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Commit 80565b6a authored by Anurag Sarkar's avatar Anurag Sarkar
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Merge branch 'main' of https://gitlab.igem.org/2024/iisc-bengaluru

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<a href="{{ url_for('pages', page='notebook') }}">Notebook</a><br>
<a href="{{ url_for('pages', page='description') }}">Description</a><br>
<a href="{{ url_for('bloglist') }}">Blogs</a><br>
<a href="{{ url_for('pages', page='human-practices') }}">Human Practices</a><br>
<a href="{{ url_for('pages', page='ihp') }}">IHP</a><br>
</div>
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wiki/menu.html
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<li><a class="dropdown-item" href="{{ url_for('pages', page='contribution') }}">Contribution</a></li>
<li><a class="dropdown-item" href="{{ url_for('pages', page='description') }}">Description</a></li>
<li><a class="dropdown-item" href="{{ url_for('pages', page='engineering') }}">Engineering</a></li>
</ul>
</li>
<!-- WET LAB -->
<li class="nav-item dropdown"></li>
<a class="nav-link dropdown-toggle" href="#" id="navbarDropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
Wet Lab
</a>
<ul class="dropdown-menu" aria-labelledby="navbarDropdown">
<li><a class="dropdown-item" href="{{ url_for('pages', page='experiments') }}">Experiments</a></li>
<li><a class="dropdown-item" href="{{ url_for('pages', page='notebook') }}">Notebook</a></li>
<li><a class="dropdown-item" href="{{ url_for('pages', page='results') }}">Results</a></li>
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<li><a class="dropdown-item" href="{{ url_for('pages', page='partcollection') }}">Best Part Collection</a></li>
</ul>
</li>
</ul>
</div>
</div>
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wiki/pages/attributions.html
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{% block lead %}In the iGEM Competition, we celebrate student effort and achievement. The Attributions form helps the judges differentiate between what students accomplished from how their external collaborators supported them. Therefore, teams must clearly explain on the standard Project Attributions form what work they have conducted by themselves and what has been done by others.{% endblock %}
{% block page_content %}
<div>
<h1 class="text-center padding">
Content will be updated soon,<br> Check back later!
<style>
p {
text-align: justify;
}
</style>
<div class="col-8">
<h1 class="text-center padding display-4">
From Genesis, till now
</h1>
<h5 class="text-center">by Subhanan Banarjee, Team Leader, iGEM IISc-Bengaluru</h5>
<hr>
<p class="padding">
It was by a mere coincidence that I came across a completely new thing in the field of biology,
just by picking a random book from our Institute library: Electrochemical Biosensors by Sergei Cosnier.
It was no sooner that the book opened the versatile interdisciplinarity of applied biology on my desk.
I read the word ‘Aptamer’ for the first time in a chapter that showed how it has been used as a probe in
electrochemical biosensors, how such molecules are synthesized and why they are strange in their ways. A
thing that immediately caught my eyes was that Aptamers have the elevated property of structural
selectivity, although they are less affine than antibodies. I was now in search of a field to apply the
‘exalted Aptamers’.
</p>
<p class="padding">
In the meantime, there was the buzz in the Institute of starting the ideation for the next iGEM cycle
and so were the newcomers now being encouraged to take a step towards being Scientists. Everyone started
making small groups of likely minds, proposing ideas, debating them, dreaming of them and so on. And so
were we, a group of three: me, Suvam and Arjun. Long held talks across the classes and messes revealed
our common interest in prion diseases. We certainly were more interested in the replication of Prions;
How could that even happen sans a genome? We were spending lots of times in the library, across Nature
and Springer or perhaps in search of a book that has all resolutions. It was the 1st of October, a
bright day in Bangalore, we found a book that had a lot to offer… Prion Biology by Stanley B. Prusiner.
It was a fallen wealth from Heaven! We learned a new thing, that some misfolded proteins can misfold
their normal versions; mathematically, this is equivalent to regeneration. That’s beautiful! We got the
key!
</p>
<p class="padding">
We had a clear version now, of how Aptamer can have a role in a field that we feared and loved too.
‘Aptamer Technology for Prion diseases’ – Doesn’t that sound revolutionary? We met Prof Varadarajan
to tell our idea, he was highly welcome and just said, ‘You never know unless you try’ Truly speaking,
iGEM was still an excuse for us, for brainstorming and intellectual discussions above academics.
A. P. J. Abdul Kalam’s quote, ‘Dream with closed eyes and fulfil them when you wake’, so now was the
second part. We must establish this now, this was not the part of science, something else, an exercise
of our characters. So, our seniors started hearing us in presentations on Sunday nights. We also had a
few other ideas like ‘Pathophysiology of auto-Erythrocytic sensitisation’ and ‘Increasing drug effectivity
at Lower Concentration by localised adsorption’. Well, the latter also could involve Aptamers, but we
loved the main idea. I remember disappointing my roommate once due to meeting in my room, that was funny,
now but a good memory. It was that Autumn evening that Suvam proposed that why not we span it across
other such conditions arising from misfolding of a protein? Now, a new challenge, what are such conditions?
