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.

Intranasal Vaccines: A Potential Off-Ramp For Coronavirus Pandemics

September 29, 2022 by Maya Posch 54 Comments

An interesting and also annoying aspect about the human immune system is that it is not a neat, centralized system where you input an antigen pattern in one spot and suddenly every T and B lymphocyte in the body knows how to target an intruder. Generally, immunity stays confined to specific areas, such as the vascular and lymph system, as well as the intestinal and mucosal (nasal) parts of the body.

The result of this is that specific types of vaccines have a different effect, as is demonstrated quite succinctly with the polio vaccines. The main difference between the oral polio vaccine (OPV) and inactivated vaccine (injected polio vaccine, or IPV) is that the former uses a weakened virus that induces strong immunity in the intestines, something that the latter does not. The effect of this is that while both protect the individual, it does not affect the fecal-oral infection route of the polio virus and thus the community spread.

The best outcome for a vaccine is when it both protects the individual, while also preventing further infections as part of so-called sterilizing immunity. This latter property is what makes the OPV vaccine so attractive, as it prevents community spread, while IPV is sufficient later on, as part of routine vaccinations. The decision to use a vaccine like the OPV versus the IPV is one of the ways doctors can tune a population’s protection against a disease.

This is where the current batch of commonly used SARS-CoV-2 vaccines are showing a major issue, as they do not provide significant immunity in the nasal passage’s mucosal tissues, even though this is where the virus initially infects a host, as well as where it replicates and infects others from. Here intranasal vaccines may achieve what OPV did for polio.

Continue reading “Intranasal Vaccines: A Potential Off-Ramp For Coronavirus Pandemics” →

HDD Centrifuge Puts COVID-19 Testing Lab In A Backpack

February 5, 2022 by Dan Maloney 11 Comments

Throughout this two-year global COVID-19 nightmare, one thing that has been sorely lacking is access to testing. “Flu-like symptoms” covers a lot of ground, and knowing if a sore throat is just a sore throat or something more is important enough that we’ve collectively plowed billions into testing. Unfortunately, the testing infrastructure remains unevenly distributed, which is a problem this backpack SARS-CoV-2 testing lab aims to address.

The portable lab, developed by [E. Emily Lin] and colleagues at the Queen Mary University of London, uses a technique called LAMP, for loop-mediated isothermal amplification. LAMP probably deserves an article of its own to explain the process, but suffice it to say that like PCR, LAMP amplifies nucleic acid sequences, but does so without the need for expensive thermal cycling equipment. The kit contains a microcentrifuge that’s fashioned from an e-waste hard drive, a 3D printed rotor, and an Arduino to drive the motor and control the speed. The centrifuge is designed to run on any 12 VDC source, meaning the lab can be powered by a car battery or solar panel if necessary. Readout relies on the trusty Mark I eyeball and a pH-indicating buffer that changes color depending on how much SARS-CoV-2 virus was in the sample.

Granted, the method used here still requires more skill to perform than a simple “spit on a stick” rapid antigen test, and it’s somewhat more subjective than the “gold standard” quantitative polymerase chain reaction (qPCR) assay. But the method is easily learned, and the kit’s portability, simple design, and low-cost construction could make it an important tool in attacking this pandemic, or the next one.

Thanks to [Christian Himmler] for the tip.

Monoclonal Antibodies: The Guided Missiles Of Medicine

September 15, 2021 by Dan Maloney 11 Comments

Whenever anyone mentions the word “antibodies” these days, it’s sure to grab your attention. Thoughts generally flow to the human immune system and the role it plays in the ongoing COVID-19 pandemic, and to how our bodies fight off disease in general. The immune system is complex in the extreme, but pretty much everyone knows that antibodies are part of it and that they’re vital to the ability of the body to recognize and neutralize invaders like bacteria and viruses.

But as important as antibodies are to long-term immunity and the avoidance of disease, that’s far from all they’re good for. The incredible specificity of antibodies to their target antigens makes them powerful tools for biological research and clinical diagnostics, like rapid COVID-19 testing. The specificity of antibodies has also opened up therapeutic modalities that were once the stuff of science-fiction, where custom-built antibodies act like a guided missile to directly attack not only a specific protein in the body, but sometimes even a specific part of a protein.

Making these therapies work, though, requires special antibodies: monoclonal antibodies. These are very much in the news recently, not only as a possible treatment for COVID-19 but also to treat everything from rheumatoid arthritis to the very worst forms of cancer. But what exactly are monoclonal antibodies, how are they made, and how do they work?

Continue reading “Monoclonal Antibodies: The Guided Missiles Of Medicine” →

A Simple But Effective High-Flow Oxygen Concentrator From Hardware Store Parts

March 24, 2021 by Dan Maloney 76 Comments

To say that a lot has happened in the year since the COVID-19 pandemic started is an understatement of epic proportions, so much so that it may be hard to remember how the hardware hacking community responded during those early days, with mass-produced PPE, homebrew ventilators and the like. But we don’t recall seeing too many attempts to build something like this DIY oxygen concentrator during that initial build-out phase.

Given the simplicity and efficacy of the design, dubbed OxiKit, it seems strange that we didn’t see more of these devices. OxiKit uses zeolite, a porous mineral that can be used as a molecular sieve. The tiny beads are packed into columns made from hardware store PVC pipes and fittings and connected to an oil-less air compressor through some solenoid-controlled pneumatic valves. After being cooled in a coil of copper pipe, the compressed air is forced through one zeolite column, which preferentially retains the nitrogen while letting the oxygen pass through. The oxygen stream is split, with part going into a buffer tank and part going into the outlet of the second zeolite column, where it forces the adsorbed nitrogen to be released. An Arduino controls the valves that alternate the gas flow back and forth, resulting in 15 liters per minute of 96% pure oxygen.

