A clear droplet sits on a blue PCB with gold traces. A syringe with a drop of clear liquid sits above the droplet.

Grow Your Own Brain Electrodes

Bioelectronics has been making great strides in recent years, but interfacing rigid electrical components with biological systems that are anything but can prove tricky. Researchers at the Laboratory for Organic Electronics (LOE) have found a way to bridge the gap with conductive gels. (via Linköping University)

Outside the body, these gels are non-conductive, but when injected into a living animal, the combination of gel and the body’s metabolites creates a conductive electrode that can move with the tissue. This is accompanied by a nifty change in color which makes it easy for researchers to see if the electrode has formed properly.

Side-by-side images of a zebrafish tail. Both say "Injected gel with LOx:HRP" at the top with an arrow going to the upper part of the tail structure. The left says "t=0 min" and "Injected with gel GOx:HRP" along the bottom with an arrow going to the lower part of the tail structure. The tail shows darkening in the later image due to formation of bioelectrodes.

Applications for the technology include better biological sensors and enhanced capabilities for future brain-controlled interfaces. The study was done on zebrafish and medicinal leeches, so it will be awhile before you can pick up a syringe of this stuff at your local computer store, but it still offers a tantalizing glimpse of the future.

We’ve covered a few different brain electrodes here before including MIT’s 3D printed version and stentrodes.

The Blue Soup Saga Is One Beefy Mystery

Beef soup! You’d normally expect it to be somewhere from reddish-brown to grey, depending on how well it was cooked and prepared. However, strangely, an assistant professor found the beef soup in their fridge had mysteriously turned blue. That spawned an investigation into the cause which is still ongoing.

[Dr. Elinne Becket] has earned her stripes in microbiology, but the blue soup astounded her. Despite her years of experience, she was unable to guess at the process or a source of contamination that could turn the soup blue. Indeed, very few natural foods are blue at all. Even blueberries themselves are more of a purple color. The case sparked enough interest that [Elinne] went back to the trash to collect photos and sample for research at the request of others.

Thus far, metagenomic DNA analysis is ongoing and samples of the soup have been cultivated in petri dishes. Early analysis shows that some of the microbes form iridescent colonies, Another researcher is trying to determine if the bugs from the soup can make blue color appear on soft cheese. There’s some suspicion that a bacteria known as pseudomonas aeruginosa could be the cause of the blue color, but that presents its own problems. P. aeruginosa is classified as a Biosafety Level 2 pathogen which would require some researchers to abandon work on the project for safety reasons.

The jury’s still out on this microbiological mystery. If you’ve got some ideas on what could be going on, let us know in the comments!

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Hackaday Links: December 18, 2022

By now everyone has probably seen the devastation wrought by the structural failure of what was once the world’s largest free-standing cylindrical aquarium. The scale of the tank, which until about 5:50 AM Berlin time on Friday graced the lobby of the Raddison Blu hotel, was amazing — 16 meters tall, 12 meters in diameter, holding a million liters of saltwater and some 1,500 tropical fish. The tank sat atop a bar in the hotel lobby and was so big that it even had an elevator passing up through the middle of it.

But for some reason, the tank failed catastrophically, emptying its contents into the hotel lobby and spilling the hapless fish out into the freezing streets of Berlin. No humans were killed by the flood, which is miraculous when you consider the forces that were unleashed here. Given the level of destruction, the displaced hotel guests, and the fact that a €13 million structure just up and failed, we’re pretty sure there will be a thorough analysis of the incident. We’re pretty interested in why structures fail, so we’ll be looking forward to finding out the story here.

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Fourteen-Legged Cell Carries Nature’s Tiny Computer

Computers are, after all, frighteningly complex state machines. Quite of bit of the software we write can be modeled as a state machine, too. A great technological achievement by humans? Turns out, state machines exist in some of nature’s tiniest natural computers, according to biologists studying Euplotes eurystomus, a kind of water-dwelling eukaryote. This single-cell organism uses fourteen protolegs known as cirri that move in a particular gait, in response to certain stimuli.

As you might expect, a single-celled organism doesn’t have the infrastructure to support a brain, so scientists wondered what could control the way the beast walks using the cirri. The answer was fibers made of bundles of microtubles that acted as a mechanical state machine.

While we are used to state machines using bi-stable electronic elements, older machines often used cams and microswitches along with a timing motor. For example, a phone answering machine might have a three-minute motor. One cam would depress a micro switch to run the outgoing message for 15 seconds. Then another cam would depress a microswitch to start recording, and a final switch and cam would keep the motor running until the very end. To start the process, a ringing phone would goose the motor so that that last cam engaged. Simple and no computer needed. The “brain fibers” of the Euplotes seem to work in a similar way. They enforce which states can be reached from what other states and react to outside stimuli, as well.

