Team:Consort Alberta/notebook

Our Notebook

   Introduction      Meetings   

Lab Work     Workshops

Introduction...

     The following notes are of our daily log book that was kept up throughout the year - the day to day activities, challenges, and solutions we come across while having our meetings or doing our lab work. Our lab work notes include the set protocols that we did and when, how, and why we did them. All of these notes are of all team member's work from several different points in time, combined together to give a full scope of what we did this year.

Meetings...

    September 16th: 3:30-4:15… Met the team from last year and the new member. We discussed the project idea that is continuing from last year's group (See last year's wiki for more information), and what synthetic biology and genetic engineering mean. We looked at a video about synthetic biology and a few other sites. Last year's Consort iGEM Team webpage was reviewed, as well as some of the other competition teams, and we looked through some of their wikis.

    September 30th: 3:30-4:30… We are getting a new Thermo-Cycler (PCR). The one we're getting is the BioRad PTC 200 (with 96 wells, like the old one, and has a heated lid). Along with new micro-pipettes (designed to measure things out in microliters). We further discussed other lab equipment that we may have to purchase. Looked over the Central Dogma of Biology, along with how different kinds of lab equipment work.

    October 7th: 3:30-4:15… Checked out other wikis for ideas for ours, and saved some links that we could refer back to and look at for inspiration.

    October 21st: 3:30-4:00… We are planning on going to present the iGEM presentation to the Consort Lions Club on November 21st to get financial and community support. We discussed who else we could talk to about support and sponsorship too, and came up with a short list of people or businesses we could contact.

    November 18th: 3:30-5:00… We looked at the iGEM poster and determined who we need to contact for the BioBricks and supplies we need for our project. The new students also looked at the process of DNA systems and about ribosomes with RNA.

    November 25th: 3:30-4:30… Darren and Sharon from the Consort Lion's Club presented our grant to us on behalf of the Consort Lions, as well as Sharon presented a second cheque on behalf of Ronwood Enterprises. On another topic, if things go well, we'll be submitting 2 BioBricks to the registry at the end of the year.

    December 2nd: 3:30-4:00… A snow day at school, so a few iGEM students hung out in the science lab and began planning our Wiki based on what we wanted, what we saw that was cool on other Wikis, and what we needed for requirements. New member to the team: Alex Coulton joined late, and so we updated him on all the science and details. We are now a team of 8 students.

    January 6th: 3:30-4:00… We received an amazing grant from Alberta Innovates who was impressed with our application, and now plus other donations. We each will kick in a potential $200 for the iGEM trip, and we are each responsible for meals and souvenirs. Today we discussed what are website will look like - Nikayla is going to take candid photos for alongside the bios within the next meeting or two, and with the help of Kris and Austin will work on the technical side of the site. We're going to write the bios so they are ready for the next meeting. Next day at lunch: determined about 200 words for the bio, including favourite Canadian stereotype. We're also going to do a "very Canadian" photo at lunch depicting a barbeque, shorts and t-shirts, and maple syrup… in the snow.

    January 13th: 3:30-5:30… Did our photo today… it was… cold. Going to have a workshop on February the 8th at the lab here at the school. Today we compared resources and website uploading options for the Wiki. We might go with OpenBexi. Going to come up with a shopping list for any supplies and such we need for the web lab.

    January 27th: 3:30-4:00… Workshop in Consort planning in progress - date is being shuffled around… not sure when or how it's going to work yet?

    February 10th: 3:30-4:30… Confirmed workshop date and time: February 23rd from 8:30am-5pm. A two people from the U of C are coming, and we are going to go over most of the procedures that we will be doing specifically. We tried downloading OpenBEXI to use on our website, but it's wonky and didn't work… so Kris contacted a student at Lethbridge to see what they used, and they used Microsoft Dreamspark - I think we'll try that out.

    February 23rd: We had our first Consort iGEM Workshop of the year with David Lloyd and Himika Dastidar from 8:30-5:00. (See this tab for more information)

    March 3rd: 3:30-4:00… Mr. Bourassa was gone, but we got all of our pages for our wiki drawn out as well as our main idea of our team descriptions and project info done. We hope to start experimenting with the website program soon!

    March 24th: 3:30-5:00… Discussed more fund raising, and got a few replies back from the letters we sent out. Any new modelling and software ideas due for this Wednesday. Protocols to follow once we get our DNA… A meeting to follow on Wednesday and Friday at lunch.

    April 14th: 3:30-5:00… Fund raising follow-up - we received gracious grants from the Veteran Lions Club, and Under Pressure. Maybe do them a presentation? Sam conducted an interview with T&E Pumps for the Human Practices portion of our website. Put Carla's Stringari as a credits for the logo and website. Alberta Innovates credits too, and we forwarded our articles to their contact as well. We also need to pick up supplies in Calgary! Once we get them, we should be able to start our plasmid switches and we need to schedule times and dates for our lab work. For flights - need names for everyone as they are on the passport plus our birthday.

