Team:Imperial College/Journal
Timeline
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Monday
First day of iGEM 2018. Everyone meets. We took the first picture in queen's tower .
Tuesday
Brainstorming day. We met our PhD supervisors: Ismael and Amrit. We also met Rodrigo, one of our two PI supervisors.
Wednesday
Lots of brainstorming again. We met Will Wright, the European iGEM ambassador. We attended an Outreach event organised by Nico McCarty. We presented to some high school kids what iGEM and synbio is. We also helped the students with some bacterial transformation tutorial (for Biopanting with GFP).
Thursday
Brainstorming is intense. So far three candidate ideas are held by the general team consensus: electronic control of patterning, biofilm lithography, control of heterocyst-cell differentiation in E. coli, Catalytic Biofilms (?!), production of quantum dots, game theory simulation, et cetera... First team trip at the union.
Friday
Breakfast reception with the High School students from wednesday in the microbiology building . Brainstorming again.
Week 1 - 02/07/18
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Monday
We visited for the first time the lab we are going to work in during the summer. It's the Phillip Lab in RCS floor 1. Thank you Eppendorf for the PCR thermocycler, centrifuge and incubator. Team PicNic in Shepherd's Bush with Rodrigo and then visit to OpenCell, where there are supercool labs inside shipping tanks.
Tuesday
Presentation of the main ideas to the Centre of Synthetic Biology. Positive feedback for the electronic control of patterning idea. The game theory simulation idea has been killed by the feedback from the PhD students (sorry Shiv...).
Wednesday
We met Alice, an artist from RCA, who crystallises sweat from people and makes fashionable pieces of clothing with it (?!). She helped us brainstorming by promoting a discussion outside of our biochemical comfort zone.
Thursday
Shiv, Alberto, Josh and Thom are in Oxford for the iGEM Meetup. The rest of the team remained in London to work on ideas and to wait for some artists from the RCA. Unfortunately, the artists never turned up. Are we really that intimidating ?!
Friday
As Thursday. We also met the iGEM president: Randy Rettberg.
Week 2 - 09/07/18
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Monday
Week three has just started. Shiv, Alberto, Josh and Thom are back from the Oxford meetup. We met Tom Ouldridge in the morning, who returned from holiday. First group problem: Lidia decided to leave the group. Everyone hopes she is coming back. Let's remember that amazing team dynamics are reached with "Radical Truth and Radical Transparency". A wild Prof. Kitney appears around lunchtime: it is the first time we see him officially. We talked about the idea of patterning. He was very chill and supportive. He also proposed to have two separate wikis: a public one with limited info (so that other teams cannot copy us) and a private full one, to be published right before the freeze. He also told us when he went to holiday with his wife in China (?!). Quote of the day: "you may have heard of me." Rodrigo and Tom Ouldridge came into our brainstorming room after lunch and we presented the main idea: "PixCell: electronic control of biopatterning". It was a constructive discussion. It's time to think about simple backup plans. What if the agar is not conductive enough and nothing works ? Rodrigo proposed that we could solve this by placing electrodes in solution and control the temporality of gene expression (perhaps of co-cultures in bioreactores to split biosynthetic pathways between different communities and prevent burden)
Tuesday
Presentation of PixCell to the centre. Kitney liked it. He suggested to think about application... think about the "so what..". Positive feedbacks from Tom Ellis, start thinking about the big picture: after all we want to control bacteria electronically: cybergenetics? PixCell has officially started. The game is on. Tom Ouldridge held a brainstorming session and we assigned roles and things to do. Roles/Responsibilities: Organising/Designing wet lab experiments (JOSH) Add/improve part in registry Proof of Concept Validate Part Ordering lab equipment/ contacting sponsors /Lab book (DIELLZA) Electric field/Redox state modelling (LUIS) Modelling Proof of Concept Transcription modelling (LUIS) Modelling Proof of Concept Building/Designing electronics (WILL) Proof of Concept Wiki (YUTONG) Wiki Human practices x2 (Events/Application research/Social Media/building outreach App etc.) (ALBERTO SIWAT THOMAS YUTONG) Integrative Human Practices Team cohesion/communication/mental health/team leader/glue/team mascot (LIDIA) Collaboration Paperwork ☹ Judging Form Attribution List Part Submission Health and Safety iGEM deadlines The Guardians (AMRIT ISMAEL) Lidia is back, stronger than ever. She is going to be our amazing group leader, the glue... Agenda for tomorrow: Luis: meet with Pascal, redox modelling Will: meet with Pascal, redox modelling, electric circuits Yutong: meet the graphic designer, design circuits and identify what we need to order Josh: design circuits Diellza: design circuits Thomas: human practice strategy in the afternoon and wet lab strategy Alberto: human practice strategy and join wet lab strategy in the morning and catalogue parts in silico Siwat: human practice strategy in the afternoon and wet lab stategy Lidia: design circuits and model transcription Shiv: unassigned yet Trip at the Union to celebrate the start of PixcCell.
