Sequencing DNA For Metagenomics

February 5, 2021 by Al Williams 15 Comments

If someone brought you an odd piece of electronic hardware and you wanted to identify it, you’d probably look for markings on the outside first. If that didn’t work out, you might look under the cover and read some markings on the board or key components. However, in a tough case, you might dump the firmware and try to guess what the device is or what it does by examining the code that makes it run. That’s kind of what [Ciro] did. Wanting to determine the bacteria in a water sample led to using relatively inexpensive DNA sequencing hardware to look at the DNA present in the samples. This would have been a huge undertaking for a well-funded lab just a few short years ago. Now it just takes a USB device and some software.

Of course, inexpensive is in the eye of the beholder. The micropore sequencer costs about $500 and has a one-time use consumable cost of about $500, although that’s enough to process about 10 human genomes. The technology depends on using a small pore only large enough to pass one strand of DNA at a time. Blocks of nucelotides cause different amounts of electrical current to flow through the pore.

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Hackaday Podcast 060: Counting Bees, DogBox Transmissions, And The Lowdown On Vents, BiPAP, And PCR

March 27, 2020 by Mike Szczys No comments

Hackaday editors Elliot Williams and Mike Szczys recount the past week in hardware hacking. There’s a new king of supercomputing and it’s everyone! Have you ever tried to count bees? Precision is just a cleverly threaded bolt away. And we dig into some of the technical details of the coronavirus response with a close look at PCR testing for the virus, and why ventilators are so difficult to build.

Take a look at the links below if you want to follow along, and as always tell us what you think about this episode in the comments!

Take a look at the links below if you want to follow along, and as always, tell us what you think about this episode in the comments!

Direct download (60 MB or so.)

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DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by Bob Baddeley 33 Comments

Technology frequently looks at nature to make improvements in efficiency, and we may be nearing a new breakthrough in copying how nature stores data. Maybe some day your thumb drive will be your actual thumb. The entire works of Shakespeare could be stored in an infinite number of monkeys. DNA could become a data storage mechanism! With all the sensationalism surrounding this frontier, it seems like a dose of reality is in order.

The Potential for Greatness

The human genome, with 3 billion base pairs can store up to 750MB of data. In reality every cell has two sets of chromosomes, so nearly every human cell has 1.5GB of data shoved inside. You could pack 165 billion cells into the volume of a microSD card, which equates to 165 exobytes, and that’s if you keep all the overhead of the rest of the cell and not just the DNA. That’s without any kind of optimizing for data storage, too.

This kind of data density is far beyond our current digital storage capabilities. Storing nearly infinite data onto extremely small cells could change everything. Beyond the volume, there’s also the promise of longevity and replication, maintaining a permanent record that can’t get lost and is easily transferred (like medical records), and even an element of subterfuge or data transportation, as well as the ability to design self-replicating machines whose purpose is to disseminate information broadly.

So, where is the state of the art in DNA data storage? There’s plenty of promise, but does it actually work?

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Put The Power Of PCR In Your Pocket With This Open-Source Thermal Cycler

January 26, 2020 by Dan Maloney 23 Comments

When the first thermal cyclers for the polymerase chain reaction came out in the 1980s, they were as expensive as a market driven by grant money could make them. Things haven’t got much better over the years, largely shutting STEM classes and biohackers out of the PCR market. That may be about to change, though, if the €99.00 PocketPCR thermal cycler takes hold.

PCR amplifies DNA in a three-step process: denaturation, which melts double-stranded DNA into single strands; annealing, which lets small pieces of primer DNA bind to either side of the region of interest; and elongation, where the enzyme DNA polymerase zips along the single strands starting at the primer to replicate the DNA. The cycle repeats and copies of the original DNA accumulate exponentially. Like any thermal cycler, [Urs Gaudenz]’s PocketPCR automates those temperature shifts, using a combination of PCB-mounted heating elements and a cooling fan. The coils rapidly heat a reaction block up to the 99°C denaturation temperature, the fan brings that down to the 68°C needed for annealing, and then the temperature ramps back up to 72°C for elongation with thermostable DNA polymerase. PID loops keep the reaction temperature precisely controlled. The whole thing is, as the name suggests, small enough to fit in a pocket, and can either be purchased in kit form or scratch-built from the build files on GitHub.

