Hi everybody and welcome to my first blog post at Albertsen Lab. As a newly started PhD student, I have engaged myself with the simple, yet Herculean task of populating the tree-of-life. As most people are aware of, microorganisms are more or less inescapably present in all places of the world — no matter how […]
Tagging of individual molecules has been used as an effective consensus error-correction strategy for Illumina data (Kivioja et al 2011, Burke et al 2016, Zhang et al 2016) and the principle is similar to the circular consensus sequencing strategy used to generate consensus reads with error rate of < 1 % on the PacBio (Travers et […]
For the first time, I am going to share something more related to my master thesis. When I started this thesis, I did not know how to use R. In order to learn R, I started using DataCamp, which is a series of interactive courses. You can start from scratch and build your skills step […]
Ever done amplicon DNA sequencing of the 16S rRNA gene to identify microbes? If so, then you must know about the challenge of analysing such complex data easily. My name is Kasper, and I am currently a master student here at the Albertsens lab. When I first learned how DNA is sequenced today, I was astonished by the rapid […]
The other day I watched my boyfriend playing the game Dark Souls III. At some point he had to step through this fog, entering a new area or a boss area or something else. You never know. It was a boss, but I don’t remember how it went from that point on. Because it got […]
My name is Peter Rendbæk, and I’m currently a master student in the Albertsen lab. The overarching aim of my master project, is as a pre-test for several of the new big projects in the group, which focus on applying the on-line bacterial identification for process control at wastewater treatment plants. Hence, last couple of months I have been working on the project “Developing methods for on-site DNA sequencing using the Oxford Nanopore MinION platform”. The MinION has improved a lot since its release three years ago, and it can now be used to make rapid determination of bacterial compositions.
The potential for this fast and mobile DNA-sequencing is mind-blowing. However, given that the technology is here now (!), there has been relatively little focus on portable, fast, easy and robust DNA extraction. Hence, I’ve spent the last months on trying to develop a fast, cheap, mobile, robust and easy to use DNA extraction method.
There is a significant amount of bias connected with DNA extraction, but the bias associated with wastewater treatment samples has been investigated in depth. However, the “optimized method” is not suited for on-site DNA-extraction. There are 3 principle steps in DNA extraction, cell lysis, debris removal and DNA isolation, which I will cover below and discuss how I simplified each step.
In general, complex samples require bead beating for cell lysis and homogenization. The problem is that our in-house bead-beating is done by a big table top tool weighing 17 kg, which makes it hard to transport. However, I came across a blog post from loman labs about sample preparation and DNA extraction in the field for Nanopore sequencing. In the blog post, the possibilities of a portable bead beater outlined, by the use of a remodeled power-tool. I thought this was interesting, so I went out and bought an Oscillating Multi-Tool cutter and tried this with lots of duct tape…
The amazing part was that it worked! But the problem was that the samples would get “beaten” differently depend on how you taped the sample to the power-tool, which could give rise to variation large variations in the observed microbial community.
I solved this by 3D printing an adapter to the power-tool that fits the bead-beater tube (Finally, a good excuse to use a 3D printer!). I used Solidworks to design the adapter and collaborated with our local department of mechanical and manufacturing engineering (m-tech) in 3D printing it. You can make your own by simply downloading my design from Thingiverse (It did take a few iterations to make it durable enough, and I still use a little duct tape..).
After the bead beating, the cell debris removal is done by centrifugation. Our “standard” protocol recommends centrifugation at 14000 x G for 10 minutes at 4 C. However, in our minds that seemed a little extensive and requires a huge non-transportable centrifuge… Alternatively, there are a lot of possibilities to use small, easy to transport and easy to use centrifuges if we do not have to centrifuge at 14.000 xG at 4 C. There is even the possibility to 3D print a hand-powered centrifuge. However, I did not follow this path, as it seems a bit dangerous… After several tests, we discovered that a simple table top centrifuge could do the job perfectly well, using 2000 xG for 1 min at room temperature if we combined it with the DNA isolation described below.
The last step is DNA isolation, I tried several different methods, but we got the idea to simply use Agencourt AMPure XP that is routinely used in e.g. PCR purification (we 10 diluted the AMPure XP beads 1:10 to save some money and it seems to work just as good). And… It works..
So, now you have an overview of the method I developed. The most amazing part is that it works! It takes 10-15 minutes from the sample is taken until you’ve got ready DNA for use, compared to 60+ minutes for our “standard” protocol. Furthermore, it requires inexpensive equipment that can be carried in a small suitcase. So, just to prove that this approach is fast, I filmed myself doing the DNA extraction with a GO-PRO camera, as you can see below.
The next part is to test the MinION in the lab. How, fast can we identify bacteria and is the extracted DNA compatible with the downstream library preparation, which we hope to do on the our new and shiny Voltrax (which is now moving liquids!).
Following our PromethION unboxing event we have finally managed to connect the machine to our University network and pass the configuration run. The configuration test demonstrates that the network can handle the data produced and transfer it fast enough to a network storage solution. Got everything up and running for @nanopore #PromethION CTC run thx to […]
As a student, you will have to present sometime during your education. Despite this, there is hardly any time allocated to learning the skills required in giving a good presentation . As part of your Masters degree at Aalborg University you’ll have to participate in at least one status seminar presenting your thesis (20 minutes). […]
Recently, I was one of 16 recipients of a 10 mill. DKK grant (1.3 mill. EUR) from the VILLUM foundation under their Young Investigator Program (YIP). The program is unique in Denmark and offers young scientists an opportunity to build a research group on their own terms. The foundation is working on the premise of the founder […]
As a newly started master student it can be a bit intimidating to attend a conference. Nevertheless, I said yes when I was offered to attend MEWE16 in Copenhagen. I had just ended a one-year maternity leave and was eager to start my thesis and talk to adult people. I quickly realized that I was […]