Wednesday
In the morning the wet lab team is bulding an inventory of parts and consumables we need. We are probably get SoxR and pSoxS with a genomic expansion (as these are endogenous in E. coli). We are also making a list of PIs and labs here at Imperial who could give us some useful reagents (such as Assembly kits). Dry lab team are full on modelling. Apparently constructing the electrode is not as complex as we expected. The graphic designer friend of yutong from CSM (virginia) had lunch with us in JCR and we discussed about our project. She is going to make our logo and help us with the aesthetics of everything. In the afternooon we constructed the inventory of materials, consumable etc... Hopefully we have the primers for the genomic expansion of SoxR by monday and we can start to pipette something ! Siwat danced Pen Pineapple Apple Pen. At 5 we had the meeting of the day with PhDs and PIs: everyone summarises the findings and achievement of the day and plan the agenda for tomorrow. Rodrigo and Tom are positive with the day. What about a team dynamics interactome ? Agenda for tomorrow: Luis: autoclave training, e-mail for ComSol, Redox modelling Will: autoclave training, redox modelling Yutong: autoclave training, contact merchandinsing, parameters for modelling Josh: autoclave training, ask Rodrigo for Cell Free, modelling Diellza: autoclave training, authorization request for ordering, DNA design Thomas: autoclave training, DNA parts design Alberto: autoclave training, modelling parameters Siwat: autoclave training, modelling parameters Lidia: autoclave training, Kirsten, modelling transcription Shiv: autoclave training, authorization request for ordering Amrit: risk assessment to order FeCN and PyO.
Thursday
In the morning a representative from BMG Labtech came in the lab. We got a microplate reader from them. We did a tutorial to learn how to use it. Lunch break in queen's lawn Luis, Will, Aberto and Siwat in the dry lab, attempting to model and find parameters (not very succesful) The wet lab team remains in RSM 1.47 designing primers and parts. Full inventory is done. Tutorial for microplate reader is on the google drive. Rodrigo: why don't you use chromoproteins istead of GFP ? At 17: lab meeting. The wet lab team completed the invetory of lab material to order. DNA sequences also have been designed. In the dry lab, Will and Luis continued working with COMSOL for the modelling of the potential at the electrode surface. Alberto and Siwat looked for parameters required for redox modelling of Fe(CN)6 and Pyocyanyn. Agenda for tomorrow: everyone risk assessement turotorial in the mornng (Phillips lab) Luis: model, plot concentration vs volum Will: model, PCB design Yutong: finish primer design, IDT order, order DJ901, talk to BMG representative for toxins on plate reader Josh: finish primer design, IDT order, order DJ901 Diellza: finish primer design, IDT order, order DJ901, Eppendorf Thomas: go to hackspace, look for collaborations and feedbacks. Alberto: list of chemists @ imperial + visit electrochemistry labs to find about redox reaction entropy (ferrocyanide) + look for parameters Siwat: list of computing/physiscs @imperial that use COMSOL, look for parameter Lidia: primer design Shiv: transcription/translation modelling, contact artists Ismael: risk assesment, iGEM kit Amrit: holidays
Friday
In the morning everybody had the safety induction in the Phillips lab with the lab manager. No students are allowed alone in the lab after 5 pm. Wet lab: filled safety forms. Designed primers. Protocols have been added here on benchling. Rodrigo apparently has the GFP in the plasmid we wanted. Yutong talked to the plate reader guy about the use of pyocyanin on their plate reader. We filled the biosafety BIO1 safety form (for the overall project). Then we need a COSHH for pyocyanyn. SOP form was not completed. We need to fill it in with our protocols. Dry lab: exercised on COMSOL again. Alberto spoke with Dr. Andrea Fantuzzi (electrochemist in 7th floor in SECB), he liked the setup but he's worried about the material of the electrode (silver can react with Cl to form AgCL which causes cytotoxicity). However, overall he seemed excited. Free cell free stuff from TXTL cell free.
