Here is an overview of what we have done throughout our project.
February notebook
February 10, 2020 - February 16, 2020
General:
We met each other for the first time, formed subgroups and decided having a meeting every Monday followed by dinner.
Wetlab:
We had a meeting for Introduction to lab Safety with the faculty members.
February 17, 2020 - February 23, 2020
General:
All subgroups had their introductory meetings where they brainstormed their goals.
February 24, 2020 - March 1, 2020
General:
We did research to get inspiration for project ideas.
Outreach:
We took over SoMe accounts and discussed logo ideas for our project.
March notebook
March 2, 2020 - March 8, 2020
General:
We brainstormed ideas for the project and read previous iGEM Judging forms. The team also submitted a Lab safety test.
Outreach:
We took over Instagram, Twitter and Facebook accounts for the DTU iGEM team.
Economy:
We took pictures of team members for funding applications and started contacting people for funding advice.
Team Building:
We had our first team building event, a fun PubQuiz at a local pub, and the second event was planned during this week.
Admin:
We prepared a team contract and got everyone’s signatures on it.
March 9, 2020 - March 15, 2020
General:
All team members pitched different ideas and received feedback from the team and supervisors. A few examples are: water remediation - to remove pesticides, psychotropic drugs - fabricating novel synthetic psychotropic drugs to fight psychological disorders, and optimizing hyphae production in filamentous fungi.
Outreach:
We attended and presented at the Open House event at our university, where we talked about synthetic biology and iGEM.
Economy:
We got the first team picture taken.
Admin:
We registered as an iGEM Team and discussed the Nordic iGEM meet up in Linköping.
March 16, 2020 - March 22, 2020
General:
We narrowed down our ideas range, and further discussed the brainstorming ideas. We set a deadline for deciding on an idea next week. We were all sent home and travel bans had come into place. DTU was closed due to Covid-19 Pandemic. We also discussed options for the BioBrick Tutorial.
Outreach:
We discussed possible future events.
Economy:
We formed a list of possible funding to apply for, taking inspiration from last year's DTU iGEM team.
Team Building:
We brainstormed ideas for future meet ups if restrictions allow it - Escape room might be a possibility.
March 23, 2020 - March 29, 2020
General:
We decided to work on improving the morphology of filamentous fungi and creating a signal peptide library. BioBrick Tutorial was postponed due to Covid-19 Pandemic, making a virtual event may not be feasible. We made a new subgroup for WIki.
Outreach:
We worked on designing a logo.
Drylab:
We started looking into previous models of morphology of filamentous fungi. We sought to find out what initiatives have been taken, what challenges have been discovered and how these have been met.
Wetlab:
Human Practice:
We brainstormed a list of people to whom we would reach out.
Economy:
We requested reference letters from supervisors and faculty personnel for funding applications. We prepared our first draft for a funding application and got our budget approved from the supervisors.
Team building:
We had an Online movie night (Netflix party).
Admin:
We started preparing for our lab work by coordinating planning and protocols, in case the restrictions are lifted later.
April notebook
March 30, 2020 - April 5, 2020
General:
We did further research on ideas and presented our research slides to the team. We continue to have meetings on Zoom in order to comply with the Danish lockdown. Our iGEM ambassador had a meeting with other iGEM ambassadors to discuss lockdown restrictions and their influence on iGEM 2020. We cancelled the BioBrick Tutorial due to Covid-19 Pandemic. We agreed on making an offline version of our wiki.
Outreach:
We prepared and posted a teaser for our project revealed on the social media platforms. We decided to do a crochet pattern of a fungus as a kind of team mascot.
Drylab:
We brainstormed different ideas for growth modelling of filamentous fungi based on the literature that we had read and furthermore, we started gathering relevant data sets of microscopic images from different papers.
Wetlab:
Human Practice:
We reviewed the list of people to contact, and took some inspiration from the list of people from last year's team.
Economy:
We got some feedback on our funding application cover letter.
April 6, 2020 - April 12, 2020
General:
We formulated a hypothesis for our project and decided to work with A. niger. We had presentations of different genes of interest for morphology and signal peptides.
