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

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               <h1 style="padding: 0;text-align:center">ARE WE EQUAL?</h1>
+
               <h1 style="padding: 0;text-align:center">CRISPeasy IMPLICATIONS AND ETHICAL ISSUES</h1>
              <h2 style="padding: 0;text-align:center">How Artificial Intelligence provides insights about iGEM teams performances</h2>
+
               <p class="p">CRISPR revolutioned 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 researches – as  in comprehend genes function – as far as CRISPR applications that will change our reality, like genetic editing of cancer cells. </p>
               <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">A tremendous range of futuristic possibilites can be turn 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 ethics 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">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">The CRISPeasy toolbox was developed to expand and further facilitate the genome engineering applying standardized BioBricks, reducing time for designing, assembling and building devices. Therefore, we aim to provide to iGEM communitythe 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">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>
+
               <p class="p">Fundamental research provides essential outputs, which is, broadly, the knowledge building block for advancing applied research projects. Bo Huang said in a 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 took less time and required less struggles. </p>
               <h2 class="p">How we did it?</h2>
+
               <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 more well fundamented.</p>
               <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">The encouragement of this kind of research cannot cease, since the improvement is continuous. By optimizating (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 considere this an important implication of our project.</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>
+
<p class="p"> One of the implications about 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 example the advent of DNA synthesis, that made possible for the Spanish influenza pandemic virus to be “ressurected”. 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>
               <h2 class="p">Data analysis</h2>
+
               <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 e quanto a análise a esses riscos, por exemplo, poderia ser usado codões de ORF de patógenos synthetized and optimized to express recombinant proteins.</p>  
<p class="p"><center><b>[INFOGRÁFICO]</b></center></p>
+
              <p class="p">Even with this high capacity of analysing and responding to risks, researchers are not exempted from taking neccessary actions to ensure biosafety. It is fundamental to considere carefully the safety implications before and during the research fulfilment. As Andrea Ventura, researcher at the Memorian 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>
<h2 class="p">Future impacts</h2>
+
              <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 accelereation 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>
<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">A resposta para o futuro ao que se diz sobre segurança biológica não está em limitar o desenvolvimento científico, e a disseminação do conhecimento através do acesso free-to-use para todo o mundo, dessa forma estaríamos parando abruptamente o desenvolvimento científico, e impedindo ou dificultando a descoberta de melhorias para, tratamentos, curas, na área biomédica e o aprimoramento de técnicas e compreensão de mecanismos na bioengenharia. A resposta está no desenvolvimento bem sucedido e em nossa agilidade para detectar, compreender e responder aos riscos biológicos, sejam eles naturais ou artificiais.</p>
 +
              <p class="p">It is necessary to put society and scientific closer, since they intimately related and influence each obter. 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 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>
 +
                                          <h2 class="p">Next steps</h2>
  
<p class="p"> &#185;&nbsp;&nbsp; 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>
 
 
              <h1 style="padding: 0;text-align:center">HAVE YOU SEEN MY DNA?</h1>
 
              <h2 style="padding: 0;text-align:center">Understanding how legislation impacts science </h2>
 
              <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">Even then, why and how did this happen?</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">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">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>
 
              <h2 class="p">How we did it</h2>
 
              <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>
 
              <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">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">Finally, to draw a comparison between different international settings, we also sent the same forms to iGEMers abroad.</p>
 
              <h2 class="p">What we found</h2>
 
              <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">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>
 
              <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>
 
              <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">
 
</script>
 
              <h2 class="p">Next steps</h2>
 
              <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>
 
<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"><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>
 
<h1 style="padding: 0;text-align:center">SYNTHETIC BIOLOGY 101</h1>
 
<h2 style="padding: 0;text-align:center">A simple method to expand scientific knowledge</h2>
 
<p class="p">Over this season scientific dissemination has been re-designed. Expanding our perspectives, we had decided to address all these community audiences through simple tools, like videos using clarifier ways. The videos were specially thought according to the target public, caring about appropriate language, addressed topics , examples for easy understanding and ways to make this available for the general community — including the iGEMers from all parts of the world, thanks to the use of subtitles in national languages.</p>
 
<p class="p">The themes ー"A brief introduction on synthetic biology"; "BioBrick concepts and definitions and BioBrick Foundation"; "Practical concepts and applications of CRISPR technology"; and “the relationship between the recombination system and CRISPR/Cas9" ー allowed us to establish a collaboration with Tübingen Team, and we provide them videos to its  online channel.</p>
 
<p class="p">Beyond that, we participated on the world's biggest technology meeting: Campus Party. Which took place in our country’s capital - Brasilia. Three of us represented our team, taking synthetic biology developed in the Amazon, and the work with CRISPR/Cas9, to national scale. We also had been present at local events, promoting lectures and workshops, like the first Academic Week of Biotechnology and Bioprocess Engineering, covering a wide range of subjects regarding these fields, such as health, genetics, bioprospecting Amazon’s biodiversity and, of course, Synthetic Biology. </p>
 
<p class="p">Finally, as restless iGEMers, we decided to spread the word of synthetic biology in a different manner. As projects communication is a fundamental part of IGEM, we thought a new way to promote the forthcoming between project-public: Augmented reality (AP), which integrates the real world to fictitious images created by the used dispositive. The great part from this is: this tool might bring an attractive visual, and, if well-used, an excellent way to simplify presentations, or simulate phenomena without its occurrence in real world.</p>
 
<p class="p">Using Augmented reality technology we aim to turn the banner interactive, with animated images, to allow the public easy understanding, further the usual and limited current physical methods. Encouraging teams around the globe to make part of an open community to share educational and knowledge values.</p>
 
 
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Revision as of 06:25, 1 November 2017

Wiki_iGEM_Amazonas

SILVER

CRISPeasy IMPLICATIONS AND ETHICAL ISSUES

CRISPR revolutioned 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 researches – 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 possibilites can be turn 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 ethics 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 time for designing, assembling and building devices. Therefore, we aim to provide to iGEM communitythe 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 a 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 took less time and required less 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 more well fundamented.

The encouragement of this kind of research cannot cease, since the improvement is continuous. By optimizating (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 considere this an important implication of our project.

One of the implications about 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 example the advent of DNA synthesis, that made possible for the Spanish influenza pandemic virus to be “ressurected”. 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 e quanto a análise a esses riscos, por exemplo, poderia ser usado codões de ORF de patógenos synthetized and optimized to express recombinant proteins.

Even with this high capacity of analysing and responding to risks, researchers are not exempted from taking neccessary actions to ensure biosafety. It is fundamental to considere carefully the safety implications before and during the research fulfilment. As Andrea Ventura, researcher at the Memorian 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 accelereation 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.

A resposta para o futuro ao que se diz sobre segurança biológica não está em limitar o desenvolvimento científico, e a disseminação do conhecimento através do acesso free-to-use para todo o mundo, dessa forma estaríamos parando abruptamente o desenvolvimento científico, e impedindo ou dificultando a descoberta de melhorias para, tratamentos, curas, na área biomédica e o aprimoramento de técnicas e compreensão de mecanismos na bioengenharia. A resposta está no desenvolvimento bem sucedido e em nossa agilidade para detectar, compreender e responder aos riscos biológicos, sejam eles naturais ou artificiais.

It is necessary to put society and scientific closer, since they intimately related and influence each obter. 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 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.

Next steps