OxiKit isn’t optimized as a commercial oxygen concentrator is, so it’s not particularly quiet. But it’s a heck of a lot cheaper than a commercial unit, and an easy build for most hackers. OxiKit’s designs are all open source, but they do sell kits and some of the harder-to-source parts and supplies, like the zeolite. We’d be tempted to build something like this just because the technology is so neat; having a source of high-flow oxygen available isn’t a bad idea, either.

Teardown Of The Singaporean COVID-19 TraceTogether Token

June 25, 2020 by Maya Posch 63 Comments

A large part of fighting against the SARS-CoV-2 pandemic is the practice of contact tracing, where the whereabouts of an infected person can be traced and anyone who has been in contact with that person over the past days tested for COVID-19. While smartphone apps have been a popular choice for this kind of tracing, they come with a range of limitations, which is what the TraceTogether hardware token seeks to circumvent. Now [Sean “Xobs” Cross] has taken a look at the hardware that will be inside the token once it launches.

Recently, [Sean] along with [Andrew “bunnie” Huang] and a few others were asked by GovTech Singapore to review their TraceTogether hardware token proposal. At its core it’s similar to the Simmel contact tracing solution – on which both are also working – with contacts stored locally in the device, Bluetooth communication, and a runtime of a few months or longer on the non-rechargeable batteries.

The tracing protocol used is BlueTrace, which is an open application protocol aimed at digital contact tracing. It was developed by the Singaporean government, initially for use with their TraceTogether mobile app.

This smartphone app showed a number of issues. First is that Apple does not allow for iOS apps to use Bluetooth in the background, requiring the app to be active in the foreground to be useful. Apple has its own tracing protocol, but it does not cover the requirements for building a full contact graph, as [Andrew] covers in more detail. Finally, the app in general is not useful to those who do not have a recent (compatible) smartphone, or who do not have a smartphone at all.

A lot of the challenges in developing these devices lie in making them low-power, while still having the Bluetooth transceiver active often enough to be useful, as well as having enough space to store interactions and the temporary tokens that are used in the tracing protocol. As Simmel and the TraceTogether tokens become available over the coming months, it will be interesting to see how well these predictions worked out.

Hackaday Links: May 31, 2020

May 31, 2020 by Dan Maloney 18 Comments

We begin with sad news indeed as we mark the passing of Marcel van Kervinck on Monday. The name might not ring a bell, but his project, the Gigatron TTL computer, certainly will. We did a deep dive on the microprocessor-less computer a while back, and Marcel was a regular at conferences and on the Gigatron forums, supporting users and extending what the computer can do. He was pretty candid about his health issues, and I’ll add that when I approached him a few weeks ago out of the blue about perhaps doing a Hack Chat about Gigatron, he was brutally honest about how little time he had left and that he wouldn’t make it that long. I was blown away by the grace and courage he displayed. His co-conspirator Walter Belger will carry on the Gigatron mission, including joining us for a Hack Chat on June 24. In the meantime, this might be a great time to pick up a Gigatron kit before they’re all sold out and get busy soldering all those delicious through-hole TTL chips.

May of 2020 is the month that never seems to end, and as the world’s focus seems to shift away from the immediate public health aspects of the ongoing COVID-19 pandemic to the long-term economic impact of the response to it, we happened across a very interesting article on just that topic. Mike Robbins from the Circuit Lab has modeled the economic impact of the pandemic using analog circuit simulations. He models people as charges and the flow of people between diseases states as currents; the model has capacitors to store the charge and allow him to measure voltages and filters that model the time delays needed for public policy changes to be adopted. It’s a fascinating mashup of engineering and policy. You can play with the model online, tweak parameters, and see what you come up with.

One of the things that the above model makes clear is that waiting to fully reopen the economy until a vaccine is ready is a long and dangerous game. But there has at least been some progress on that front, as Massachusetts biotech firm Moderna announced success in Phase 1 clinical trials of its novel mRNA vaccine against SARS-CoV-2. It’s important to temper expectations here; Phase 1 trials are only the beginning of human testing, aimed at determining the highest treatment dose that won’t cause serious side effects. Phase 2 and Phase 3 trials are much more involved, so there’s a long way to go before the vaccine, mRNA-1273, is ready for use. If you need to brush up on how these new vaccines work, check out our handy guide to mRNA vaccines.

In happier news, the “moar memory” version of the Raspberry Pi 4 is now on sale. Eben Upton announced that the 8GB version of the Pi 4 is now available for $75. The upgrade was apparently delayed by the lack of an 8GB LPDDR SDRAM chip in a package that would work in the Pi manufacturing process. They’ve also released a beta of a 64-bit version of the Raspberry Pi OS, if you’re interested in a bleeding-edge flex.

And finally, for those who missed the first wave of the computer revolution and never had a blinkenlight machine, you can at least partially scratch that itch with this Internet-connected Altair 8800. Jesse Downing has written a queueing system that allows users to connect to the machine via ssh and use Microsoft BASIC 5.0 on CP/M. Need to see those glorious front panels lights do their thing? Jesse has kindly set up a live stream for that, with an overlay of the current console output. It’s a great way to relive your misspent youth, or to get a taste of what computing was like when soldering skills were a barrier to entry.