Outreach:
We made our first draft of the logo/mascot and worked on creating crochet mascots.
Drylab:
We started our discussion of what features would be relevant to include in our growth model, we were also granted access to the growth model developed by the DTU biobuilders 2018, which could then take part in our discussions.
Wetlab:
April 13, 2020 - April 19, 2020
General:
We had Easter holiday in Denmark. Therefore, no iGEM meetings were held this week.
April 20, 2020 - April 26, 2020
General:
We discussed the goal of the project: a better fungal cell factory?
Outreach:
We contacted photographers for headshots of each team member.
Drylab:
We worked on converting the model from the DTU BioBuilders 2018 from R to Python to use it as a starting template. We continued the discussion of potential parameters of interest for modelling the morphology of A. niger, in particular we discussed branching frequency, hyphal length, and hyphal densities.
Wetlab:
Human Practice:
We sent emails to bioindustry personnel. We also discovered that we needed to contact people with a bioinformatics viewpoint.
April 27, 2020 - May 3, 2020
General:
We found out that this year’s Jamboree will be online.
Outreach:
We were contacted by IIT Madras regarding a collaboration. We discussed a Wetlab-based collaboration idea with a Norwegian team.
Drylab:
We discussed how to improve the growth models that had already been developed, such as graph based models, using 2D/3D images and mixing. We continued the discussion of what other parameters to consider, and we finished the conversion of the 2018 growth model from R to python.
Wetlab:
Human Practice:
We had meetings with Mhairi McIntyre Workman (Associate Manager - Novo Nordisk), Kim Hansen (Senior science manager - Novozymes), Jens Frisvad (Professor - DTU Bioengineering), Dr. Edyta Szewczyk (Senior Scientist in Biology - Bolt Threads), and Kenneth Jensen (Science Manager and Project Leader - Novozymes).
Economy:
We discussed different costs related to the project. More recommendation letters were received during this week.
May notebook
May 4, 2020 - May 10, 2020
General:
We discussed different options for filming for the promotional and presentation videos.
Outreach:
We had a meeting with IIT Madras, they had to withdraw due to Covid-19 Pandemic.
Drylab:
We wanted to base our growth model on experimental data, so we started looking into methods for doing good microscopy of fungi and we also looked at different image analysis tools that could help us extract parameters from the data sets that we had received.
Wetlab:
Human Practice:
We had meetings with Morten Skov Jacobsen (Head of fermentation pilot plant - Novozymes) and José Luis Martinez Ruiz (Associate Professor - DTU Bioengineering).
May 11, 2020 - May 17, 2020
General:
We had no meetings or work on iGEM during this week due to exams at DTU.
May 18, 2020 - May 24, 2020
General:
We had no meetings or work on iGEM during this week due to exams at DTU.
May 25, 2020 - May 31, 2020
General:
We discussed our prospects for lab work with our supervisors. They promised to find some spots for us. We made a new subgroup for making project videos.
Outreach:
We held a discussion as a follow up on our collaboration with IIT-Madras.
Drylab:
We continued our work on investigating microscopy protocols and started testing different image analysis tools on the data sets that we had received.
Wetlab:
Human Practice:
We held a meeting with Drylab to discuss model ideas with different bioindustry personnel.
Economy:
We got a sponsorship from Amplicon.
Admin:
We also discussed different medal criteria with the team.
June notebook
June 1, 2020 - June 7, 2020
General:
We all signed up for Benchling and Kyle gave a Benchling tutorial.
Outreach:
We published two crochet patterns for our team mascots on Ravelry. We are still working on the IIT-Madras collaboration. We set a date for team photography.
Drylab:
We worked on modeling.
Wetlab:
Human Practice:
We worked on documenting talks from bioindustry personnel.
June 8, 2020 - June 14, 2020
General:
We went to the lab for the first time! With initial restrictions only allowing three people to be in our lab at any one time
Outreach:
A collaboration agreement document was prepared with IIT-Madras. We participated in the COPI (Corona Outreach Program Initiative) started by Uppsala iGEM team.
