Team:ULaval/Notebook
Notebook
January 23rd 2019
Helping during Career Day at Université Laval to fund the team
François, Nathan, Pascale, Marianne, Florian and Catherine
January 2019 - February 2019
Recruitment and committee formation
François, Nathan, Élodie, Catherine, Florian, Marianne, Pascale, Lucas
Planned our comitee's objectives and size, tried to broaden the disciplins from which the new students could come from, as last year it was mostly from our biochemitry, microbiology and bioinformatic's department.
February 14th, 2019
Project design and planification
Whole team
Meetings discussing our objectives and the parts of the project.
February 27th, 2019
Science committee job distribution
François, Angel, Carla, Pascale, Guillaume, Ahmed
We decided who would focus their efforts on which scientific aspects of the project.
March 19th, 2019
First experience with NUPACK to model RNA secondary structure
Angel, Elodie
Learning how to use NUPACK by modeling structures in their server and with their command-line tool.
April 1st, 2019
First Toehold designed by hand
François, Elodie
First try at designing ToeHold switches by hand. This proved very complex, and was partly what motivated us to work on the tool.
April 15th, 2019
Project presentation in our department
François and Nathan (presenters), Carla, Angel, Pascale, Guillaume, Elodie, Catherine
Meeting with the department's researchers to receive feedback on our design and our understanding of the problem.
April 18th, 2019
Best Scientific Project winner at the Gala de la vie étudiante
Whole team
May 8th, 2019
First full version of the toehold design script (designing a toehold for a trigger)
Angel
Writing Python code to run NUPACK automatically and analyze the results.
May 10th, 2019
Submission of our presentation plan to the TEDxQuebec coordinator
Martine and Nathan
We had to submit a plan and summary about our presentation. We also had to tell them how our presentation would be interesting to their public. We also had to submit a small video summarizing our talk.
May 19th, 2019
First 3D model of a toehold riboswitch
Angel
Designed the model of the riboswitch with RNAComposer and evaluated its quality with MOLProbity.
May 22th, 2019
Pint of Science Québec organization + presentation
Elodie, Florian and Martine
Presenting our 2018 project and vulgarizing synthetic biology to the general public in a pub.
June 1st, 2019
Extension of the script to look at all candidate triggers in a gene of interest
Angel
Tried with different triggers in a gene to study which ones have the most desirable energetic parameters.
June 8th, 2019
First coaching for the TEDxQuébec presentation
Nathan and Catherine
Practicing the TEDxQuébec presentation with the other speakers and three communication coaches.
June 23rd, 2019
Toehold gBlocks received from IDT, cloning starts
François
Cloning toehold inserts
July 2nd, 2019
First design of microfluidics circuit
Francois, Ahmed and Nastaran
A two-level microchip with three reaction chambers, but lacked waste disposal on one step as it was fixed later.
July 5nd, 2019
Interview with a journalist from the Quebec Science magazine
Martine and Karine
The magazine's goal is to inform people about the current advances in science. The journalist (Joel Leblanc) mainly asked questions about the projects the team has carried out until now; AdrenaYeast and ADN. He also asked questions about synthetic biology and its ethical implications. The article should be published between December and February.
July 6th, 2019
Collaborative comic submission to iGEM Wroclaw
Martine, Jean-Michel and Angel
Taking photos in specific places for Wroclaw to build their comic
July 14th, 2019
Started molecular dynamics simulations (MDS) with the toehold 3D structure
Angel, assisted by Patrick Lagüe
Ran MDS with NAMD in our server to study the dynamics of the 3D structure.
July 16th, 2019
Skype call to discuss collaborations with iGEM Concordia
Nathan and Angel
Planning modelisation and computation sharing
July 20th, 2019
Participation in the meetup organized by iGEM Western Ontario
Angel and François
Presenting the advancements so far with other Canadian teams.
July 27th, 2019
Competent cells
Carla
We made the competent cells using the CaCl2 method.
July 30th, 2019
Alternative innovative funding opportunity launched
Florian
We put remaining designs from diverse activities and new ones on the subject of synthetic biology or microbiology on shirts to both promote science and find a new way for the student community to get involved with our activities
August 1st, 2019
Change in cloning design
Francois
We had a problem with one of our plasmids, so we changed the backbone on one of our PI's instruction.
August 5th, 2019
Participation in the meetup organized by iGEM MIT
Angel and Nathan
We showed our general structure with human practices and public engagement, and the judge's comments helped us shape more thouroughly our approach
August 8th, 2019
Popular Science On microbiolgy presentation at Club des petits débrouillards Summer Camp
Julien, Florian and Guillaume
Presentation on microbiology where kids can participate through quiz and are invited to "contaminate" petri dishes to observe what can't be seen on their hands.
