March
1st week (March 16th to March 30th)
This is the first time we heard about iGEM. Two weeks before the first official meeting we were informed of the possibility to participate in this event. It was also raised the possibility of having a meeting with students that participated in the previous year to share their experience and what we could expect if we embark on this adventure.
2nd week (March 30th to April 5th)
So, on the 30th of March 2021, the first meeting occurred, where we for the first time informed about our interest in participating in iGEM. It was also at this meeting that we got together with previous students who participated in the previous year, to answer some doubts we had about participation in iGEM and to get some knowledge of the experience that the two students had during their participation. Additionally, the brainstorming about the suitable theme for development has begun.
April
3rd week (April 6th to April 12th)
In this meeting, several ideas for the iGEM project were discussed. Our advisor has proposed the repartition of students into small groups for further research on the proposed ideas and then share their findings the following week. We also created our official email to address further needs.
4th week (April 13th to April 19th)
There were many ideas presented in this meeting:
1) The removal of plastics from the ocean water through a vacuum cleaner like machine;
2) The substitution of the Haber-Bosch process;
3) Trying to combat a plant plague, preferably, a portuguese associated one was also an idea in discussion.
Afterwards, we made the following groups to come up with solid and attractive presentations for further voting. Groups composition: Haber-Bosch (Guilherme, Ana, Fábio, André and Bárbara), Microplastic Degradation (Olga, Rodrigo, Vitor, Rita, Henrique, Alexandre) and Plant Plague (Francisco, David, Marta, Fredi and Diogo).
5th week (April 20th to April 26th)
We proceeded with the presentations. All presentations were catchy, informative and compelling. It will be a tough decision to make.
6th week (April 27th to May 3rd)
After a whole week of deliberation, the most voted project proposal, the bacterial degradation of microplastics. We have decided our theme! Let’s get to work! For logistic matters team members were divided into 3 (bibliographic) research teams, proposed to address distinct aspects of the project: (i) microplastic composition; (ii) microorganisms and/or enzymes involved in microplastic degradation; and (iii) technologies involved in the collection and/or treatment of microplastics.
Now the fun part has begun, the search to make our project come true. Baby steps!
May
7th week (May 4th to May 13th)
We got to share our first finding with each other. The following subtopics were focused:
1) Microplastics Composition;
2) Microorganisms/Enzyme capable of Degrading Plastics ;
3) Technologies for harvesting and processing microplastics .
This meeting was also extremely exciting since we had to proceed with the election of the Student Leader. First thing first, we started with nominations and applications, and the following week was to vote on who we though would suit the best in this position.
8th week (May 14th to May 17th)
This week was only about good news, we chose our team leader – Guilherme Alves. Furthermore, our team had a little member growth. With the join of new members, we made a quick tour on what have been discussed so far and proceeded with the exposition of our analysis: microorganisms used to degrade the microplastics, such as E.coli, Bacillus and Pseudomonas.
It was suggested by our supervisor to focus on some microorganisms like Pseudomonas and to search for different metabolic pathways related to degradation of microplastics.
9th week (May 18th to May 27th)
We manage to come down to two microorganisms possible for our project, now only left to choose which one is better. To do so – we need a little bit of research. The following task consisted in gathering the molecular information on Bacillus and Pseudomonas.
However, the project is not only the research we also did a little brainstorming on the next steps of the project (possible application of this project in beach cleaners) and some doubts were clarified. Our meeting started to be more lively and fuller, like this:
10th week (May 28th to May 30th)
After having our project and our microorganism chosen, B. subtilis, we started to collect the information on laboratorial procedures and the products needed for our research. Well, smells like another task is coming up.
June
11th week (June 1st to June 17th)
The meeting started with the sequence analysis of our bacteria. after we proceeded with the order of the peptides and sequence that will possibly be used in experimental work. Really exciting and important task.
The new assignments were distributed to groups, as listed below:
1) Mutant enzyme sequence: Ana, Francisco, Vítor
2) Promoter and signal sequence: Guilherme, Marta, César, Fábio, Alexandre
3) List of protocols and reagents: Rodrigo, Bárbara, David, Fredi, André
4) Plasmid Cloning and Terminators: Pedro, Olga, Henrique
At this point we have many things to do, no time for slaking.
12th week (June 18th to June 21st)
At this point, we are already choosing our project name, we came up with idea of P(L)AST the ocean cleaner. Cool right, it is like a band-aid you put on your wound to protect, the same as with our project, that is meant to protect the oceans.
During previous week, we conducted an interview to Paula Sobral where she gave her specialist opinion. She also proposed and mentioned the necessity of biosensors in this area, in order to identify microplastic, which made us wonder about our original idea.
