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.
[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 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.
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.
[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.