Week 3 - 16/07/18
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Monday
In the morning, we completed the BIO1 form and all the relevant SOP forms for biosafety. The dry lab team made progresses in the modelling. Basic deterministic TXTL is running, reasonably simplified. Start working on a stochastic model as well. We are still waiting for the electrochemistry package in COMSOL. Wet lab managed to get hold to a new vector that converts Golden gate into BioBricks (developed by Marko, a researcher in Geoff Baldwin's Lab). We have ordered Pyocyanin, petri dishes, glycerol, ethanol, and most importantly primers. Alberto and Thomas spoke with Charlie Keyzor (president of SynBIC) and we are going to have part of the SynBIC stand on Fresher's Fair to showcase our iGEM project. Yutong's friend is deisgning a pixcell mascot. At 5 meeting as usual. Apparently we did not fill all the forms to receive all the payments. Tom updates us on the plan for the Jamboree. Agenda for tomorrow: everybody at 10 a.m. in Phillips lab for nanodrop tutorial Luis: contact comsol for sponsor Will: arduino Yutong: not in the morning (bank), go through all the wikis and see if there's a team workig on similar project (for collab) Josh: collect expression vectors, miniprep/glycerol stock Diellza: dry lab autoclave, anitibotic solution Thomas: meet SciCom guy Alberto: meet SciCom guy, e-mail bioethicisic fro European commission Siwat: meet SciCom guy Lidia: e-mail Sara Biol, Molly Stevens and Collab presentation Shiv: find hardware teams
Tuesday
Today was the first day in the wet lab. In the mornig we had the NanoDrop turorial. Alberto, Thomas and Siwat had the meeting with Dr. Sternberg (senior lectures in science communication) who gave helpful advices on how to comunicate complex foundational technology. Wet lab team and dry lab team remained in the Phillips lab. We then headed off to farmer's market for lunch. In the afternoon we prepared the antibiotics aliquot, the LB agar and the solvent solutions. We also picked up the MG1655 strain lines and Turbocompetent cells. from Tom Ellis -80 freezer. At 5 pm meeting in the lab with Amrit and Tom.
Wednesday
In the morning we received the parcel with pyocyanin and also the NEB free stuff. We did everything in the checklist. We make Agar-LB plates. We also resurrected the old plasmid (pBR322) and spreaded the SoxR-containing E. coli strain (MG1655) into plates. Primers have been shipped. Dry lab: RBS and promoter strength does not seem to affect the system. We thought that the general theme of our human practice is communication (exchange of information): Communication between scientists and general public. Communication between individual cells to form complex patterns Communication between individuals within a team Communication between machines and organisms (computers connected to bacteria) After lunch, Alberto and Shiv met two artsts from UAL and presented PixCell and proposed the Art exhibition. We received the confimation e-mail for the jamboree. At 5pm usual meeting with T.O. and Amrit.
Thursday
One of the hottest day so far (around 35 °C). First failures in the lab: our GFP overnight cultures did not grow. Primers haven't arrived yet and so we could not do much more. Also we found out that the sterile loops are not autoclavable... we found them melted in the morning. The modelers are trying to see if they can code the electrochemical model with MATLAB, as COMSOL people did not reply yet.
Friday
We finally received the primers and performed colony PCR to extract SoxR from an old strain, a sample of which was in some freezers in Tom Ellis lab. Shiv, Lidia and Siwat met representatives of KCL, UCL and Westmisnter Uni to oganise a London iGEM Meetup. Alberto, Thomas and Amrit met with Albert Fabregas, a PhD student from Guy Bart-Stan lab who is working with optogenetics. He told us that for 2D applications he can do the same with optogenetics and does not see the benefit of electricity. However, it would be cool to develop a toolkit for electronic gene expression --> we now have chemical toolkits, light, temperature, pressure and even pH toolkits to activate gene expression... but what about an electrical input?? Improvements on the wiki and human practice. Also we have 300£ in the VWR stores account, so that "we can buy cheap ethanol and get fucked up" - Josh. In the dry lab we received the carbon electrodes to test. Luis is working on a very comprehensive modelling guide. The Arduino also arrived in the lab.
