Team:UFMG Brazil/Notebook




Project

Overview

Problem and
Solution

Chassis

Devices and
kill switch

Lab Work

Safety

Notebook

Protocols

Results

Modeling

Practices

Overview

Integrated Human
Practices

Public
Engagement

Synenergene

Overview

Application
Scenarios

Techno-moral

Team

Our Team

Attributions

Collaborations

Sponsors




Notebook

  • November/2014:
    • Brainstorming ideas for the 2015’s project.

  • December/2014:
    • The idea of teaching an “Engineered Machines” summer course at the university surges.

  • January:
    • Week 1: vacation
    • Week 2: vacation
    • Week 3: Definition of this year’s project: To modify a Leishmania so that it treats inflammatory articular diseases. Plus: A new chassis for iGEM!!
    • Week 4: Begin of theoretic research for the project.
      • Week 5: Begin of theoretic research for the project.

  • February:
    • Week 6: Planning and advertising the summer course.
    • Week 7: Planning and advertising the summer course.
    • Week 8: End of course’s registry. Over 800 people applied, which was a big surprise for us! We decided to have a big lecture for everybody who registered, and selected 40 people to participate of the Summer Course.
    • Week 9: 1rst Engineered Machines Summer Course”, held at UFMG’s campus.

  • March:
    • Week 10: Such was the success of our Summer Course, we decided to admit new members on our team. Interviews with the candidates and posterior selection of new team members were made this week.
    • Week 11: First meeting with the whole team! We greeted the new members and put them up to date on the project.
    • Week 12: We divided the team into groups, so that the research would be done quicker. During the weekly meeting we had the idea to start a group on UFMG to discuss synthetic biology (synbio) with anyone who wished to do so, bringing together people from different backgrounds.
    • Week 13: The project logo was presented by our team designer. An official letter asking for sponsorship was written and sent to several institutions and companies.

  • April:
    • Week 14: Meeting with a team member to learn how to use a specific protozoan databank. Team’s registration on iGEM!
    • Week 15: Drawing biobricks, studying vector use in Leishmania and kill switch elaboration. In parallel, the idea of creating a weekly discussion group to the university community (maybe a Journal Club) came up. Team members joined the UFMG_Brazil team on iGEM’s website.
    • Week 16: Lecture given by the team at “ExpoEngenharia”, an engineering exhibition fair at UFMG. An amastigote-specific vector was defined and drawn. Contact with Dr. Hira Nikhasi, from the FDA, the Leishmania donovani Centrin-1-/- non-virulent strain creator, to get his approval to use it on our project. Modeling brainstorm on how to inject Leishmania into humans. Thinking about doing a R statistics course and a synbio workshop to raise funds for the team.
    • Week 17: Modeling approach was decided: simulate intravenous systemic injection as well as intra synovial joint injection. Primers were drawn. The Biobricks arrived in Brazil, but are retained by Brazil’s Health Surveillance National Agency (ANVISA).
    • Week 18: Professor Flávio Almeida Amaral was a guest on our meeting and gave us a lecture about inflammatory joint diseases and animal usage on such studies. Thinking about a mosquito-based kill switch. Synenergene project submission.

  • May:
    • Week 19: Lecture given by the team at “ENAPEBI - VII Encontro de Pesquisa em Bioquímica e Imunologia”, a biochemistry and immunology search meeting, held at UFMG. Our team got fundings from the UFMG’s research and extension dean to hold a SynBio Workshop.
    • Week 20: Synenergene project submission. Skype meeting with UFSCar-Brasil Team to discuss a possible collaboration. Possibility to use a technetium Leishmania staining to determine its distribution pattern on mice.
    • Week 21: Submission of the project on a Brazilian crowdfunding platform, Benfeitoria.
    • Week 22: Gene sequences sent to IDT for synthesis. Partnership with Oswaldo Cruz Foundation (Fiocruz) to cultivate Leishmania. Discussion of the wiki’s theme. Contact with some inflammatory joint diseases patients. Possibility of making the “Idea Incubator” a formal discipline at UFMG, planning the course.

  • June:
    • Week 23: We received the biobricks. Our team got selected to be a part of the Synenergene project! Problems with the gene synthesis, IDT sent us a technical report. We will repair the sequences’ problems as soon as possible. Professor Gonçalo Amarantes from UNICAMP and Professor Francis Nunes from UFSCar accepted our invitation to give a lecture on our SynBio Workshop. The Brazilian Ministry of Science and Technology wants to support us, and will pay one of the advisor’s trip to Boston.
    • Week 24: Skype meeting with all the other teams that got selected to the Synenergene project. We started to write the wiki’s texts and defined some aspects of it.
    • Week 25: Sign up for the InterLab measurement studies. First “Idea Incubator” meeting with over 40 students from different areas. Meeting to decide the details of the SynBio Workshop. The funding for our community lab project was approved.
    • Week 26: Skype meeting with our Synenergene supervisor, Kjetil Rommetveit. Our team got invited to participate of the iGEM’s Brazilian meeting, Jamboré, promoted by the UFSCar-Brasil team. Team members Ana Carolina Prado, Tiago Mendes, Rodrigo Baptista and Natália Souza were interviewed by BH News TVand team member Cristiane Toledo got interviewed bt TV UFMGchannel; about the iGEM competition and our project. Safety form submitted. The kill switch had too many problems to be synthesized, so we chose to synthesize just the INF-ß construction for now.

