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Arina Filatova authoredArina Filatova authored
Contribution.vue 15.55 KiB
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<h3>Connecting iGEM Past, Present, and Future</h3>
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src="https://static.igem.wiki/teams/5306/contribution/contributionscutiesgood.webp"
alt="Contribution Image"
width="300"
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<p>
Our team, MSP-Maastricht, is dedicated to being an active and ongoing contributor to the iGEM community. We believe that science and engineering bridge the past and future, as all research builds on the knowledge of those who came before us. A key part of this tradition is our Contributions page, which showcases the innovative solutions we are developing to tackle real-world challenges. By sharing our strategies, methodologies, and findings, we aim to enhance the accessibility and application of synthetic biology techniques. Through facilitating such knowledge transfer, we hope to benefit future iGEM teams and the broader SynBio community.
</p>
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<h3>Our Specific Contributions</h3>
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<!-- Vibrio Natriegens Protocol Booklet -->
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Vibrio natriegens Protocol Booklet
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<div v-if="sections.protocolGuide" class="content">
<p>
With the growing popularity of <i>Vibrio natriegens</i> as a chassis organism and its relatively new use within synthetic biology and iGEM, the consolidation of protocols is crucial. To fulfill this need, we aim to provide future iGEM teams a strong foundation to build upon through our comprehensive protocol guide for <i>Vibrio natriegens</i>. This guide will provide step-by-step instructions on obtaining, culturing, manipulating, and utilizing <i>Vibrio natriegens</i>, making it easier for other researchers to adopt this organism in their work. Additionally, the guide also includes tips and tricks we have learned through our experience working with this novel bacterium. By providing this resource, we hope to save teams valuable time and effort during the competition and beyond.
</p>
<iframe
src="https://static.igem.wiki/teams/5306/contribution/the-maastricht-booklet.pdf"
width="100%"
height="600px"
style="border: none;"
title="The Maastricht Booklet"
></iframe>
</div>
</div>
<!-- Vibrio Natriegens Snapgene Codon Optimization Table -->
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Vibrio natriegens Snapgene Codon Optimization Table
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<p>
In addition to our protocol guide, Natronaut has created an easily accessible codon optimization table specifically for <i>Vibrio natriegens</i> that can be directly used in Snapgene. This table will assist researchers in selecting the most efficient codons for gene expression, optimizing the performance of genetic constructs, and improving experimental outcomes for future teams working with <i>Vibrio natriegens</i>.
</p>
<img
src="https://static.igem.wiki/teams/5306/contribution/codon-opt-table.webp"
alt="Codon Optimization Table"
width="100%"
/>
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<h4>Download the Codon Optimization Table</h4>
<button @click="downloadTable">Download Codon Optimization Table</button>
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<p>
To download the <i>Vibrio natriegens</i> codon optimization table for use in Snapgene click on the button above. Once downloaded, select the xml file in your downloads. From here you can chose to open the xml file with straight into Snapgene and just in these few clicks you are ready for codon optimization.
</p>
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<!-- Registry Parts -->
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Registry Parts
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<p>
Natronaut is proud to introduce several new BioBrick Parts to the iGEM Parts Registry. The iGEM Registry is the best way to contribute to future iGEM teams, who can find and utilize well-characterized parts with increased ease. Our registered parts consist of six new basic parts and the composite part they contribute to. Below is a brief description of each part we contributed, including their roles in the full Assimilatory Nitrate Reduction to Ammonium (ANRA) pathway and other potential applications:
</p>
<ul>
<li><b>Periplasmic Binding Protein (nasF) - BBa_K5306000</b><br>
The periplasmic binding protein binds to extracellular nitrates with high affinity, starting the uptake process necessary for the functioning of the ANRA pathway and overall nitrate capture.</li>
<li><b>Homodimeric Transmembrane Protein (nasE) - BBa_K5306001</b><br>
This transmembrane protein facilitates the uptake of nitrate through the lipid bilayer, acting as a vital link in the transport of nitrates into the cell.</li>
<li><b>Dimeric ATP-Binding Protein (nasD) - BBa_K5306002</b><br>
The nasD part encodes a dimeric ATP-binding protein that hydrolyzes ATP. This protein powers the transport processes necessary for the uptake of nitrates, ensuring that the pathway operates efficiently under varying conditions.</li>
<li><b>Molybdoenzyme (nasA) - BBa_K5306005</b><br>
This part encodes a molybdoenzyme that reduces nitrates. It performs the enzymatic processes required for efficient nitrogen conversion.</li>
<li><b>Nitrate Reductase (nasC) - BBa_K5306003</b><br>
This enzyme is responsible for catalyzing the conversion of nitrate (NO₃⁻) to nitrite (NO₂⁻) once it enters the bacterial cell. Nitrate reductase is NADH-dependent and consists of a large catalytic subunit containing the active site for reduction and a smaller NADH oxidoreductase subunit, facilitating electron transfer.</li>
<li><b>Nitrite Reductase (nasB) - BBa_K5306004</b><br>
The nitrite reductase enzyme converts nitrites (NO₂⁻) into ammonium (NH₄⁺). As a cytochrome enzyme, it employs various heme groups to facilitate the reduction process, ensuring efficient conversion. The sequence encoding nasB also includes a 6x His tag, enabling protein localization.</li>
<li><b>Composite Part: ANRA Pathway (BBa_K5306006)</b><br>
This composite part encodes the three primary enzymes involved in the ANRA pathway: the transporter (ABC enzyme), nitrate reductase, and nitrite reductase. By integrating these components, the ANRA pathway enables the efficient conversion of nitrates to ammonium.</li>
</ul>
<p>
These parts not only play key roles both individually and as part of the ANRA pathway but also facilitate the collaborative research and development that is central to the iGEM community. These parts can be utilized independently or in combination to engineer innovative solutions.
