Team:UPF Barcelona/Education
Human Practices
Education
We firmly believe that real changes can only be achieved through social awareness. We want an effective solution against antibiotic resistance to be possible. With this purpose, on the one hand we have actively worked to disseminate this health problem to the whole population and to promote the role of synthetic biology and artificial intelligence as a fundamental part of our fight. On the other hand, at the same time we have worked on our own education by gaining knowledge not only from the team instructors but also from experts in and out of the field.
All in all, we have engaged with the non-scientific community and seek help from experts to unite both worlds and achieve a common goal: win the battle against the upcoming resistant bacteria pandemic by becoming aware of its urgency.
Education is the most powerful weapon you can use to change the world.
- Each team has to hit members of the opposing team.
- If hit, the kid has to run back home to rejoin the field.
- There were 3 different colours of water balloons (yellow, blue and red).
- When the medic team has been hit four times, the game would be paused and, from now on, one balloon colour cannot be used by the medic team anymore. This represents the concept of acquiring resistance to a certain antibiotic by the bacteria.
- The medic team has the goal to prevent this situation.
- Eventually, the bacteria team would be immune to all the balloons thrown to them, which is a metaphor of the problem we’re trying to solve.
- After each game, the teams are swapped.
- No one is going to get mad at you for hearing opinions that are different from yours.
- Learn a lot from outside our own field. Be it pharmacy, medicine, biology...
- Schedule what we are going to do together.
- Listening to each other.
- Try to get the opinion of as many people as possible, not just ourselves.
- Safe environment: all opinions are valid and should be respected.
- Whenever you want to give your opinion, you are free to raise your hand.
- If we ask for an opinion and no one is speaking, you can open the microphone directly.
- Introduction
- Short talks
- Introduction talk → Led by Joel Romero, dealt with an explanation of the problem we aim to tackle, deeply digging into how complex it is antibiotic resistance. Afterwards, he gave an overview of ARIA’s approach, the details of its three main components and its potential clinical applications.
- Bacteria: XXI century robots → Led by Auba Fuster, dealt with the potential of using bacteria systems as machines that can produce whatever it is desired. Together with this, the wide range of applications of genetic engineering and synthetic biology were pointed out.
- CRISPR Technology → Led by Laisa Bonin, dealt with the basics of such a powerful technique that changed science, the market and consequently, the world. Then, she explained how ARIA does make a special and particular use of the CRISPR-Cas12 method.
- Machine Learning Fundamentals → Led by Isaac Capallera, dealt with the general description of the functionalities and possibilities in which ML sheds light to, and how did we make the most of them.
- Questions & Answers
- Conclusion and acknowledgements
- Jordi Pla, PhD in the Complex Systems lab.
- Jordi G. Ojalvo, PI in the Dynamical Systems Biology lab.
- Guillem Murciano, PhD in Oxidative Stress and Cell Cycle Research Group lab.
- Head of the Department of Infectious Diseases, Coordinator of the Infection Control Program and President of the Infection Control Committee at Hospital del Mar, Parc de Salut MAR (Barcelona, Spain).
- Coordinator of the Infectious Pathology and Antimicrobials Research group (IPAR) at the Hospital Del Mar Research Institute (IMIM) (Barcelona, Spain).
- Head of the Catalan Society of Infectious Diseases and Clinical Microbiology (Barcelona, Spain).
- Professor of Medicine at Pompeu Fabra University (Barcelona, Spain).
- Member of the Infection Control Committee at l'Esperit Sant Hospital (Santa Coloma Gramenet, Spain).
- Member of the Technical Committee at VINCat (Catalonia, Spain).
- Associate Professor of Medicine at University of Barcelona (Barcelona, Spain).
- Coordinator of the Infectious Diseases Department, Paediatric Research Institute. Sant Joan de Déu Barcelona Children's Hospital (Barcelona, Spain).
- President of the Catalan Society of Infectious Diseases and Clinical Microbiology (Catalonia, Spain).
- Head of CIBERESP (Biomedical Research Networking Centre for Epidemiology and Public Health) Group 57(Madrid, Spain).
