Difference between revisions of "Team:BioIQS-Barcelona/Public Engagement"

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                 <h2 class="section-heading orange">Publication in the News AIQS Magazine</h2>
 
                 <h2 class="section-heading orange">Publication in the News AIQS Magazine</h2>
 
                 <div class="col-md-auto">
 
                 <div class="col-md-auto">
                     <h4 class="book orange block-sept comas">We had the opportunity to announce our project to the IQS
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                     <h4 class="book orange block-sept comas" id="eliminateOverflowcommas">We had the opportunity to present our project to the IQS
                         Alumni Association in an interview that was published on the News AIQS magazine in October
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                         Alumni Association in an interview that was published on the News AIQS magazine in September
 
                         2018. Being present in the newspapers brings us the opportunity to reach more people.</h4>
 
                         2018. Being present in the newspapers brings us the opportunity to reach more people.</h4>
 
                 </div>
 
                 </div>
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                         <p class="book orange">We baked around fifty cakes, most of them gluten-free, for demonstrating
 
                         <p class="book orange">We baked around fifty cakes, most of them gluten-free, for demonstrating
 
                             that life without gluten is pretty tasty.</p>
 
                             that life without gluten is pretty tasty.</p>
                         <p class="book orange">During two days we sold cakes, cookies, and candies at the entry hall of
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                         <p class="book orange">During two days we sold cakes, cookies and candies at the entry hall of
 
                             our university. We also made a challenge that consisted of eating two pieces of cakes, one
 
                             our university. We also made a challenge that consisted of eating two pieces of cakes, one
 
                             with gluten and the other one gluten-free, and students had to guess which one was suitable
 
                             with gluten and the other one gluten-free, and students had to guess which one was suitable
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                     </div>
 
                     </div>
 
                     <div class="col-md-6 left center">
 
                     <div class="col-md-6 left center">
                         <p class="book orange">We had the occasion to share our iGEM experience with undergraduate
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                         <p class="book orange">We had the opportunity to share our iGEM experience with undergraduate
                             students of Biotechnology, Chemistry and Bioengineering from IQS. We explained how is to
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                             students of Biotechnology, Chemistry, and Bioengineering from IQS. We explained the satisfactions and struggles found when
                             start a project from scratch, how important it is to work together as a team, all the
+
                             starting one project from scratch, how important it is to work together as a team, all the
 
                             achievements, the new skills we have acquired and everything that we have learn from this
 
                             achievements, the new skills we have acquired and everything that we have learn from this
 
                             project.</p>
 
                             project.</p>
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                     <div class="col-md-6 right">
 
                     <div class="col-md-6 right">
 
                         <p class="book orange">During the divulgation sessions in which we explained our personalized
 
                         <p class="book orange">During the divulgation sessions in which we explained our personalized
                             sensor project we noticed that many people was surprised by the fact that the sensor would
+
                             sensor project, we noticed that many people were surprised by the fact that the sensor would
                             be build upon their DNA sequence.</p>
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                             be built upon their DNA sequence.</p>
 
                     </div>
 
                     </div>
 
                     <div class="col-md-6 left">
 
                     <div class="col-md-6 left">
 
                         <p class="book orange">As we decided to keep the focus of our education and public engagement
 
                         <p class="book orange">As we decided to keep the focus of our education and public engagement
 
                             activities on the necessities of the people who participated in it, we realized that we
 
                             activities on the necessities of the people who participated in it, we realized that we
                             could do some kind of workshop to let to know the information storage capability of DNA.
+
                             could do some kind of workshop to let them know the information storage capability of DNA.
 
                             This is how the DNA information storage workshop was born.</p>
 
                             This is how the DNA information storage workshop was born.</p>
 
                     </div>
 
                     </div>
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                                         way, everyone without biology or computation* knowledge could also imagine the
 
                                         way, everyone without biology or computation* knowledge could also imagine the
 
                                         quantity of information.</p>
 
                                         quantity of information.</p>
                                     <p class="orange block-sept">*(sometimes the quantity of DNA information it is
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                                     <p class="orange block-sept">*(sometimes the quantity of DNA information is
                                         expressed in bytes, which is not suitable for general population, especially
+
                                         expressed in bytes, which is not suitable for the general population, especially
                                         older people) It turns out that a normal somatic human female cell has 2
+
                                         older people). It turns out that a normal somatic human female cell has 2
 
