Open-Source LAMP Instrument Aimed At Clinicians And Biohackers Alike

July 14, 2023 by Dan Maloney 28 Comments

Over the last few years, we’ve all been given a valuable lesson in both the promise and limitations of advanced molecular biology methods for clinical diagnostics. Polymerase chain reaction (PCR) was held up as the “gold standard” of COVID-19 testing, but the cost, complexity, and need for advanced instrumentation and operators with specialized training made PCR difficult to scale to the levels demanded by a pandemic.

There are other diagnostic methods, of course, some of which don’t have all the baggage of PCR. RT-LAMP, or reverse transcriptase loop-mediated amplification, is one method with a lot of promise, especially when it can be done on a cheap open-source instrument like qLAMP. For about 50€, qLAMP makes amplification and detection of nucleic acids, like the RNA genome of the SARS-CoV-2 virus, a benchtop operation that can be performed by anyone. LAMP is an isothermal process; it can be done at one single temperature, meaning that no bulky thermal cycler is required. Detection is via the fluorescent dye SYTO 9, which layers into the base pairs inside the amplified DNA strands, using a 470-nm LED for excitation and a photodiode with a filter to detect the emission. Heating is provided by a PCB heater and a 3D-printed aluminum block that holds tubes for eight separate reactions. Everything lives in a 3D-printed case, including the ESP32 which takes care of all the housekeeping and data analysis duties.

With the proper test kits, which cost just a couple of bucks each, qLAMP would be useful for diagnosing a wide range of diseases, and under less-than-ideal conditions. It could also be a boon to biohackers, who could use it for their own citizen science efforts. We saw a LAMP setup at the height of the pandemic that used the Mark 1 eyeball as a detector; this one is far more quantitative.

Coronavirus Testing: CRISPR Technology Set To Streamline Viral Testing

May 27, 2020 by Dan Maloney 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 Orlando Hoilett 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 Dan Maloney 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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Simple, Low-Cost Rig Lets The Budding Biohacker Run DNA Gels

December 1, 2018 by Dan Maloney 12 Comments

We all the know the basic components for building out an electronics lab: breadboards, bench power supply, a selection of components, a multimeter, and maybe an oscilloscope. But what exactly do you need when you’re setting up a biohacking lab?

That’s the question that [Justin] from The Thought Emporium is trying to answer with a series of videos where he does exactly that – build a molecular biology lab from scratch. In the current installment, [Justin] covers the basics of agarose gel electrophoresis, arguably the fundamental skill for aspiring bio-geeks. Electrophoresis is simply using an electric field to separate a population of macromolecules, like nucleic acids and proteins, based on their sizes. [Justin] covers the basics, from building a rig for running agarose gels to pouring the gels to doing the actual separation and documenting the results. Commercial grade gear for the job is priced to squeeze the most money out of a grant as possible, but his stuff is built on the cheap, from dollar-store drawer organizers and other odd bits. It all works, and it saves a ton of money that can be put into the things that make more sense to buy, like fluorescent DNA stain for visualizing the bands; we’re heartened to see that the potent carcinogen ethidium bromide that we used back in the day is no longer used for this.

We’re really intrigued with [Justin]’s bio lab buildout, and it inspires us to do the same here. This and other videos in the series, like his small incubators built on the cheap, will go a long way to helping others get into biohacking.

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Françoise Barré-Sinoussi: Virus Hunter

July 17, 2018 by Steven Dufresne 13 Comments

It was early 1983 and Françoise Barré-Sinoussi of the prestigious Pasteur Institute in Paris was busy at the centrifuge trying to detect the presence of a retrovirus. The sample in the centrifuge came from an AIDS patient, though the disease wasn’t called AIDS yet.

Barré-Sinoussi and Montagnier in 1983, Image source: Le Globserver

Just two years earlier in the US, a cluster of young men had been reported as suffering from unusual infections and forms of cancer normally experienced by the very old or by people using drugs designed to suppress the immune system. More cases were reported and US Centers for Disease Control and Prevention (CDC) formed a task force to monitor the unusual outbreak. In December, the first scientific article about the outbreak was published in the New England Journal of Medicine.

By May 1983, researchers Barré-Sinoussi and Luc Montagnier of the Pasteur Institute had isolated HIV, the virus which causes AIDS, and reported it in the journal Science. Both received the Nobel prize in 2008 for this work and the Nobel prize citation stated:

Never before have science and medicine been so quick to discover, identify the origin and provide treatment for a new disease entity.

It’s only fitting then that we take a closer look at one of these modern detectives of science, Françoise Barré-Sinoussi, and what led to her discovery.

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Synthetic Biology Creates Living Computers

August 9, 2017 by Al Williams 25 Comments

Most people have at least a fuzzy idea of what DNA is. Ask about RNA, though, and unless you are talking to a biologist, you are likely to get even more handwaving. We hackers might have to reread our biology text books, though, since researchers have built logic gates using RNA.

Sometimes we read these university press releases and realize that the result isn’t very practical. But in this case, the Arizona State University study shows how AND, OR, and NOT gates are possible and shows practical applications with four-input AND gates and six-input OR gates using living cells. The key is a construct known as an RNA toehold switch (see video below). Although this was worked out in 2012, this recent study shows how to apply it practically.

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