- Head of the Catalan Public Health Agency Support Laboratory for pneumococcal and meningococcal disease and pertussis (Catalonia, Spain).
- Associate lecturer at the International University of Catalonia (online university).
- Lecturer on the Master's degree in Microbiology at University of Barcelona - Autonomous University of Barcelona (Bellaterra and Barcelona, Spain).
- Lecturer on the BIOLAC Master's degree (Clinical Analysis Laboratory) at Pompeu Fabra University(Barcelona, Spain).
- Pilar Rivera Gil, PI in the Integrative Biomedical Materials and Nanomedicine lab.
- Robert Castelo, Associate Professor at Universitat Pompeu Fabra.
- Andreas Meyerhans, ICREA Research Professor at Universitat Pompeu Fabra.
- Preventing individuals from acquiring resistant infections: Broad awareness and education strategies are needed to advance infection prevention.
- Treating existing AMR-related infections appropriately: Giving patients with AMR-related infections the best chance at recovery requires preserving and extending the effectiveness of current therapies.
- Discovering and developing new tools to reverse the trend of growing drug resistance: Infectious pathogens will continue to evolve and develop resistance to new and existing therapies. New diagnostics are essential to ensure antimicrobial use is limited to those with appropriate infections.
- WIKI basics and medal criteria
- WIKI designing
- WIKI programming and content
- Coding tips
- HTML: hypertext markup language, by TutorialsPoint [1].
- HTML, CSS and JavaScript, by Nematrian 2020 [2].
- Sams Teach Yourself HTML, CSS and JavaScript, All in One, by Julie C. Meloni [3].
1. General Population Survey
Intending to know how the relationship of the general population with antibiotics is, as well as their general knowledge of antibiotic resistance, we designed the following survey, available in three different languages (English, Spanish and Catalan). Our idea was to make people think about this matter.
The survey was distributed mainly through our own social networks, the secretary of our university, Universitat Pompeu Fabra, and other centers associated with the research park in which we are based.
The results can be found here.
2. Approaching Science to Children
Divulgation plays a key role in the scientific community as well as in society. Moreover, younger generations are being increasingly focused in this part, since being approached to this field may not only catch their attention, but could also be beneficial for the entire scientific world in the near future. Furthermore, we as a team were highly interested in viewing and explaining antimicrobial resistance from different levels of complexity, from children to experts. Altogether, the overall simplification of the problem in order to be understandable for children in elementary and high school was considered a challenge for us. To do so, a bunch of activities mixing knowledge with entertainment had to be designed for such purposes. The first one was aimed at high school students, which is the reason why it was a bit more technical, while the others were designed for elementary school children.
Introduction
A crucial part of science is sharing what makes it so fascinating. That is why divulgation and reaching different communities is crucial in spreading knowledge around society. Moreover, reaching out to younger generations can be interesting in various ways: while they get the opportunity to understand and learn about the world around them, a spark of curiosity and interest can arise. It can be the beginning of someone’s personal growth, building interests and choosing an educational path.
Approaching Science to High Schools
Every divulgation activity or event starts with reflecting on what concepts the target audience already has. Understanding which is their starting point, and from there aim to give further knowledge about the field. In the case of high school students, we had to put ourselves in their shoes and remember what we knew about biology at that time. So, in 15-16 year old teens we expected basic notions on cellular biology and biochemistry, and so we planned a DNA extraction experiment.
Moreover, we opted to complement our explanations with the following questions:
"Why do we feel dehydrated when we drink sea water?"
This first question aims to reflect on how a hypertonic salt solution will induce the loss of water from the organism or the cell, for this reason when we drink sea water we become more thirsty.
"Why do you think detergent dissolves the lipidic membrane?"
This question is used to explain how a domestic detergent used to remove grease can also dissolve the lipidic cell membrane.
