How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Conclusions by 
Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16- against all odds, the experiment worked and we got DNA out of the water, despite a bunch of non-bio newbs actively messing with random parts of the experiment
- PuntSeq and Biomakespace people, and all those tho do scientific outreach, are awesome!
- biology is hard
- creating insanely media rich articles like this is also hard, but the following helped enormously:
- Wikimedia Commons to store large media files out of Git
- Asciidoctor extensions to easily include those media files. The lessons learnt in this article were then an important motivation for Ciro's OurBigBook Markup, to which this article was later migrated.
- Nomacs to give Google Photos photos meaningful names and to edit people's faces out of pictures ;-)
- some scientific Wikipedia pages may or may not have been edited with better pictures during the course of writing this article
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen DNeasy PowerWater Kit by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.qiagen.com/gb/products/discovery-and-translational-research/dna-rna-purification/dna-purification/microbial-dna/dneasy-powerwater-kit (archive) Here is its documentation: www.qiagen.com/gb/resources/download.aspx?id=bb731482-874b-4241-8cf4-c15054e3a4bf&lang=en (archive).
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Qiagen QIAquick PCR Purification Kit by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16www.qiagen.com/us/products/discovery-translational-research/dna-rn-a-purification/dna-purification/dna-clean-up/qiaquick-pcr-purification-kit/#orderinginformation (archive)
Manual archive: web.archive.org/web/20190911100243/https://www.qiagen.com/us/resources/download.aspx?id=e0fab087-ea52-4c16-b79f-c224bf760c39&lang=en
Removes PCR byproducts from purified DNA.
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Oxford Nanopore SQK-LSK109 Ligation Sequencing Kit by Ciro Santilli 40 Updated 2025-07-16
Ciro Santilli 40 Updated 2025-07-16Repairs the ends of DNA, and also attaches an adapter protein to the DNA that makes them go through the pores of e.g. an Oxford Nanopore MinION.
Note that this is a specific application of de novo DNA synthesis, e.g. polymerase chain reaction primers is another major application that does not imply creating genes.
Using de novo DNA synthesis to synthesize entire Chromosomes.
For parallels between nazi Germany and the cirosantilli.com/china-dictatorship/nazi
Natural pseudodistance is a concept used in mathematical biology and ecology, particularly in the study of population genetics and evolutionary theory. It is typically used to quantify the genetic differences or relationships between populations or individuals based on genetic data. In general, a pseudodistance is a metric that measures how "far apart" two entities are within a particular space or context, but it may not fulfill all the properties of a true distance metric (such as the triangle inequality).
The third one from Cambridge after:
Synthesizing the DNA itself is not the only problem however.
You then have to get that DNA into a working living form state so that normal cell processes can continue:
Multicellular questions:
Apparently achieved for the first time in 2021: www.jcvi.org/research/first-self-replicating-synthetic-bacterial-cell by the J. Craig Venter Institute.
Man-made virus!
TODO: if we had cheap de novo DNA synthesis, how hard would it be to bootstrap a virus culture from that? github.com/cirosantilli/cirosantilli.github.io/issues/60
Is it easy to transfect a cell with the synthesized DNA, and get it to generate full infectious viral particles?
If so, then de novo DNA synthesis would be very similar to 3D printed guns: en.wikipedia.org/wiki/3D_printed_firearms.
It might already be possible to order dissimulated sequences online:
We get the time-independent Schrödinger equation by substituting this into Equation "time-independent Schrödinger equation for a one dimensional particle":
Now, there are two ways to go about this.
The first is the stupid "here's a guess" + "hey this family of solutions forms a complete basis"! This is exactly how we solved the problem at Section "Solving partial differential equations with the Fourier series", except that now the complete basis are the Hermite functions.
The second is the much celebrated ladder operator method.
The first found and most important known epigenetic marker.
Happens only on adenine and cytosine. Adenine methylation is much less common in mammal than cytosine methylation, when people say "methylation" they often mean just cytosine methylation.
It often happens on promoters, where it inhibits transcription.
Pinned article: Introduction to the OurBigBook Project
Welcome to the OurBigBook Project! Our goal is to create the perfect publishing platform for STEM subjects, and get university-level students to write the best free STEM tutorials ever.
Everyone is welcome to create an account and play with the site: ourbigbook.com/go/register. We belive that students themselves can write amazing tutorials, but teachers are welcome too. You can write about anything you want, it doesn't have to be STEM or even educational. Silly test content is very welcome and you won't be penalized in any way. Just keep it legal!
Intro to OurBigBook
. Source. We have two killer features:
- topics: topics group articles by different users with the same title, e.g. here is the topic for the "Fundamental Theorem of Calculus" ourbigbook.com/go/topic/fundamental-theorem-of-calculusArticles of different users are sorted by upvote within each article page. This feature is a bit like:
- a Wikipedia where each user can have their own version of each article
- a Q&A website like Stack Overflow, where multiple people can give their views on a given topic, and the best ones are sorted by upvote. Except you don't need to wait for someone to ask first, and any topic goes, no matter how narrow or broad
This feature makes it possible for readers to find better explanations of any topic created by other writers. And it allows writers to create an explanation in a place that readers might actually find it.
Figure 1. Screenshot of the "Derivative" topic page. View it live at: ourbigbook.com/go/topic/derivativeVideo 2. OurBigBook Web topics demo. Source. - local editing: you can store all your personal knowledge base content locally in a plaintext markup format that can be edited locally and published either:This way you can be sure that even if OurBigBook.com were to go down one day (which we have no plans to do as it is quite cheap to host!), your content will still be perfectly readable as a static site.
- to OurBigBook.com to get awesome multi-user features like topics and likes
- as HTML files to a static website, which you can host yourself for free on many external providers like GitHub Pages, and remain in full control
Figure 3. Visual Studio Code extension installation.
Figure 4. Visual Studio Code extension tree navigation.
Figure 5. Web editor. You can also edit articles on the Web editor without installing anything locally.Video 3. Edit locally and publish demo. Source. This shows editing OurBigBook Markup and publishing it using the Visual Studio Code extension.Video 4. OurBigBook Visual Studio Code extension editing and navigation demo. Source. 
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