Difference between revisions of "Team:Amazonas Brazil/HP/Silver"

 
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         <li><a class="bar_text"  href="https://2017.igem.org/Team:Amazonas_Brazil/HP/Gold_Integrated">Integrated Human Practices</a></li>
 
         <li><a class="bar_text"  href="https://2017.igem.org/Team:Amazonas_Brazil/HP/Gold_Integrated">Integrated Human Practices</a></li>
 
         <li><a class="bar_text"  href="https://2017.igem.org/Team:Amazonas_Brazil/Engagement">Education and Public Engagement</a></li>
 
         <li><a class="bar_text"  href="https://2017.igem.org/Team:Amazonas_Brazil/Engagement">Education and Public Engagement</a></li>
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        <li><a class="bar_text"  href="https://2017.igem.org/Team:Amazonas_Brazil/Notebook">Notebook</a></li>
 
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              <h1 style="padding: 0;text-align:center">ARE WE EQUAL?</h1>
 
              <h2 style="padding: 0;text-align:center">How Artificial Intelligence provides insights about iGEM teams performances</h2>
 
              <p class="p">Why does China has more teams? How the United States get to win more medals over the years? Why Africa only has two registred teams? Why there’s no team from Central America in the competition?</p>
 
              <p class="p">iGEM teams are broadly distributed all around Earth. Geographical location, culture and economy are some factors which impact directly on participation and performance of teams from the biggest competition of synthetic biology in the world. All over these 13 years of iGEM, many teams started these journey, grew bigger and became reference to other iGEMers, due to extraordinary projects developed in the lab or social work engaged directly to the community.</p>
 
              <p class="p">And how to know or predict which factor can influence directly one team on being successful and achieve medals? To answer this, we united knowledge in Machine Learning&#185; and Pattern Recognition. By identifying patterns present on iGEM teams it’s possible to predict which factors really affect directly the prizes they win and the medals they achieve.</p>
 
              <h2 class="p">How we did it?</h2>
 
              <p class="p">The idea originated from our curiosity in verifying if there were any correlation between iGEM medal winners and their continent of origin, since the first edition, 2004.  From each team, we collected name, country they belong to, continent and medals won by year. We also identified and correlated geographically  “Grand Prize” winners. In this query, we considered a large spectre, identifying how many and which were the medals winner per year; compiling all data in algorithmic scales, which gave us pattern of recognition of what makes a winning team.</p>
 
              <p class="p">During the data query, we noticed that not everything was organized and disposed in the same places, and it lead us to conclude that iGEM data are constantly being transformed and structured. In this step, a great came from iGEM Foundation, providing data by “iGEM Meta”. Therefore, the data that could be better analyzed and understood are from 2014 on, our starting point . Finally, we divided teams according to their countries’ respective continents. </p>
 
              <h2 class="p">Data analysis</h2>
 
<p class="p"><center><b>[INFOGRÁFICO]</b></center></p>
 
<h2 class="p">Future impacts</h2>
 
<p class="p">Many variables could’ve been utilized to perform patterns recognition. However, some websites don’t have recent data about their countries, difficulting the choice of variables. Students from all around the world have an enormous potential in elaborating strategical solutions to problems in their communities through synthetic biology. However, not every continent has an expressive amount of teams as, for example, Africa, Central and South America. In these places, talented students have to face struggles as general socioeconomical issues and lack of investment in education, science and technology, which difficult the journey of their teams to the Giant Jamboree.</p>
 
  
<p class="p"> &#185; We can say that Machine Learning is a kind of artificial intelligence, where machines are able to predict outcomes with help from algorithm and patterns. This technology is present in our daily life. For example, when your phone organizes your photos by location, or recognizes your voice, it is using machine learning.</p>
+
            <img width="90%" height="90%" src="https://static.igem.org/mediawiki/2017/c/c0/Amazonas2017_Silver_Implication.png">
  
