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Commit 4590e4d8 authored by Meera Bobzin's avatar Meera Bobzin
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static/style.css
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......@@ -119,6 +119,32 @@ a[href^="#ref"] { /* Styling all hyperlinks */
width: 50%;
}
}
/* Video styling */
.video-container {
position: relative;
width: 560px; /* Default size for larger screens */
max-width: 100%; /* Ensures it adapts to smaller screens */
padding-top: 56.25%; /* 16:9 aspect ratio */
margin: 0 auto; /* Center align */
overflow: hidden;
}
.video-container iframe {
position: absolute;
top: 0;
left: 0;
width: 100%;
height: 100%;
}
/* Responsive adjustments */
@media (max-width: 768px) {
.video-container {
width: 100%; /* Span the full width of smaller screens */
}
}
/* -=-=-=-=-=-=-=-= Progress bar -=-=-=-=-=-=-=-= */
#progress-bar {
position: fixed;
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wiki/pages/collaboration.html
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<div class="row mt-4" id="scavenger">
<h3 class="text-center">Protocol for Scavenger Hunt</h3>
<img src="https://static.igem.wiki/teams/5250/team/collaborations/img-03-min.jpg" alt="Scavenger hunt" class="img-fluid" style="width: 50%; display: block; margin: 0 auto; padding: top 30px;">>
<img src="https://static.igem.wiki/teams/5250/team/collaborations/img-03-min.jpg" alt="Scavenger hunt" class="img-fluid" style="width: 50%; display: block; margin: 0 auto; padding: top 30px;">
</div>
<div class="row mt-4 justify-content-center">
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wiki/pages/description.html
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......@@ -143,9 +143,11 @@
<div class="row mt-4">
<div class="col-lg-12">
<h2>Watch Our Presentation Video</h2>
<hr>
<iframe width="560" height="315" src="https://video.igem.org/videos/embed/b2a999ad-14d2-4a4e-b0cb-b9fc67681cf5" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
<h2>Watch Our Presentation Video</h2>
<hr>
<div class="video-container">
<iframe src="https://video.igem.org/videos/embed/b2a999ad-14d2-4a4e-b0cb-b9fc67681cf5" frameborder="0" allow="autoplay; encrypted-media" allowfullscreen></iframe>
</div>
</div>
</div>
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wiki/pages/experiments.html
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The positive control entails a plasmid that constitutively expresses GFP.
</p>
<p>
Before starting the actual experiment we adjusted the cultures to OD 0.01 and into each well of a 96-well plate we added 20 μl of xylose and 180 μl of our adjusted culture .
Before starting the actual experiment we adjusted the cultures to OD 0.01 and into each well of a 96-well plate we added 20 μl of xylose and 180 μl of our adjusted culture.
In order to measure the fluorescence we used a plate reader.
We tested different xylose concentrations to find the optimum and to determine the amount of xylose the plant would need to exude in order to activate our promoter: 20mM, 10mM, 5mM, 2mM, 1mM, 0.5 mM, 0.2 mM, 0.1 mM, 0.01 mM.
We used a 24-hours program to measure OD and fluorescence every 30 minutes.
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wiki/pages/model.html
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......@@ -53,8 +53,9 @@ Holmes M, et al. (2003),", "title": "Pseudomonas putida KT2440 [ppu].", "link":
"https://www.sciencedirect.com/science/article/abs/pii/S0010482523002986?via%3Dihub"},
{"names": "[20] Purtschert-Montenegro, G., Cárcamo-Oyarce G., Pinto-Carbó M., Agnoli K., Bailly A., und Eberl L.",
"title": "„Pseudomonas Putida Mediates Bacterial Killing, Biofilm Invasion and Biocontrol with a Type IVB Secretion
System“. Nature Microbiology 7, Nr. 10 (19. September 2022): 1547–57.", "link": "
https://doi.org/10.1038/s41564-022-01209-6"}
System“. Nature Microbiology 7, Nr. 10 (19. September 2022): 1547–57.", "link": "https://doi.org/10.1038/s41564-022-01209-6"},
{"names": "[21] ",
"title": "", "link": ""}
] %}
{% extends "layout_TOC.html" %}
......@@ -1142,24 +1143,23 @@ https://doi.org/10.1038/s41564-022-01209-6"}
<h2>Update</h2>
<hr>
<p>
In the time between wiki freeze and the Grand Jamboree, we continued tp work on our models and achived some
more results, which we would like to present in this section.