                                         dotations of 23 chromosomes (including 2 X sex chromosomes) and mitochondrial
 
                                         dotations of 23 chromosomes (including 2 X sex chromosomes) and mitochondrial
 
                                         DNA. This is a total of two times 3,088,286,401 base pairs, according to the
 
                                         DNA. This is a total of two times 3,088,286,401 base pairs, according to the
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                                         pairs written on it. Therefore, to write all the information stored in the base
 
                                         pairs written on it. Therefore, to write all the information stored in the base
 
                                         pairs of the genome of a single human cell it would be needed to print
 
                                         pairs of the genome of a single human cell it would be needed to print
                                         2,186,117 pages on one face. If this pages are then piled up to form a tower
+
                                         2,186,117 pages on one face. If these pages are then piled up to form a tower
 
                                         (considering the height of a single paper is 0.1mm), it would be 218.61 meters
 
                                         (considering the height of a single paper is 0.1mm), it would be 218.61 meters
 
                                         tall (717.2 ft)! Just between the Agbar Tower (the taller building in our city,
 
                                         tall (717.2 ft)! Just between the Agbar Tower (the taller building in our city,
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                                         microbiota). So...to write all the information condensed in the DNA of one
 
                                         microbiota). So...to write all the information condensed in the DNA of one
 
                                         human body it would take a large amount of DINA-4 papers. This amount is so
 
                                         human body it would take a large amount of DINA-4 papers. This amount is so
                                         huge that if the papers were arranged in a straight line, light would spend
+
                                         huge that if the papers were arranged in a straight line, the light would spend
                                         2553 years traveling from one end to the other. This is 2553 light years long!
+
                                         2553 years traveling from one end to the other. This is 2553 light-years long!
                                         Keep in mind that the distance from sun to earth is just 8.3 light minutes, so
+
                                         Keep in mind that the distance from the sun to the earth is just 8.3 light-minutes, so
 
                                         imagine the amount of data stored in such a low volume like your body.</p>
 
                                         imagine the amount of data stored in such a low volume like your body.</p>
                                     <p class="orange block-sept">Using this examples, general population can easily
+
                                     <p class="orange block-sept">Using these examples, the general population can easily
 
                                         understand the information storage capability of DNA. Nearly everyone
 
                                         understand the information storage capability of DNA. Nearly everyone
 
                                         (including ourselves) was pretty amazed to realize how much information human
 
                                         (including ourselves) was pretty amazed to realize how much information human
 
                                         bodies contain stored in DNA. After this examples, we explained that our sensor
 
                                         bodies contain stored in DNA. After this examples, we explained that our sensor
 
                                         was based on a piece of information stored in two genes of the DNA. So this
 
                                         was based on a piece of information stored in two genes of the DNA. So this
                                         comparisons helped general population to understand that DNA contains many
+
                                         comparisons helped the general population to understand that DNA contains much
 
                                         useful information, which is different between us and that we can extract this
 
                                         useful information, which is different between us and that we can extract this
 
                                         information to create a personalized product. This helped us to explain the DNA
 
                                         information to create a personalized product. This helped us to explain the DNA
                                         extraction and PCR process of our project to general population. This way, they
+
                                         extraction and PCR process of our project to the general population. This way, they
 
                                         are much better informed about the project and can have an opinion about it.
 
                                         are much better informed about the project and can have an opinion about it.
 
                                         Then, we integrated that informed opinion from the general population in the
 
                                         Then, we integrated that informed opinion from the general population in the
 
                                         design of our project. Dedicating effort in explaining the projects in a simple
 
                                         design of our project. Dedicating effort in explaining the projects in a simple
 
                                         but rigorous way can help teams to receive feedback from the target population.
 
                                         but rigorous way can help teams to receive feedback from the target population.
                                         This feedback can be incorporated in the design of the project and hence make
+
                                         This feedback can be incorporated into the design of the project and hence make
 
                                         it more suitable for the real world.</p>
 
                                         it more suitable for the real world.</p>
 
                                 </div>
 
                                 </div>
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                                 <div class="card-body">
 
                                 <div class="card-body">
 
                                     <p class="orange block-sept">Synthetic biologists engineer nature to create
 
                                     <p class="orange block-sept">Synthetic biologists engineer nature to create
                                         solutions to real world problems. We decided to incorporate some synthetic
+
                                         solutions to real-world problems. We decided to incorporate some synthetic
                                         biology in our DNA information storage workshop to expand the general
+
                                         biology into our DNA information storage workshop to expand the general
 
                                         population knowledge about that field. If DNA is able to compact such a large
 
                                         population knowledge about that field. If DNA is able to compact such a large
                                         amount of data in a very small volume, why not use it as a information storage
+
                                         amount of data in a very small volume, why not use it as an information storage
 