               <h1 style="padding: 0;text-align:center">HAVE YOU SEEN MY DNA?</h1>
+
               <p class="p">CRISPR revolutionised genome editing. When compared to older techniques, CRISPR machinery has overcome obstacles as efficiency, experimental time and, mainly, expenses. One milestone of this scientific ascension is its power of democratization: to turn available cutting-edge techniques to researchers from different nationalities, distributed worldwide, in a way that everyone has tools to develop research without demanding a great lab structure and huge amounts of investment. This democratic revolution that CRISPR has brought to science is fantastic and goes beyond the importance of promoting science for all. It’s in the building of this future that we will progress faster, not only in discovering of basic aspects and fundamental researchers as in comprehend genes function as far as CRISPR applications that will change our reality, like genetic editing of cancer cells. </p>
              <h2 style="padding: 0;text-align:center">Understanding how legislation impacts science </h2>
+
<center><img src="https://static.igem.org/mediawiki/2017/thumb/2/28/Imagem1_silver.png/777px-Imagem1_silver.png"></center>
               <p class="p">One of the most important milestones for an iGEM team is when the biological parts kit arrives. It is a long way from Boston for every team around the world to receive their packages. How much time did we lose waiting for ours to arrive instead of doing lab work?</p>  
+
               <p class="p">A tremendous range of futuristic possibilities can be turned into reality through CRISPR/Cas9-based genome editing system. Even with these rapid advances and the vast applications of this technique, it is essential to pave the way to discuss the social and ethical implications of CRISPR, taking into account the impact in the world and society. By standardizing a “toolbox”, CRISPeasy, to be implemented on standardized genome editing in bacteria, we considered fundamental to be aware of it and discuss the implications of our project.</p>
            <p class="p">Even then, why and how did this happen?</p>
+
              <p class="p">The CRISPeasy toolbox was developed to expand and further facilitate the genome engineering applying standardized BioBricks, reducing the time for designing, assembling and building devices. Therefore, we aim to provide to iGEM community the power of genetic editing in a few steps. We believe that by through applying bioengineering principles, like standardization and abstraction, we can go fast forward.  </p>
               <p class="p">For the kits to finally get to our hands, they must go through scrutiny and analysis by the Brazilian Regulatory Importing Agency, and, only upon lengthy inspection, they are finally cleared to their final destinations. That, of course, considering everything goes well.</p>
+
               <p class="p">Fundamental research provides essential outputs, which is, broadly, the knowledge building block for advancing applied research projects. Bo Huang said in an interview for Nature that he and his lab team took two months to adapt CRISPR to image study in his project “Imaging genomic elements in living cells using CRISPR/Cas9”. Thus, he highlighted that if there were as a more basal knowledge, like design optimization of guide RNAs, it would take less time and required fewer struggles. </p>
               <p class="p">However, as the Second Law of Thermodynamics (scientist’s very own Murphy’s Law), things can derail quite quickly. As the kits may get entrenched in the entropy of trade legislation, the material may be returned to the sender, be lost midway or, most simply, be denied shipping fulfillment due to biosafety issues. Considering the kit survives this internal process, it can take a good few months of waiting time and unnecessary anxiety. </p>
+
               <p class="p">Then, we could realize the value of “foundational advances”, that contribute so much to improve the technique, regarding its efficiency, off-target effects and to comprehend CRISPR utilization, that over time might be applied to more complexes organisms, as humans and other animals. Until then, CRISPR needs to be even better fundamented.</p>
              <p class="p">This long and inefficient process - unknown by many iGEMers – was addressed by our team. We longed to understand the importing and exporting policies for biological parts in Brazil, and worked alongside ANVISA (the Brazilian Agency responsible for regulating the traffic of these materials), to find ways to solve this problem.</p>
+
      <p class="p">The encouragement of this kind of research cannot cease since the improvement is continuous. By optimizing (and improving) a specific element of CRISPR, as we did with CRISPeasy toolbox, doesn’t represent the end, but the beginning or continuity to collaborations and related projects. We consider this an important implication of our project.</p>
              <h2 class="p">How we did it</h2>
+
<p class="p"> One of the implications of the development, simplification and free-to-use access, the Foundational Technologies, it’s our exposure to dangers, which can be natural or artificial, caused unexpectedly by bioengineering. However, the analysis of these risks cannot be direct – What? Drew Endy addresses this question in his article “Foundations for Engineering Biology”, and cites as an example the advent of DNA synthesis, that made possible for the Spanish influenza pandemic virus to be “resurrected”. With the article of Trumpey T. M., called “Characterization of the reconstructed 1918 Spanish influenza pandemic virus”, it was possible to understand details about its virulence. </p>
               <p class="p">The National Agency For Sanitary Surveillance (ANVISA in Portuguese) is the federal entity that inspects and regulates Food, Drugs, and other products potentially harmful products (analogous to the FDA in the United States), being responsible for devising the policies and norms regarding biological material distribution throughout the country.</p>