</p>
<p class="padding">
In gradual pace, we found that Alzheimer’s, Parkinson’s, Huntington etc are all real-world examples.
In fact, most neurodegenerative diseases are because of protein misfolding oriented cascades! We wanted
to believe that Aptamers can be solution to all of them but were sceptical enough, we understand now
that’s how science works. We realised that doing experiments with Prion sis a bit impractical for us,
so we kept it for another day.
</p>
<p class="padding">
Then came the winter, homecoming season for most of us. Suvam made an WhatsApp group and christened
it ‘Misfolded Folks’!
</p>
<p class="padding">
The second semester was perhaps a bit filled one, due to optional subjects, assignments, quizzes and
exams. So, our frequency of meeting was a bit less now. It was on a Sunday night after meeting the
seniors I remember that I spoke to Anurag, who was by then in another team with Avani and just preceded
the moment speaking about Alzheimer’s theranostics. I said like a salesperson ‘You may like to use Aptamers’.
That was the birth of a new collaboration and slowly the two teams became one (Unification of Germany!).
We now wanted to select any one disease as a model… So, we distributed the diseases among us! Suvam was
on Parkinson’s, Manya who had recently joined our team was on Huntington’s, Anurag and Avani were on
Amyotrophic Lateral Sclerosis (ALS), Arjun on Alzheimer’s and I was on Tauopathies in general.
We figured out! Tau phosphorylation had something to do with the misfolding and we were clear we
wanted to use it as a Biomarker. We met Prof Muddashetty from the Centre of Brain Research and
realised that we may have a solution but with yet got posed with another challenge: Tau phosphorylations
leads to misfolding and the cascade of neurodegeneration but are highly variable. He said that it is
only the average phosphorylation that increases up to 8 and is still not well established. Statistics!
Now we understand why statistical physics was developed, macroscopic properties are oftentimes more
reliable than individualised properties.
</p>
<p class="padding">
This was February, and we were heading to decide a team representing the Institute. But how could it
be done unbiased and well-spirited? There were two major groups now, us and Parth’s. Parth’s team was
initially working on strategies for Diabetes control using some genetic modifications. Suvam proposed a
panel consisting of our iGEM experienced seniors and an anonymous voting after successive presentation.
I heard Parth’s idea that day, properly and completely and realised it was as good if not better. It was
completely something else than expected. The seniors stepped back from choosing! I personally, who was
thinking Parth as a competitor, was stunned when he joined hands with us happily on his own. Now, there
was one single team, unified with science, bonded with dreams.
</p>
<p class="padding">
The team had to get the coordinators and leader and that’s why the experience in the cycle wasn’t only
of a scientific rollercoaster. The team voted me as the Team Leader and Suvam as the co-Team Leader.
From administering a team to facing the issues with the administration, it was all like the lines of a
bildungsroman novel.
</p>
<p class="padding">
The intermittently worked day and night to resolve the flaws in the idea, checked with professor
Varadarajan and Muddashetty frequently. Our PI, Prof Deepak gave us the contact of a few experienced
researchers on the relevant field at the Brigham and Women’s Hospital; Dr Nagendran, Dr Lei Liu and
Dr Jean-Pierre Bellier. We obtained lots of prospects from them.
</p>
<p class="padding">
During the summer, everyone went to some lab or the other for training and internship. It was too,
an exercise of balancing all your interests after all… We met every week during this time, planned
the experiments and ordered the materials. Well, after all when the wet lab started, we faced several
issues and failures. But that’s a part of life, right? Trying our best is the only thing we have in our
hands. The semester also started by then. I remember how hard Suvam used to work in the labs, he really
sacrificed a bounty of sleep. Nevertheless, we still had a lot of fun… We oftentimes met in front of
the main building of IISc, which is itself an inspiration that helped us keep going. And I remember,
on one such meeting Avani ordered a huge pack of ice cream and we all shared from the same. We never
realised when a team crafted for a motive, slowly transformed into a group of friends, where each one
was a peculiar character: Parth the teacher, Suvam the happy-go-lucky guy, Anurag the chemi-passionate,
Manya the reserved lady, Avani the bold girl, Arjun the innocent, Anushka the illustrator, Geeth with the
distinctive accent, Harish who laughs more than he speaks, Shouvik the Neuroscientist and many more…
</p>
<hr>
<div style="height: 5rem;"></div>
</div>
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{% extends "layout.html" %}
{% block title %}iHP{% endblock %}
{% block lead %}Integrated Human Practices of iGEM IISc-Bengaluru{% endblock %}
{% 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>
</div>
<div class="row mt-4">
<div class="col-lg-8">
<h2>Overview</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>
<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>
</div>
</div> -->
{% endblock %}
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