Between the wiki freeze and the Grand Jamboree, we continued working on our models and achieved additional results, which we present in this section.
</p>
<p>
We focused on the competition test mentioned in the <a href="#section-15" class="hyperlink-under">outlook</a> section.
As a proof of concept, we chose two models of bacteria that our bacterium would most likely be competing against and decided to use one gram positive and one gram negative.
For the gram positive we used models <i>Bacillus subtilis str. 168 </i>(iYO844) and for the gram negative <i>Xanthomonas phaseoli pv. manihotis </i>(iXpm1556).
We adapted our pre-established soil conditions to these models and looked at the biomass production.
Assuming that growth rate is a reasonable approximation of competitiveness, in the sense that a bacterium has an advantage if it can outgrow the others, we compared the levels at which the bacteria could grow biomass.
We focused on the competition test described in the <a href="#section-15" class="hyperlink-under">outlook</a> section.
As a proof of concept, we selected two GEMs of soil bacteria, a gram-positive and a gram-negative strain, that our bacterium would likely compete with in field applications.
For the gram-positive bacterium, we used <i>Bacillus subtilis</i> str. 168 and used its GEM, iYO844 <a href="#ref18">18</a>, and for the gram-negative bacterium, we chose <i>Xanthomonas phaseoli pv. manihotis </i>, using its GEM, iXpm1556<a href="#ref21">21</a>.
We adapted both models to our established soil conditions <a href="#section-11" class="hyperlink-under">in stage 3</a> and analyzed their biomass production in the given environment.
Assuming that growth rate is a reasonable proxy for competitiveness - where a bacterium gains a competitive advantage by outgrowing others - we compared their biomass production levels to those of our pre-established <i>P. putida</i> KT2440 model.
</p>
<div class="row mt-4 image-model">
<img src="https://static.igem.wiki/teams/5250/model/5-2-competitiontest-cell.webp"
alt="Dependence of Biomass Production on Cellulose Excretion in the Rhizosphere" class="img-fluid d-block mx-auto responsive-img">
<p><b>Figure 24:</b> <i>P. putida</i> KT2440 shows a metabolic competition advantage to two other soil bacteria even when producing biofilm component cellulose.</p>
<p><b>Figure 24:</b> <i>P. putida</i> KT2440 shows a metabolic competition advantage to two other soil bacteria even when producing the biofilm component cellulose.</p>
</div>
<p>
As shown in the graph, the <i>P. putida K2440</i> model outperforms both and can even be forced to produce cellulose before the cost becomes too high and the growth rate falls below that of the others.
This result is very promising, but it needs to be followed up with more such tests and verification from the wet lab.
As shown in Figure 24, the <i>P. putida </i>KT2440 model outperforms both competitors and can even be induced to produce cellulose before the cost becomes too high and the growth rate falls below that of the others.
This result is very promising, but it requires further testing and verification/validation from the wet lab.
</p>
</div>
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wiki/pages/new-basic-part.html
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<hr>
<div class="highlight">
<p>
<b>We successfully modified a diguanylate cyclase (DGC) native to <i>Pseudomonas species</i> IsoF to stop c-di-GMP from binding to the negative allosteric binding site which effectively enhanced the enzyme’s activity.</b>
<b>We modified a diguanylate cyclase (DGC) native to <i>Pseudomonas species</i> IsoF to stop c-di-GMP from binding to the negative allosteric binding site which effectively enhanced the enzyme’s activity.</b>
</p>
</div>
<p>
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<div class="row mt-0">
<div class="col">
<div class=image-model>
<p style="text-align:center;"><b>Figure 2,3:</b>Fluorescence Intensity from c-di-GMP Assay across different Strains.</p>
<p style="text-align:center;"><b>Figure 2,3:</b> Fluorescence Intensity from c-di-GMP Assay across different Strains.</p>
</div>
</div>
</div>
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wiki/pages/results.html
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wiki/pages/safety.html
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......@@ -67,7 +67,7 @@
<p>
At the current stage, the nationwide moratorium on GMOs in Switzerland would significantly complicate the field testing and application of our product<a href="#ref3">3</a>.
However, as of 2024, the longevity of this law is under discussion.
To find out more about the implications of the moratorium on our project, visit our <a href="{{ url_for('pages', page='entrepreneurship') }}" class="hyperlink-under">Implementation and Entrepreneurship page</a>.
