Team:DTU-Denmark/Journal


Journal

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Protocols

Needed materials: 100 ml TAE buffer, 1gr. agarose, ethidium bromide.
Mix 100 ml. TAE buffer with 1 gr. agarose powder, heat in microwave till the agarose is disolved, let it cool till it can be handled with bare hands, add 10 µl ethidium bromide. Then pour the mixture into a mold containing slots for wells, and let cool.
Set gel into electrophoresis chamber filled with 1X TAE buffer so the wells are covered. 
Mix 5 µl of your PCR reactions/sample with 1 µl 6X loading buffer.
Pipette 5 µl into each well, pour 2-3 µl ladder in some so the size can be seen.
Run at 140 V, for 30-40 min.
Chemo competens is a way of getting E. coli to be able to take up new DNA, since this cant be done naturally like B. subtilis, then chemocompetent cells have to be made.
Protocol can be found here
Needed materials: a 40% glycerol solution, bacteria of your choice, cryo tubes.
Mix glycerol and bacteria 50/50 in a cryo tube and place in a -80 frezzer till needed.

A lot of lab work requires plates in order to produce results, and often you need a special concentration, a unique antibiotic mixed into the plates or a different composition than what is available at the lab you are in. If that is the case, the plate needs to be made from scratch, or somewhat along the way.

Protocol can be found here.

For the experiments a minimal media designed for B. subtilis has been used. The plates have been made by following this protocol (for 1 liter).
Protocol can be found here.
In order to work with plasmids, then they needs to be purified and condensed, this is done bu minipreping the bacteria, and afterwards the concentration can be investigating using NanoDrop™.
Protocol can be found here.
Bacillus can be made competent allowing an easy alteration of the genome and so wanted mutaions can be inserted, this is a unique way of investigateing new pathways.
Protocol can be found here.
Electrotoration of bacteria is used in order to introduce mutations in the lagging strand of the strain, this technique are used in order to incorporate wanted mutations in a strain of Bacillus subtilis 168.
Protocol can be found here.
Electro competent cells are used in our MAGE part of the project, so a batch of cells was prepared using the following protocol.
Protocol can be found here

Lab Notebook

The lab book for expression of tyrocidine can be found here. 
The lab book for the generation of oligo-competent strains can be found here.
To approve a lab-on-a-disc concept as a screening device, the UV-vis abasobancee were measured here. 
See our labnotebook here.

Timeline

  • Biology of the Future

    2015-09-14

    Our team member Pernille spent an afternoon giving a presentation on cell factories and synthetic biology to 30 highschool students. She says: "Synthetic biology is all about being creative and use your imagination to design bio-solutions that can impact the world. For that exact reason, it is neccesary to discuss which ethical values tat should drive research". The highschool students had lots of questions and opinion for the discussion about ethics.

     

  • VWR to the rescue!

    2015-09-01

    We are happy to announce that the VWR is contributing our team with their awesome products!

     

  • Visit from Fisher Scientific!

    2015-08-26

    Today we had a visit by Susanne Basse from Fisher Scientific. She came by our office with a wagon full of items, Thanks! 

  • Contribution from Macrogen!

    2015-08-20

    We are pleased to announce that Macrogen is sponsoring our team with sequencing!

  • Contributions from AKG!

    2015-08-19

    We are happy to announce that AKG Acoustics is sponsoring our team with headphones for presentations in Boston! 

  • Contributions from VWR - Bie & Berntsen A/S

    2015-08-11

    We are happy to announce that VWR - Bie & Berntsen A/S is sponsoring our team with lab consumeables!

  • Contributions from Fisher Scientific

    2015-08-11

    We are happy to announce that Fisher Scientific is sponsoring our team with lab materials! 

  • Canoeing

    2015-08-07

    Today we took a day off from lab to go canoeing, followed by a barbeque at Chris' place.

  • Contribution from SnapGene

    2015-08-03

    We are happy to announce that the SnapGene is contributing our team with lisences to their awesome product!

  • Wiki Wizard

    2015-07-30

    We have uploaded the first beta version of the Wiki Wizard to GitHub

  • First BioBrick cloned into B. subtilis

    2015-07-30

    An expression cassette with lambda beta recombinase was sucesfully transformed into Bacillus subtilis. First step towards establishing MAGE in Bacillus subtilis completed!

  • BioBrick High School Project

    2015-07-23

    3 high school students; Simran, Noor, and Charlotte, joined us and Biotech Academy for 5 days to make biosensors that changes color, when water is poluted. Read more at the Human Practice and http://biotechacademy.dk.

  • First sequencing results

    2015-07-22

    We received our first sequencing results. One step closer to our first BioBrick!

  • Brevibacillus parabrevis arrives

    2015-07-16

    Brevibacillus parabrevis produces a lot of different antibiotics including tyrocidine. We will transfer the tyrocidine operon to our chassis Bacillus subtilis.

  • Contribution from the Lundbeck Foundation!

    2015-07-15

    We are happy to announce that the Lundbeck Foundation is contributing financially to our team!

  • Contributions from In Vitro!

    2015-05-06

    We are happy to announce that In Vitro A/S is sponsoring our team with lab consumeables! 

  • Contributions from Frisnette

    2015-04-30

    We are happy to announce that Frisnette is sponsoring our team with lab consumeables! 

  • We get our strain

    2015-04-28

    We get a plate of our chassis strain Bacillus subtilis W168.
    We can now begin the work in the laboratory.

  • BioBrick Workshop

    2015-04-24

    Southern University of Denmark and University of Copenhagen joined us for a three-day BioBrick tutorial, where we spent three days in the laboratory cloning, learning about iGEM, wiki design, and getting to know each other through social activities.

  • Contribution from the Otto Mønsted Fonden!

    2015-03-08

    We are happy to announce that the Otto Mønsted Fonden is contributing financially to our team!

  • First official team meeting

    2015-01-14

    Today we had our first official team meeting. We talked about the project and got to know each other.

  • Introductory meeting

    2014-11-25

    This day, last years team held an introductory session about iGEM for interested people.

Technical University of Denmark
Department of Systems Biology
Søltofts Plads 221
2800 Kgs. Lyngby
Denmark
P: +45 45 25 25 25
M: dtu-igem-2015@googlegroups.com