Drylab:
We started a journal club.
Wetlab:
Team building:
We had an outdoor meetup in a park for games and as we say in Denmark “hygge”.
Admin:
We reached out to the Dusseldorf iGEM team. We met up with SDU and KU online to plan a Danish iGEM meetup.
June 15, 2020 - June 21, 2020
Outreach:
We are in discussions regarding collaborations with Mexico and Dusseldorf. We received the team headshots.
Drylab:
We asked paper authors for image data and received some more. We continued testing different image analysis packages for microscopic image analysis and we started discussing how to do good microscopy, considering what we learned from literature.
Wetlab:
Economy:
We submitted our abstract to ASBE V.
June 22, 2020 - June 28, 2020
Outreach:
We planned a possible collaboration and meeting with FCB-UANL from Mexico. We are doing Instagram presentations of team members.
Drylab:
We discussed pros and cons of the different image analysis tools that we had tested. We also discussed the microscopy protocols that we had seen and we met with Claus Sternberg to test the confocal microscope.
Wetlab:
Human Practice:
We had an online meeting with IIT-Madras.
Team building:
We had a Grill & Chill with all the supervisors this week and are planning further events.
July notebook
June 29, 2020 - July 5, 2020
Outreach:
We had meetings with IIT-Madras, FCB-UANL, and Korea-HS about collaborations.
Drylab:
We met with Claus Sternberg regarding microscopy, and agreed on doing microscope training on July 8th. We received better image data from paper authors to test out the imaging tools that we found.
Wetlab:
Admin:
We submitted our preliminary safety form.
July 6, 2020 - July 12, 2020
Outreach:
We are looking at a collaboration with Maastricht about an article for an iGEM journal. We will participate in DTU intro week with a talk on iGEM and synthetic Biology.
Drylab:
We continued discussing
Wetlab:
Team building:
We went on a sailing trip around Copenhagen harbour.
July 13, 2020 - July 19, 2020
Drylab:
We will be working on image analysis because we want to improve estimates of parameters for branching angles, growth rate, and branching rate compared to the existing model. We are testing out tools for segmentation, binarization and vectorisation. We will work with image data from papers for now until we can get images of our own fungi.
Wetlab:
July 20, 2020 - July 26, 2020
Outreach:
We had a meeting with FCB-UANL. Some of the team went to a Danish iGEM meetup at SDU.
Drylab:
We continued to test out different image analysis tools on paper data sets and sent out requests for more data sets from other papers.
Wetlab:
July 27, 2020 - August 2, 2020
Outreach:
We had some follow-up meetings on collaborations.
Drylab:
Claus is be back next week, so we can get some microcopy instruction and start taking pictures. Therefore, we started planning our microscopy. We also talked to people from SDU regarding 3D printing of microscope chambers.
Admin:
We selected our iGEM track: Manufacturing.
August notebook
August 3, 2020 - August 9, 2020
Outreach:
We met with Aakii from PF, the DTU students’ association, regarding our participation in the Masters’ introduction week.
Drylab:
We selected and ordered stain (calcufluor-white) and perfusion chambers for microscopy. We scheduled time with Claus for microscope instructions. We also started working on our own image analysis tool as the majority of image analysis tools were not flexible enough to tune to our needs.
Wetlab:
August 10, 2020 - August 16, 2020
Drylab:
We attempted our first microscopic slides with help from the wetlab team. We held a Wiki meeting for assigning tasks to all team members and the wetlab team came up with the idea of computing wide-functioning synthetic signal peptides.
Wetlab:
August 17, 2020 - August 23, 2020
General:
We filmed our promotion video. We also talked about options for meetups for the Giant Jamboree.
Outreach:
We will participate in Naturvidenskabsfestivalen, where several pairs of team members will present workshops on filamentous fungi at primary schools in the greater Copenhagen area.
Drylab:
We continued working on achieving better microscopic images - thanks to the wetlab team for preparing the slides! We met with Henrik Nielsen to learn more about his program SignalP and how we could apply it for predicting synthetic signal peptides.