  • July:
    • Week 27: Public survey for Synenergene in several locations in the city of Belo Horizonte. Begin of the InterLab experiments with the expansion of XL1-blue and BL-21 bacteria. Advertising our SynBio Workshop, which will happen on August 5th. Team advisor Tiago Mendes was interviewed by Rádio UFMGabout iGEM and our project.
    • Week 28: Further work on the organization of the SynBio Workshop, including buying airplane tickets and booking hotel rooms for the speakers from São Paulo. Synenergene text alterations and addition of more details. Our team received an invitation to give a lecture at UnB (Brasília’s University) in october, about synbio and the iGEM. Jamboré participation via Skype. InterLab experiments are going wrong, as we are facing an antibiotic problem. To solve that, we will buy new antibiotics and restart the experiments. Last Idea Incubator class before vacations, we will return in early August, when classes return.
    • Week 29: Giant Jamboree registration of 3 team members. Further advertisement of our SynBio Workshop. Synenergene text modifications. Meeting to create a text-delivery schedule for the wiki. InterLab: antibiotics problem solved, new bacteria produced. We can now carry on with the experiments. Modelling meeting to discuss some project approaches.
    • Week 30: Synenergene restructuralization of the project according to Kjetil Rommetveit’s suggestions, focusing more on the social implications of our LeishMANIA project. Meeting to define wiki’s design. Presentation of of the modelling’s progress done so far, discussion to refine the parameters. IDT genes arrived, so we planned the project’s experiments.

  • August:
    • Week 31: Collaboration with Aix-Marseille team by answering their survey. UFMG’s techno-administration employees are on strike, therefore the semester’s registration is suspended, as well as every class, postponing the Idea Incubator’s return. SynBio workshop happened this week, and it was a total success! Professor and instructor Liza Felicori was interviewed by the newspaper “O Tempo”, and the article got the front page! Bacterial expansion of the plasmid containing IFN-ß and further clone miniprep.
    • Week 32: Kelly Drinkwater asked us to better explain some safety aspects of our project and update the “About Our Project” text on iGEM’s website. The synthesized primers arrived, so we could continue the experiments. Amplification of the IFN-ß biobrick by PCR, followed by its digestion and binding to pGEM and pSB1C3 plasmids. InterLab: successful cloning of the P1-22A; P1-22K; P1-20K and P4-21J promoters. That was necessary due to the low amount of biobricks sample. Replacing the modelling with real data, adding clearance, phagocytosis and half-life of macrophages and Leishmania. Starting to come up with the Giant Jamboree’s presentation. Wiki design and content meeting. Synenergene meeting to improve project’s aspects and survey.
    • Week 33: Wiki’s animation sketch in progress; texts starting to be written. Modelling data were optimized, plotting for wiki. Scheduling technetium Leishmania staining (to determine its spreading pattern on mice) with collaborator. Scheduling interview with RA patients for Human Practices. Writing Techno-moral Scenarios for Synenergene.
    • Week 34: Idea Incubator’s return. Our InterLab experiments went completely wrong: we had a major setback because of the Brazilian import policy, and the biobricks only arrived in July; also, we spent a lot of time standardizing the protocols, the bacteria did not glow as it should, and the limited amount of DNA made it hard to transform the biobricks. Problems in cloning IFN-ß as well. Interview with RA patients was made.

  • September:
    • Week 35: Definition of the topics to be discussed in the presentation at the Giant Jamboree. Problems in cloning IFN-ß were solved. Establishing protocols for technetium Leishmania staining. Defining a practical action to inform the society about our project.
    • Week 36: Discussing presentation for Giant Jamboree. Requesting an interview with rheumatologist specialist doctor about arthritis.
    • Week 37: Discussing presentation for Giant Jamboree. We went to the streets of Belo Horizonte to promote synthetic biology and our project for society.
    • Week 38: Social action LeishMania at Praça da Liberdade (Portuguese form for Liberty Square), Belo Horizonte. We took a glove which simulates RA symptoms to sensitize society about how limited are the joints of patients affected by this disease. Also, we collected people’s opinions on the acceptance of the use of our chassis to treat RA and asked for their ideas on how science could make the world better. Wiki upload.
    • Week 39: Giant Jamboree!