Welcome to my logbook and documentation page ;)

My inspiration comes from Joi Ito, the director of the MIT Media Lab. At the Solid Conference 2015 he gave a talk about the future of technology. His statement is ‘Bio is the New Digital’. His quote on which my project it based is: ‘The design of the future is hardware, it’s software, it’s biology and it’s complex.. But you have to know math.’

My goal of the Biohack Academy is to try and tinker with the future of biotechnology myself.

Presentation

Take a look at my presentation for an update (and pictures): https://docs.google.com/presentation/d/1iQGf3zNRhKPUyp9L-tkgpL7eB5ZujxsHIc1U7SvHuCM/edit?usp=sharing

The design of the future is … hardware … biology

The first two elements are finished. These were:

• building a simple 3d printed webcam microscope
• doing dirty DNA extraction from strawberries
  The documentation is in the week 8 blogpost https://peterjoostennet.github.io/week8/

The design of the future is … biology (part 2)

When I started with Biohack Academy course, I really wanted to do a project with genetic engineering.

My first idea was to work with a CRISPR/cas9 kit, because I am fascinated by the possibilities of gene-editing for agriculture, in healthcare, for industrial use, etc.

Because of European regulations I am not allowed to work with CRISPR/cas9 on living organisms (including myself) at the Waag. A fellow student at the Waag is doing her project about the ins and outs of this regulation, so I am following her insights with a lot of anticipation.

As an alternative I ordered a Biotechnology Explorer kit of Bio-rad, namely the Restriction digestion and analysis of Lambda DNA kit. Because restriction enzymes (RE) are cutting DNA and not cutting and pasting (like CRISPR/cas9), I allowed to work with this experiment at the Waag.

The steps in the proces were 1) restriction digestion, 2) gel electrophoresis and 3) staining DNA. The kit also came with a very insightfull manual. With this manual I got a better understanding of the workings of RE and gel elecrophoresis, but it also gave me another change to practice in the lab. All the steps and details are not that important (and you can look it up on the website of Bio-rad or in Youtube video’s). That is why I want to share all the failures, mistakes and lessons learned :)

In the week 8 blog you can read about my lessons and faillures from last week, because I had not the outcome which I hoped for: https://peterjoostennet.github.io/week8/

New lessons and failures

These are my lessons learned with the RE kit this week:

• I am allowed at De Waag to work with the lambda bacteriophage DNA, because I am only working with DNA (not with a living organism)
• If I would change DNA inside an organism, it would be a GMO. This is not allowed because of EU regulations.
• This is also the difference between in vitro (in a lab) and in vivo (inside an organism)
• I cut into the DNA of a bacteriophage, which is a virus (not a bacteria)
• An awesome video about bacteriophages and their use in medicine is made by Kurtzgesagt: https://www.youtube.com/watch?v=YI3tsmFsrOg
• Experiments in the lab are timebound, so you need to start early or at least be aware of the planning of your project.
• It is always a good habit to note all the quantities. For the second run of the experiment, I had some trouble to see how much agarose and buffer I needed the last time.

Outcome of the experiment

With Roland I ran through all the steps in the experiment to see where things could go wrong. For example, this time we used a second gelbox to use the SYBR stain instead of the Fast Blast of Bio-rad. Because I had to leave, my fellow BA students finished the project (i.e. the gel electroproses). Based on the pictures, it seemed that it worked out this time!

The design of the future is … software

I want to order a part of a DNA strand at Eurofins Genomics.
First I copied a sample out of Benchling and also tried to work with BLAST and N20. I think it is a great idea to order the lambda DNA like in my RE kit.

In the week 8 blog you can read about the previous steps: https://peterjoostennet.github.io/week8/

Preparation

These were the steps in the preparation:

• I ordered the synthetic DNA from Eurofins
• Based on the Primer Designer I could choose from 5 standard primers (forward and reverse primers)
• I called with Eurofins customer support: do I need all 5 primers or do I need to choose one?
• For the purpose of my project (a.k.a. just playing around) they advised me to compare the location of the primers with the DNA code
• The primers do not neatly start at the first basepairs and end at the last. This is based on the molecule structure, which needs to be strong enough.
• I did an analysis and found out that primer 1 gave me the ‘most bang for the buck’
• The DNA should be delivered in six days, so that would be Monday the 24th of March
• This week we had a practicum about Bioinformatics, so I copied the DNA code in Blastx and tinkered around. Which proteins sequence will be produced based on the DNA code?

Execution

These are the next steps:

• Multiply the DNA with the PCR
• If I have time: do the RE kit experiments one more time with the Lamda DNA (of the kit) and the synthetic (part of the) Lambda DNA.