                                         system? - would a synthetic biology scientist think. Furthermore, digital
 
                                         system? - would a synthetic biology scientist think. Furthermore, digital
 
                                         information is being generated at an increasing rate and the storage of this
 
                                         information is being generated at an increasing rate and the storage of this
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                                         (A,T,C,G), while one bit can only take up to two values (0 or 1 in binary
 
                                         (A,T,C,G), while one bit can only take up to two values (0 or 1 in binary
 
                                         code). So one DNA base pair could contain two binary code bits of information
 
                                         code). So one DNA base pair could contain two binary code bits of information
                                         (i.e. A=00, T=01, C=10, G=11). Therefore, theoretically information is much
+
                                         (i.e. A=00, T=01, C=10, G=11). Therefore, theoretically, information is much
 
                                         more condensed in DNA than in bits.</p>
 
                                         more condensed in DNA than in bits.</p>
 
                                     <p class="orange block-sept">Actually, there are still several factors making DNA
 
                                     <p class="orange block-sept">Actually, there are still several factors making DNA
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                                         system. For this reason, <a class="link" href="http://science.sciencemag.org/content/337/6102/1628"
 
                                         system. For this reason, <a class="link" href="http://science.sciencemag.org/content/337/6102/1628"
 
                                             target="_blank">Church et al, 2012</a> encoded multiple copies of the book
 
                                             target="_blank">Church et al, 2012</a> encoded multiple copies of the book
                                         he wrote, Regenesis, in DNA and then used next generation sequencing to read
+
                                         he wrote, Regenesis, in DNA and then used next-generation sequencing to read
 
                                         it. Instead of using the maximum compaction system that DNA offers (2 bits per
 
                                         it. Instead of using the maximum compaction system that DNA offers (2 bits per
 
                                         base), the authors used one bit per base (A or C for 0, G or T for 1). This has
 
                                         base), the authors used one bit per base (A or C for 0, G or T for 1). This has
 
                                         multiple advantages, one of it being avoiding extreme GC content.</p>
 
                                         multiple advantages, one of it being avoiding extreme GC content.</p>
                                     <p class="orange block-sept">To integrate system biology in our DNA storage
+
                                     <p class="orange block-sept">To integrate synthetic biology in our DNA storage
 
                                         workshop we reproduced the work done by Church et al, 2012 to write our own DNA
 
                                         workshop we reproduced the work done by Church et al, 2012 to write our own DNA
 
                                         messages. While the authors considered secondary structure, designed a block
 
                                         messages. While the authors considered secondary structure, designed a block
                                         system to order their data from DNA and encoded words, images and a javascript
+
                                         system to order their data from DNA and encoded words, images, and a javascript
 
                                         file, our system only considered GC content to write messages of a few words or
 
                                         file, our system only considered GC content to write messages of a few words or
 
                                         mp3 files in binary code. However, our system was perfectly usable for our
 
                                         mp3 files in binary code. However, our system was perfectly usable for our
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                                         message was being encoded in binary and then in DNA.</p>
 
                                         message was being encoded in binary and then in DNA.</p>
 
                                     <p class="orange block-sept">We used this program to convert several short text
 
                                     <p class="orange block-sept">We used this program to convert several short text
                                         messages about synthetic biology to DNA sequences. We then printed only this
+
                                         messages about synthetic biology into DNA sequences. We then printed only this
 
                                         DNA sequences with their title and including a guide on how this information is
 
                                         DNA sequences with their title and including a guide on how this information is
 
                                         encoded on the other face of the paper. We printed nearly 300 copies of the
 
                                         encoded on the other face of the paper. We printed nearly 300 copies of the
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                                     <p class="orange block-sept">Furthermore, it was very satisfactory for us to see
 
                                     <p class="orange block-sept">Furthermore, it was very satisfactory for us to see
 
                                         the enthusiastic attitude of the students towards that workshop. It seems that
 
                                         the enthusiastic attitude of the students towards that workshop. It seems that
                                         most of them finds special the fact of having a personal message stored in a
+
                                         most of them find special the fact of having a personal message stored in a
                                         DNA sequence which could be then synthetized and introduced and replicated by a
+
                                         DNA sequence which could be then synthesized, introduced to and replicated by a
 
                                         living organism. The program we developed based on the coding system of Church
 
                                         living organism. The program we developed based on the coding system of Church
 
                                         et al, 2012, helped the students to integrate into the topic by engaging on it
 
                                         et al, 2012, helped the students to integrate into the topic by engaging on it

Revision as of 00:09, 17 December 2018

BIO IQS

Outside the Lab | Education & Engagement

Have a look!

