From 4cf3b820e5fee58d68673f2102a05a4cd22fe622 Mon Sep 17 00:00:00 2001
From: Nathan Gillespie <crookedtwig4@gmail.com>
Date: Tue, 1 Oct 2024 21:05:47 -0700
Subject: [PATCH] Nate does stuff
---
wiki/pages/human-practices.html | 9 ++++-
wiki/pages/model.html | 72 ++++++++++++++++++++++-----------
2 files changed, 56 insertions(+), 25 deletions(-)
diff --git a/wiki/pages/human-practices.html b/wiki/pages/human-practices.html
index 5d8aad2..4db4d9f 100644
--- a/wiki/pages/human-practices.html
+++ b/wiki/pages/human-practices.html
@@ -59,10 +59,15 @@
<h2>Social media</h2>
<hr>
<p>
- Sample Text <strong>ADD ACTUAL TEXT</strong>
+ Our first post was called Astronaut DNAid. The main aim of this post was to educate the community about our project for iGEM. The post consisted of a short description of the issue we were tackling and our solution.
+ Later we posted our RBHS IGEM 2024 Human practices survey. This was because we needed more data for our survey and decided social media would be an effective outreach method.
+ Ten days later, we posted our "Goals of iGEM". We were setting our goals for iGEM this year and informing social media users about the organization as a whole.
+ Our fourth post was our pictures at SDSU in Dr. Love's lab. We posted this to advertise our club activities. It gives a good example of what we did in the lab during the summer. People can see the post as a reference to know what activities we do in IGEM.
+ Then we posted a lab overview for our team. We posted the process of our lab with brief descriptions for each step. This shows the order of the lab process with images to inform our lab process.
+ Subsequently we posted a short post of Photolyase. We posted the introduction of photolyase in order to let people know what photolyase does and how it is important to complete our lab.
+ Finally, we posted some random facts about a person's DNA. We wrote that our DNA all put together is about twice the diameter of the solar system. We thought this was interesting and educational to post it on our iGEM Instagram.
</p>
<br>
-
</div>
</div>
diff --git a/wiki/pages/model.html b/wiki/pages/model.html
index fe5453f..3d4cee7 100644
--- a/wiki/pages/model.html
+++ b/wiki/pages/model.html
@@ -6,35 +6,61 @@
{% block page_content %}
<div class="row mt-4">
- <div class="col">
- <div class="bd-callout bd-callout-info">
- <h4>Best Model</h4>
- <p>Models and computer simulations can help us understand the function and operation of BioBrick Parts and Devices. Simulation and modeling are critical engineering skills that can contribute to project design or provide a better understanding of the modeled process. These processes are even more useful and/or informative when real world data are included in the model. This award is for teams who build a model of their system and use it to inform system design or simulate expected behavior before, or in conjunction with, experiments in the wetlab.</p>
- <p>To compete for the Best Model prize, select the prize on the <a href="https://competition.igem.org/deliverables/judging-form">judging form</a> and describe your work on this page.</p>
- <hr>
- <p>Please see the <a href="https://competition.igem.org/judging/awards">2024 Awards Page</a> for more information.</p>
- </div>
+ <div class="col-lg-8">
</div>
</div>
<div class="row mt-4">
- <div class="col-lg-8">
- <h2>Overview</h2>
+ <div class="col-lg-7">
+ <h2>Introduction</h2>
<hr>
- <p>Mathematical models and computer simulations provide a great way to describe the function and operation of Parts and Devices. Synthetic Biology is an engineering discipline, and part of engineering is simulation and modeling to determine the behavior of your design before you build it. Designing and simulating can be iterated many times in a computer before moving to the lab.</p>
- </div>
- <div class="col-lg-4">
- <h2>Inspirations</h2>
+ <p>
+ Our plan is to use the Michaelis-Menten (MM) equation to model the kinetics of the photoenzymatic repair of UV-induced pyrimidine dimers in E. coli. By understanding the reaction rate constants and enzyme kinetics, we aim to quantify the efficiency of photolyase in repairing DNA damage. This serves as a foundational model for further investigating DNA repair mechanisms under UV stress, and we were particularly helped most by lower-bound rate constants available from existing literature.
