How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Fisher Scientific UVP LM-26E Benchtop 2UV Transilluminator by 
Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21www.bidspotter.com/en-us/auction-catalogues/bscsur/catalogue-id-bscsur10011/lot-c6605b41-1a14-40e5-a255-a5c5000866e0 (archive) Cannot exact same product on official website, but here is a similar one: www.fishersci.co.uk/shop/products/lm-26-2uv-transilluminator/12382038 (archive).
How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Filtration with vacuum pump by Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21The first thing we did was to filter the water samples with a membrane filter that is so fine that not even bacteria can pass through, but water can.
Therefore, after filtration, we would have all particles such as bacteria and larger dirt pieces in the filter.
From the 1 liter in each bottle, we only used 400 ml because previous experiments showed that filtering the remaining 600 ml is very time consuming because the membrane filter gets clogged up.
Therefore, the filtration step allows us to reduce those 400 ml volumes to more manageable Eppendorf tube volumes: Figure 1. "An Eppendorf tube". Reagents are expensive, and lab bench centrifuges are small!
Labelled Eppendorf tubes on a rack
. Source. Since the filter is so fine, filtering by gravity alone would take forever, and so we used a vacuum pump to speed thing up!
For that we used:
Peeling the vacuum pump filter protection peel before usage
. Source. 
Placing the vacuum pump filter
. Source. How to use an Oxford Nanopore MinION to extract DNA from river water and determine which bacteria live in it Post filtration purification by Ciro Santilli 40 Updated 2026-08-21
Ciro Santilli 40 Updated 2026-08-21After filtration, all DNA should present in the filter, so we cut the paper up with scissors and put the pieces into an Eppendorf: Video 1. "Cutting vacuum pump filter and placing it in Eppendorf".
Cutting vacuum pump filter and placing it in Eppendorf
. Source. Now that we had the DNA in Eppendorfs, we were ready to continue the purification in a simpler and more standardized lab pipeline fashion.
First we added some small specialized beads and chemicals to the water and shook them Eppendorfs hard in a Scientific Industries Inc. Vortex-Genie 2 machine to break the cell and free the DNA.
Once that was done, we added several reagents which split the solution into two phases: one containing the DNA and the other not. We would then pipette the phase with the DNA out to the next Eppendorf, and continue the process.
In one step for example, the DNA was present as a white precipitate at the bottom of the tube, and we threw away the supernatant liquid: Figure 1. "White precipitate formed with Qiagen DNeasy PowerWater Kit".
At various stages, centrifuging was also necessary. Much like the previous vacuum pump step, this adds extra gravity to speed up the separation of phases with different molecular masses.
Then, when we had finally finished all the purification steps, we measured the quantity of DNA with a Biochrom SimpliNano spectrophotometer to check that the purification went well:
arstechnica.com/information-technology/2016/11/private-microwave-networks-financial-hft/ The secret world of microwave networks (2016) Fantastic article.
Apparently, DC current comes in, and microwaves come out.
TODO: sample power efficiently of this conversion and output spectrum of this conversion on some cheap device we can buy today.
Device that Won WW2 by Curious Droid
. Source. For the most part, a great pseudo-country to live in with lots of cultural diversity, art and safety.
However, Europe is in economic decline after all its Jewish and German geniuses fled in/after World War II and due to having more than one natural language is bad for the world.
Ciro Santilli moved to Europe in 2010.
Exist because double bonds don't rotate freely. Have different properties of course, unlike enantiomer.
Key exmaple: d and L amino acids. Enantiomers have identical physico-chemical properties. But their biological roles can be very different, because an enzyme might only be able to act on one of them.
Example:
- the three most table polymorphs of calcium carbonate polymorphs are:
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. 
- Infinitely deep tables of contents:
All our software is open source and hosted at: github.com/ourbigbook/ourbigbook
Further documentation can be found at: docs.ourbigbook.com
Feel free to reach our to us for any help or suggestions: docs.ourbigbook.com/#contact