Reverse Engineering A DNA Sequencer

August 9, 2018 by Tom Nardi 19 Comments

Improvements in methodology have dramatically dropped the cost of DNA sequencing in the last decade. In 2007, it cost around $10 million dollars to sequence a single genome. Today, there are services which will do it for as little as $1,000. That’s not to bad if you just want to examine your own DNA, but prohibitively expensive if you’re looking to experiment with DNA in the home lab. You can buy your own desktop sequencer and cut out the middleman, but they cost in the neighborhood of $50,000. A bit outside of the experimenter’s budget unless you’re Tony Stark.

But thanks to the incredible work of [Alexander Sokolov], the intrepid hacker may one day be able to put a DNA sequencer in their lab for the cost of a decent oscilloscope. The breakthrough came as the result of those two classic hacker pastimes: reverse engineering and dumpster diving. He realized that the heavy lifting in a desktop genome sequencer was being done in a sensor matrix that the manufacturer considers disposable. After finding a source of trashed sensors to experiment with, he was able to figure out not only how to read them, but revitalize them so he could introduce a new sample.

To start with, [Alexander] had to figure out how these “disposable” sensors worked. He knew they were similar in principle to a digital camera’s CCD sensor; but rather than having cells which respond to light, they read changes in pH level. The chip contains 10 million of these pH cells, and each one needs to be read individually hundreds of times to capture the entire DNA sequence.

Enlisting the help of some friends who had experience reverse engineering silicon, and armed with an X-Ray machine and suitable optical microscope, he eventually figured out how the sensor matrix worked electrically. He then designed a board that reads the sensor and dumps the “picture” of the DNA sample to his computer over serial.

Once he could reliably read the sensor, the next phase of the project was finding a way to wash the old sample out so it could be reloaded. [Alexander] tried different methods, and after several wash and read cycles, he nailed down the process of rejuvenating the sensor so its performance essentially matches that of a new one. He’s currently working on the next generation of his reader hardware, and we’re very interested to see where the project goes.

This isn’t the first piece of DIY DNA hardware we’ve seen here at Hackaday, and it certainly won’t be the last. Like it or not, hackers are officially fiddling with genomes.

Shining A Light On Hearing Loss

July 26, 2018 by Brian McEvoy 16 Comments

When auditory cells are modified to receive light, do you see sound, or hear light? To some trained gerbils at University Medical Center Göttingen, Germany under the care of [Tobias Moser], the question is moot. The gerbils were instructed to move to a different part of their cage when administrators played a sound, and when cochlear lights were activated on their modified cells, the gerbils obeyed their conditioning and went where they were supposed to go.

In the linked article, there is software which allows you to simulate what it is like to hear through a cochlear implant, or you can check out the video below the break which is not related to the article. Either way, improvements to the technology are welcome, and according to [Tobias]: “Optical stimulation may be the breakthrough to increase frequency resolution, and continue improving the cochlear implant”. The first cochlear implant was installed in 1964 so it has long history and a solid future.

This is not the only method for improving cochlear implants, and some don’t require any modified cells, but [Tobias] explained his reasoning. “I essentially took the harder route with optogenetics because it has a mechanism I understand,” and if that does not sound like so many hackers who reach for the tools they are familiar with, we don’t know what does. Revel in your Arduinos, 555 timers, transistors, or optogenetically modified cells, and know that your choice of tool is as powerful as the wielder.

Optogenetics could become a hot ticket at bio maker spaces. We have talked about optogenetics in lab rodents before, but it also finds purchase in zebrafish and roundworm.

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An MRI-Safe 3D Printed Pneumatic Stepper Motor

July 26, 2018 by Tom Nardi 33 Comments

You will no doubt have seen those videos where MRI machines suck up all sorts of metallic objects with hilariously disastrous results. The magnetic field in one of these machines can easily pull in metal objects from across the room, exerting a force of several hundred pounds on any ferrous object unlucky enough to wander too close. As you can probably imagine, designing mechanical devices that can operate in such an intense magnetic field is exceptionally difficult.

But this fully 3D printed pneumatic stepper motor designed by [Foad Sojoodi Farimani] might one day change that. The PneuAct, which he presented at the recent International Conference on Robotics and Automation (ICRA) in Brisbane, Australia, manages to run at up to 850 RPM with full position control using bursts of air rather than electronic pulses. Made entirely of plastic and without any electronic components, the PneuAct can not only operate in intense magnetic fields but also areas with flammable gases where sparks could potentially cause an explosion.

We often say that a design is “fully” 3D printable, even though it might require screws or other bits of hardware. But in the case of the PneuAct, it’s truly all printed. It has to be, or else the whole thing would be ripped apart when it got to close to the MRI machine. Each and every piece of the motor is printed in ABS, and can be used without any additional machining or cleanup. No lubrication is required, and [Foad] mentions that the whole thing is so cheap that it can be disposable. Which is a huge advantage in medical environments where contamination could be a concern.