</p>
<p>
For more detailed information about Natronaut's parts, please refer to the <a href="https://2024.igem.wiki/msp-maastricht/engineering.html" target="_blank">Engineering</a> and <a href="https://2024.igem.wiki/msp-maastricht/part-collection.html" target="_blank">Parts</a> pages.
</p>
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</div>
<!-- Sustainable Development Booklet -->
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Sustainable Development Booklet
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<p>
The SDG Booklet is aimed at guiding future iGEM teams through the Sustainable Development Goals (SDGs) in addition to self-assessing what SDGs teams decide to fall into and focus on. Questions such as “How many SDGs should a team focus on?” and “How should each SDG be tackled?” are answered in this 16-paged booklet. Moreover, the special prize awarded to iGEM teams who undertake SDG consideration is described and tackled via a step-to-step instruction which Natronaut hopes will reach and be made great use of by iGEM generations to come.
</p>
<iframe
src="https://static.igem.wiki/teams/5306/contribution/sustainabledevelopmentimpact-msp-maastricht24.pdf"
width="100%"
height="600px"
style="border: none;"
title="Sustainable Development Booklet"
></iframe>
</div>
</div>
<!-- iGEM Surivival Kit -->
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<h4 @click="toggleSection('survivalKit')">
The iGEM Survival Kit Series
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<div v-if="sections.survivalKit" class="content">
<p>
The iGEM Survival Kit is a series of educational content created by the MSP-Maastricht iGEM team for future iGEM teams. It covers a variety of topics, from dry lab tasks like primer design, gBlock design, and parts registration to wet lab protocols such as liquid broth preparation, transformations, and sequencing preparation. Additionally, the guide takes teams through basic requirements and necessary documentation practices specific to iGEM. It acts as a set of tutorials for future iGEM teams, providing audio-visual guidance for tasks tailored to their needs in the iGEM competition, all in one place.
</p>
<p>
This is especially useful for teams that may struggle to find up-to-date, comprehensive, and specialized video tutorials online, as we initially did. These videos also serve as aids for the greater SynBio community. While tailored to help future iGEM teams through their journey, we have already received positive feedback from students in genetic engineering disciplines.For more detailed information about
the series, please refer to the <a href="https://2024.igem.wiki/msp-maastricht/education.html" target="_blank">Education</a> page.
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<!-- Notion Organisation Template -->
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Notion Organisation Template
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<p>
Based on our experience, organization and management are foundational to a successful project. To help future iGEM teams organize and manage their projects effectively and seamlessly, we have created a Notion template that our team has personally used within our project. To keep track of everything in our project, the Natronaut team made great use of a customized iGEM Notion template developed in collaboration with Chris Damour, a former MSP-Maastricht iGEM member. Notion is a powerful productivity and note-taking web application that serves as an invaluable organizational tool. We at Natronaut truly believe in the template's ability to guide, document, and standardize the work and data of future iGEM teams.The template is designed to encompass all the necessary information from the iGEM wiki while providing a structured way to meet iGEM criteria. It centralizes all medals, deadlines, wiki pages, and more in one location. The customized iGEM template supported us throughout our project, from the very beginning to the end. It facilitated our brainstorming stages with an integrated idea voting system, aided in literature research, and streamlined our time spent in the laboratory. Moreover, it simplified the process of uploading information to the MSP iGEM Wiki, allowing wiki editing to become the responsibility of only a few people.We believe that this template will be a game-changer for future iGEM teams, providing a clear framework and an organized workspace customized to iGEM. By enhancing efficiency and collaboration, it will foster a sense of community and empower future teams to share their knowledge and experiences, paving the way for innovation and growth in synthetic biology.
</p>
:::tip
Check out our Notion template:
<a href="https://curvy-caribou-2c5.notion.site/iGEM-Notion-11010f1720c0805d8e12f4e8b2943349?pvs=4" target="_blank">Click here to view the Notion template</a>.
:::
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<h3>Conclusion</h3>
<p>
Together, these contributions aim to empower future researchers, especially iGEM teams, promote the responsible use of synthetic biology, and facilitate advancements in addressing pressing environmental issues. We believe that sharing our insights and tools will not only enhance our own project but also benefit the global iGEM community and beyond.
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<UsageTable type="C" name="Vibrio Natriegens" geneticCode="1" frequencies="GCG:0.27;ATC:0.41;CTG:0.22;ACG:0.23;CCA:0.39;AGC:0.19;CGG:0.03;TTC:0.4;AGG:0.03;GAT:0.6;CCT:0.31;GAA:0.65;GGT:0.45;GGC:0.32;ATG:1;TCG:0.12;CGT:0.42;TAG:0.19;CAA:0.59;TTT:0.59;TGA:0.15;CGC:0.26;CTT:0.18;CAC:0.49;CCG:0.22;ACA:0.22;AAT:0.43;TAA:0.65;AAG:0.31;ATA:0.1;CAG:0.41;GTT:0.33;ATT:0.48;GTG:0.25;GGA:0.12;TGG:1;GCT:0.26;CGA:0.14;GGG:0.09;GAG:0.34;TAC:0.56;GTA:0.22;AAC:0.56;TCC:0.07;GAC:0.39;TAT:0.43;CTA:0.13;AGA:0.1;GTC:0.18;TGT:0.66;TGC:0.33;TTA:0.31;CAT:0.3;AAC:0.57;CAG:0.47;TGT:0.58;TCG:0.14;CCG:0.26;AAG:0.22;CGA:0.31;CTC:0.21;ACA:0.19;TCC:0.22" />
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