs, which subsequently serve as templates in generating addition full-length
+
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genomes and speed up the virus replication [3] .<br></br>
+
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Despite how fast medical and pharmaceutical technologies are improving, there is
+
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currently still no cure for COVID-19, and vaccines are not yet available. However, some
+
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medications are prescribed to relieve the severity of the symptoms experienced by patients,
+
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including fever, cough, and bone pain. Hypothetically, if COVID-19 affected half the world&#39;s
+
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current population over a year with a 1% fatality rate, the death toll would be 35 million, and
+
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thus increasing the number of deaths worldwide, which is already around 60 million for all
+
−
causes in a typical year [4] . Therefore, scientists are in a hurry to develop an efficient and fast
+
−
vaccine to save the world.<br></br> <p style="text-align:center;">COVID-19 total cases (world map image). <br></br>Retrieved from
+
−
https://coronavirus.jhu.edu/data/animated-world-map
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</p> <img style = "width: 500px; margin-left: 250px;" src= "https://static.igem.org/mediawiki/2020/2/26/T--AUC-EGYPT--descpmap.jpg"><img>
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<br></br> <p style="text-align:center;">Total cases, total deaths, recovered cases, and active cases that get updated daily:
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Retrieved from: https://www.worldometers.info/coronavirus/ 
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It could be something like that:
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<section class="facts section-bg" data-aos="fade-up">
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<div class="col-lg-3 col-6 text-center">
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<span data-toggle="counter-up">7</span>
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<p>Speakers</p>
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</div>
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<div class="col-lg-3 col-6 text-center">
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<span data-toggle="counter-up">10</span>
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<p>Partners</p>
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</div>
+
−
+
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<div class="col-lg-3 col-6 text-center">
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<span data-toggle="counter-up">25</span>
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<p>Research Competitors</p>
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</div>
+
−
+
−
<div class="col-lg-3 col-6 text-center">
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−
<span data-toggle="counter-up">1,200</span>
+
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<p>Attendees</p>
+
−
</div>
+
−
+
−
</div>
+
−
+
−
</div>
+
 
</section>
 
</section>
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</div>
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<h2 >Mission Luciferin: an interactive twist on the AFCM-SynFair</h2><br></br>
−
 
+
<p style="font-size:medium;">This year, we wanted to focus strongly on science communication and education as a part of our core values and social responsibility. Rather than reinvent the wheel, we wanted to build on already existing resources that were tried and true. During our early meetings with AFCM, we learned that they had an activity called the SynFair where they host students from all over the country in their campus for SynBio educational workshops. As COVID-19 precautions also caused their campus to close, they had begun to consider the challenges of having their SynFair activity be a face-to-face interaction. During one of our regular meetings, we came up with the idea of turning their educational content into an interactive app that they could deploy to school children. This endeavor would also strongly help them in future iterations of the SynFair activity as they would be able to deliver their content to an even wider base of students. Two of their team members, Ahmed Adel and Ahmed Wael met with our Biology team (Salma Abou Elhassan, Rana Salah and Ahmed Magdy) and provided us with their educational content. Our teams worked together to turn this content into a set of engaging games and activities. Our awesome game developer, Dalia Waleed, then worked using Unity on stringing together the game: Mission Luciferin. Mission Luciferin follows the adventures of a family of fireflies on a quest to get their daughter firefly to light up again. On their journey, they enter a SynBio Lab and learn all about how to design circuits and use them. The game was showcased in AFCM’s virtual SynFair and was heavily praised.
−
<section id="WF">
+
</p>
 +
 
 +
    <br></br>
 +
<section id="model">
 
<br></br>
 
<br></br>
 
<br></br>
 
<br></br>
 
</section>
 
</section>
−
 
+
<h2 >Modeling</h2><br></br>
−
<h2 >Approach and Project Description</h2>
+
<p>Early on in our project, we knew that due to our campus closure and restricted access to the lab we needed to count heavily on various modeling and simulation techniques to evaluate our design. Our team members had strong mathematical backgrounds, yet we still needed help in applying this background in a biological setting. Once we had settled on using toehold switches, we realized that we needed to perform extensive structural modeling and to have a go at modeling the kinetics of our circuit. Back in June we met with Ahmed Gamal and Mohamed Tarek, 2 AFCM iGEMers responsible for modeling within their project. They began helping us by introducing us to the various modeling techniques we could use and how to create mathematical models that would be useful in a therapeutic context. After that, we regularly checked in with updates of our work progress and troubleshooted various hurdles in our models including but not limited to parameter selection, equation formulation and data plotting. In a later check-in, they noticed that we were sketching MATLAB codes from scratch and recommended that we use MATLAB’s SynBiology software for our models.
−
 