Next, groups were made:
1) Wet Lab: Ana Ferreira, André Piteira, Bárbara Fernandes, César Duarte, David Cortiço, Fábio Queiróz, Francisco Sobral, Fredi Brigham, Guilherme Alves, Henrique Silva, Marta Cação, Olga Chervonovska, Rodrigo Barriga Alves e Vitor Mordido
2) Engineering: Alexandre Coelho, André Piteira, César Duarte, Guilherme Alves, Marta Cação
3) Sponsors & Financial Analysis: Diogo Torres, Olga Chervonovska, Inês Ventura
4) Computational/Modelling: Alexandre Coelho, Fábio Queiróz, Francisco Sobral, Fredi Brigham, Henrique Silva, Rodrigo Barriga Alves
5) Human Practices/Impact: Ana Ferreira, Bárbara Fernandes, Pedro Nunes, Rodrigo Barriga Alves, Vitor Mordido, Inês Ventura
6) Communication: David Cortiço, Diogo Torres, Pedro Nunes, Rita Teixeira, Inês Ventura, Olga Chervonovska, Rodrigo Barriga Alves
13th week (June 22nd to June 29th)
After Paula’s Sobral interview the group was divided between biosensor and degrading technology. After some voting and discussion, we finally managed to come up with the final decision! Which one is it going to be?
We choose our original idea the degrading technology. Well, they always say, original is always better! We thought so too!
14th week (June 30th to July 6th)
Since we already have the groups established each has now a specific task to do.
1) Informatics/Modelling: this week was about organization and task distribution.
2) Wet Lab: MHETase strategies (Marta, André, Henrique, Fábio, Bárbara). We ordered our material, however there were delay and problems in the customs, we wonder when our plasmids are going to come so we can start our work. We have this idea of implementing the Idionella PETase and MHETase into Bacillus, by doing this we hope to power up Bacillus and make it more efficient in microplastic degradation.
3) Engineering: state point and discussion of project, how we can implement it, what are the best ideas and ways of doing it.
4) Finances: have already started doing powerpoint for companies and gathering possible sponsors and contacts. As soon as the powerpoint is finished we will send it to the companies.
5) Communication: this one had the most work to do. Starting with the promotional video. We choose to make video a little bit cartoonish. Everyone loves watching cartoons, right? Not only we could attract older audience but also the younger one! Also we discussed several ideas for Educational purposes: the idea of “Synthetic Biology Event” – mainly directed to university students; environmental side – directed to primary or secondary classes; taking part in beach cleaning activities; solidary events; example: bottle lids. The most talented ones are also starting to create our logo. So excited about the outcome!
6) Human Practices: they also did not waste time, started right away gathering the information on contacts for collaboration, related projects and further collaboration possibilities.
July
15th week (July 7th to July 12th)
We conducted different meetings during the week, and present the highlight on general meeting, so everyone is aware of all the work.
Engineering: it was presented which type of microplastic is most problematic - particularly PET and PE. The reason behind it is that most microplastics were found in sediments, mainly PET - because it has a higher density than water. Additionally, a reaction caused by UV radiation leads to PE precipitation.
It was also discussed microplastics separation strategies, it was proposed a two steps purification protocol: one at the local of collection, to limit sediments quantity transferred; another later to obtain a more purified and enriched sample in microplastics - since some sediments and microplastics might present similar characteristics.
For a location to implement the system, it was first suggested ETARs (Estações de Tratamento de Águas Residuais - residual water treatment facilities). Another possibility for an application site would be piscatory regions, as the fishing nets are one of the causes of microplastics in water.
For the collection of sediments and water it was suggested the use of dredgers, a boat designed for dredging harbors. However, further research are required in terms of the legislation and companies interested in it.
Communication, Sponsors, and Human Practices: In the meeting with the ITQB communication office, it was considered the possibility of organizing a workshop for ITQB, IGC, and iMM about the reduction of plastic consumption in the laboratories, as well as, implementing plastic recycling in ITQB. They will also provide help with institutional contacts (such as the Pavilhão do Conhecimento, Oceanário, and Aquário Vasco da Gama) and promote communication with the city councils.
Regarding the possibility of making a construction with collected plastics, it was suggested sending an email to all ITQB personnel – all ideas are welcome, the more the merrier. Another option was doing it as a project with different schools.
The communication group has also finished the presentation of the project, and the guide for the promotion video has been written – next stop: execution and drawing!
Wet Lab: In the previous meeting, work was divided into the search for more appropriate protocols, define the MHETase strategy, and identify the best mutant enzymes.
Our first first results and our lab WORK! We started with the performance of a PCR to amplify the genes with the ordered primers and the amplification quality was verified. So, later they can be inserted into the plasmids.
Modelling: Currently, it is being researched multiple Bacillus models, for comparison, to identify which would be the best model to use.
Who said research work is easy? We need to search and compare different models and find the most suitable one! Chop chop, time wait for no one!
16th week (July 13th to July 19th)
Wet Lab: it was presented the best mutant enzymes. We found that relative to PETase mutation there are a lot of mutants, to be more precisely there are 13 of them which lead to an increase of activity. There is also a linker which binds PETase and MHETase also increasing their activity. It is a promising start!