Publication in the News AIQS Magazine

We had the opportunity to present our project to the IQS Alumni Association in an interview that was published on the News AIQS magazine in September 2018. Being present in the newspapers brings us the opportunity to reach more people.

Divulgation Activities in Barcelona

“The closer we get to people, the more they sympathize with the cause.”

Spain is the country that has more bars per inhabitant in the world. Therefore, if you ever want to catch people attention, you better go to any bar and present your project to the audience.

Since our project aims to ease celiac people life, we arranged divulgation activities over the summer in bars and coffee shops that compromise with scientific divulgation. It was a must that all bars had gluten-free meals in their menu.

“Learning by playing”

We offered games based on educational technology using Kahoot (game-based learning platform). We asked a set of questions to the audience:

What is gluten, a protein or a sugar? What is cross-contamination? Does gluten apports nutritional value to the food?

By answering this questions, we were expecting to clear up misunderstandings related to celiac disease. Over the project, we realized there are yet several myths associated with gluten-free food.

There is much work yet to do!

We also brought the audience the opportunity to know more about the iGEM competition and synthetic biology.

Introducing gluten free food at the University

“Time to cook! The BioIQS Barcelona team changed the laboratory for the kitchen for a while.”

We baked around fifty cakes, most of them gluten-free, for demonstrating that life without gluten is pretty tasty.

During two days we sold cakes, cookies and candies at the entry hall of our university. We also made a challenge that consisted of eating two pieces of cakes, one with gluten and the other one gluten-free, and students had to guess which one was suitable for celiac people.

Collaborations

We visited the iGEM UPF CRG Barcelona Team. Being able to share what we were investigating, how we managed to deal with deadlines and fundraising was such a good experience.

It took part in front of the PRBB (The Barcelona Biomedical Research Park), where the IGEM UPF CRG Team is working. Since this Research Park is placed in front of the beach, we took advantage of it and played volleyball towards the Mediterranean sea.

This meeting set the beginning of a new collaboration. Over the summer, our team designed a novel strategy to extract the alpha and beta chains of the HLA-DQ from a celiac patient's DNA using PCR. We invited them to test our protocol using a different DNA sample to determine whether our protocol was robust or not.

Sharing the IGEM experience

We had the opportunity to share our iGEM experience with undergraduate students of Biotechnology, Chemistry, and Bioengineering from IQS. We explained the satisfactions and struggles found when starting one project from scratch, how important it is to work together as a team, all the achievements, the new skills we have acquired and everything that we have learn from this project.

DNA information storage workshop

During the divulgation sessions in which we explained our personalized sensor project, we noticed that many people were surprised by the fact that the sensor would be built upon their DNA sequence.

As we decided to keep the focus of our education and public engagement activities on the necessities of the people who participated in it, we realized that we could do some kind of workshop to let them know the information storage capability of DNA. This is how the DNA information storage workshop was born.

We prepared a postcard to explain how many information is stored in the genome of a single cell or in a single human body. To give sense to that large amount of data we calculated the quantity of DIN-A4 papers that would be needed in order to write all the DNA sequence of the genome of a single cell in a standard font (Courier New, 12) and standard margins. This way, everyone without biology or computation* knowledge could also imagine the quantity of information.

*(sometimes the quantity of DNA information is expressed in bytes, which is not suitable for the general population, especially older people). It turns out that a normal somatic human female cell has 2 dotations of 23 chromosomes (including 2 X sex chromosomes) and mitochondrial DNA. This is a total of two times 3,088,286,401 base pairs, according to the latest human genome sequence release (GRCh38.p12). A single DINA-4 page full of characters in Courier New, 12 and standard margins could contain 2773 base pairs written on it. Therefore, to write all the information stored in the base pairs of the genome of a single human cell it would be needed to print 2,186,117 pages on one face. If these pages are then piled up to form a tower (considering the height of a single paper is 0.1mm), it would be 218.61 meters tall (717.2 ft)! Just between the Agbar Tower (the taller building in our city, Barcelona; 142m) and the Eiffel Tower (324m). Scientists have estimated that the human body contains nearly 37.2 trillions of human cells (note that this does not include the microbiota). So...to write all the information condensed in the DNA of one human body it would take a large amount of DINA-4 papers. This amount is so huge that if the papers were arranged in a straight line, the light would spend 2553 years traveling from one end to the other. This is 2553 light-years long! Keep in mind that the distance from the sun to the earth is just 8.3 light-minutes, so imagine the amount of data stored in such a low volume like your body.