+
<center><img src="https://static.igem.org/mediawiki/2017/thumb/8/84/Imagem3_silver.png/777px-Imagem3_silver.png"></center>
               <p class="p">We studied the Brazilian legislation, focusing on the procedures regarding importing of nucleic acids and proteins. We collaborated with professor Carlos Gustavo and Matheus Costa, both having expertise in this area and clarified us about the legal aspect of it. We concluded that there is no specific policy concerning importing and exporting of biological parts in Brazil.</p>
+
               <p class="p">Now, it is possible to make Smallpox genome, with easily accessible DNA sequences. The free-to-use access of these informations allows to construct variants of this vírus, and many others as well. However, the emerging of DNA synthesis could quickly and efficiently come with solutions to these risks, as occurs when we deal with natural biological risks, Through high capacity of response to risks, vaccines and its precursors could be synthetized and about the analysis of these risks, for example, ORF codons of pathogens synthetized and optimized to express recombinant proteins.</p>
               <p class="p">Aiming to map the obstacles, we developed a survey and sent it to many research groups and laboratories in Brazil, with questions regarding the waiting time, the accessibility of the legislation and beyond.</p>
+
               <p class="p">Even with this high capacity of analyzing and responding to risks, researchers are not exempted from taking necessary actions to ensure biosafety. It is fundamental to consider carefully the safety implications before and during the research fulfillment. As Andrea Ventura, a researcher at the Memorial Sloan Kettering Cancer Center in New York,  tells Nature in interview with Heidi Ledford, it is important to foresee even remote risks and that, when working with lung cancer model in mouses using CRISPR, he had carefully designed guide RNAs that don’t cleave human DNA, highlighting  that “It’s not very likely, but still needs to be considered”. </p>
               <p class="p">Finally, to draw a comparison between different international settings, we also sent the same forms to iGEMers abroad.</p>
+
               <p class="p">The risk analysis for Foundational Technologies, depend on its applications, that can impact positively or negatively. We saw that these technologies show potential to solve these conceivable risks. In a nearer moment, the most important and certain about these Foundational Technologies is the acceleration of continuous and constructive experimental research. A scientist using technologies that optimize the phase of experimental processing will have an increase in productivity, reducing experimental time and improving the efficiency of research.</p>
              <h2 class="p">What we found</h2>
+
               <p class="p"> The answer to the future when it comes to biosafety does not reside in limiting scientific development and knowledge dissemination through free-to-use access, that way we would be stopping abruptly science’s progress and hindering the discovery of novel treatments and cures in the biomedical field and the improvement of techniques in bioengineering. The answer consists in our agility in detecting, understanding and responding to biological risks, natural or artificial.</p>
               <p class="p">While studying the normative laws, we realized that there aren’t specific laws for biological parts – nucleic acids and proteins. Generally, in Brazil, the approval or confiscation of biological material is decided on the inspector’s interpretation of the case. Beyond this bibliographical research, the analysis of the forms and comparison of the responses from Brazilian and International perspectives revealed some alarming bureaucratic questions.</p>
+
               <p class="p">It is necessary to put society and scientific community closer since they are intimately related and influence each other. Just as society drives the direction science goes, science also influences society’s lifestyle, in the way we eat, what we think and so on. Jennifer Doduna said in an interview about CRISPR for The Guardian: “History and evidence points to the fact that when we inspire and support our scientific community we advance our way of life and thrive.” Therefore, it is important to keep encouraging society as a whole to support a global community for Synbio and be aware of its importance, so together we can move further to advance bioengineering.</p>
              <p class="p">The lack of specific legislation governing biological parts would give the scientific community the security and legal support to import these materials, vastly reducing the amount of time necessary to access these components. We then met with the ANVISA representatives once more to discuss what could be done in the legislative sphere and presented suggestions for the importing process of biological materials.</p>
+
<p class="p">CRISPR made possible the insertion of the Amazon in a scenario of scientific-technological advances. Scientific development in the Amazon is difficult for a number of reasons, including logistics, because it is a region with few possibilities for access and investment, which for science is somewhat limited. There are many research challenges with state-of-the-art technologies in the Brazilian Amazon, because the majority of them has a high cost. In the midst of so many challenges and difficulties, we have been able to carry out state-of-the-art and highly effective research. CRISPR has made this possible, especially for its practicality and low investment cost. This achievement represents scientific-technological advances for the Amazon region, where it is possible to form a network of national collaborators and even international laboratories, drawing attention to this region, which may imply greater investments, more young people in science and development of more complex projects to contribute to a global scientific and social community.</p>
               <h2 class="p">Data analysis</h2>
+
 
