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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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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Optogenetics For 100 Euros

August 3, 2017 by Michael Uttmark 4 Comments

Larval zebrafish, Drosophila (fruit fly), and Caenorhabditis elegans (roundworm) have become key model organisms in modern neuroscience due to their low maintenance costs and easy sharing of genetic strains across labs. However, the purchase of a commercial solution for experiments using these organisms can be quite costly. Enter FlyPi: a low-cost and modular open-source alternative to commercially available options for optogenetic experimentation.

One of the things that larval zebrafish, fruit flies, and roundworms have in common is that scientists can monitor them individually or in groups in a behavioural arena while controlling the activity of select neurons using optogenetic (light-based) or thermogenetic (heat-based) tools.

FlyPi is based on a 3D-printed mainframe, a Raspberry Pi computer, and a high-definition camera system supplemented by Arduino-based optical and thermal control circuits. FlyPi features optional modules for LED-based fluorescence microscopy and optogenetic stimulation as well as a Peltier-based temperature simulator for thermogenetics. The complete version with all modules costs approximately €200 with a layman’s purchasing habits, but for those of us who live on the dark side of eBay or the depths of Taobao, it shouldn’t cost more than €100.

Once assembled, all of the functions of FlyPi can be controlled through a graphical user interface. As an example for how FlyPi can be used, the authors of the paper document its use in a series of “state-of-the-art neurogenetics experiments”, so go check out the recently published open access paper on PLOS. Everything considered the authors hope that the low cost and modular nature, as well as the fully open design of FlyPi, will make it a widely used tool in a range of applications, from the classroom all the way to research labs. Need more lab equipment hacks? Don’t worry, we’ve got you covered. And while you’re at it, why not take a spin with the RWXBioFuge.

The Quest For Mice With Frickin’ Laser Beams (Pointed At Their Brains), Building A Laser Controller

August 13, 2016 by Gerrit Coetzee 16 Comments

The logo for the field is kind of cute though.

[Scott Harden] is working on a research project involving optogenetics. From what we were able to piece together optogenetics is like this: someone genetically modifies a mouse to have cell behaviors which can activated by light sensitive proteins. The mice then have a frikin’ lasers mounted on their heads, but pointing inwards towards their brains not out towards Mr. Bond’s.

Naturally, to make any guesses about the resulting output behavior from the mouse the input light has to be very controlled and exact. [Scott] had a laser and he had a driver, but he didn’t have a controller to fire the pulses. To make things more difficult, the research was already underway and the controller had to be built

The expensive laser driver had a bizarre output of maybe positive 28 volts or, perhaps, negative 28 volts… at eight amps. It was an industry standard in a very small industry. He didn’t have a really good way to measure or verify this without either destroying his measuring equipment or the laser driver. So he decided to just build a voltage-agnostic input on his controller. As a bonus the opto-isolated input would protect the expensive controller.

The kind of travesty that can occur when [Stefan Kiese] doesn't have access to nice project boxes. — The kind of travesty that can occur when [Scott] doesn’t have access to nice project boxes.

The output is handled by an ATtiny85. He admits that a 555 circuit could generate the signal he needed, but to get a precision pulse it was easier to just hook up a microcontroller to a crystal and know that it’s 100% correct. Otherwise he’d have to spend all day with an oscilloscope fiddling with potentiometers. Only a few Hackaday readers relish the thought as a relaxing Sunday afternoon.

He packaged everything in a nice project box. He keeps them on hand to prevent him from building circuits on whatever he can find. Adding some tricks from the ham-radio hobby made the box look very professional. He was pleased and surprised to find that the box worked on his first try.

Mouse Brain with neurons exhibiting GFP expression

UC Davis Researchers Use Light To Erase Memories In Genetically Altered Mice

October 13, 2014 by Theodora Fabio 23 Comments

Much like using UV light to erase data from an EPROM, researchers from UC Davis have used light to erase specific memories in mice. [Kazumasa Tanaka, Brian Wiltgen and colleagues] used optogenetic techniques to test current ideas about memory retrieval. Optogenetics has been featured on Hackaday before. It is the use of light to control specific neurons (nerve cells) that have been genetically sensitized to light. By doing so, the effects can be seen in real-time.

For their research, [Kazumasa Tanaka, Brian Wiltgen and colleagues] created genetically altered mice whose activated neurons expressed GFP, a protein that fluoresces green. This allowed neurons to be easily located and track which ones responded to learning and memory stimuli. The neurons produced an additional protein that made it possible to “switch them off” in response to light. This enabled the researchers to determine which specific neurons are involved in the learning and memory pathways as well as study the behavior of the mouse when certain neurons were active or not.

Animal lovers may want to refrain from the following paragraph. The mice were subjected to mild electric shocks after being placed in a cage. They were trained so that when they were put in the cage again, they remembered the previous shock and would freeze in fear. However, when specific neurons in the hippocampus (a structure in the brain) were exposed to light transmitted through fiber optics (likely through a hole in each mouse’s skull), the mice happily scampered around the cage, no memory of the earlier shock to terrify them. The neurons that stored the memory of the shock had been “turned off” after the light exposure.

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Backyard Brains: Controlling Cockroaches, Fruit Flys, And People

July 18, 2014 by Brian Benchoff 16 Comments

[Greg Gage] and some of the other crew at Backyard Brains have done a TED talk, had a few successful Kickstarters, and most surprisingly given that pedigree, are actually doing something interesting, fun, and educational. They’re bringing neuroscience to everyone with a series of projects and kits that mutilate cockroaches and send PETA into a tizzy.

[Greg] demonstrated some of his highly modified cockroaches by putting a small Bluetooth backpack on one. The roach had previously been ‘prepared’ by attaching small electrodes to each of its two front antennas. The backpack sends a small electrical signal to the antennae every time I swiped the screen of an iPhone. The roach thinks it’s hitting a wall and turns in the direction I’m swiping, turning it into a roboroach. We seen something like this before but it never gets old.

Far from being your one stop shop for cockroach torture devices, Backyard Brains also has a fairly impressive lab in the basement of their building filled with grad students and genetically modified organisms. [Cort Thompson] is working with fruit flies genetically modified so a neuron will activate when they’re exposed to a specific pulse of light. It’s called optogenetics, and [Cort] has a few of these guys who have an ‘I’m tasting something sweet’ neuron activated when exposed to a pulse of red light.

Of course controlling cockroaches is one thing, and genetically engineering fruit flies is a little more impressive. How about controlling other people? After being hooked up to an EMG box to turn muscle actuation in my arm into static on a speaker, [Greg] asked for a volunteer. [Jason Kridner], the guy behind the BeagleBone, was tagging along with us, and stepped up to have two electrodes attached to his ulnar nerve. With a little bit of circuitry that is available in the Backyard Brains store, I was able to control [Jason]’s wrist with my mind. Extraordinarily cool stuff.

There was far too much awesome stuff at Backyard Brains for a video of reasonable length. Not shown includes projects with scorpions, and an improved version of the roboroach that gives a roach a little bit of encouragement to move forward. We’ll put up a ‘cutting room floor’ video of that a bit later.