Also, good news, our plasmid kit directly from Headquarters is finally here! How let’s get our hand dirty! If you know what we mean!
Great news! Our dear friend Beatriz Almeida has finished drawing the promotional video! Now we are going to do a voice over! Our lovely Inês Ventura was chosen to be the narrator, unanimously. And it is done!
17th week (July 27th to August 2nd)
Communication: A weekly news system regarding microplastics was created to keep the team updated on current events concerning the topic. Also, we created our social media account (Instagram) for this as an outreach strategy. We also discussed the enrollment on the Latin American encounter. Our team members were challenged to make a small video explaining why they wanted to join the team, how they know about iGEM, and their interests.
Sponsors: Details regarding the proposal pitch were discussed and adjusted, as were optimal contact dates to potential sponsors. A crowdfunding project (GoFundMe®) was created for the team in order to collect the donations.
Wet Lab: We had a little trouble, since the plasmid was nonfunctioning, so we managed to contact the Uppsala team to help solve the problem. However, it did not stop us from doing another essential task such as elaboration of a list of programmed activities (cloning strategies, tests involving signal peptides, PET degradation assays).
August
18th week (August 3rd to August 9th)
Communication: It started by defining the strategy to promote GoFund Me, using ITQB communication services and later sending emails to all ITQB members.
Wet Lab: Plasmids have not arrived yet, however the design strategy, protocols and mutants are defined, André compiled the work that has been done so far and the work plan (English).
Human Practices: document compiled with contacts, document with structured events (powerpoint), beach cleaning event (with town hall, with NAS, with scouts) were made. Our team members are so organized!
Informatics Modelling: checking if Bacillus can degrade ethylene glycol, which enzymes we need to add. The main focus is, however, ethylene glycol since it is the energy source of system.
We started organizing the Wiki and we are participating in LATAM, so we are looking for volunteers to do the presentation!
19th week (August 10th to August 16th)
Each group discussed what had been done during that week, progress, and the difficulties they had encountered. We are taking shifts to go to the laboratory. Everyone is eager to go!
20th week (August 17th to August 23rd)
Starting with good news, we have our LATAM speakers: André Luís, Guilherme Alves, Olga Chervonovska, Henrique Pereira
Wet Lab: Since there is a delay in laboratory work, research on following matters was requested: conditions to be used in the bioreactor (tolerance of bacteria, preferential conditions, alternative carbon/energy sources).
Modelling: already has the idea of the pathway degradation of PET to generate energy through plastic. They are undecided whether to use glycolate, but apparently there may be other alternatives, and the first way is not easily executed, they are studying other possibilities. The model does not have a shuttle that is required. Further research is needed.
21st week (August 24th to August 31st)
We are preparing for LATAM! The presentation is on the 28th - this is the main event this week. Everyone is excited. While our volunteers are dedicated to this presentation, the rest of the team is working hard on further research.
Engineering is looking for ways to conciliate our degrading bacteria with ETAR’s bioreactors. Either with the insertion of a new tank only meant for microplastic treatment or combining other tanks with bacteria. Pretty genius, right?
Human Practices: this part of the team is preparing Conferência do Mar. Event where we invite other iGEM teams and specialists to talk about their project and work.
September
22nd week (September 1st to September 6th)
Our university has a lot of events coming up, and we are thinking of making our presence there. There are a lot of logistics behind every little event, our hardworking bees haven´t stopped yet.
23rd week (September 7th to September 14th)
We received a proposal from a Mexican team for collaboration. Fingers crossed; we hope everything will be fine.
We are having problems with our plasmids, so we need to change our strategies, we need to use different sets of primers. We are confident in our work, we know everything will be fine.
24th week (September 15th to September 20th)
Everyone is so busy with their master thesis. However, there is always time for iGEM. Wet Lab proceeded with the creation of an experimental protocol for tag exportation efficiency in Bacillus Subtilis, alternative protocols were set to be discussed further. HumanPractises planned for upcoming public events.
Creation of drafts with information for the teams Wiki page were set to be created for each group. It has begun. One month until official wiki FREEZE.
25th week (September 21st to September 30th)
We are working on parts for Wet lab. Our biochemist Barbara is responsible for this task, it is important since this work will be left for following iGEM generations get inspired and guided. Another good news, we are having success in the Lab! Check this out:
October
26th week (October 1st to October 8th)
It is now 21 days left for wiki freeze. Our team started to fill what is missing. We are not panicking. Yet. We are just stressed.
27th week (October 9th to October 16th)
This week our three volunteers - André, José and Olga - went to primary school; this visit meant to sensitize on the issue of microplastics and the excessive use of plastics. Well, what can we say, the children were amazing, really smart and really curious. A lot of them have good daily habits so we really felt that our purpose was understood. It was such a pleasure!
28th week (October 17th to October 21st)
We are really working on Wiki, there were some delays, but this won´t stop us from finishing our wiki. Some sleepless nights won’t harm anyone.