+ </p>
+ <h2>Methods</h2>
+ <hr>
+ <p>
+ To construct our model, we employ data from both the papers blah blah. Specifically, we use the Michaelis-Menten equation:
+ Vmax=k3×[enzyme concentration] = MIT PAPER
+ where:
+ <ul>
+ <li>kâ‚ = 1.1 × 10ⶠMâ»Â¹sâ»Â¹: rate at which photolyase combines with pyrimidine dimers to form an enzyme-substrate complex</li>
+ <li>â‚‚ = 1.9 × 10â»Â³ sâ»Â¹: the rate of dissociation of the enzyme-substrate complex into photolyase and pyrimidine dimers</li>
+ <li>k₃ = 10³ sâ»Â¹: the rate of photolyase catalysis (also equal to k_pI) for UV lesion repair.</li>
+ </ul>
+ We modeled the repair process by assuming Michaelis-Menten kinetics, taking into account these lower-bound values for K_m, k₃, and k₂. The substrate in our model is pyrimidine dimers, and enzyme concentrations were chosen based on available literature.
+ </p>
+ <h2>Results and Analysis</h2>
<hr>
- <ul>
- <li><a href="http://2018.igem.org/Team:GreatBay_China/Model">2018 GreatBay China</a></li>
- <li><a href="http://2018.igem.org/Team:Leiden/Model">2018 Leiden</a></li>
- <li><a href="https://2019.igem.org/Team:IISER_Kolkata/Model">2019 IISER Kolkata</a></li>
- <li><a href="https://2019.igem.org/Team:Exeter/Model">2019 Exeter</a></li>
- <li><a href="https://2019.igem.org/Team:Mingdao/Model">2019 Mingdao</a></li>
- <li><a href="https://2020.igem.org/Team:Harvard/Model">2020 Harvard</a></li>
- <li><a href="https://2020.igem.org/Team:Leiden/Model">2020 Leiden</a></li>
- </ul>
+ <p>
+ The figures illustrate how the rate of DNA repair varies with different enzyme concentrations and UV damage levels. Following typical Michaelis-Menten behavior, these figures should show the expected hyperbolic relationship between substrate concentration and repair rate. We should see that photolyase operates efficiently at normal physiological concentrations and that the lower-bound rate constants used still provide realistic repair rates.
+ Our calculations of K<sub>m</sub> and V<sub>max</sub> allow us to predict the behavior of photolyase under varying conditions, giving insight into how effective photolyase can be in repairing DNA lesions under specific UV exposures. We need to talk more about the assumptions and the impact of those here too.
+ </p>
+ <h2>Future Implementations</h2>
+ <hr>
+ <p>
+ This model can be extended to calculate the effects of photolyase in various biological and environmental conditions. Refining the model with more specific data on enzyme concentrations and substrate types can be used to:
+ <br>
+ <ul>
+ <li>Predict photolyase activity in other organisms or cellular environments.</li>
+ <li>Investigate repair kinetics for other UV-induced lesions like 6-4 photoproducts.</li>
+ <li>Explore how environmental factors like light intensity and temperature impact DNA repair.</li>
+ </ul>
+ Additionally, this model serves as a proof of concept for general photolyase mechanisms, providing a foundation for future experimental validation and refinements.
+
+ </p>
+ <h2>Conclusion</h2>
+ <hr>
+ <p>
+ Our current model using Michaelis-Menten kinetics provides a basic framework for studying photolyase activity and DNA repair efficiency. Since lower-bound estimates from multiple sources were used for critical parameters, the model's predictive capability can be enhanced by incorporating more accurate measurements from more integrated and recent studies. This is a solid first step to further exploring photolyase DNA repair mechanisms and their potential applications in biotechnology and medicine.
+ </p>
+ </div>
+ <div class="col-lg-5">
+ <img src="https://static.igem.wiki/teams/5135/images/modeling1.png" width="100%">
+ <br>
+ <img src="https://static.igem.wiki/teams/5135/images/modeling2.png" width="100%">
+ <br>
+ <img src="https://static.igem.wiki/teams/5135/images/modeling3.png" width="100%">
</div>
</div>
--
GitLab