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Devyani Ravi authoredDevyani Ravi authored
Contribution.vue 12.09 KiB
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<div class="contribution">
<h3>Connecting iGEM Past, Present, and Future</h3>
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<img
src="https://static.igem.wiki/teams/5306/contribution/contributionscutiesgood.webp"
alt="Contribution Image"
width="300"
/>
<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>
</div>
<h3>Our Specific Contributions</h3>
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<!-- Vibrio Natriegens Protocol Booklet -->
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<h4 @click="toggleSection('protocolGuide')">
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%"
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title="The Maastricht Booklet"
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</div>
<!-- Vibrio Natriegens Snapgene Codon Optimization Table -->
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<h4 @click="toggleSection('codonTable')">
Vibrio natriegens Snapgene Codon Optimization Table
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<div v-if="sections.codonTable" class="content">
<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.
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</div>
<!-- Registry Parts -->
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<h4 @click="toggleSection('registryParts')">
Registry Parts
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<div v-if="sections.registryParts" class="content">
<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.
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</div>
</div>
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<h4 @click="toggleSection('sustainableBooklet')">
Sustainable Development Booklet
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<p>
Sustainability is an integral part that is inherently integrated into our project. Given our experience in this area, Natronaut is currently developing a Sustainable Development Booklet. This booklet will share our experiences with the community, as an outline for how iGEM projects can align with global sustainability goals.
</p>
<iframe
src="https://static.igem.wiki/teams/5306/contribution/sdi-booklet-msp-maastricht24.pdf"
width="100%"
height="600px"
style="border: none;"
title="Sustainable Development Booklet"
></iframe>
</div>
</div>
<!-- Notion Organisation Template -->
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<h4 @click="toggleSection('notionTemplate')">
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.
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</div>
</div>
</div>
<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.
</p>
</div>
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// Define the XML content for the codon optimization table
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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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