This experiment can be carried out with basic, day-to-day material, and it allows for a better understanding of the characteristics of the cell, as well as how interactions with different substances affect it. The main object of the procedure is the fruit from which DNA will be extracted, which in our case were strawberries. To get that DNA, three different compounds are needed: pineapple juice, salt and detergent. The pineapple juice is employed due to the presence of a protease in it, which is employed in order to destroy the proteins that help keep the DNA compacted and packed in chromosomes (histones). Salt is employed to extract the DNA from the fruit thanks to the osmotic process, which will pump water out of the cell to reduce the gradient. Lastly, detergent is used to dissolve the lipids found in the cellular membrane, which will enable the DNA to get out of the cell and be extracted. Another component employed to finally separate the genetic material from the fruit is alcohol, where DNA will end up suspended and can be seen.
To do this experiment, you first need to wash and crush the fruit. Then, this paste of fruit has to be filtered, so that only liquid and small molecules pass, and the solid part is left out. Then, you create the extraction solution which will be formed by the three elements mentioned earlier, used to separate the DNA from the rest. This solution is mixed with the liquid obtained from the fruit, and then alcohol is slowly poured onto it so that DNA is suspended in it. Afterwards, the genetic material could be manipulated with a glass rod to better visualize the DNA and the success of the experiment.
So the main concepts acquired and reinforced with this experiment were the basic components of the cell structure, DNA biochemistry characteristics, and basic laboratory protocols such as filtration and organic liquid extraction. A basic cell scheme was used to illustrate the basic components of the cell, such as the nucleus, genetic material, plasmatic membrane and cytoplasm. Furthermore, the high level of compaction of the genetic material was explained using the analogy of a magnet: the DNA is negatively charged so it binds with high intensity to proteins that are positively charged. Also, the solubility properties of nucleic acids explain why the DNA was finally extracted from the solution using alcohol. The complementary explanation we gave was that "DNA likes alcohol very much ;)".
The kids were engaged with the activity during the whole process and showed interest in the explained topics. A positive aspect to take into account is that such an intuitive protocol let them work quite independently, they performed each step with autonomy and could take decisions on their own. Every student judged their own mistakes and proposed solutions and alternatives in order to progress with the experiment.
During the development of the experiment we had to face several problems. For instance, when filtering the strawberries with filter paper we could not do it, as the crushing of strawberries was too dense.
Then all together we started thinking about how we could solve it with the materials we had in the lab. We found some plastic plates and decided to drill holes in them and use them as strainers. We saw that it worked, but to get more accurate results we re-filtered it with strainers that were bought while looking for alternative ways to solve the problem.
We all learned that in science not only knowledge is needed, but also the ability to solve the problems presented to us.
Introduction
In this event, we tried to approach 9-10 year old children to science by virtue of simple and fun activities that provide them with fundamental knowledge regarding microbial antibiotic resistance, and how it can be developed. This event was part of a higher organization called “Edunauta”, which helps children reinforce their knowledge in a wide variety of fields through dynamic activities. Hence, our activity had to incorporate simple yet useful explanations related to how antibiotic resistance works, and how this problem may evolve in the near future.
Activity 1
With the aim of teaching a basic concept of resistance, we designed a game based on a water balloon contest between two teams. We divided the kids into two teams, the first one represented the antibiotics while the other were team bacteria. Each team had a different purpose and a set of rules:
This game is created so the bacteria team always wins, to put emphasis on the situation that is likely to happen in the future.
Activity 2
The second activity had the aim to reinforce the same concept: bacteria acquiring resistance to a certain antibiotic.
This time, only one person would be part of the doctors team while all the others were in team bacteria. The game was similar to “Infected” but with certain rules we were imposing while playing.
At the beginning of the game, the doctor had to catch as much bacteria as possible. After some time, we imposed the rule that kids with pink clothes cannot be infected, these rules were imposed until only one kid would fulfill all the rules, practically becoming untouchable and, therefore, winning the game.
Our point was for the kids to realize that, in the beginning, they could catch a lot of bacteria and, for every bacteria “turned” doctor, their job was only easier. But after each rule, catching people was more difficult and, eventually, there was nothing they could do to win against the resistant child, thus putting the scope on the big problem we are trying to solve in a more fun and simple way.
3. Dissemination events
National Student Congress for Antibiotic Resistance (feat. AECS & FEEF)
After having carried out activities in schools and institutes, we also reconsidered the idea of reaching other more specialized groups, such as students of health sciences who are training to become health professionals. Because of that, we decided to collaborate with two other health associations of students to organize a National Student Congress for antibiotic resistance.