               <p class="p">Our sample consisted of 29 surveys from Brazil and 15 from iGEM teams worldwide. There were six questions in the study and, after comparing both groups, we observed exciting trends.</p>
+
               <h1 style="padding: 0;text-align:center">Building Synbio legacy in our community</h1>
              <script id="infogram_0_843cbb65-859e-488c-b47b-d9d241b28ef5" title="infografico_hp_pag1" src="https://e.infogram.com/js/dist/embed.js?SZ6" type="text/javascript">
+
               <p class="p">One of the greatest achievements of Synbio is to be broadly present in diverse backgrounds: from high tech institutes to local communities all around the world. We stand proudly as the first iGEM team to work with CRISPR in Latin America and the first research group to work with it in the Amazon. Therefore, we felt the urge to implement the first building block of Synbio (and CRISPR) in our community, through educational engagement.</p>
</script>
+
               <p class="p">On our community, we raised awareness for Synbio and the significance of building foundational advances to standardize CRISPR, through broadcasted interviews and social media, highlighting CRISPR as a revolutionary technique that has plenty of potentials to solve real-world problems. To the academic community, we kept promoting Synbio principles, by giving lectures and workshops introducing concepts such as biological parts and standardization. We also mobilized all spheres of society into discussing the importance of science and its role as powerful and transforming tool to improve human life and the world, by organizing the March for Science at our city, in partnership with Brazilian Society For Science’s Progress (SBPC in portuguese).</p>
              <h2 class="p">Next steps</h2>
+
            <center><img src="https://static.igem.org/mediawiki/2017/thumb/8/8a/19442084_1567122646666097_6736605394802004815_o.jpg/800px-19442084_1567122646666097_6736605394802004815_o.jpg">
               <p class="p">As iGEMers, after verifying the disparity of answers, we decided to bring to ANVISA our necessity to make the entry and exit of biological material less bureaucratic and more efficient, allowing Brazilian scientists to have practicality and allow open discussion about how these problems negatively influence the national scientific development efforts. We reunited with regional representatives and established that current laws regarding the subject are limited to the human genetic material (body fluids, cells, tissues, blood, organs). Thus, alongside them, we demanded ANVISA what could be done to address this lack of specific policy for biological parts and urged for them to regulate it. Going further, we also developed a guideline to aid researchers to import and export biological material, validated by ANVISA as well.</p>
+
<p class="p"></p><i> Our team and  everyone who engaged at the March For Science in Manaus, capital of Amazonas state.</i><center>
<center><img src="https://static.igem.org/mediawiki/2017/thumb/2/2d/Human_Practice_Educational_and_Public_Engagement.jpeg/800px-Human_Practice_Educational_and_Public_Engagement.jpeg">
+
              <p class="p">In addition, we tried not to stick only to our regional community, but in showing the world what the Amazon has to offer in terms of Synbio and cutting-edge technologies. By lecturing at Campus Party - the biggest event of technology in the world - we’ve got the chance to reach a more distinct audience than that we were used to since Campus Party is more appealing to a public which has a technologic background but not necessarily a biotech one. For the first time, many of these people from different scenarios heard about CRISPR and its outstanding perspectives, and that all of this revolution in genome editing is not strictly happening in the biggest institutes of research in the world, but in the Brazilian Amazon as well.</p>
<p class="p"><i>Our Human Practices members Maria Cecília and Wlademir meeting regional representative of ANVISA (National Agency For Sanitary Surveillance)  Marco Antonio Pinto to discuss the current legislation to import biological parts in Brazil.</i></p><center>
+
<p class="p">So, in the future, iGEMers in situations like these can develop their activities in a similar fashion, promoting positive impacts in their communities and removing barriers for synthetic biology growing. As perspective, we believe that what we’ve done can help, guide and inspire fellow iGEM teams to create a more connected and integrated community, with free-to-use DNA parts; get, give and share, paving the way to make synthetic biology more and more greater.</p>
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Latest revision as of 04:00, 2 November 2017