+
</p>
−
<p><br></br> Unlike other treatments that focus on treating the side complications and symptoms of COVID-
+
−
19, AUC-EGYPT iGEM tackles the problem from the root by developing an innovative
+
−
therapeutic to stop the viral replication and thereby its invasion to the host cells. <br></br>
+
−
Consequently, our project proposes a synthetic biology approach for COVID-19
+
−
treatment through a designed circuit to control the expression of the hybrid transcriptional
+
−
activator GAL4-VP16, which is a potent transcriptional activator that is orthogonal to
+
−
mammalian cells, using a toehold switch device that allows the translation of a downstream
+
−
mRNA upon base pairing with a complementary mRNA trigger [5,6] . The switch gets activated
+
−
upon sensing SARS-CoV-2 mRNA, inducing the expression of GAL4-VP16 which in turn
+
−
activates the siRNA expression through binding to its upstream UAS promoter, and, thus,
+
−
initiating an RNA interference (RNAi) pathway against SARS-CoV-2 mRNA [7] . This RNAi is
+
−
achieved in the circuit using 2 de novo double-stranded siRNA, targeting the viral mRNA coding
+
−
for replicase proteins [8, 9] . Each siRNA sequence comprises 21 nucleotides that were selected
+
−
using computational inferences by siDirect software tool and were then subjected to a BLAST search to ensure the lack of homology with any other off-target genes from the host. <br></br>
+
−
<img style = "width: 600px; margin-left: 180px;" src="https://static.igem.org/mediawiki/2020/8/8c/T--AUC-EGYPT--Descp4.jpeg"></img></p>
+
 
<br></br>
 
<br></br>
−
 
+
<section id="entr">
−
Having our circuit completed, it will be delivered to the targeted cells through a virus-
+
−
like particle system (VLPs) which are non-replicating particles that lack the viral genome, yet
+
−
can mimic the cell entry of the actual virus [10] . Here, we will have a baculovirus-mediated
+
−
lentivirus vectors’ production as they have not only shown clinical success and high transduction
+
−
rates in gene therapy but also a great transduction efficacy of the inserted gene of interest greater
+
−
than 90% to the mammalian cell cultures [11,12] . Then we will modify those lentivirus vectors by
+
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changing them to a SARS-CoV-2 Pseudo-Virus, resulting in dealing with viruses that have
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biosafety level 2 instead of biosafety level 3, and allowing the specific targeting of the cells
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expressing the ACE2 receptor [1,4] . Consequently, we will be delivering our designed construct
+
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only to the cells that are most likely to be infected by SARS-CoV-2. We created four baculovirus
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donor plasmids: Two code for the essential elements for the production of the third generation,
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self-inactivating lentiviruses [11,12] , one codes for the SARS-CoV-2 Spike protein to replace the
+
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normal envelope glycoprotein of the lentivirus vectors [13] , and one to transfer the genes encoding
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for our toehold switch and siRNAs construct [12] . Through this delivery system, our designed
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sensing-interfering circuit will be successfully transduced into infected cells expressing the
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ACE2 receptor.<br></br>
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<img style = "width: 600px; margin-left: 200px;" src="https://static.igem.org/mediawiki/2020/e/ec/T--AUC-EGYPT--Descp5.png"></img></p>
+
−
 
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−
<section id="Ipt">
+
 
<br></br>
 
<br></br>
 
<br></br>
 
<br></br>
 
</section>
 
</section>
 +
<h2>Entrepreneurship</h2><br></br>
 +
<p style="font-size:medium;">During our first preliminary meetings with AFCM, we learned from them that they had always wanted to explore the entrepreneurial potential of their iGEM projects. They had been participating in the competition for four years conceptualizing cancer therapies but had never actually begun to create a business model for a therapeutic solution. Their only currently available business model was for custommune, a software tool for hotspot identification and epitope prediction. Our team includes Muhammad Hasan and Sawsan Ali, two team members from who have experience in preparing business models both our team members worked closely with Saif Wahba and Aly Morsy, 2 AFCM team members tasked with working on the business model. <br></br>
 +
Together we began exploring the current regulatory framework in Egypt for therapy for therapies utilizing SynBio, we helped them identify the unmet needs and their UVP, look into potential stakeholders and identify the challenges and potential hurdles they might encounter in the real world implementation of their project.
  