Objectives
The Congress was organized for the weekend of October from the 1st to the 3rd in an online format in Spain, to ensure that, due to the current COVID-19 situation, safety measures and social distancing were maintained. Moreover, in this way, we were able to contact students from all corners of Spain and invite experts from different cities.
The objective of this event was to raise awareness of the current problem with antibiotic resistance that has been overshadowed by the COVID-19 pandemic situation. In addition, we took the opportunity to emphasize the importance of working in multidisciplinary teams to be able to face and effectively fight these kinds of complex problems in the not-too-distant future.
Organizing committee
The entities that collaborated with us were the Association of Health Sciences Students of Catalonia (AECS) and the Spanish Federation of Pharmacy Students (FEEF). Parts of these institutions, the organizers of the congress were: Julio de Oliveira (AECS National Public Health Coordinator), Nour Hammouch (FEEF Vice President of Communication and External Relations) and Isabel Ramón (FEEF External Relations Coordinator). Manuel Recuerda (FEEF Vice President of International Relations) also collaborated with his contribution and design of the Escape room.
Public engagement
The congress was attended by students from different fields of health sciences from all over Spain. In order to promote the congress, we created a specific Instagram account (@vsresistencias) where we posted all the information about the activities that would take place. We were active on social networks for a period of one month, during which we gradually revealed the experts who would be participating. We even raffled off some small stuffed bacteria toys, to motivate people to join in.
Finally, we passed out a registration form, so that we could later grant a certificate of attendance signed by the three associations.
Congress structure
The congress was divided into three days: Friday afternoon, all day Saturday and Sunday morning. Each presentation was scheduled for approximately 40-60 minutes, with up to 30 minutes for questions afterwards. Each day of the congress was attended by an average of 100 people in total.
Along with the registration form, we also passed a short survey where we were able to find out what topics students were most interested in or where they might be less informed. After obtaining the results, we decided to look for professionals who could address the points that students were most concerned about. Our objective was also to contact experts from different areas in order to provide a global vision of this problem and to be able to deal with it from different points of view.
To start the congress, we organized an introductory talk to the general problem presented by the organizing committee, in order to introduce the topic, welcome all the participants and explain the ground rules so that they would be comfortable during the whole congress. We also organized a small game on the longest day of presentations, an Escape room based on antibiotic resistance, with the aim of changing the dynamics a little and motivating participants to learn in a different way.
On the last day, our team also gave a presentation on our ARIA project, the challenges we are facing and the techniques we are using. The speakers were Joel Romero, introducing the paradigms involved in the problem, Auba Fuster on genetic engineering, Isaac Capallera on Neural Networks and Teresa Castaño on CRISPR-Cas.
Finally, we concluded the congress with another short presentation by the organizing committee, where a brief summary of the objectives and most important points of the congress were made. At the end, a survey was passed again to assess whether the knowledge imparted during the congress had been useful and to receive feedback on improvements from the public.
Ground rules
We established ground rules for ourselves that we tried to maintain throughout the organizing time of the congress so that the working environment would be appropriate. In order to do this, we posted some questions such as: “What do we think is important? What do we not want to lose sight of in all that we do/will do? What values are important to us in working with others?”. With this, the ground rules were the following:
We also established other ground rules during the congress so that both listeners and speakers could feel at ease and have good communication:
Speakers list
Within the list of speakers we found a variety of different disciplines, among which we found pharmacists and doctors who explained the workings of antibiotic resistance, a science communicator who explained the importance of good communication and, finally, our instructor Dr. Marc Güell, an expert in Synthetic Biology, together with our group ARIA, provided an innovative and motivating point of view to change the functioning of science for the better and to address important situations such as antibiotic resistance.
As can be noticed, the list of speakers itself also reflects the importance of working in a multidisciplinary team, a concept that we felt it was important to emphasize repeatedly during the congress.
Survey results and Feedback
One of the first questions we asked in the survey was: “On a numerical scale, with 1 being nothing and 5 being everything, how much do you consider yourself to know about antibiotic resistance?”