Is any of this practical? Maybe not, although we often see technology mimic biological systems. But we can’t help but wonder if future microscopic-scale machines might not need this same sort of mechanical state machine for many purposes, including locomotion.

You can apparently make single-cell organisms your servants, more or less. We’ve covered state machines many times if you need a refresher.

Tube Tumbler Provides The Perfect Culture

We’ve all had to shake jars of nail polish, model paint, or cell cultures. Mixing paint is easy – but bacteria and cells need to be agitated for hours.  Happily, laboratory tube tumblers automate this for us. The swishing action is handled with rotation. The vials are mounted at angles around a wheel. The angular offset means the tubes are inclined as they rise, and declined as they fall. This causes the liquid in the tube to slosh from one side to the other as the wheel rotates.  [Sebastian S. Cocioba] aka [ATinyGreenCell] released his plans through Tinkercad and GitHub, and with a name like Sir Tumbalot, we know he must be cultured indeed.

Grab your monocles. Version 2 features a driven wheel lined with magnets to attach tube adapters, and he’s modeled 50mL and twin 15mL tube holders. The attachment points look like a simple beveled rectangle with a magnet pocket, so if you’re feeling vigorous for vials, you can whip up custom sockets and tumble any darn thing. A Trinamic StealthChop chip on a custom PCB controls the pancake stepper, and the whole shebang should cost less than $50USD. We’re wondering what other purposes this modular design could have, like the smallest rock tumbler or resin print rinser.

Making lab equipment is phenomenal for saving money for things that just spin up to a biotech lab.

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PiSpy, The Camera Setup Designed To Make Biological Observations Better

Back in grad school, we biology students were talking shop at lunch one day. We “lab rats” were talking about the tools of the trade, which for most of us included things like gel electrophoresis, restriction endonucleases, and polymerase chain reaction. Not to be left out, a fellow who studied fire ants chimed in that his main tool was a lawn chair, which he set up by a Dumpster in a convenience store parking lot to watch a fire ant colony. Such is the glamor of field biology.

Ants on the march. Tough luck for the crickets, though.

What our colleague [Mike] wouldn’t have given for something like PiSpy, the automated observation tool for organismal biology by [Greg Pask] of Middlebury College, et al. As discussed in the preprint abstract, an automated imaging platform can be key to accurate observations of some organisms, whose behavior might be influenced by the presence of a human observer, or even a grad student in a lawn chair. Plus, PiSpy offers all the usual benefits of automation — it doesn’t get tired, it doesn’t need to take bathroom breaks, and it can even work around the clock. PiSpy is based on commonly available components, like laser-cut plywood and a Raspberry Pi and camera, so it has the added advantage of being cheap and easy to produce — or at least it will be when the Pi supply picks back up again. PiSpy takes advantage of the Pi’s GPIO pins to enable triggering based on external events, or controlling peripherals like lights or servos.

While built for biological research, there are probably dozens of uses for something like PiSpy. It could be handy for monitoring mechanical testing setups, or perhaps for capturing UI changes during embedded device development. Or you could just use it to watch birds at a feeder. The source is all open-sourced, so whatever you make of PiSpy is up to you — even if it’s not for watching fire ants.

When Hacking And Biosensing Collide

[Prof. Edwin Hwu] of the Technical University of Denmark wrote in with a call for contributions to special edition of the open-access scientific journal Biosensors. Along the way, he linked in videos from three talks that he’s given on hacking consumer electronics gear for biosensing and nano-scale printing. Many of them focus on clever uses of the read-write head from a Blu-ray disc unit (but that’s not all!) and there are many good hacks here.

For instance, this video on using the optical pickup for the optics in an atomic force microscope (AFM) is bonkers. An AFM resolves features on the sub-micrometer level by putting a very sharp, very tiny probe on the end of a vibrating arm and scanning it over the surface in question. Deflections in the arm are measured by reflecting light off of it and measuring their variation, and that’s exactly what these optical pickups are designed to do. In addition to phenomenal resolution, [Dr. Hwu’s] AFM can be made on a shoestring budget!

Speaking of AFMs, check out his version that’s based on simple piezo discs in this video, but don’t neglect the rest of the hacks either. This one is a talk aimed at introducing scientists to consumer electronics hacking, so you’ll absolutely find yourself nodding your heads during the first few minutes. But then he documents turning a DVD player into a micro-strobe for high speed microfluidics microscopy using a wireless “spy camera” pen. And finally, [Dr. Hwu’s] lab has also done some really interesting work into nano-scale 3D printing, documented in this video, again using the humble Blu-ray drive, both for exposing the photopolymer and for spin-coating the disc with medium. Very clever!

If you’re doing any biosensing science hacking, be sure to let [Dr. Hwu] know. Or just tear into that Blu-ray drive that’s collecting dust in your closet.

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