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<h2>Inspiration</h2>
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</p>
−
<p>
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−
During our brainstorming sessions for the project, our team had a wide variety of ideas that
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coupled synthetic biology utilization in therapeutic applications of genetic engineering, which
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also grasped our attention because of their potential to directly not only diagnose but also treat
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harmful diseases. Several viral diseases were researched, including developing vaccines for HIV
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and Ebolavirus.<br></br>
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However, we wanted our project to have a maximal as well as a global impact in addition to its
+
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availability to every individual. During that time, the COVID-19 pandemic had just started, and
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our university (AUC) was the leading university in Egypt to emphasize the importance of
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quarantine and preventing access to campus. Moreover, some members of our team have lost
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their close ones due to the pandemic. Since then, we have realized how dangerous the novel
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coronavirus is, and the necessity of not downplaying it. And, that is how the idea of working on
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SARS-CoV-2 came to us.<br></br>
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Since many of us were concerned about the looming threat of the virus&#39;s rapid spread and
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infection among people, we thought about uprooting the virus and inhibiting its replication in the
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first place to eliminate its severity and invasion to neighboring cells.<br></br>
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Our vision became much clearer when we discovered that small interfering RNAs (siRNAs) is a
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highly conserved gene silencing mechanism that plays a significant role in antiviral therapeutic
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and prophylactic applications [14] . And, that was the first component in our circuit to knockdown
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the viral mRNA coding for the replicase proteins. Then, we have searched for the current
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treatments for COVID-19 that utilize synthetic biology platform, and we discovered that
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scientists from Ellington’s group can diagnose patients applying toehold circuits [15] . Thus, we
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agreed on attaching our toehold switch, which is turned on through the UAS promoter, to the
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siRNA sequences to control their activation with the aid of the hybrid transcriptional activator
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GAL4-VP16 if and only if they bind to a SARS-CoV-2 mRNA, and thus increase the specificity
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of our treatment in a cost-effective way. Together, they completed our circuit.<br></br>
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We designed 2 de novo siRNA sequences that play a significant role in our antiviral therapeutic
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approach through the knockdown of the SARS-CoV-2 mRNA coding for the replicase proteins,
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which are responsible for the virus replication.<br></br>
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Having decided on the circuit, we wanted to maximize the specificity and efficiency of our
+
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treatment. However, we have faced an obstacle when it comes to the circuit delivery inside the
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targeted lung cells without getting degraded from the cell environment. As a result, we want a
+
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solution to boost patients&#39; immunity on one hand and carry our circuit safely to the cell on the <br></br>
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other hand. After an intensive search, this problem does no more exist when we discovered that
+
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both requirements are becoming amenable with the use of Virus-Like Particles (VLPs) that are
+
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self-assembled into a capsule in which we can load our circuit as cargo inside it [16] . Thus, we
+
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believe we have made a great advance in the eventual completion of this project, providing a
+
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specific, efficient, and cost-effective solution that helps in the struggle against COVID-19.<br></br>
+
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</p>
+
  
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<section id="instl">
 
 
<br></br>
 
<br></br>
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<br></br>
 
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</section>
 
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<h2>References</h2>
 
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<p>
 
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1. Coronavirus (COVID-19) Cases - Statistics and Research. 2020; Retrieved from
 
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https://ourworldindata.org/covid-cases <br></br>
 
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2. Coronavirus: the economic impact. 2020; Retrieved from
 
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https://www.unido.org/stories/coronavirus-economic-impact-10-july-2020<br></br>
 
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3. Boopathi, S., Poma, A. B., &amp; Kolandaivel, P. (2020). Novel 2019 coronavirus structure,
 
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mechanism of action, antiviral drug promises and rule out against its treatment. Journal of
 
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Biomolecular Structure and Dynamics, 1-10. doi: 10.1080/07391102.2020.1758788<br></br>
 
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4. Ioannidis, J. P., Axfors, C., &amp; Contopoulos-Ioannidis, D. G. (2020). Population-level COVID-
 