We were happy and proud that we had achieved our main objective: to make students aware of the problem of antibiotic resistance. We managed to get 6.9% of people who did not know anything, to learn about this issue.
The feedback received by the participants was very positive. The most repeated comments were those highlighting the organization and dynamism of the congress, as well as its interest. They also left us with other proposals for the future, such as holding another congress at an international level or of the same style but for neuronal topics.
To see all the results of the survey and feedback comments click on the following button:
Conference at UPF
In order to create awareness of the antibiotic resistance phenomenon, which is on its way to become the next pandemic for the XXI century, we organized an international conference on October 15th that was about exposing tools that may avoid this worrying future antibiotic resistance pandemic.
The conference took place in the UPF Poblenou Auditorium, and we had the opportunity to expose the status of our project. Following the sanitary protocols, the in-person assistance was limited to 208 individuals, the ones that, preferably, were first invited thanks to their positions as academic researchers related to the field, scientific students or professors. Before attending, a survey and a preregistration were required.
Besides, a virtual audience was present as well through a live retransmission platform. This allowed us to invite in advance other iGEM teams from all around the world to connect and stay tuned during our event in a synchronous way. Once our intervention was over, there was time and space for debate. Our main aim was to enjoy interactivity and a collaborative environment.
Finally, to every attendee, we issued a participation certificate. This way, we had the chance to appear in many other iGEM teams Human Practices wiki pages.
How did we organize it
Since the event was conducted in a public facility from UPF Barcelona, we needed to request permission and free renting to the University. In this context, we were given this space for organizing the Congress.
The needed assets were: armchairs, projector, microphones, attendee control and a live broadcasting service.
How did we promote it
Since an event like that one required a massive dissemination and promotion, we considered writing down invitation texts in different languages, to get not only attendees from Barcelona but also virtual ones from the rest of iGEM worldwide teams.
Besides that, by means of our auxiliary web, we promoted the event as well, having an official link from which to enroll and stay tuned about any novelty that might have arisen.
How did we conduct the talk
The talk was intended to last an approximate slot of 60 minutes, in which a thorough planning of the interventions was ideated. In this context, the aim was to create public concern about the AR phenomenon, at the same time that we kept satisfactory scientific and technical language coherence. This way, we were able to inform the general audience about what we consider an international problem to be addressed and solved, at the same time that we fed the academics and researchers that assisted with new proposals, ideas and shedding light to the field.
Summing up, the event architecture followed an organization distributed in mainly the next points:
The very first point was to answer the rhetorical question “what is iGEM?”. This way, the attendees were able to know why we were there and why we were focusing so much effort on our project. Once this was done, we went for the second question to be addressed, the one that defined our main project headline, “why is it so important to take into consideration the antibiotic resistance phenomenon?”.
By answering to them both, the context of the conference was understood. Finally, in order to talk about the whole project and its development during several months, we needed to make a laborious resumé of such a vast quantity of tasks and focus on the general architecture from our ARIA project.
After having made the introduction and prolegomena, we entered more in detail by means of four short talks given by some of our representatives in different project fronts (synbio, laboratory and computational scope). The short talks, whose presentation slides can be checked below, were:
Interactive chat discussing with the virtual and in-person attendees. With this purpose, for the virtual assistants, a Q&A forum online chat was fitted out previous to the start of the conference, through a platform called Slido.
At the end of the session, we tried to acknowledge everybody involved in our R&D path and in the event organization, so that this conference was a place to express, in an official manner, the thankfulness of every single ARIA member towards the people that helped us reach that point.
Assistance metrics
This conference had almost a hundred (100) attendees combining the both modalities (in-person and virtual). This allowed us to spread knowledge and create concern about which was the headline of our project: disseminating metrics, new technologies and a pioneer approach to fight back the AR phenomenon.
Below, one can appreciate the space of the event, a few minutes before the opening of doors.
Feedback report
Since one of the main goals of our conference was to create a collaborative and interactive atmosphere, we engaged and cheered both the in-person and virtual assistants (coming from other iGEM teams as well) to come up with their comments, suggestions and doubts. These were attended either with the portable microphone we handed them if they wanted to take part in, or via the Q&A forum mentioned above. Some of the very best virtual interventions we had are shown below.