Wetlab:
Human Practice:
We contacted people from DSM and Chr. Hansen.
Admin:
We started planning a trip to a summer house in our autumn break to write the bulk of our wiki.
August 24, 2020- August 30, 2020
Outreach:
We presented a workshop for DTU Masters' introduction week.
Drylab:
We improved at growing our fungi for microscopic images, but we had some issues with contamination, so we started thinking about how to solve this. We started working on SignalPrepper, following ideas from Henrik Nielsen.
Wetlab:
September notebook
August 31, 2020 - September 6, 2020
General:
The promo video is on it’s way!
Drylab:
We worked on improving our microscopy, and we continued working on the image analysis tool. Furthermore, we finished SignalPrepper and gave the resulting best scoring synthetic signal peptides to the Wetlab team.
Wetlab:
Human Practice:
We met with Kenneth from Novozymes.
Team Building:
The team had a great evening trying to escape the clutches of a criminal mastermind in an Escape room. We, of course, prevailed!
September 14, 2020 - September 20, 2020
General:
We participated in the Nordic iGEM conference and presented our preliminary work. The final cut of our promo video was ready for upload!
Drylab:
We took many pictures this week including the ΔchsC_ΔspaA double knockout. Work on the image analysis model progressed, particularly we created target segmentation, cut the images into tiles, made a ‘data loader’, and started setting up the model itself. Work on the simulation model also progressed as we decided to implement substrate diffusion, lateral branching and chemotropism.
Wetlab: We started the first round of bioreactor runs! We also did Glucoamylase and BCA assays of morphology strains.
September 21, 2020 - September 27, 2020
General:
We worked on the concepts for the presentation video.
Outreach:
This week was Naturvidenskabsfestivalen and though we could not visit schools we gave several presentations virtually.
Drylab:
We continued our work on getting good microscopic images of all mutant strains, but some mutants were difficult to grow in such a way that we could get good pictures. We also continued working on the image analysis and the simulation models.
Wetlab:
We ran Bioreactor experiments with the reference strain, ΔchsC and ΔspaA. We performed glucoamylase assay and BCA performed the samples form these runs.
Human Practice:
We set up a presentation with Novozymes for a week before the wiki freeze.
September 28, 2020 - October 4, 2020
Outreach:
We had a meeting with FCB-UANL.
Drylab:
We took a lot of microscope images, worked on the simulation, and discussed benchmarking with Dennis from Novozymes. For the simulation we worked with the code to model a substrate gradient and to allow for directional changes in hyphal growth.
Wetlab:
We ran Bioreactors with reference strain, ΔracA and ΔchsC_Δgul and performed Glucoamylase and BCA assays on them. The biolectors reactors runs will be repeated during the next weeks, as pH was not controlled during fermentation. We ran the Biolector with the morphology strains in YPD + MM with maltose instead of glucose.
Bioreactors for lab-scale testing of our K/O strains.
October notebook
October 5, 2020 - October 11, 2020
Drylab:
We finished most of our image analysis work, now only missing a few mutants. The simulation model is almost ready, just need to get the results looking their best and then run all the simulations for the different mutants.
Wetlab:
We ran Bioreactors with reference strain, ΔracA and ΔchsC_Δgul and performed Glucoamylase and BCA assays on them. The biolectors reactors runs will be repeated during the next weeks, as pH was not controlled during fermentation. We ran the Biolector with the morphology strains in YPD + MM with maltose instead of glucose.
October 12, 2020 - October 18, 2020
General:
The team spent the week together in a summer house working on data analysis, the wiki, and presentations.
October 19, 2020 - October 25, 2020
General:
The team spent the week working on the wiki. We also presented our project for DTU Bioengineering - the section we worked at during our project.
Drylab:
We got a final round of microscope images for image analysis and did some bug fixing in the simulation model.
Human Practice:
We presented our project to Novozymes for a final round of feedback from the industry stakeholders.
October 26, 2020 - November 1, 2020
General:
The team spent the first part of this week finishing the wiki, then finishing up the presentation video and the judging form. We also presented our project at the DTU blue dot ceremony.