I have bought once a used (very used) Stratagene MX4000 qPCR for about $400 (plus $500 for delivery from the US to Switzerland, as it is really bulky and heavy). I wrote to Agilent asking for the drivers, and they kindly sent it to me for free. I was able to run a few qPCR experiments successfully (never found a SARS-CoV-2 sample in the wild, but control RNA worked).
And I opened an account at Sigma-Aldrich, declaring myself as a hobbyist researcher. There were quite friendly, too.
Why do these machines have so much thermal mass in the cycling part of the machine?
A series of wells a few micrometers wide in a silicon substrate, doped to make use of the thermoelectric effect, ought to be able to do temperature cycling at kilohertz, by 50+ degrees C.
It's the kind of thing that could be built in a university silicon lab too.
If you're using off the shelf plastics as your reaction vessel (which most of these do), then you're immediately stuck with these large thermal mass systems.
A few reasons why many of these machines stay away from microfluidics:
PCR reactions are notoriously susceptible to cross-contamination, so microfluidics wells would either need to be thoroughly cleaned (a pain), or just single use (this is what we do with most plastics... - which would be expensive).
How do you get your stuff into the well! Current scale plastics had amendable to human operators (infinitely flexible, minimal capital cost, easy to replace). The equipment you need (basically a good pipette and tips) is relatively cheap and well understood. To do this at the microfluidics scale would be much more expensive (and see the same cleaning concern from above).
What are you doing with your PCR result? Assuming that you're just going with florescent probes, having the giant macro-scale lump of liquid gives you both a physically very large target, and a relatively brighter target to look for. This can certainly be overcome, but is more engineering work.
If you were using PCR as an upstream process (dunno how common this is now anymore), then you need to generate enough volume to be useful in your downstream process... and if your downstream process is human scale, then you're PCR reaction needs to be as well.
Oh, and finally the actual PCR bio-chemical reactions take a finite amount of time to work, so you can't really temperature cycle by the kilohertz. Probably the fastest you can take it is... dunno, 10 seconds per cycle? The literature is a little weird here.
Cycling will be rate limited by the speed of the polymerase involved in the reaction. Short sequences are usually fairly quick regardless, but the extension period is still measured in seconds per kilobase.
Also, some primers really do not cooperate at fast cycle speeds. PCR is really quirky even in optimized conditions.
In my experience it’s easier to measure and thus control the temperature of a thermal mass that is much much larger than both the sensors (thermocouples) attached to it and the samples inside of it.
The large thermal mass of the heating block in a traditional thermocycler vs the relatively tiny masses of the samples inside the pcr tubes contained within means that the samples are basically always at the temperature of the block, which means the control loop for the heating/cooling system can be modeled and controlled with just a PID feedback loop.
This is pretty cool! Big fan of hobby biology experiments.
I've never tried running PCRs w/o a heated lid, and I know that the mineral approach is the way things used to be, but I imagine that it'd make PCRing things way more of a chore.
At first, I didn’t realize the the disk on the left was being used to hold down tubes in the thermal block. I thought you might load the tubes into it and then it would turn to put tubes in smaller blocks that were at different temperatures. If it did this, then that would be the ultimate throwback to when we would actually move tubes between water baths/heat blocks to manually “cycle” the tubes.
PCR is literally the lowest hanging fruit. It is a glorified rice cooker. There are many bigger open hardware problems to tackle in biology such as sequencing, anything optics related, and general process automation. It is not good for hardware and software people entering the field to get distracted with making PCR machines.
To put it in context, take for example web collaborative software. They are very hard to build correctly and get right so most collaborative software in general are close sourced SaaSes. Imagine if a bunch of native/desktop software engineers decided to take a look at the problem and suggest that, hey, we need more open source real time collaborative software so let's build yet another web framework. Another web framework isn't needed and doesn't solve the problem! The problem is lack of correct CRDT and operational transform libraries. We don't need yet another web framework. I hope this analogy makes sense because everytime a biology thread comes up on HN the discussion pivots to "how can I help by focusing on x y z bioinformatics etc" and completely misses the point. Hard problems sometimes need to be tackled head on.
Leave low hanging fruits to academia and interns. If you are a software/hardware engineer with >5 years of experience then recreating the Todo MVC equivalent in biomedical engineering isn't helping anyone. Many of the bio posts here feels like those low effort and inaccurate web dev tutorials on medium.com written by bootcamp grads that would never make it to the front of HN, but for some reason the people here are happy to swallow the equivalent in life science hook, line, and sinker.
I think you're right, but considering there hasn't been any good open PCR machines (openPCR is functionally dead), this feels more like the early days of web development, where there are no good web frameworks or standards yet.
I have no idea what this does or how it works, but it looks really cool.
We've put microchips of all kinds into the hands of people to make them electrical engineers. Let's do the same for biology and make some more scientists.
PCR (Polymerase Chain Reaction) is the standard procedure for duplicating DNA, which is a critical step to many different protocols, including COVID tests (real-time PCR) and DNA sequencing. This device is a miniaturized thermo cycler, which heats up and cools down a sample in a small test tube according to a pre-programmed sequence. Heating/cooling cycles are necessary for the enzymes involved in PCR to do their jobs.
The FAQ seems to answer that you can't use it for COVID tests. Are there resources out there for beginner friendly experiments you can do with this kit?
Sorry but the idea of abstracting bio hacking for the unwashed masses seems like a horrible idea. Sequencing and info extraction sure, but you don’t want Joe Dirt having an automated way to synthesize anything that can augment biological processes.
This is a snarky way to express a valid concern of progress and ‚democratization’ of technology in general, namely that increasing capabilities of individuals can endanger an ever larger number of people. So far we have been lucky but I’m not convinced that this (increasing power of individuals, not only diy-biology) might not turn out as being the Great Filter.
Democratization works both ways. The more people who can build, the more people who can cure. From COVID19, at least, I think we need more people who can cure.
Also I can’t really imagine a biological mechanism that can lead to human extinction that can’t be solved with technology, so that would probably be a tough nut to crack.
The problem is you only need one insane individual or group to abuse the technology once to make something extremely contagious with a 2 month incubation period that has a 99% lethality. We simply can’t rely on trusting the good of humanity on this one.
Fun fact: The company that makes it is called GaudiLabs and they sell it in their GaudiShop. This is a play on the founders name Urs Gaudenz but a the same time the German word "Gaudi" means fun from latin gaudium = joy. So essentially they are FunLabs selling products in their FunShop.
This is a good remark. Covid19 is detected using so called q(quantitative)PCR or Real-Time PCR. This indeed requires real time fluorescence detection as the thermal cycle at which your signal starts to ramp up is a measure for the amount of DNA or RNA molecules present in the original sample.
It’s just a basic thermal cycler, not a real-time one with fluorescence detectors. You would need something like a gel electrophoresis system and a transilluminator to check the results.
>“It is very nice.” >Yanwu Guo, Head Engineer >University of Oslo (UiO)