lab technique

COVID-19 tests encased on coffee machine capsules

Transitioning to home working had its challenges for us all, but when your job involves researching biological applications for nanotechnology, those trials are a little more complicated than juggling the household’s broadband usage. So barred from his lab, you might reasonably expect the research by organic chemist Vittorio Saggiomo, from the Bionanotechnology group at Wageningen University & Research in the Netherlands, to have come to a grinding halt.

But Saggiomo is a creative, imaginative type, and so he began to wonder if he could turn common household appliances to good use in the fight against COVID-19. More specifically, could he create a cheap, highly sensitive home test for the virus? It turns out he could. His team has now posted the idea on a preprint server, ChemArxiv. The paper is yet to be reviewed by other scientists.

At the moment, there are two main types of COVID-19 test: the PCR test and the lateral flow test (LFT). The gold-standard PCR test checks for the presence of the virus by detecting its genetic material known as RNA. But there are vanishingly small amounts of viral material in a swab, so the material has to be converted into DNA and amplified before it can be detected. And this is achieved by the “polymerase chain reaction”, which is what PCR stands for.

The process involves repeated cycling through a range of temperatures between 50°C and 90°C. During each cycle, the amount of DNA doubles, so after 30 cycles over a billion copies of the viral material can be created from just one strand of starting material. The amplified material is then detected with fluorescent labels that attach themselves to the viral DNA sequences.

As such, PCR is a highly sensitive technique, but it needs specialist materials and equipment to perform. This is why the tests are sent off to a lab, and it takes a day or two to get the result.

The second common test is the lateral flow test (LFT). These work by detecting fragments of viral protein shells. Embedded within the strips of the LFTs are antibodies that bind to the virus. These antibodies are labelled with tiny gold particles, which appear red, allowing you to see them on the test device. The labelled antibodies accumulate on distinct bands on the LFT depending on whether the virus is present or not.

The LFTs are fast, cheap and easy to use, making them ideal for community and home testing. But they are nowhere near as sensitive as the PCR tests – they will only identify people with high viral loads. This means many people who are infected will get a false negative result from such tests.

CoroNaspresso tests

Ideally, we need a home test that’s as easy to use as the LFTs but as sensitive as the PCR test. An excellent candidate is a method called loop-mediated isothermal amplification (Lamp). This works along very similar principles to PCR, producing multiple copies of the starting genetic material – which you can get from a swab – but has some key advantages.

For example, it can be combined with a handy “colour readout”. When the Lamp reaction occurs, it causes an increase in the acidity of the sample. That means you can add a substance that changes colour according to pH value in the reaction mix, providing a visual indication of a positive or negative result. Another advantage is that Lamp reactions are carried out at a fixed temperature (about 65°C) instead of needing constant cycling through a range of temperatures.

Nevertheless, Lamp still needs fine temperature control. Temperature control systems – be they in a PCR machine, a Lamp instrument or household oven – are usually achieved with electronic thermostats. However, making and shipping new electronic devices specifically designed for home Lamp tests is impractical (especially in the middle of a pandemic). So Saggiomo tried to find a way around this. He hit upon substances called phase change materials that absorb energy (heat) as they melt and so maintain a constant temperature.

After finding a wax made of such a material that melted at exactly the required temperature, Saggiomo set about constructing a device to house the Lamp reaction tubes and chunks of wax. This then needed to be inserted into some other material that could be heated. The perfect housing turned out to be staring him in the face while making his morning coffee: Nespresso coffee machine capsules.

The final step was just finding the right way to heat the capsules. After trying the dishwasher (it worked but samples kept getting lost), the microwave oven (failed, because the tubes overheated and lids popped off) and cups full of hot water (not enough control on the temperature), Saggiomo settled on a simple pan of simmering water on a stovetop. The resulting “CoroNaspresso” device, when tested by other members of the team, with swabs from six people, correctly identified three cases of COVID-19 (these had a different colour to the negative tests).

Home covid test.
Tweet by @V_Saggiomo

The test, including the capsules, phase changing wax and vials in which to insert genetic material, would be easy to produce in millions. People could then swab for genetic material at home and heat the capsules to get their results. These devices are also cheap (about €0.20), easy to make, easy to use and largely recyclable. Maybe we’ll see the CoroNespresso tests in our homes soon, just don’t get them confused with your regular coffee pods.The Conversation

Mark Lorch, Professor of Science Communication and Chemistry, University of Hull

This article is republished from The Conversation under a Creative Commons license. Read the original article.

By April 9, 2021 1 comment lab technique, science news

Hack your inkjet printer and turn it into a lab robot

If you stop and think about it for a moment, you will realise what an astonishing feat of precision engineering your colour printer is. It can take the primary colours – cyan, yellow, magenta and black – and mix them together carefully enough to achieve more than a million different hues and shades. Not only that but the drops of colour are mere nanolitres (billionths of a litre) in volume, each of which is then placed on the paper – assuming its not jammed in the feeder tray – with better than pinpoint accuracy.

