dna

43 Articles

Sequencing DNA For Metagenomics

February 5, 2021 by 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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Coronavirus Testing: CRISPR Technology Set To Streamline Viral Testing

May 27, 2020 by 3 Comments

If we could run back 2020 to its beginning and get a do-over, chances are pretty good that we’d do a lot of things differently. There’s a ton of blame to go around on COVID-19, but it’s safe to say that one of the biggest failures of this whole episode has been the lack of cheap, quick, accurate testing for SARS-CoV-2, the virus behind the current pandemic. It’s not for lack of information; after all, Chinese scientists published the sequence of the viral genome very early in the pandemic, and researchers the world over did the same for all the information they gleaned from the virus as it rampaged around the planet.

But leveraging that information into usable diagnostics has been anything but a smooth process. Initially, the only method of detecting the virus was with reverse transcriptase-polymerase chain reaction (RT-PCR) tests, a fussy process that requires trained technicians and a well-equipped lab, takes days to weeks to return results, and can only tell if the patient has a current infection. Antibody testing has the potential for a quick and easy, no-lab-required test, but can only be used to see if a patient has had an infection at some time in the past.

What’s needed as the COVID-19 crisis continues is a test with the specificity and sensitivity of PCR combined with the rapidity and simplicity of an antibody test. That’s where a new assay, based on the latest in molecular biology methods and dubbed “STOPCovid” comes in, and it could play a major role in diagnostics now and in the future.

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Defense Department Funds Wearables To Detect COVID-19

May 17, 2020 by 10 Comments

As many countries across the globe begin loosening their stay-at-home orders, we’re seeing government agencies and large companies prepare for the lasting effects of the pandemic. A recent solicitation from the United States Department of Defense (DoD) indicates they are investing $25 million into wearable devices that can detect early signs of COVID-19.

Based on a few details from the request for project proposals, it looks like the DoD is targeting mostly companies in this particular solicitation, but have left the door open for academic institutions as well. That makes intuitive sense. Companies can generally operate at a faster pace than most academic research labs. Given the urgency of the matter, faster turnarounds in technological development are imperative. Nonetheless, we have seen quite a bit of important COVID-19 work coming from academic research labs and we imagine that battling this pandemic will take all the brilliant minds we can muster together.

It’s good to see the DoD join the fight in what could be a lengthy battle with the coronavirus.

Please feel free to read through the request for project proposals for more details.

So What Is Protein Folding, Anyway?

April 14, 2020 by 26 Comments

The current COVID-19 pandemic is rife with problems that hackers have attacked with gusto. From 3D printed face shields and homebrew face masks to replacements for full-fledged mechanical ventilators, the outpouring of ideas has been inspirational and heartwarming. At the same time there have been many efforts in a different area: research aimed at fighting the virus itself.

Getting to the root of the problem seems to have the most potential for ending this pandemic and getting ahead of future ones, and that’s the “know your enemy” problem that the distributed computing effort known as Folding@Home aims to address. Millions of people have signed up to donate cycles from spare PCs and GPUs, and in the process have created the largest supercomputer in history.

But what exactly are all these exaFLOPS being used for? Why is protein folding something to direct so much computational might toward? What’s the biochemistry behind this, and why do proteins need to fold in the first place? Here’s a brief look at protein folding: what it is, how it happens, and why it’s important.

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Hackaday Links: February 23, 2020

February 23, 2020 by 19 Comments

If you think your data rates suck, take pity on New Horizons. The space probe, which gave us lovely pictures of the hapless one-time planet Pluto after its 2015 flyby, continued to plunge and explore other, smaller objects in the Kuiper belt. In January of 2019, New Horizons zipped by Kuiper belt object Arrokoth and buffered its findings on the spacecraft’s solid-state data recorders. The probe has been dribbling data back to Earth ever since at the rate of 1 to 2 kilobits per second, and now we have enough of that data to piece together a story of how planets may have formed in the early solar system. The planetary science is fascinating, but for our money, getting a probe to narrowly miss a 35-kilometer long object at a range of 6.5 billion km all while traveling at 51,500 km/h is pretty impressive. And if as expected it takes until September to retrieve all the data from the event at a speed worse than dialup rates, it’ll be worth the wait.

Speaking of space, if you’re at all interested in big data, you might want to consider putting your skills to work in the search for extraterrestrial intelligence. The Berkeley SETI Research Center has been feeding data from the Green Bank Telescope and their Automated Planet Finder into the public archive of Breakthrough Listen, a 10-year, $100 million initiative to scan the million closest stars in our galaxy as well as the 100 nearest galaxies for signs of intelligent life. They’re asking for help to analyze the torrents of data they’re accumulating, specifically by developing software and algorithms to process the data. They’ve set up a site to walk you through the basics and get you started. If you’re handy with Python and have an interest in astronomy, you should check it out.

Staying with the space theme, what’s the best way to get kids interested in space and electronics? Why, by launching a satellite designed to meme its way across the heavens, of course. The Mission for Education and Multimedia Engagement satellite, or MEMESat-1, is being planned for a February 2021 launch. The 1U cubesat will serve as an amateur radio repeater and slow-scan TV (SSTV) beacon that will beam down memes donated to the project and stored on radiation-hardened flash storage. In all seriousness, this seems like a great way to engage the generation that elevated the meme to a modern art form in a STEM project they might otherwise show little interest in.

It looks as though Linux might be getting a big boost as the government of South Korea announced that they’re switching 3.3 million PCs from Windows to Linux. It’s tempting to blame Microsoft’s recent dropping of Windows 7 support for the defenestration, but this sounds like a plan that’s been in the works for a while. No official word on which distro will be selected for the 780 billion won ($655 million) effort, which is said to be driven by ballooning software license costs and a desire to get out from under Microsoft’s thumb.

And finally, in perhaps the ickiest auction ever held, the “Davos Collection” headed to the auction block this week in New York. The items offered were all collected from the 2018 World Economic Forum in Davos, Switzerland, where the world’s elites gather to determine the fate of the 99.999%. Every item in the collection, ranging from utensils and glassware used at the many lavish meals to “sanitary items” disposed of by the billionaires, and even hair and fluid samples swabbed from restrooms, potentially holds a genetic treasure trove in the form of the DNA it takes to be in the elite. Or at least that’s the theory. There’s a whole “Boys from Brazil” vibe here that we find disquieting, and we flatly refuse to see how an auction where a used paper cup is offered for $8,000 went, but if you’d like to virtually browse through the ostensibly valuable trash of oligarchs, check out the auction catalog.

Hackaday Podcast 055: The Most Cyberpunk Synthesizer, Data In Your Cells, Bubbly In Your Printer, And The Dystopian Peepshow

February 21, 2020 by 2 Comments

Hackaday editors Mike Szczys and Elliot Williams discuss the many great hacks of the past week. Just in case you missed the fact that we’re living in the cyberpunk future, you can now pop off your prosthetic hand and jack directly into a synthesizer. The robot headed for Mars has a flying drone in its belly. Now they’re putting foaming agent in filament to make it light and flexible. And did you ever wonder why those pinouts were so jumbled?

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!

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DNA Now Stands For Data And Knowledge Accumulation

February 18, 2020 by 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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