August 23th, 2019
Popular Science on microbiology presentation at Club des petits Débrouillards Summer Camp
Julien and Florian
Presentation on microbiology where kids can participate through quiz and are invited to "contaminate" petri dishes to observe what can't be seen on their hands
September 1st, 2019
Cloning: Digestion and plasmid purification
Carla
We did the digestion and purification of the plasmid with the new backbone proposed for cloning
September 8th, 2019
Received 3D modelling results from iGEM Concordia
Angel
Exploiting different software allowed us to compare RNAComposer to Rosetta and verifying the RNA folding, with the essential region conserving its behaviour, and observing disparities in the non-specific part's folding
September 9th, 2019
Extension of the script to do alignments to reference genomes to test specificity
Angel
Wrote the necessary code to run the alignments and made it versatile so that users could easily specify the genomes of interest.
September 10th, 2019
Expo Synthbio - Morrin Centre
Julien, Florian and Guillaume
Exploiting different software allowed us to compare RNAComposer to Rosetta and verifying the RNA folding, with the essential region conserving its behaviour, and observing disparities in the non-specific part's folding
September 11th, 2019
Day of the committees of the AESGUL
Angel, François, Florian and Carla
We showed our project to the members of the university community and we did a survey with people to complete our part of human practices.
September 16th, 2019
First round of parts characterization
Francois and Pascale
Expression of freen fluorescent protein previously characterized in vivo, here measured in cell-free media, but the results were confusing.
September 17th, 2019
Presentation at Cabaret ad Lab (Université Laval)
Florian and Nathan
Ultra-vulgarized presentation for students at the Département de biochimie, microbiologie et bio-informatique.
September 19th, 2019
Second coaching for the TEDxQuébec presentation
Nathan and Catherine
Practicing the TEDxQuébec presentation with the other speakers and three communication coaches.
September 24th, 2019
Prepared the Github repository
Angel
Uploaded our scripts to Github to make them available to the synthetic biology community.
September 27th-28th, 2019
Participation in the meetup organized by iGEM Concordia
Angel, François, Florian and Nathan
Presented our project and poster at a Mini Jamboree hosted by Concordia that also included Queen's.
October 3th, 2019
Bartending at a university party to fund the team
Catherine, Jean-Michel, Florian, François, Guillaume, Angel, Marianne, Nathan and Christina, a friend of us
October 5th, 2019
Third coaching for the TEDxQuébec presentation
Nathan and Catherine
Practicing the TEDxQuébec presentation with the other speakers and three communication coaches.
October 8th, 2019
Second design of microfluidics circuit
Nastaran and Francois
We modified our microfluidics circuit after feedback from experts. The design was streamlined and the protocol adapted.
October 8th, 2019
Successfully finished raising money to participate at the competition.
Catherine, Martine, Jean-Michel and Lucas
October 9th, 2019
Successful clones for ToeHolds
Francois
Final parts that were selected for characterization were tested in cell-free media and their efficiency was assessed.
October 10th, 2019
Final round of parts characerization
Pascale and Francois
Fluorescence calibration curve and testing the GFP parts in cell free media, found what was missing the last try.
October 11th, 2019
Toehold test in presence of trigger sequence, confirmation of system efficiency
Francois
We tested our most efficient ToeHold switch in cell-free expression system using isolated bacterial mRNA to test our design in conditions closer that what they will be in our tool.
October 11th, 2019
Finished modeling collaboration with Concordia
Angel
Wrote MATLAB code that Concordia could use to model the difusion of amilCP in their gel.
October 11th, 2019
Hydrogen bond analysis from molecular dynamics simulations.
Angel and Florian
Analyzed the hydrogen bonds in the simulations to look at the most stable ones and the least stable ones. Designed a figure to convey this information clearly.
October 14th, 2019
Building microlfuidics device chip
Nastaran
The newly designed microfluidics design was prepared and printed according to the protocol.
October 15th, 2019
Wrote code to obtain consensus secondary structures.
Angel
This new code allows us to see the consensus structures from the designed toeholds to prove that they are similar to the intended one.
October 16th, 2019
Designed new toeholds for measles virus, chickenpox virus, and norovirus
Angel and Pascale
We used our software to produce new toeholds that would allow the detection of viruses of interest and submitted them to the iGEM registry.
October 16th, 2019
Presentation at the Interlabs at Université Laval
Nathan, François, Angel and Florian
Presenting the advancements so far to faculty members and students at Université Laval.
October 31st to November 5th, 2019
GIANT JAMBOREE!
Nathan, François, Florian, Julien, Guillaume, Angel, Carla, Martine, Catherine, Pascale, Lucas and Marianne
November 7th, 2019
Presenting iGEM to High School students and teachers at Musée de la civilisation
Martine and François
January 11th, 2020
TEDxQuébec Presentation
Nathan and Catherine
Presenting a vulgarized presentation about synthetic biology and its benefits and the importance of communicating science to the general public. The presentation will be filmed and available on the Web.