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19 mortality risk for non-elderly individuals overall and for non-elderly individuals without
 
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underlying diseases in pandemic epicenters. medRxiv. doi: 10.1101/2020.04.05.20054361<br></br>
 
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5. Green, A. A., Silver, P. A., Collins, J. J., &amp; Yin, P. (2014). Toehold switches: de-novo-
 
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designed regulators of gene expression. Cell, 159(4), 925–939. doi: 10.1016/j.cell.2014.10.002<br></br>
 
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6. Pardee, K., Green, A. A., Takahashi, M. K., Braff, D., Lambert, G., Lee, J. W., Ferrante, T.,
 
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Ma, D., Donghia, N., Fan, M., Daringer, N. M., Bosch, I., Dudley, D. M., O&#39;Connor, D. H.,
 
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Gehrke, L., &amp; Collins, J. J. (2016). Rapid, Low-Cost Detection of Zika Virus Using
 
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Programmable Biomolecular Components. Cell, 165(5), 1255–1266.
 
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doi:10.1016/j.cell.2016.04.059<br></br>
 
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7. Sadowski, I., Ma, J., Triezenberg, S., &amp; Ptashne, M. (1988). GAL4-VP16 is an unusually
 
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potent transcriptional activator. Nature, 335(6190), 563–564. doi: 10.1038/335563a0<br></br>
 
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8. He, M. L., Zheng, B. J., Chen, Y., Wong, K. L., Huang, J. D., Lin, M. C., ... &amp; Kung, H. F.
 
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(2006). Kinetics and synergistic effects of siRNAs targeting structural and replicase genes of
 
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SARS-associated coronavirus. FEBS letters, 580(10), 2414-2420.
 
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doi:10.1016/j.febslet.2006.03.066<br></br>
 
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9. Levanova, A., &amp; Poranen, M. M. (2018). RNA interference as a prospective tool for the
 
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control of human viral infections. Frontiers in microbiology, 9, 2151.
 
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doi:10.3389/fmicb.2018.02151<br></br>
 
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10. Naskalska, A., Dabrowska, A., Nowak, P., Szczepanski, A., Jasik, K., Milewska, A.,
 
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Ochman, M., Zeglen, S., Rajfur, Z., &amp; Pyrc, K. (2018). Novel coronavirus-like particles targeting<br></br>
 
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cells lining the respiratory tract. PLoS ONE, 13(9). doi: 10.1371/journal.pone.0203489
 
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11. Milone, M.C. &amp; O’Doherty, U. (2018). Clinical use of lentiviral
 
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vectors. Leukemia, 32, 1529–1541. doi: 10.1038/s41375-018-0106-0<br></br>
 
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12. Lesch, H., Turpeinen, S., Niskanen, E. et al. (2008). Generation of lentivirus vectors using
 
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recombinant baculoviruses. Gene Therapy, 15, 1280–1286. doi: 10.1038/gt.2008.76<br></br>
 
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13. Crawford, K.H.D., Eguia, R., Dingens, A.S., Loes, A.N., Malone, K.D., Wolf, C.R.;, Chu,
 
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H.Y., Tortorici, M.A., Veesler, D., Murphy, M., Pettie, D., King, N.P., Balazs, A.B. &amp; Bloom,
 
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J.D. (2020). Protocol and Reagents for Pseudotyping Lentiviral Particles with SARS-CoV-2
 
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Spike Protein for Neutralization Assays. Viruses. doi: 10.3390/v12050513<br></br>
 
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14. Villegas, P. M., Ortega, E., Villa-Tanaca, L., Barrón, B. L., &amp; Torres-Flores, J. (2018).
 
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Inhibition of dengue virus infection by small interfering RNAs that target highly conserved
 
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sequences in the NS4B or NS5 coding regions. Archives of virology, 163(5), 1331-1335. doi:
 
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10.1007/s00705-018-3757-2<br></br>
 
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15. Shen, M., Zhou, Y., Ye, J., Al-Maskri, A. A. A., Kang, Y., Zeng, S., &amp; Cai, S. (2020).
 