Week 4 - 23/07/18
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Monday
In the morning we performed the colony PCR to clone SoxR from MG1655. Siwat is working on the interactive HTML Science Communication guideline. Yu is making progresses in outlining the HTML architecture of the wiki. Alberto is also working on the HTML code of the Team Cohesion questionnaire. Luis and Will talked with Tom Ouldridge, who suggested to model a square wave form of Pyo as input to GFP as output (to see resoponse of different concentration of pyocyanin). Still no response from COMSOL, is it possible that at Imperial nobody works on electrochemistry? The electrodes also have been built. Lunch break in SAF cafe. After lunch, we went to the VWR store downstairs in SAFB to pick up an Eppendorf parcel and bought some Ethanol. We did three colony PCR, the first 2 did not work (too long elongation time probably); finally the last one of the day worked.
Tuesday
In the morning we performed gel extraction of the succesful colony PCR gel from yesterday. We managed to collect 33 ng/ul of DNA of SoxR. Not a lot, but enough to engineer some genetic circuits. Also we performed the Golden Gate assembly for construct 1. We have all the parts for the 1-state system. Josh looked back at the paper and found out that even at 0-voltage, the fluorescence is marginal. General consensus is that perhaps a degradation tag on the GFP would delete the bleed that might appear. An alternative is to set the zero point at -0.5 V. Alberto, Thom and Siwat met Dr. Stephen Webster, a science communication professor, who gave hepful feedback on the science comm framework. He also really liked the philosophical perspective of PixCell (the nature-machine interface). Also today we finally received our stipends ! Also we received sponsorship for molecular Maya, a super cool software to model and animate proteins, and DNA in 3D. Also we received sponssorship from SnapGene, amazing! Next monday we have the presentation to the centre, we need to start thinking about real applications. Tom Ouldridge proposed a system to keep cells spatial separated by making that some cells survive only at certiain voltages. You can do a lot of "interesting things in non-homogenous pots".
Wednesday
Today, in wet lab the Kanamycin V3 worked but the V4 did not. In the afternoon, Thomas and Alberto miniprepped the sucessful V3. Josh updated the protocols. Luis and Will got comsol licence from a chemical engineering professor and had a talk with Tom about modelling. They decided to continue to use Matlab and maybe use comsol when it is needed. Luis and Will coninued working on modelling the redox small molecules. People were also preparing the ppt for next Monday's presentation.
Thursday
Cell growth curve on the plate reader was set up. Luis, Will and Josh spent a lot of time with Tom Ouldridge discussing about the model. Also Alberto and Josh prepared the pyocyanin solution in the fume hood, as it is very toxic. And it's an amazing prussian blue color. Ferrocyanide is a "mediterranean sun" yellow. At 5, Ben Reeve (CSO from CustoMem and former Imperial iGEMer) came into the lab to chat with us about our project and how to improve team dynamics. A flat structure is ideal. It is important to do social activities outside the lab as well.
Friday
It is Lidia's birthday today ! Also welcome to Luca, her boyfriend. The cell growth curve does not look very good. The plate reader was not shaking... that explains why perhaps... We plated agar+kan+pyo+FeCN and tested the electrode. Oxidised Pyo is blue and indeed in the proximity of an oxidising electrode there is blue spot ! this is a "tantalising result" -[Tom Ouldridge]. Will went to Westiminster for a collaboration, he had to do a voiceover for the iGEM team as he has a very deep and sexy voice.
Week 5 - 30/07/18
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Week 6 - 06/08/18
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Week 7 - 13/08/18
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Week 8 - 20/08/18
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Week 9 - 27/08/18
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Week 10 - 03/09/18
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Week 11 - 10/09/18
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Week 12 - 17/09/18
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Week 13 - 24/09/18
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Week 14 - 01/10/18
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Week 15 - 08/10/18
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Week 16 - 15/10/18