Using these examples, the general population can easily understand the information storage capability of DNA. Nearly everyone (including ourselves) was pretty amazed to realize how much information human bodies contain stored in DNA. After this examples, we explained that our sensor was based on a piece of information stored in two genes of the DNA. So this comparisons helped the general population to understand that DNA contains much useful information, which is different between us and that we can extract this information to create a personalized product. This helped us to explain the DNA extraction and PCR process of our project to the general population. This way, they are much better informed about the project and can have an opinion about it. Then, we integrated that informed opinion from the general population in the design of our project. Dedicating effort in explaining the projects in a simple but rigorous way can help teams to receive feedback from the target population. This feedback can be incorporated into the design of the project and hence make it more suitable for the real world.

Synthetic biologists engineer nature to create solutions to real-world problems. We decided to incorporate some synthetic biology into our DNA information storage workshop to expand the general population knowledge about that field. If DNA is able to compact such a large amount of data in a very small volume, why not use it as an information storage system? - would a synthetic biology scientist think. Furthermore, digital information is being generated at an increasing rate and the storage of this information requires a huge amount of servers which take up a lot of space. So why not using DNA to store digital data?

A single DNA base contains more information than one bit. DNA is made from a combination of four different nucleotide residues (A,T,C,G), while one bit can only take up to two values (0 or 1 in binary code). So one DNA base pair could contain two binary code bits of information (i.e. A=00, T=01, C=10, G=11). Therefore, theoretically, information is much more condensed in DNA than in bits.

Actually, there are still several factors making DNA information storage not as practical as current systems. However, the increase in efficiency and the drop in the cost of DNA synthesis and sequencing has dramatically increased the likelihood of using DNA as an information storage system. For this reason, Church et al, 2012 encoded multiple copies of the book he wrote, Regenesis, in DNA and then used next-generation sequencing to read it. Instead of using the maximum compaction system that DNA offers (2 bits per base), the authors used one bit per base (A or C for 0, G or T for 1). This has multiple advantages, one of it being avoiding extreme GC content.

To integrate synthetic biology in our DNA storage workshop we reproduced the work done by Church et al, 2012 to write our own DNA messages. While the authors considered secondary structure, designed a block system to order their data from DNA and encoded words, images, and a javascript file, our system only considered GC content to write messages of a few words or mp3 files in binary code. However, our system was perfectly usable for our purpose. We created a bash script which takes a text input message and converts it to binary by the ASCII code using the xxd command. Then, using a random function, the program assigns a DNA nucleotide to each binary value (A or C to 0, G or T to 1). Finally, it checks if the GC content is between the specified boundaries (by default, 40-60%). Thanks to the random function, the GC content is usually between 50%. Only when encoding single ASCII characters the program needs to perform more than one iteration to get the appropriate GC content. The generated output consists of the written message in the input format, in binary and in DNA. It also incorporates a title recreating the FASTA format used to identify the DNA sequences (and in this case, the message). The program was also adapted to convert songs in mp3 format to DNA sequences, to convert multiple text messages in the same file and to send the generated DNA messages by mail. In addition, the program displayed in a very visual way how the message was being encoded in binary and then in DNA.

We used this program to convert several short text messages about synthetic biology into DNA sequences. We then printed only this DNA sequences with their title and including a guide on how this information is encoded on the other face of the paper. We printed nearly 300 copies of the messages and gave it to students in our university. The message contained information about where to locate the DNA information workshop and an invitation to come in order to decode their DNA message.

This way, we attracted the students to the workshop, where we told them the information about natural information on DNA. In addition, we organized some other small activities related to science and celiac disease (i.e. a guess what contest, in which the participants tried to identify the content of a science picture between two possible options). All the students who came had their message decoded by us. We could quickly identify the message by its title and write down the content of the message in text format in their DNA message paper.

Finally, if the participants correctly identified more than 2 of 3 scientific pictures, we gave them the opportunity to write their own message and have it coded in DNA and sent to their mail by the program we created. Most of the messages consisted of the name of the participants and some student jokes. However, the final objective was to have fun while learning about DNA information storage, so mission accomplished!

Furthermore, it was very satisfactory for us to see the enthusiastic attitude of the students towards that workshop. It seems that most of them find special the fact of having a personal message stored in a DNA sequence which could be then synthesized, introduced to and replicated by a living organism. The program we developed based on the coding system of Church et al, 2012, helped the students to integrate into the topic by engaging on it hands on. Like the examples provided before, this section of the workshop helped translate a difficult concept in a simple but rigorous way to general population. In addition, it served us as a tool to attract people to the workshop and explain them a little bit more about iGEM, synthetic biology and our project.