    April 27th: We had our second workshop of the year, with Emily Hicks and Robert Mayall from 8:30-5:00. (See this tab for more information)

    April 28th: 3:30-5:00… More fundraiser follow-up and general part ordering and organization discussions. Website is well in progress, and a new modelling software is downloaded and begun to be experimented with.

    May 5th: 3:30-4:30… We will get some parts in later this week so we organized the cabinets. Returned our incubator to the Kindergarteners too. Arranging to go to a workshop in Calgary at the end of the month, seeing how that will go.

    May 12th: 3:30-4:30… On May 8th Kris happened to fix the autoclave… then we ran into some… uh… issues with the apparently heat-resistant bottles that we put into the sterilizing machine… they kinda melted, but they're sterilized! Website is in further progress, other teams are starting to do theirs a little too, but we are overall ahead of the game. Workshop on Saturday May 24th, and we will leave right after school to head to Calgary. We booked our geekStarter tickets and got them ready too.

    May 19th: 3:30-4:30… General meeting, getting ready to make some LB Broth and going over procedures. For making the LB Broth, see the lab work for more information.

    May 20th: 3:30-4:30… Made LB Broth with no complications. Also worked on modelling and website afterwards until 6:00. The beginning phases of mathematical modelling are appearing after the extra help from Robert Mayall.

    May 21st: 3:30-5:00… Took LB Broth out of the autoclave today. Before dealing with the more serious synthesized DNA, we are following our 3A Assembly Kit and Transformation Efficiency Kit from the iGEM Headquarters, which outline basic procedures that we'll use with our synthesized DNA later on. This book will take us through step by step and show us how to, in the end result, make E. coli cells produce a Red Fluorescent Protein that can directly tell us whether or not we did the procedure properly, as it has a strong reporter. Did some agar plates (SOB) and we are growing cultures overnight on the shaker table. Made 3 plates - two from the 2014 distribution and one from the 2013. For making the Agar Plates, see the lab work for more information.

    May 26th: 3:30-6:00… Today we made more plates and did agar stabs from the Kit and grew our E. coli. Tomorrow at lunch and after school we are going to rehydrate the reporter genes, and hopefully transform into E. Coli and make them competent. And then culture and grow them. We did 6 agar stabs on plates, and got together the materials and procedures that we need for tomorrow. We've planned a mini-prep for Wednesday. Also worked on modelling afterwards. To look at our procedure, see the lab work for more information.

    May 28th: 3:30-5:00… We have our E. Coli successfully cultured and growing on the agar plates overnight, to be checked out in the morning.

    May 29th: 3:30-4:30… We used a spectrophotometer to get an optimal density reading on our culture tubes. To look at our results, see the lab work for more information.

    June 2nd: 3:30-4:30… Getting prepared for our next procedures, and planning a second human practices interview with Dave Bruha, and potentially other people. Did a mini-prep today with our cultures. To look at our procedure, see the lab work for more information.

    June 4th: 3:30-5:00… Worked on some modelling and generally getting ready for a restriction digest. Also completed the interview with Dave Bruha of the Consort Enterprise as a part of our Human Practices portion of our project.

    June 5th: 3:30-5:00... We used a spectrophotometer to get an optimal density reading of our newly growth cultures. To look at our results, see the lab work for more information.

    June 6th: 3:30-5:00... At lunch today we did a ligation, followed by a transformation of the plasmids into the cells after school. We're letting them sit over the weekend, and then see if they glow red on Monday. To look at our procedure, see the lab work for more information.

    June 9th: 3:30-5:30… Our RFP cells didn't glow red, and we determined that something went wrong during the transformation stage - we are going to try it again and see what exactly went wrong.

    June 10th: 3:30-5:30… We finished making the competent cells then doing the transformation using a different protocol SEE HERE, and there was a two hour incubation on plates.

    June 11th: 3:30-5:30… Our cultures still aren't glowing red, and this was trial number three. SEE HERE We contacted Emily Hicks for discussing our problems, and she gave us advice and trouble-shooting tips. We think that it was the competency protocol that went wrong, as well as the level of growth that our cells were at. When we did the optical density test, our results varied from 0.7-1.2 range, and they should be at about 0.4 for the best growing rate. And so after re-doing SOME PROTOCOL?, we did another optical density test SEE HERE, and got much more optimal results, which may be to blame for the lack of RFP transformation.

    June 12th: 3:30-11:00… Got several more protocols in place and reviewed our handbooks for tomorrow, including the making of competent cells and transformation, and figured out the variations of the concentration of the CaCl and the different types of growth media added to the cells. We then plated them out on different types of media.