We applaud [Urs]’ efforts to get the power of PCR into the hands of citizen scientists. Quick and dirty thermal cyclers are one thing, but Pocket PCR has a great fit and finish that makes it more accessible.

Thanks to [Abe Tusk] for the tip.

OSM (Pronounced Awesome) Hardware Makes DNA In Space

April 27, 2017 by Michael Uttmark 21 Comments

OSM stands for Oligonucleotide Synthesizer designed for use in Microgravity, meaning that it’s a device that makes arbitrary DNA strands (of moderate length) in space. Cool eh? I’ve been working on this project for the last eight months with a wonderful team of fellow hackers as part of the Stanford Student Space Initiative, and I’d like to share what we’re doing, what we’ve already done, and where we’re going.

Why space? Well, first of all, space is cool. But more seriously, access to arbitrary DNA in space could accelerate research in a plethora of fields, and the ability to genetically engineer bacteria to produce substances (say on a martian colony) could mean the difference between death and a life-saving shot. In short, it’s hard to predict the exact DNA one might need for research or practical use before hand.

First, as Hackaday tends to be a little light on biology terminology, we need to get a little vocabulary out of the way to grease the ways of communication. If you have a Ph.D. in synthetic biology, you might want to skip this section. Otherwise, here are five quick terms that will make your brain bigger so stay with me!

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Enzymes From The Deep – The Polymerase

March 22, 2016 by Nava Whiteford 46 Comments

Our bodies rely on DNA to function, it’s often described as “the secret of life”. A computer program that describes how to make a man. However inaccurate these analogies might be, DNA is fundamental to life. In order for organisms to grown and replicate they therefore need to copy their DNA.

dna-replication — DNA structure and replication

Since the discovery of its structure in 1953, the approximate method used to copy DNA has been obvious. The information in DNA is encoded in 4 nucleotides (which in their short form we call A,T,G, and C). These couple with each other in pairs, forming 2 complimentary strands that mirror each other. This structure naturally lends itself to replication. The two strands can dissociate (under heat we call this melting), and new strands form around each single stranded template.

However, this replication process can’t happen all by itself, it requires assistance. And it wasn’t until we discovered an enzyme called the DNA polymerase that we understood how this worked. In conjunction with other enzymes, double stranded DNA is unwound into 2 single strands which are replicated by the polymerase.

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THP Entry: Polymerase Chain Reaction, Cheaper Than A Hamburger

July 14, 2014 by Brian Benchoff 15 Comments

PCR Invented 30 years ago, polymerase chain reaction , or PCR, is one of the greatest inventions of the 20th century. It’s the technique that allows researchers to map genomes, find genetic causes of diseases, create Jurassic Park, and match crime scene DNA to suspects. When PCR was first invented it was extraordinarily expensive, and even today commercial PCR machines cost about the same as a new car. There is an open source project for a PCR machine that costs about $600, but for his Hackaday Prize entry, [David] is knocking a few more zeros off that cost and building a machine for less than the cost of a fast food meal.

Despite being the work behind a Nobel Prize, PCR is conceptually fairly simple: A strand of DNA is unwound into two strands, an enzyme, or primer, is annealed onto these single strands, and then biochemistry happens, turning those single helix strands of DNA into a complete double helix, ready for the next replication cycle. The key of the PCR technique is getting the enzymes and primers to react. This is only done at a fairly fine range of temperatures, cycling between 90°C, then 60°, then 72°C.

The oldest models of PCR machines used multiple water baths, with newer commercial machines using something that probably justifies their cost. The OpenPCR project uses an aluminum heater block, but [David] is going for a modern twist on the old-school method. He’s trying to figure out how to exploit convection to get local temperature variations in a single vessel. How he’s going to do this is anyone’s guess, but building a PCR machine for $5 is pretty cool.

The project featured in this post is an entry in The Hackaday Prize. Build something awesome and win a trip to space or hundreds of other prizes.