Team:Slovenia/PROJECT/practice

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<div id="naslov">introduction</div>
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<div id="naslov">human practice</div>
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<h2 style="font-size:145%">Human practice - how to increase the public awareness of synthetic biology</h2>
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<p>&nbsp;</p>
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The most obvious problem of placing the synthetic biology into a societal context is that most people are just not aware of it. While this is common to most fields of science, people are more aware of the end products of the technology that are used to improve the quality of life. We were discussing what could improve the awareness of synthetic biology in public and come up with the list of the following most important factors.<br><br>
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<p><span style="font-size: 20px; line-height: 25px;">DNA as the program</span></p>
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<p>&nbsp;</p>
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As DNA molecule is so extensively characterized, being sort of a pop culture molecule, finding a completely novel way of using it presents quite a challenge. DNA is the basic linear carrier of information and we thought that it could represent an ideal scaffold for information processing.&nbsp;Instead of seeing DNA in a traditional way, where triplet codons guide the ribosome to incorporate a defined sequence of amino acids into a newly formed protein, we envisioned a completely new way of coding the information using DNA scaffold. Instead of triplets, binding sites for different DNA-binding proteins could be used as functional units. For example, we can select blocks of nine nucleotides that act as the sites for binding different DNA-binding proteins.
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<p>&nbsp;</p>
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<p><span style="font-size: 20px; line-height: 25px;">Outline of the idea </span></p>
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<p>&nbsp;</p>
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How does this idea work? DNA sequence represents a program consisting of a series of blocks which determine the arrangement of DNA binding factors along the DNA. The main twist comes with the requirement that each of those DNA-binding proteins is fused to a different functional protein. Therefore, the sequence of target motifs encoded by DNA program defines also the arrangement of those functional proteins along with the order of DNA-binding factors. What is so powerful about this idea is the fact that by only changing the sequence of a DNA program, either switching positions or adding new target sequences, the outcome can be predicted in advance.
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<p>&nbsp;</p>
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<p>&nbsp;</p>
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<p><span style="font-size: 20px; line-height: 25px;">Expansion of the number of tools for synthetic biology </span></p>
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While there are 64 nucleotide triplets that in the nature code for 20 aminoacids, there could be as many as 262,144 different motifs consisting of nine nucleotides. Zinc-fingers and TAL elements can be&nbsp;designed to bind to almost any desired nucleotide sequence ranging from 9 to as many as 18 nucleotides. While this is sometimes a laborious process we don&rsquo;t really need to do this. We can reverse the problem and select the target nucleotide sequence for each available DNA-binding factor. There are more than 700 experimentally determined zinc fingers in the database ZIFDB, offering a huge choice of tools for synthetic biology. Moreover zinc fingers have similar properties, such as binding affinity or stability, which is important since we don&rsquo;t need to adjust properties of each separate part. DNA program therefore represents a modular approach for various synthetic biology applications. This could be an important step towards moving the synthetic biology from being a craft of tinkering peculiar biological elements towards becoming a truly engineering science. At the moment there is only one experimentally verified repressilator composed of three specific bacterial transcription factors, meaning a bacterial device that can count to three. Using the available natural elements those devices can never be extended above 5 or maximally 10 naturally available elements. Our approach therefore represents a completely new perspective of synthetic biology.
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<p><span style="font-size: 20px; line-height: 25px;">Applications of DNA-guided programming</span></p>
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What could be the specific implementations of this idea?
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<p style="margin-left: 48px;">1.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; The first big application is to use the DNA program <strong>to arrange the sequence of biosynthetic reaction enzymes</strong> and therefore guide the biosynthetic flow towards the desired products. We decided to test this idea on a previously characterized biosynthetic pathway, demonstrating the advantages of DNA programming. One important advantage is to increase the reaction rate of the overall biosynthetic pathway but it can also guide the biosynthetic flow towards one or other product and prevent side reactions. We have demonstrated both effects on the biosynthesis of violacein, a five step reaction, which can, by the addition of enzymes, yield three different products. This approach offers several potential advantages in comparison to protein-based scaffolds.</p>
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<p>&nbsp;</p>
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<p style="margin-left: 48px;">2.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; We can also envision the use of this approach to <strong>perform information processing</strong> that offers many advantages over traditional genetic switches, as the flow of information can be restricted to the reactions occurring along the linear DNA instead of throughout the cell. Attachment of the cascade of proteases, phosphatases or other enzymes/protein interaction domains to the DNA scaffold could result in a rapid information processing depending on the input of particular DNA sequence and initiation reaction.</p>
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<p>&nbsp;</p>
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<p style="margin-left: 48px;">3.&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; Another application of the same principle is to use DNA-binding factors to <strong>extend and simplify the construction of oscillators</strong>. Modeling two different types of oscillators indicates that the use of synthetic DNA-binding proteins can provide tools to prepare orthogonal oscillators for both prokaryotic and eukaryotic cells, add new features to increase the robustness and independence of stochastic initial conditions and increase the selection of their frequency. For this purpose the basic type of building block was demonstrated to function in mammalian cells.</p>
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<p>&nbsp;</p>
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<p><span style="font-size: 20px; line-height: 25px;">Conclusions</span></p>
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It can be said that our project has shuffled the way DNA is seen and regarded in the field of synthetic biology, meaning this view will never be the same again. To conclude, the perspective of sequential ordering of functional fusion proteins on a DNA scaffold ''on demand'', could soon lead into novel computer-biotech hybrid science, changing fundamental paradigms of both fields, employing engineering principles of synthetic biology in highly predictive fashion using DNA program.