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Recent advances and perspectives of nucleic acid detection for coronavirus. Journal of
 
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Pharmaceutical Analysis. doi: 10.1016/j.jpha.2020.02.010<br></br>
 
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16. Onodera, T., Hashi, K., Shukla, R. K., Miki, M., Takai-Todaka, R., Fujimoto, A., ... &amp; Ato,
 
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M. (2019). Immune-focusing properties of virus-like particles improve protective IgA
 
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responses. The Journal of Immunology, 203(12), 3282-3292. doi: 10.4049/jimmunol.1900481<br></br>
 
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Latest revision as of 03:01, 19 December 2020







Partnership: leveraging resources in a resource-limited setting



Early in the season when we started to prepare for the competition, we realized that there were so many aspects that we needed help in navigating. Our team is a multidisciplinary one with members from Computer Science, Engineering, Actuarial Sciences and of course biology. However, the nature of the competition was so unique that we needed guidance navigating it.

We knew that AFCM has been Africa’s longest standing team in the competition, yet we also knew that they are a medical college and thus may also need help in navigating non-biology components of iGEM. The fact that both of our teams are based in Egypt gave us a boost to pursue a partnership with them.

Throughout the season, we held many meetings where both teams helped each other in navigating various challenges in the competition starting from modeling, entrepreneurship and education all the way to networking and hosting mutual feedback sessions. In our feedback sessions, we would each present our current progress and identify strengths and weaknesses as well as next steps. Two of AFCM's instructors actually dedicated their time with us as advisors following us along each step of the way.







Mission Luciferin: an interactive twist on the AFCM-SynFair



This year, we wanted to focus strongly on science communication and education as a part of our core values and social responsibility. Rather than reinvent the wheel, we wanted to build on already existing resources that were tried and true. During our early meetings with AFCM, we learned that they had an activity called the SynFair where they host students from all over the country in their campus for SynBio educational workshops. As COVID-19 precautions also caused their campus to close, they had begun to consider the challenges of having their SynFair activity be a face-to-face interaction. During one of our regular meetings, we came up with the idea of turning their educational content into an interactive app that they could deploy to school children. This endeavor would also strongly help them in future iterations of the SynFair activity as they would be able to deliver their content to an even wider base of students. Two of their team members, Ahmed Adel and Ahmed Wael met with our Biology team (Salma Abou Elhassan, Rana Salah and Ahmed Magdy) and provided us with their educational content. Our teams worked together to turn this content into a set of engaging games and activities. Our awesome game developer, Dalia Waleed, then worked using Unity on stringing together the game: Mission Luciferin. Mission Luciferin follows the adventures of a family of fireflies on a quest to get their daughter firefly to light up again. On their journey, they enter a SynBio Lab and learn all about how to design circuits and use them. The game was showcased in AFCM’s virtual SynFair and was heavily praised.







Modeling



Early on in our project, we knew that due to our campus closure and restricted access to the lab we needed to count heavily on various modeling and simulation techniques to evaluate our design. Our team members had strong mathematical backgrounds, yet we still needed help in applying this background in a biological setting. Once we had settled on using toehold switches, we realized that we needed to perform extensive structural modeling and to have a go at modeling the kinetics of our circuit. Back in June we met with Ahmed Gamal and Mohamed Tarek, 2 AFCM iGEMers responsible for modeling within their project. They began helping us by introducing us to the various modeling techniques we could use and how to create mathematical models that would be useful in a therapeutic context. After that, we regularly checked in with updates of our work progress and troubleshooted various hurdles in our models including but not limited to parameter selection, equation formulation and data plotting. In a later check-in, they noticed that we were sketching MATLAB codes from scratch and recommended that we use MATLAB’s SynBiology software for our models.







Entrepreneurship



During our first preliminary meetings with AFCM, we learned from them that they had always wanted to explore the entrepreneurial potential of their iGEM projects. They had been participating in the competition for four years conceptualizing cancer therapies but had never actually begun to create a business model for a therapeutic solution. Their only currently available business model was for custommune, a software tool for hotspot identification and epitope prediction. Our team includes Muhammad Hasan and Sawsan Ali, two team members from who have experience in preparing business models both our team members worked closely with Saif Wahba and Aly Morsy, 2 AFCM team members tasked with working on the business model.

Together we began exploring the current regulatory framework in Egypt for therapy for therapies utilizing SynBio, we helped them identify the unmet needs and their UVP, look into potential stakeholders and identify the challenges and potential hurdles they might encounter in the real world implementation of their project.