4. Post-iGEM: future dissemination events
Catalunya-La Pedrera Conference
Thanks to the networking we have done through LinkedIn, a member of the team of the Catalunya-La Pedrera foundation got in touch with us to offer us support.
This foundation was born in 2013 to promote knowledge, scientific and cultural vocations. In fact, it sponsors various research and innovation programs for students in the last years of high school. These allow them to stay in top scientific and technological centers in Catalonia, but also in various parts of the world.
Sayansi Podcast Interview
Sayansi's team also wrote to us on LinkedIn. They are a group of young researchers passionate about scientific communication who have just started a podcast and a Youtube channel. They aim to bring scientific research closer to the community by showing its most human face; through the telling of the stories behind the whole research process.
Two members of our team will represent ARIA in an interview that will be recorded in both audio and video and will last a maximum of one hour.
ASBTEC: Association of Biotechnologists of Catalonia
ASBTEC is a professional young non-profit entity from Catalunya whose main objectives are entrepreneurship development in the biotechnological sphere as well as networking in the same field. They contacted us showing interest on our project and proposed some activities to do together: a streaming interview in their youtube channel and participation in Bionorth, a congress organized by the Spanish Biotechnological Federation.
1. Advisors
Since ARIA is divided into three fundamental parts, we needed instructors and collaborators from different backgrounds who would be able to give us advice and support to shape the direction and workflow of our project.
i) Instructors
We have had four instructors during the project, Javier Santos Moreno, Nastassia Knödlseder, Guillermo Nevot Sánchez, and Sira Mogas Díez. The first three belong to the Translational Synthetic Biology lab, while the latter belongs to the Synthetic Biology for Biomedical Applications lab. The wetlab team is the one that has called on her help the most because they are experts in laboratory work. However, they have also advised the computational group in making decisions for their application in the practical laboratory part.
Marc Güell Cargol, PI of the Translational Synthetic Biology lab, and Javier Macia Santamaria, PI of the Synthetic Biology for Biomedical Applications lab, have also guided and helped us in making decisions in order to bring our project on track. In addition, they have provided us with new ideas and solutions to the problems we have encountered during the development of ARIA.
ii) Collaborators
Apart from the help of our official instructors, we have had the additional aid of several collaborators such as:
He works with synthetic criticality and complex systems. His help has consisted of general advice on iGEM (since he is a former competitor and instructor), advice on lab techniques and use of the plate reader. Moreover, Jordi Plà also helped us with the wiki programming, specially solving some problems regarding the competition server.
He studies multiple phenomena, driven by processes such as gene regulation and information processing, observed in living systems as are bacteria, stem cells, the immune system and the brain. Due to his deep knowledge in modelling, his contribution to our project mainly consisted of giving feedback and advice about the ARIA model based on lab experimental data (see CRISPR-Cas12 enzyme kinetics model), built by two wetlab team members.
His work consists of using CRISPR-Cas9 for genome editing in S. pombe. Guillem advised us on methods to check the efficiency of cloning in a fast way by adding a GFP reporter together with the plasmid to be cloned.
2. Experts feedback
i) Medical doctors and researchers
Our project is designed with the aim of helping the healthcare system in antibiotic resistance detection and characterization. For our system to meet all the needs of clinicians, we have met with experts to evaluate it and ensure that our final development meets all their requirements.
Given that all the interviewed doctors have a healthcare vocation, but are also very involved in biomedical research, they gave us excellent advice in both directions.
Affiliations:
Medical needs against AR?
The mechanisms of resistance in patients with bacteremia are very urgent to detect. Working with blood is complicated because of clotting, protein matrix resistance, etc. In addition, the handling of blood samples in the laboratory is complicated. Currently, scientists are working with serum after having centrifuged the blood. Clinicians, however, want to work with the whole blood to see the effect of bacteria on the immune system.
