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How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Overview of the experiment Updated 2025-07-16
For those that know biology and just want to do the thing, see: Section "Protocols used".
The PuntSeq team uses an Oxford Nanopore MinION DNA sequencer made by Oxford Nanopore Technologies to sequence the 16S region of bacterial DNA, which is about 1500 nucleotides long.
This kind of "decode everything from the sample to see what species are present approach" is called "metagenomics".
This is how the MinION looks like: Figure 1. "Oxford Nanopore MinION top".
Oxford Nanopore MinION top open
. Source. 
Before sequencing the DNA, we will do a PCR with primers that fit just before and just after the 16S DNA, in well conserved regions expected to be present in all bacteria.
The PCR replicates only the DNA region between our two selected primers a gazillion times so that only those regions will actually get picked up by the sequencing step in practice.
Eukaryotes also have an analogous ribosome part, the 18S region, but the PCR primers are selected for targets around the 16S region which are only present in prokaryotes.
This way, we amplify only the 16S region of bacteria, excluding other parts of bacterial genome, and excluding eukaryotes entirely.
Despite coding such a fundamental piece of RNA, there is still surprisingly variability in the 16S region across different bacteria, and it is those differences will allow us to identify which bacteria are present in the river.
The variability exists because certain base pairs are not fundamental for the function of the 16S region. This variability happens mostly on RNA loops as opposed to stems, i.e. parts of the RNA that don't base pair with other RNA in the RNA secondary structure as shown at: Code 1. "RNA stem-loop structure".
This is how the 16S RNA secondary structure looks like in its full glory: Figure 5. "16S RNA secondary structure".
Since loops don't base pair, they are less crucial in the determination of the secondary structure of the RNA.
The variability is such that it is possible to identify individual species apart if full sequences are known with certainty.
With the experimental limitations of experiment however, we would only be able to obtain family or genus level breakdowns.
Sandy Maguire Updated 2025-07-16
Lots of similar ideologies to Ciro Santilli, love it:
- sandymaguire.me/blog/reaching-climbing/: don't be a pussyOne is also reminded of Gwern Branwen. Sandy is also into self-improvement stuff, so even more like Gwern. This is a point Ciro diverges on. Ciro works actively on self-worsening.
Last Friday was my final day at work. According to my facebook profile, I am now "happily retired." As of today, I don't plan to do another day of "traditional work" in my life. That's not to say that I'll be sitting idle playing tiddly winks. I want to build things, to dedicate my life to independent study, and to get really, really good with building communities. I don't have time for any of this "work" stuff that somehow pervades our entire culture, choking our inspiration and sapping our energy away from the things we'd rather be doing.
- he thinks university is useless:
- sandymaguire.me/blog/where-uni-fails/ Where University Fails (2018), mostly talking about backward design
- sandymaguire.me/blog/gatekept/ rejected from Imperial College PhD program due to grade being slightly too low for their stupid requirements, even though he had a referral already, and an amazing CV
- he likes jazz: sandymaguire.me/blog/too-smart/
Other interesting points:
- sandymaguire.me/blog/sandy-runback/ he changed his own name to Sandy because he didn't like it, he was born Alexander
- algebradriven.design/ closed source books though, ouch. At least they seem to have been made with leanpub though, could be worse.
Scientific Autobiography by Max Planck translated by Frank Gaynor (1949) Updated 2025-07-16
Published as Scientific Autobiography and Other Papers by Max Planck translated by Frank Gaynor (1949) which also contained other papers.
This section refers just to the translation of Scientific autobiography by Max Planck (1948).
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This actually happens in spring. But because they are so euphemistic winter had to be removed from the calendar, it gets shifted a left.
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