To find out more about the implications of the moratorium on our project, visit our <a href="{{ url_for('pages', page='entrepreneurship') }}" class="hyperlink-under">Entrepreneurship and Implementation page</a>.
Regardless, our product accounts for a safe application and prevents a release beyond containment through several approaches:
</p>
</div>
......@@ -81,10 +81,10 @@
<div class="row">
<div class="col-12">
<p><b>Killswitch:</b> An important part of RhyzUp is our antitoxin-toxin based Killswitch. This part of our construct ensures the bacteria stays contained in the deliberately inoculated plant’s rhizosphere, as the survival of the bacteria is directly linked to its direct sensing of the plant roots.
To learn the specifics of our Killswitch system and how we developed and tested it visit our <a href="{{ url_for('pages', page='engineering') }}" class="hyperlink-under">Engineering page</a>.</p>
To learn the specifics of our Killswitch system and how we developed and tested it, visit our <a href="{{ url_for('pages', page='engineering') }}" class="hyperlink-under">Engineering page</a>.</p>
<p><b><i>P. sp.</i> IsoF - a rhizosphere regulator:</b> Though known for its competitiveness and ability to protect crops against pathogenic microbes, partially through active killing, our bacteria has a positive environmental impact. As RhyzUp de-deseritfies soil, it aids in the re-stabilization of a healthy rhizobiome, potentially boosting microbial diversity. These benefits would be most prevalent when implemented in controlled, closed system fields, such as greenhouses, or soils with a poor microbial diversity.
To learn more about our plans of implementation visit our<a href="{{ url_for('pages', page='entrepreneurship') }}" class="hyperlink-under"> Implementation and Entrepreneurship page</a>.</p>
To learn more about our plans of implementation visit our<a href="{{ url_for('pages', page='entrepreneurship') }}" class="hyperlink-under"> Entrepreneurship and Implementation page</a>.</p>
<p><b>Spread of antimicrobial resistances:</b> In order to stop the potential horizontal transfer of antibiotic resistance genes through our plasmid’s backbones, we plan to integrate all our parts in our chassi’s genome in the future.</p>
</div>
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We ensured sterile conditions by working under bunsen burners and laminar flow hoods.
All surfaces were routinely decontaminated with 70% ethanol and hands were periodically washed.
All waste was autoclaved according to BSL2 regulations before being disposed of appropriately.
Find more information on our safe lab techniques in our <a href="https://teams.igem.org/5250/safety/74a59fdc-35c7-4567-86fd-3bea339286b0" class="hyperlink-under">safety</a>
on our <a href="https://teams.igem.org/5250/safety/74a59fdc-35c7-4567-86fd-3bea339286b0" class="hyperlink-under">Team page</a>.
Find more information on our safe lab techniques in our <a href="https://teams.igem.org/5250/safety/74a59fdc-35c7-4567-86fd-3bea339286b0" class="hyperlink-under">safety form</a>
on our <a href="https://teams.igem.org/5250" class="hyperlink-under">Team page</a>.
</p>
</div>
</div>
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<div class="row mt-0">
<div class="col-lg-3 col-md-3 col-sm-12">
<div class="contribution-box" style="height: 550px;">
<div class="contribution-box">
<h3>Written consent</h3>
<p>
We received written, informed consent of all interviewees to record the interviews and use the material appropriately.
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</div>
</div>
<div class="col-lg-9 col-md-9 col-sm-12">
<div class="contribution-box" style="height: 550px;">
<div class="contribution-box">
<h3>Political awareness</h3>
<div class="image-description">
<img src="https://static.igem.wiki/teams/5250/project/safety/s-3-min.jpg" alt="Discussion on the topic “designer babies” at our lab workshop for highschool students" class="img-fluid d-block mx-auto responsive-img-smaller">
......@@ -183,7 +183,7 @@
<p>
As mentioned in Environmental safety, the use of GMOs and the study of synthetic biology are topics of political debate globally as well as locally in Switzerland.
We were cautious not to display any political opinions toward the matter. This applies especially to our wiki, lecture series, educational visits to schools and our lab workshop.
To find out more about the educational aspect of our project check out our<a href="{{ url_for('pages', page='parts') }}" class="hyperlink-under"> Education page</a>.
To find out more about the educational aspect of our project check out our<a href="{{ url_for('pages', page='education') }}" class="hyperlink-under"> Education page</a>.
</p>
</div>
</div>
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