    June 15th: 10:00-5:00… Yesterday we researched troubleshooting solutions for both transformations and for making chemically competent cells. Today we prepared to make more competent cells using THIS PROCEDURE (page 96ish in the huge email book) followed by some poster brainstorming and fixing up the wiki as we waited 2 hours for the LB Broth mixture to sit on the shaker table. Afterwards, we ____.

   June 16th: 3:30-5:00… Phoned Emily Hicks and asked for some more help... her one suggestion was that maybe something was wrong with the DNA. She's going to talk with her colleagues tonight and let us know tomorrow. Another thing that may be wrong is that our centrifuge holds less than what the protocols ask for, so we had to split it up into smaller volumes, which could be a problem.

Lab Work...

The following are the protocols in which we followed for our lab work, along with the book or web handbooks references, the dates when we did the protocol, and how the protocol went overall.

    ~LB Broth (May 19th): Materials: LB broth powder, Glass bottle. Protocol: Weigh out 20g of LB broth powder and mix with 1L of water. Scale up or down as desired. Autoclave (sterilize) the broth at 121°C for 15 minutes. We made 1.5ml of Broth, and we had no problem following the procedure. Since then we have made a few other broths as well, such as SOC and SOB.("International Genetically Engineered Machines Competition Guidebook for High School Students and Instructors", page 96-97)

    ~Agar Plates (May 21st): Materials: LB-agar powder mix, Plates. Protocol: 1. Weigh out 35g of LB-agar powder mix per litre of media desired. One litre makes 40-50 plates. Ensure that the mixture volume does not exceed half of the volume of the flask/container used, otherwise it will boil over in the autoclave. 2. Dissolve the LB-agar, using water from one of the wall mounted Nanopure filters. Add a stir bar and use a magnetic stirrer to facilitate mixing. 3. Cover the flask with aluminium foil, and secure the foil with autoclave tape. The foil should be somewhat loose (to avoid building pressure in the flask while sterilizing), but not so loose that lots of liquid can escape. 4. Put the flask in a plastic autoclave tray, load into the autoclave, and sterilize using the 20 minute liquid program. 5. Allow the media to cool until it can be handled. 6. Once media is cool, add other desired ingredients. Use the magnetic stirrer to mix, do NOT add a stir bar now, or the media will be contaminated. (If one wasn't added before, you must do without.) 7. Add the antibiotic that will select for your plasmid. The following antibiotic concentrations are used commonly in iGEM: Ampicillin (stock 100mg/ml, final 100μg/ml); Kanamycin (stock 50mg/ml, final 50μg/ml); Chloramphenicol (stock 50 mg/ml, final 10μg/ml) Note: To achieve final concentrations, add 1mL of stock per 1L of culture media, except for chloramphenicol, where 0.6mL stock per 1L of media is added instead. 8. Pour the sterile, antibiotic-containing broth directly from the flask into the sterile Petri plates carefully to avoid trapping air bubbles. 9. Allow the plates to stand right side up overnight, and then store them at 4°C (in fridge). We had no trouble making these either. ("International Genetically Engineered Machines Competition Guidebook for High School Students and Instructors", page 97-98)

    ~Streaking From Agar Stabs and Growing Up Cell Cultures (May 26th): We made 6 plates, 3 Part A and 3 Part B, following this procedure. After our incubation, our cells were cloudy as the procedure said they would be. ("3A Assembly kit and Transformation Efficiency", page 9-11)

    ~Spectrophotometer Test #1 (June 5th): Using our spectrophotometer (GeneQuant), we tested our cultures to see what their optical density was in order to judge whether they were at their optimal growing stage or after their growing was finished. Our results were as follows... Test blank: LB Broth with Amp and Kan read 0.365. Actual testing: Test Tube 1 (Part B): 0.792, Test Tube 1 (Part A): 1.762, Test 2 (Part B): 0.778, Test Tube 2 (Part A): 0.752, Test Tube 3 (Part B): 0.882, Test Tube 3 (Part A): 1.102. Observation: Part A seemed to grow faster. We were surprised at the huge optical density though, and we considered testing it further but decided not to.

    ~Mini Prep #1 (June 2nd): ("3A Assembly kit and Transformation Efficiency", page 12-14)

    ~Spectrophotometer Test #2 (June 5th): Sample 1: 0.948, Sample 2: 0.736, Sample 3: 0.924, Sample 4: 1.208.

    ~Transformation #1 (June 6th): ("3A Assembly kit and Transformation Efficiency", page 19-20)

Workshops...

    Our first workshop this year was...

    References: International Genetically Engineered Machines Competition Guidebook for High School Students and Instructors,  iGEM High School Handbook