Although it is possible to work with different types of samples (whole blood, plasma, serum, respiratory secretions, peritoneal fluid, bile, etc.), the one that has faster applicability is urine. This is because it has a higher concentration of bacteria. However, its applicability presents more restrictions. To be more scalable, he recommends using blood, although it has a low concentration of bacteria, and it is more difficult to work with it.
Research proposals?
During the development of Alpha, it is important to consider those bacteria that express mechanisms of resistance to antibiotics only in the presence of the antibiotic and not before.
In Omega, it is essential to pay attention to the patient's immune system as the patient's main data.
Affiliations:
Medical needs against AR?
Healthcare workers in front of a sick patient need to know two main things: which microorganism is the one that presents resistance, and which is the pattern of bacterial resistance it has. This would significantly reduce the inappropriate use of broad-spectrum antibiotics.
It is also important that the device is point-of-care and that samples can be analyzed within the hospital itself, rather than being transferred to a laboratory, which would save a lot of time and money.
Research proposals?
It would be interesting to incorporate into the ARIA AI system a mechanism that analyzes the infectious pathology of the patient and that determines the risk that the patient has of suffering complications in the future due to the infection. If the chances of danger are moderate, the user might be recommended to use a broad-spectrum antibiotic. On the contrary, the medical user must establish a more specific treatment.
Affiliations:
Medical needs against AR?
It is very important to know which bacterial species we are fighting against and to detect resistance quickly and cheaply. A paper-based detection panel is a fantastic solution.
Applying the ARIA project to already grown bacteria is an interesting and applicable step to later improve the system to patient samples.
Research proposals?
Before doing CRISPR-Cas12 detection directly with blood samples, it is very important to add a previous amplification step since the blood has very little bacterial concentration and CRISPR system has not enough sensitivity.
As it is necessary to identify the bacterial species, the 16S RNA gene, which is common in all bacteria, can be identified first. Subsequently, once only organisms belonging to bacterial populations are available for the following steps, amplify these genomes in parts using specific primers in each matrix spot: according to specific genes.
ii) Multidisciplinary researchers
Once the project approach was defined, we considered constructive the fact of consulting specific professional academic researchers non-directly related to our field of study, so that we obtained a multidisciplinary vision about every single aspect from our proposal from their feedback, impressions and possible enhancements about the development status we had accomplished.
Pilar Rivera is the head of the UPF Integrative Biomedical Materials and Nanomedicine lab, whose main research lines reside in nanomedicine, nanotoxicity, biological and functional characterization of nanostructured materials and nanomaterials for intracellular ion sensing and microcapsules for controlled and remote release.
Robert Castelo is the head of the IMIM-UPF Functional Genomics Group and of the Research Programme on Biomedical Informatics (GRIB). Associate professor of Bioinformatics and Biostatistics at the UPF as well.
His main research line is based on narrowing the gap between sequence and function by developing computational tools to build network models of molecular regulatory mechanisms from high-throughput genetic and genomics data.
Andreas Meyerhans is the head of the UPF Biology of the Infection Lab. His main research lines are focused on virus evolution and lymphocyte responses in persistent human infections (HIV, HCV, CMV and Mycobacterium tuberculosis).
After sending, to the three of them, a document prepared for their peer-review and receiving their feedback, we summarized all their comments and advices in the following attached PDF:
3. Johnson&Johnson Antimicrobial Resistance Webinar
Communication coming from an outer source was enriching as well, since with this chance, ARIA would receive points of view that were coming from an Antimicrobial Resistance R&D program leaded by a multinational association such as J&J. Thus, we attended 15th september a webinar about innovation and breakthrough in this hot topic science field.
Lecturers
Niels Wheeler: Innovation Activation Manager.
He had experience managing infectious diseases & vaccines therapeutic area of Janssen as well as in the roll-out of Janssen’s Ebola Vaccine.
Elena Fernández-Kleinlein: Head of JLABS EMEA.
She catalyzes the translation of science and technology into valuable solutions for patients and consumers across pharma, medical devices and consumer healthcare.
Alfred Tonelli: Head External Innovation, Global Public Health and R&D, Janssen.
Experience in pharma companies where he initially functioned as a Senior level Functional Leader. He headed Early Development in Janssen's first External Innovation Department.