Design-wise the PneuAct is essentially an expanded version of the 3D printed air motors we’ve seen previously, but it would be fair to say that none has ever been studied so closely before.

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Help With Stuttering Could Come From Electricity

July 24, 2018 by Brian McEvoy 10 Comments

At the University of Oxford, [Jen Chesters] conducts therapy sessions with thirty men in a randomized clinical trial to test the effects of tDCS on subjects who stutter. Men are approximately four times as likely to stutter and the sex variability of the phenomenon is not being tested. In the randomized sessions, the men and [Jen] are unaware if any current is being applied, or a decoy buzzer is used.

Transcranial Direct Current, tDCS, applies a small current to the brain with the intent of exciting or biasing the region below the electrode. A credit-card sized card is used to apply the current. Typically, tDCS ranges from nine to eighteen volts at two milliamps or less. The power passing through a person’s brain is roughly on par with the kind of laser pointer you should not point straight into your eyeball and is considered “safe,” with quotation marks.

A week after the therapy, conversational fluency and the ability to recite written passages shows improvement over the placebo group which does not show improvement. Six weeks after the therapy, there is still measurable improvement in the ability to read written passages, but sadly, conversational gains are lost.

Many people are on the fence about tDCS and we urge our citizen scientists to exercise all the caution you would expect when sending current through the brain. Or, just don’t do that.

This Smart Pill Uses A Stomach Acid Battery

July 7, 2018 by Steven Dufresne 34 Comments

[Curt White] is working on a smart pill whose copper-zinc battery will use his own stomach acid as the electrolyte. It’s not that unusual of an idea, MIT tested a similar approach in a pig. It’s also better than using lithium ion batteries, something we covered in this PSA.

His starting point is a small, hacked activity tracker with its Nordic nRF51822 ARM Cortex-M0 and Bluetooth LE SoC. Most everything else is removed. The battery electrodes are sewn onto a plastic mesh cut to the activity tracker’s dimensions. Three coin type super capacitors and a boost converter sit between the battery and the SoC.

He uses the Bluetooth LE for communication, sort of. BLE devices constantly transmit information about themselves and it’s this which you see when scanning for available devices. Included in that transmission is a UUID (Universally Unique Identifier) and a name (e.g. “smartpillxyz”). He has the pill transmit data by putting it in that name. This saves power by minimizing the time which the pill’s Bluetooth radio is turned on. The smartphone app extracts the data from these transmissions without ever connecting.

His goal is to monitor the voltage and the maximum current. This will tell him if his stomach acid battery works and what can be powered by it. First tests will use regurgitated gastric fluid and then later he’ll swallow the pill himself. As he puts it, why not, “people swallow and pass all kinds of weird stuff without a problem.” Thay may sound cavalier but judging by his hackaday.io page, he’s doing his homework.

DIY Socket For Prosthetics Contains Power Supply, Charger

July 6, 2018 by Donald Papp 4 Comments

Innovation in prosthetics is open to anyone looking to enhance the quality of life, but there’s an aspect of it that is sometimes under-served. The DIY Prosthetic Socket entry to the Hackaday Prize is all about the foundation of a useful prosthesis: a custom, form-fitting, and effective socket with a useful interface for attaching other hardware. While [atharvshringaregt] is also involved with a project for a high-tech robotic hand with meaningful feedback, socket fitting and design is important enough to be its own project.

The goal is not just to explore creating these essential parts in a way that’s accessible and affordable to all, but to have them include a self-contained rechargeable power supply that can power attachments. Thoughtful strap placement and a power supply design that uses readily available components with a 3D printed battery housing makes this DIY prosthetic socket a useful piece of design that keeps in mind the importance of comfort and fitting when it comes to prosthetics; even the fanciest robot hand isn’t much good otherwise.

Reverse-Engineering Brains, One Neuron At A Time

June 30, 2018 by Roger Cheng 10 Comments

Most posts here are electrical or mechanical, with a few scattered hacks from other fields. Those who also keep up with advances in biomedical research may have noticed certain areas are starting to parallel the electronics we know. [Dr. Rajib Shubert] is in one such field, and picked up on the commonality as well. He thought it’d be interesting to bridge the two worlds by explaining his research using analogies familiar to the Hackaday audience. (Video also embedded below.)

He laid the foundation with a little background, establishing that we’ve been able to see individual static neurons for a while via microscope slides and such, and we’ve been able to see activity of the whole living brain via functional MRI. These methods gradually improved our understanding of neurons, and advances within the past few years have reached an intersection of those two points: [Dr. Shubert] and colleagues now have tools to peer inside a functional brain, teasing out how it works one neuron at a time.

[Dr. Shubert]’s talk makes analogies to electronics hardware, but we can also make a software analogy treating the brain as a highly optimized (and/or obfuscated) piece of code. Virus stamping a single cell under this analogy is like isolating a single function, seeing who calls it, and who it calls. This pairs well with optogenetics techniques, which can be seen as like modifying a function to see how it affects results in real time. It certainly puts a different meaning on the phrase “working with live code”!

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