Team:ULaval/Notebook

Team:ULaval - 2019.igem.org


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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

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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.

igem@bcm.ulaval.ca