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<p>&nbsp;</p>
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<li>The best promotion of synthetic biology are '''success stories'''. If synthetic biology can be used to solve important problems of the humanity (health, energy, environment), its public awareness will definitely increase. </li>
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<li>Make it '''exciting and interesting''' (approaching the solution of a problem from a fresh perspective rather than with brute force). Here is where iGEM comes to stage as the playground for new and inventive ideas in synthetic biology.</li>
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<li>'''Explain it simply''', so that your grandmother understands it and your little brother will keep attention. Science is complex and we need to have some understanding of basic concepts, but is it really impossible to explain an idea to be comprehensible to nonspecialists ?</li>
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<li>Crossing borders between disciplines.</li>
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We believe that our project may lead to real world applications that could lead to technological solutions and improvement of the quality of life, therefore we are working towards the success story.
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We certainly feel that our project, as many other iGEM projects, bring innovative and fresh perspectives that stimulate thinking &ldquo;out of the box&rdquo;.
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Those conclusions led us to prepare the presentation of our project in &raquo;plain english&laquo; and tested it on our grandmothers (and grandfathers, aunts, nieces...). Perhaps they just wanted to be kind to their grandchildren but they said they understood it. You should judge for yourself. <br><br>
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<h2>Our project in plain english</h2>
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<center><object width="443" height="370"><param name="movie" value="http://www.youtube.com/v/jVA6qS8YPgg?fs=1&amp;hl=sl_SI"></param><param name="allowFullScreen" value="true"></param><param name="allowscriptaccess" value="always"></param><embed src="http://www.youtube.com/v/jVA6qS8YPgg?fs=1&amp;hl=sl_SI" type="application/x-shockwave-flash" allowscriptaccess="always" allowfullscreen="true" width="443" height="370"></embed></object></center>
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<h2>DNA Explorer board game</h2>
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What is the best way to learn new things? When you are having fun! That is why we also created a game in which anybody can learn about synthetic biology through a game. '''DNA explorer''' is a board game with elements from our project, BioBrick system and DNA in general, with a goal to introduce the field of synthetic biology to general public, break the stereotype of science being boring and with some luck inspire future iGEM participants. So grab a dice and start playing!<br>
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<center><a href="https://static.igem.org/mediawiki/2010/1/17/SLO_boardgame_A3.pdf"><img src="https://static.igem.org/mediawiki/2010/c/c8/SLO_icon_DNA_explorer.png"></a></center>
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<center><a href="https://static.igem.org/mediawiki/2010/e/e0/SLO_boardgame_A4.pdf">(A4 format version)</a></center>
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Reviews from high school students, who volunteered to try out our board game:<br>
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"DNA explorer is an amazing game. I love it because I had fun and learned a lot at the same time!"<br>
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"I really like this game because I learned so much without even realizing it."<br>
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"DNA explorer is such a great game because it sums up everything an average person should know about DNA. But unlike school books it does this in a fun and interesting way."<br>
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"DNA explorer is a game which has helped me to understand the world of synthetic biology a lot better. It is fun and educational but more importantly it is simple. I believe that many schools could benefit from using this game because it explains things that are difficult to understand for children in a simple and fun way."
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<br><br>
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This year, four students of computer sciences were also included in the team. This is their story.
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'''Students of computer science and the beginning of their journey in the world of synthetic biology:'''
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<br><br>
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"Four poor students were brought from the world of zeros and ones to the world of proteins and DNA. Those students only heard rumors that in synthetic biology bugs are good. We joined the iGEM Team Slovenia in search of an insight of this universe, because we are aware that the not so distant future of computer science will inevitably be built with BioBricks. The summer of 2010 ended and we are now convinced that these parallel universes are closer than they appear. After all these months our lab skills may still be on a waterboy/girl level, but we can now tell our colleagues of a house they/we will some day live in. The walls of that house are being built with BioBricks."
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'''Bio aspect on the cooperation with computer part of the team'''
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Bridging sciences has always been a great challenge. Nowadays interdisciplinarity, despite this term being a little cliche, is somewhat encoded into the minds of the scientists almost by default.
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When starting this years iGEM project, student members of the biological part of the team didn't know excatly where to put the enthusiastic team colleagues from the computer science and how this cooperation will proceed. To put it differently, the project at its roots and the idea behind it undoubtedly promised interwinding both disciplines, but this was not that clear at the moment. It is something we agreed on after the project. Nevertheless, both parts of the team were demanding and curious enough to have a tip of each others study fields in order to break the ''bridge'' between the sciences. Eventhough, it was a great challenge to find a common path which ultimately unified both parts of the team beyond the scope of our expectations. We were enrolled in every day cooperation in order to improve their understanding of fundamental properties of biological system functioning as well as our understanding of what modelling is all about. We were therefore encouraged by them to get involved into their work, as well as they had to approach us in order to get the real life data, needed for their model to function properly and as realistically as possible. We considered and still consider this kind of cooperation extremely beneficial and by observing how our project was actually supported by the modelling outcomes, we can conclude it is of extreme importance to select forecoming teams as interwinding as this years'. Synthetic biology is definetely a place for such scientific overlaps.
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Latest revision as of 00:16, 28 October 2010