Now a group of enterprising chemists from Tsinghua University are exploiting that precision engineering, which normally results in high-resolution colour prints, to screen millions of different chemical reactions. Their results have been published in the journal Chemical Communications.

Yifei Zhang and colleagues have been trying to understand reaction pathways in living things. Every chemical process that goes on in living organisms is controlled by a cascade of reactions. The steps in a cascade are mediated by protein molecules called enzymes. Each enzyme makes a small chemical alteration, like workers on a production line, to a molecule before passing its product onto the next enzyme. In this way, for example, plants build sugars from carbon dioxide and your food gets broken down and then reconstructed into other useful chemicals for your body.

The problem is that to understand these complicated processes by reconstructing them outside of a living cell is difficult. The concentrations of an enzyme relative to the next in the line is key. Get this wrong and bottle necks are formed in the production line, as one enzyme works faster than the next.

To figure out what are the right conditions to replicate a living cell’s workings, chemists must set up and monitor a vast number of reactions. Screening large numbers of reactions like this is often done using “96-well plates”, which are 96 tiny containers with a unique combination of chemicals in each. These reactions might be set up manually or, if the lab is well-funded, by an expensive robot. But even with the best robots available it can still be a slow process.

Colour printers are a lot cheaper than robots. And if the inks are replaced by solutions of enzymes then suddenly you have a device that has the potential to dispense more than a million different reaction mixtures.

That is just want Yifei and colleagues have done. Their printers were loaded with a series of enzymes that, when they work together in the correct ratios, produce coloured reaction products. These were printed directly onto paper where it was immediately obvious, from the intensity of a coloured dot, which reaction mixtures worked best.

In the test cases reactions were deliberately chosen that resulted in colour changes. This made for a nice quick visual indication of whether the system worked well. So for example one test started with glucose and a chemical called ABTS in the magenta cartridge, then the enzymes glucose oxidase (GOx) and horse-radish peroxidase (HRP) in the yellow and cyan cartridges. When they are mixed together the GOx removes a hydrogen from the glucose and adds it to oxygen, producing hydrogen peroxide. Next the HRP reacts this with the ABTS, which results in a green chemical.

The potential applications for these printer-based mixtures extend beyond curiosity-driven research on biological pathways. Yifei and colleagues have already shown that by loading the printer cartridges with the right enzymes they can use the set up to indicate the presence of glucose in a sample. Glucose in urine is a indication of diabetes, so their printer-based chemistry already has the potential to diagnose diabetes.

The result then could be a future where a trip to the doctors results in a printout of, quite literally, your urine and some enzymes alongside, after 30 seconds or so, a diagnosis and the prescription.

The Conversation

Mark Lorch does not work for, consult to, own shares in or receive funding from any company or organisation that would benefit from this article, and has no relevant affiliations.

This article was originally published on The Conversation.
Read the original article.

By September 16, 2014 6 comments lab technique

TedED: Increasing Reaction Rates, or How to Get A Date

From the Chemistry Reddit, a TedED animation by Aaron Sams describing 5 ways to increase the rate of a chemical reaction. I’m not following all the analogies, but it’s still a pretty good teaching tool.

Nitroolefins – The Crying Game

(This post was written for the ‘Toxic Chemicals’ carnival, over at ScienceGeist)

Let me tell you about the time I broke down crying in lab. No, it wasn’t an epic breakup, or even a death in the family. It was…a nitroolefin.

Many summers ago, I worked as a pharma intern, a small flywheel in a then-huge drugmaking machine. My supervisor, a kind, safety-conscious scientist, begged me to come straight to him if I had any questions about my reactions.

We were synthesizing a small nitroolefin – 2-nitropropene, to be exact – for some nitro-Michael additions. If you look at the Org. Syn. prep, it warns, right at the top in red letters, that the compound is a potent lachrymator. The term, from the Latin word for “teardrop,” describes compounds that irritate the eyes to such an extent that tears freely flow.

I carefully piloted the reaction, distilled the greenish-yellow product, and then watched it run up my TLC plate. Beautiful! Now, I just needed an NMR sample.

Gingerly, I dissolved a drop into some chloroform. Forgetting for an instant, I pulled the NMR tube out of the hood to cap it, and within seconds crumpled to the bench. It felt as if someone had stabbed smoldering iron toothpicks into my eyes. I stumbled around until my labmates dragged me over to the eyewash; later, I became well acquainted with our local safety officer. My eyes remained bloodshot for the rest of the day. Lesson learned: Lachrymators are not to be taken lightly! (I’ve experienced similar, though milder, reactions to benzyl bromide and thionyl chloride).

For those younger chemists thinking about summer lab work, take a few minutes to find out if your reagents might cause uncontrollable crying. Cautious handling, and a well-fit respirator, can go a long way towards your future safety and comfort.