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".
The 16S region codes for one of the RNA pieces that makes the bacterial ribosome.
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".
A-U
/ \
A-U-C-G-A-U-C-G C
| | | | | | | | |
U-A-G-C-U-A-G-C G
\ /
U-A
| || |
+-------------++----+
stem loopCode 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.
Literally: West of the Mountain.
This actually happens in spring. But because they are so euphemistic winter had to be removed from the calendar, it gets shifted a left.
Eccentric nerdy slow speaking physicist mostly based in University of Cambridge.
Created the Dirac equation, what else do you need to know?!
QED and the men who made it: Dyson, Feynman, Schwinger, and Tomonaga by Silvan Schweber (1994) chapter 1.3 "P.A.M. Dirac and the Birth of Quantum Electrodynamics" quotes Dirac saying how being at high school during World War I was an advantage, since all slightly older boys were being sent to war, and so the younger kids were made advance as fast as they could through subjects. Exactly the type of thing Ciro Santilli wants to achieve with OurBigBook.com, but without the need for a world war hopefully.
Dirac was a staunch atheist having said during the Fifth Solvay Conference (1927)[ref]:
If we are honest - and scientists have to be - we must admit that religion is a jumble of false assertions, with no basis in reality. The very idea of God is a product of the human imagination. It is quite understandable why primitive people, who were so much more exposed to the overpowering forces of nature than we are today, should have personified these forces in fear and trembling. But nowadays, when we understand so many natural processes, we have no need for such solutions. I can't for the life of me see how the postulate of an Almighty God helps us in any way. What I do see is that this assumption leads to such unproductive questions as why God allows so much misery and injustice, the exploitation of the poor by the rich and all the other horrors He might have prevented. If religion is still being taught, it is by no means because its ideas still convince us, but simply because some of us want to keep the lower classes quiet. Quiet people are much easier to govern than clamorous and dissatisfied ones. They are also much easier to exploit. Religion is a kind of opium that allows a nation to lull itself into wishful dreams and so forget the injustices that are being perpetrated against the people. Hence the close alliance between those two great political forces, the State and the Church. Both need the illusion that a kindly God rewards - in heaven if not on earth - all those who have not risen up against injustice, who have done their duty quietly and uncomplainingly. That is precisely why the honest assertion that God is a mere product of the human imagination is branded as the worst of all mortal sins.
Paul Dirac and the religion of mathematical beauty by Royal Society (2013)
Source. This is one of the prime examples of Europe's decline.
Instead of trying to dominate the sequencing market and gain trillions of dollars from it, they local British early stage investors were more than happy to get a 20x return on their small initial investments, and sold out to the Americans who will then make the real profit.
And now Solexa doesn't even have its own Wikipedia page, while Illumina is set out to be the next Microsoft. What a disgrace.
Here are some good articles about the company:
Cambridge visitors can still visit the Panton Arms pub, which was the location of the legendary "hey we should talk" founders meeting, chosen due to its proximity to the chemistry department of the University of Cambridge.
In 2021 the founders were awarded the Breakthrough Prize. The third person awarded was Pascal Mayer. He was apparently at Serono Pharmaceutical Research Institute at the time of development. They do have a wiki page unlike Solexa: en.wikipedia.org/wiki/Serono. They paid a 700 million fine in 2005 in the United States, and sold out in 2006 to Merck for 10 billion USD.
Basically a subset of the boundary condition for when one of the parameters is time and we are specifying values for the time 0.
Beautifully argued at: Can't get you out of my head by Adam Curtis (2021).
There are unlisted articles, also show them or only show them.