Chuck Norris facts:

human practice

Contents


Human practice - how to increase the public awareness of synthetic biology

The most obvious problem of placing the synthetic biology into a societal context is that most people are just not aware of it. While this is common to most fields of science, people are more aware of the end products of the technology that are used to improve the quality of life. We were discussing what could improve the awareness of synthetic biology in public and come up with the list of the following most important factors.

  • The best promotion of synthetic biology are success stories. If synthetic biology can be used to solve important problems of the humanity (health, energy, environment), its public awareness will definitely increase.
  • Make it exciting and interesting (approaching the solution of a problem from a fresh perspective rather than with brute force). Here is where iGEM comes to stage as the playground for new and inventive ideas in synthetic biology.
  • Explain it simply, so that your grandmother understands it and your little brother will keep attention. Science is complex and we need to have some understanding of basic concepts, but is it really impossible to explain an idea to be comprehensible to nonspecialists ?
  • Crossing borders between disciplines.


We believe that our project may lead to real world applications that could lead to technological solutions and improvement of the quality of life, therefore we are working towards the success story.

We certainly feel that our project, as many other iGEM projects, bring innovative and fresh perspectives that stimulate thinking “out of the box”.

Those conclusions led us to prepare the presentation of our project in »plain english« and tested it on our grandmothers (and grandfathers, aunts, nieces...). Perhaps they just wanted to be kind to their grandchildren but they said they understood it. You should judge for yourself.

Our project in plain english



DNA Explorer board game

What is the best way to learn new things? When you are having fun! That is why we also created a game in which anybody can learn about synthetic biology through a game. DNA explorer is a board game with elements from our project, BioBrick system and DNA in general, with a goal to introduce the field of synthetic biology to general public, break the stereotype of science being boring and with some luck inspire future iGEM participants. So grab a dice and start playing!

(A4 format version)

Reviews from high school students, who volunteered to try out our board game:
"DNA explorer is an amazing game. I love it because I had fun and learned a lot at the same time!"
"I really like this game because I learned so much without even realizing it."
"DNA explorer is such a great game because it sums up everything an average person should know about DNA. But unlike school books it does this in a fun and interesting way."
"DNA explorer is a game which has helped me to understand the world of synthetic biology a lot better. It is fun and educational but more importantly it is simple. I believe that many schools could benefit from using this game because it explains things that are difficult to understand for children in a simple and fun way."

This year, four students of computer sciences were also included in the team. This is their story.
Students of computer science and the beginning of their journey in the world of synthetic biology:

"Four poor students were brought from the world of zeros and ones to the world of proteins and DNA. Those students only heard rumors that in synthetic biology bugs are good. We joined the iGEM Team Slovenia in search of an insight of this universe, because we are aware that the not so distant future of computer science will inevitably be built with BioBricks. The summer of 2010 ended and we are now convinced that these parallel universes are closer than they appear. After all these months our lab skills may still be on a waterboy/girl level, but we can now tell our colleagues of a house they/we will some day live in. The walls of that house are being built with BioBricks."


Bio aspect on the cooperation with computer part of the team


Bridging sciences has always been a great challenge. Nowadays interdisciplinarity, despite this term being a little cliche, is somewhat encoded into the minds of the scientists almost by default.

When starting this years iGEM project, student members of the biological part of the team didn't know excatly where to put the enthusiastic team colleagues from the computer science and how this cooperation will proceed. To put it differently, the project at its roots and the idea behind it undoubtedly promised interwinding both disciplines, but this was not that clear at the moment. It is something we agreed on after the project. Nevertheless, both parts of the team were demanding and curious enough to have a tip of each others study fields in order to break the bridge between the sciences. Eventhough, it was a great challenge to find a common path which ultimately unified both parts of the team beyond the scope of our expectations. We were enrolled in every day cooperation in order to improve their understanding of fundamental properties of biological system functioning as well as our understanding of what modelling is all about. We were therefore encouraged by them to get involved into their work, as well as they had to approach us in order to get the real life data, needed for their model to function properly and as realistically as possible. We considered and still consider this kind of cooperation extremely beneficial and by observing how our project was actually supported by the modelling outcomes, we can conclude it is of extreme importance to select forecoming teams as interwinding as this years'. Synthetic biology is definetely a place for such scientific overlaps.


Retrieved from "http://2010.igem.org/Team:Slovenia/PROJECT/practice"