Wiki_iGEM_Amazonas

SILVER

CRISPR revolutionised genome editing. When compared to older techniques, CRISPR machinery has overcome obstacles as efficiency, experimental time and, mainly, expenses. One milestone of this scientific ascension is its power of democratization: to turn available cutting-edge techniques to researchers from different nationalities, distributed worldwide, in a way that everyone has tools to develop research without demanding a great lab structure and huge amounts of investment. This democratic revolution that CRISPR has brought to science is fantastic and goes beyond the importance of promoting science for all. It’s in the building of this future that we will progress faster, not only in discovering of basic aspects and fundamental researchers as in comprehend genes function as far as CRISPR applications that will change our reality, like genetic editing of cancer cells.

A tremendous range of futuristic possibilities can be turned into reality through CRISPR/Cas9-based genome editing system. Even with these rapid advances and the vast applications of this technique, it is essential to pave the way to discuss the social and ethical implications of CRISPR, taking into account the impact in the world and society. By standardizing a “toolbox”, CRISPeasy, to be implemented on standardized genome editing in bacteria, we considered fundamental to be aware of it and discuss the implications of our project.

The CRISPeasy toolbox was developed to expand and further facilitate the genome engineering applying standardized BioBricks, reducing the time for designing, assembling and building devices. Therefore, we aim to provide to iGEM community the power of genetic editing in a few steps. We believe that by through applying bioengineering principles, like standardization and abstraction, we can go fast forward.

Fundamental research provides essential outputs, which is, broadly, the knowledge building block for advancing applied research projects. Bo Huang said in an interview for Nature that he and his lab team took two months to adapt CRISPR to image study in his project “Imaging genomic elements in living cells using CRISPR/Cas9”. Thus, he highlighted that if there were as a more basal knowledge, like design optimization of guide RNAs, it would take less time and required fewer struggles.

Then, we could realize the value of “foundational advances”, that contribute so much to improve the technique, regarding its efficiency, off-target effects and to comprehend CRISPR utilization, that over time might be applied to more complexes organisms, as humans and other animals. Until then, CRISPR needs to be even better fundamented.

The encouragement of this kind of research cannot cease since the improvement is continuous. By optimizing (and improving) a specific element of CRISPR, as we did with CRISPeasy toolbox, doesn’t represent the end, but the beginning or continuity to collaborations and related projects. We consider this an important implication of our project.

One of the implications of the development, simplification and free-to-use access, the Foundational Technologies, it’s our exposure to dangers, which can be natural or artificial, caused unexpectedly by bioengineering. However, the analysis of these risks cannot be direct – What? Drew Endy addresses this question in his article “Foundations for Engineering Biology”, and cites as an example the advent of DNA synthesis, that made possible for the Spanish influenza pandemic virus to be “resurrected”. With the article of Trumpey T. M., called “Characterization of the reconstructed 1918 Spanish influenza pandemic virus”, it was possible to understand details about its virulence.

Now, it is possible to make Smallpox genome, with easily accessible DNA sequences. The free-to-use access of these informations allows to construct variants of this vírus, and many others as well. However, the emerging of DNA synthesis could quickly and efficiently come with solutions to these risks, as occurs when we deal with natural biological risks, Through high capacity of response to risks, vaccines and its precursors could be synthetized and about the analysis of these risks, for example, ORF codons of pathogens synthetized and optimized to express recombinant proteins.