Background of the webinar
The spread of drug-resistant pathogens, known as antimicrobial resistance (AMR), is a growing public health concern. Overuse of antibiotics, or not using them as prescribed, contributes to growth of resistant bacteria, which renders antibiotics less effective or ineffective. It is estimated that by 2050, AMR infections could cause 10 million deaths annually. Furthermore, the increase in hospitalizations and antibiotic use in COVID-19 treatment have been predicted to further exacerbate AMR. Johnson & Johnson has a commitment to develop and deploy innovative technologies and treatments to combat the growing threat of AMR.
Antimicrobial resistance (AMR) is one of the defining scientific, health and economic challenges of our time. Without urgent and meaningful action to address specific diseases and system-level issues, patients, families and communities around the world will face a tremendous threat in the years ahead from untreatable infections. While AMR is fundamentally driven by the ability of pathogens to evolve, its impact is amplified by factors that span economic, healthcare and agricultural domains.
Together, we must improve how we prevent infections in the first place, effectively deploy and deliver current tools across all countries, and spur the development of new innovations. We must address multiple AMR systemic failures, including lack of early research; the high costs and risks of developing new medications and diagnostics; and the barriers to finding, diagnosing and treating patients across all geographies and economic backgrounds.
Thoughts about Antimicrobial Resistance
Resistant pathogens can cause outbreaks locally or be carried within and across national borders. While the impact and threat of AMR are global, the main causes and consequences of AMR play out differently in developing and emerging markets compared to developed countries. That said, three responsive strategies are critical in every context:
Collective action to address antimicrobial resistance
Johnson & Johnson announced it has joined more than 80 companies and organizations in signing the Declaration on Combating Antimicrobial Resistance (AMR). The declaration outlines for the first time how industry and governments can work together to support sustained innovation to address the growing problem of AMR, common yet life-threatening infections difficult or even impossible to treat.
Inspirational quotes
For many diseases, patients have few options for treatment. Therefore, safeguarding appropriate use of current options is critical to ensure patients do not develop resistance.
The emergence of so-called 'superbugs,' or drug-resistant bacteria, forces our attention to the inadequacy of our therapeutic arsenals and the need for new incentive frameworks for antibiotics to stimulate the level of R&D investments so critically needed to strike back at drug-resistant infections.
4. WIKI formation
One of the main milestones to be accomplished during iGEM Competition is the construction of a WIKI page, which integrates the status of the scientific approach that was conducted during months. The WIKI includes all the information that ARIA wants to communicate their project to the whole world, and it is because of this that its proper development is extremely important.
As we already knew, a vast number of past teams received formation and tips about how to design, construct and code the aforementioned WIKI.
Therefore, we found it really useful to attend a master-class organized by the predecessors UPF iGEMERs, HORMONIC, aimed at several Spanish iGEM teams. This workshop addressed all that aspects encompassed by the WIKI page, from how to properly organize the content to more technical aspects as it is the coding itself.
Speakers
More specifically, the ones that were responsible for instructing us in the Workshop were Miriam Caravaca, Nerea Álvarez de Eulate and Quim Martí, from HORMONIC 2020 iGEM Project.
Outline
The structure of this WIKI workshop was based on the following points:
General introduction of the main characteristics to be included in a WIKI template. Apart from that, specific medal criteria were summarized, in order for the attendant teams to be eligible for them.
How to make the appearance as clear as possible and how to find the balance between simplicity and technicalities in terms of the scientific language used.
Based on three main blocks, in this workshop we received tips about the information in form of text, the pictures and images and finally the videos and animations.
Finally, when it came to becoming more technical, we were given short live-demos on how to combine different programming languages, and how to test them interactively so that the coding experience was as instructive and guided as possible.
Apart from the workshop, in order to develop our WIKI page, we did a deep research over the internet to find guidance and support when it came to the coding of the WIKI. This includes YouTube tutorials provided by other iGEM teams from previous years and also literature as the following:
Finally, after having developed our WIKI page, we wanted to also make a little contribution to future iGEM teams, which consists of some guidelines that we found useful to point out and that can be found in the Contribution section.
