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Commit d7f38fc6 authored by mablin7's avatar mablin7
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wip: engineering

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static/page.css
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......@@ -1387,3 +1387,21 @@ body {
.results-dataframe td:nth-child(3) {
font-style: italic;
}
.engineering-dbtl {
display: flex;
flex-direction: row;
gap: 2em;
}
.engineering-dbtl + .engineering-dbtl {
margin-top: 2em;
}
.engineering-dbtl .engineering-dbtl-icon {
background-position: center;
background-size: cover;
background-repeat: no-repeat;
min-width: 200px;
height: 200px;
}
wiki/pages/engineering.html
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{% extends "layout.html" %}
{% block title %}Engineering Success{% endblock %}
{% block lead %}Demonstrate engineering success in a technical aspect of your project by going through at least one iteration of the engineering design cycle. This achievement should be distinct from your Contribution for Bronze.{% endblock %}
{% extends "layout.html" %} {% block title %}Engineering Success{% endblock %}
{% block lead %}Demonstrate engineering success in a technical aspect of your
project by going through at least one iteration of the engineering design cycle.
This achievement should be distinct from your Contribution for Bronze.{%
endblock %}
<!-- page content -->
{% block page_content %}
<div class="row mt-4">
<div class="col">
<div class="bd-callout bd-callout-info">
<h4>Silver Medal Criterion #1</h4>
<p>Demonstrate engineering success in a part of your project by going through at least one iteration of the engineering design cycle. This achievement should be distinct from your Contribution for Bronze.</p>
<p>If you plan to show engineering success by creating a new Part that has been shown to work as expected, you must document your contribution on the Part's Main Page on the <a href="https://parts.igem.org/Main_Page">Registry</a> for your team to be eligible for this criteria.</p>
<hr>
<p>Please see the <a href="https://competition.igem.org/judging/medals">2024 Medals Page</a> for more information.</p>
<div class="pagecontainer">
<div class="title2">
<span>Engineering</span>
</div>
<div class="pagebody">
<div class="pagenav">
<!-- <div onclick="goTo(document.getElementById('one'))"><span id="subtitle1" style="color: #62D881;"><strong>DRY LAB</strong></span></div>
<div onclick="goTo(document.getElementById('two'))"><span id="subtitle2" style="color: #62D881;">The uTP sequence</div>
<div onclick="goTo(document.getElementById('three'))"><span id="subtitle3" style="color: #62D881;"><strong>WET LAB</strong></span></div>
<div onclick="goTo(document.getElementById('four'))"><span id="subtitle4" style="color: #62D881;">uTP expression</div>
<div onclick="goTo(document.getElementById('five'))"><span id="subtitle5" style="color: #62D881;">UCYN-A fusion</div>
<div onclick="goTo(document.getElementById('six'))"><span id="subtitle6" style="color: #62D881;"><strong>References</strong></div> -->
</div>
<div class="pagecontent">
<p>
Our iGEM project aims to develop a suitable environment for the
nitrogen-fixing organelle
<em>Candidatus Atelocyanobacterium thalassa</em> (UCYN-A) or
“nitroplast" in the model organisms
<em>​Saccharomyces cerevisiae</em> and
<em>Chlamydomonas reinhardtii</em>. To achieve this, we have divided the
project into several key engineering modules, iterating through the
design-build-test-learn cycle to refine our approach and address
challenges encountered along the way.
</p>
<div class="h" id="m-1">
<div class="h1">Dry-lab characterization of uTP sequences</div>
</div>
<div class="h" id="m1-c1">
<div class="h2">Cycle 1</div>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-1.svg');
"
></div>
<p>
The plan for finding a uTP sequence was initially based on results
from Coale et al (2024): identify the conserved C-terminal region,
find repeating motifs, and create a consensus sequence.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-2.svg');
"
></div>
<p>
The analysis and filtering code was implemented in Python and the MEME
suite (ref) was used for motif analysis.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-3.svg');
"
></div>
<p>We visualized the motifs and their co-occurrences.</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-4.svg');
"
></div>
<p>
We found that there are multiple variations in which motifs occur,
yielding different uTP variants, with some shared properties.
</p>
</div>
<div class="h" id="m1-c2">
<div class="h2">Cycle 2</div>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-1.svg');
"
></div>
<p>
We decided to test whether certain uTP variations correlate with
certain sequences.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-2.svg');
"
></div>
<p>
Machine learning classifiers were trained on the sequence data to
predict the corresponding uTP motifs from the protein’s main body.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-3.svg');
"
></div>
<p>
The classifiers were evaluated using 5-fold cross-validations and
permutation test.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-4.svg');
"
></div>
<p>
We found that 3 of the classifiers have indicated a statistically
significant correlation between protein sequences and motif
variations. We used the top classifier, Logistic Regression, to design
a uTP sequence for our fluorescent proteins.
</p>
</div>
<div class="h" id="m1-c3">
<div class="h2">Cycle 3</div>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-1.svg');
"
></div>
<p>
To evaluate the constructed fluorescent uTP proteins, we decided to
investigate their 3D structure using prediction tools.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-2.svg');
"
></div>
<p>
The structures of al uTP-containing B. bigelowii proteins and the uTP
constructs were predicted using AlphaFold 3.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-3.svg');
"
></div>
<p>
The structures were analyzed using PyMol and Python and a consensus
structure was created from the native uTP sequences to show the
structurally conserved regions.
</p>
</div>
<div class="engineering-dbtl">
<div
class="engineering-dbtl-icon"
style="
background-image: url('https://static.igem.wiki/teams/5054/dbtl-4.svg');
"
></div>
<p>
Analysis identified a region in the uTP sequences exhibiting a highly
conserved structure. The superimposition of this region onto our
construct structures demonstrated a correspondence between the two.
</p>
</div>
</div>
</div>
</div>
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