Even with this high capacity of analyzing and responding to risks, researchers are not exempted from taking necessary actions to ensure biosafety. It is fundamental to consider carefully the safety implications before and during the research fulfillment. As Andrea Ventura, a researcher at the Memorial Sloan Kettering Cancer Center in New York, tells Nature in interview with Heidi Ledford, it is important to foresee even remote risks and that, when working with lung cancer model in mouses using CRISPR, he had carefully designed guide RNAs that don’t cleave human DNA, highlighting that “It’s not very likely, but still needs to be considered”.

The risk analysis for Foundational Technologies, depend on its applications, that can impact positively or negatively. We saw that these technologies show potential to solve these conceivable risks. In a nearer moment, the most important and certain about these Foundational Technologies is the acceleration of continuous and constructive experimental research. A scientist using technologies that optimize the phase of experimental processing will have an increase in productivity, reducing experimental time and improving the efficiency of research.

The answer to the future when it comes to biosafety does not reside in limiting scientific development and knowledge dissemination through free-to-use access, that way we would be stopping abruptly science’s progress and hindering the discovery of novel treatments and cures in the biomedical field and the improvement of techniques in bioengineering. The answer consists in our agility in detecting, understanding and responding to biological risks, natural or artificial.

It is necessary to put society and scientific community closer since they are intimately related and influence each other. Just as society drives the direction science goes, science also influences society’s lifestyle, in the way we eat, what we think and so on. Jennifer Doduna said in an interview about CRISPR for The Guardian: “History and evidence points to the fact that when we inspire and support our scientific community we advance our way of life and thrive.” Therefore, it is important to keep encouraging society as a whole to support a global community for Synbio and be aware of its importance, so together we can move further to advance bioengineering.

CRISPR made possible the insertion of the Amazon in a scenario of scientific-technological advances. Scientific development in the Amazon is difficult for a number of reasons, including logistics, because it is a region with few possibilities for access and investment, which for science is somewhat limited. There are many research challenges with state-of-the-art technologies in the Brazilian Amazon, because the majority of them has a high cost. In the midst of so many challenges and difficulties, we have been able to carry out state-of-the-art and highly effective research. CRISPR has made this possible, especially for its practicality and low investment cost. This achievement represents scientific-technological advances for the Amazon region, where it is possible to form a network of national collaborators and even international laboratories, drawing attention to this region, which may imply greater investments, more young people in science and development of more complex projects to contribute to a global scientific and social community.

Building Synbio legacy in our community

One of the greatest achievements of Synbio is to be broadly present in diverse backgrounds: from high tech institutes to local communities all around the world. We stand proudly as the first iGEM team to work with CRISPR in Latin America and the first research group to work with it in the Amazon. Therefore, we felt the urge to implement the first building block of Synbio (and CRISPR) in our community, through educational engagement.

On our community, we raised awareness for Synbio and the significance of building foundational advances to standardize CRISPR, through broadcasted interviews and social media, highlighting CRISPR as a revolutionary technique that has plenty of potentials to solve real-world problems. To the academic community, we kept promoting Synbio principles, by giving lectures and workshops introducing concepts such as biological parts and standardization. We also mobilized all spheres of society into discussing the importance of science and its role as powerful and transforming tool to improve human life and the world, by organizing the March for Science at our city, in partnership with Brazilian Society For Science’s Progress (SBPC in portuguese).

Our team and everyone who engaged at the March For Science in Manaus, capital of Amazonas state.

In addition, we tried not to stick only to our regional community, but in showing the world what the Amazon has to offer in terms of Synbio and cutting-edge technologies. By lecturing at Campus Party - the biggest event of technology in the world - we’ve got the chance to reach a more distinct audience than that we were used to since Campus Party is more appealing to a public which has a technologic background but not necessarily a biotech one. For the first time, many of these people from different scenarios heard about CRISPR and its outstanding perspectives, and that all of this revolution in genome editing is not strictly happening in the biggest institutes of research in the world, but in the Brazilian Amazon as well.