Greetings, this is Trevor coming live from Ann Arbor in a basement…
We have one week left in the internship and things are finally starting to come together. Last time I made a post, I was without a doubt on the struggle bus in terms of getting data worthy of a poster, let alone a journal article. Since that point I have learned a hell of a lot of what not to do while recording data. First, always make sure everything is plugged in, second, make sure your specimen is alive, and last always make sure your equipment is hooked up everywhere it should be. You may think I’m weird for this, but I think my moths are pretty cute. A couple weeks ago I was having a really hard time getting clear recording from the BYB Spikerbox due to so much activity happening in the antennae, and as a result we switched to the SpikerShield to get an electroantennogram recordings. Electroantennogram recordings are low frequency, are the preferred way to record antennae stimulus and look like this:
Before I started testing the sex pheromone bombykol on the moths, I characterized how the male moths responded when introduced to their female counterparts, and it is best described as a circling motion in a zigzag path towards the female. It happens almost every time a female is brought within a couple feet of a male, but is not present when stimulated with just any odorant, like lemon oil or peppermint.
The male seems significantly less enthused about the lemon than about the female-I wonder why?
Once I had that complete I began trials with bombykol using a new delivery system that went through many revisions. At first we were using a valve system to deliver odors via an air stream, but we observed a change in airflow when opening valves, which meant we couldn’t be sure if the neuronal responses we got were from the change in airflow or the added odorant. To fix this problem, we inserted syringes into the piping with some T-junctions on the way to the moth, thus keeping a constant air stream.
Now I needed a way to consistently empty the syringes, so for that I added a linear actuator and a wood based housing to hold the actuator and syringes. The housing, entitled “Mr. Orange” due to its bright orange paint job and my love for Reservoir Dogs, has three ports for three syringes, to serve as an air control, other odorant positive control, and pheromone syringes all in one recording. Along the way, thanks to our fearless leader Greg I had to edit the housing from two to three syringe ports just minutes after completing the project…
Are you happy now, Greg?
Before “Mr. Orange” was built I was able to successfully record a bombykol stimulus on the last day of my second batch of moths. Displayed below is Bombykol compared to a negative control, aka clean air. Remember they only live 5-10 to days, and have to be ordered, so my time working with them is precious! I am currently awaiting new moths so that I can do my final trials which will involve mulberry leaves, which their caterpillars live on and eat, as a positive control for both male and female moths. This will allow me to show that both males and females react similarly to one stimulus (and ensure the prep is working), but also that they have evolved such that males are much more sensitive to bombykol than females.
Last but not least, the interns all presented last week at MID-SURE, a poster session on Michigan State University’s campus in East Lansing, and I have included my poster below for anyone curious.
Hello my name is Bailey! I am a junior majoring in electrical engineering at Michigan State University and am doing an internship at Backyard Brains this summer. Sorry I missed the first blog post, I was travelling in Japan with my sister!
Left-my sister, Right-me
I know it doesn’t look like it from the picture, but I was doing some important background research for my project.
I mean…circuits were involved
Ok, so it was just for fun.
After getting over my jetlag it was time to get back to work. My project this summer involved mormyrid fishes. What’s so special about these fish? Mormyrid fish are awesome because they both emit and detect electric signals. Unlike an electric eel, however, their electrical discharges are too weak to harm other fish. Instead, they use electric signals to navigate their environment, which is naturally very cloudy, and communicate with each other. A lot can be learned about these fishes’ behavior and even evolutionary history just by studying their electric organ discharges (EODs). Unfortunately the equipment used to record their EODs is quite costly, often prohibitively so-especially for those who live in the same area as the fish. This is where we come in. My goal this summer was to build an inexpensive, easy to use, and open source device that can record EODs from weakly electric fish.
Since the EODs occur at very high frequencies, a simpler microcontroller like an Arduino is not sufficiently powerful to record their EODs in real time. Enter the BeagleBone Black.
The BeagleBone Black has a 1GHz processor and 4GB of storage (that can be supplemented with a micro SD card) as well as running a full Linux OS, making it perfect for collecting the EOD data.
Now I need something to convert the analog EOD signals to digital so that the BeagleBone can process them. For this project I am using the MCP3008 analog to digital converter. Initially, I started by using a cape that had the chip on it.
Analogs, prepare to be converted!
The cape worked well for testing the setup with low frequency sine waves, however, the inputs it normally connected to on the BeagleBone were not able to handle the high speed data collection I needed and the data was not being recorded in real time. To work around this issue, I had to individually connect each pin to the appropriate input on the BeagleBone. This lead to the setup appropriately nicknamed “The Shiva”.
Not pictured: the additional arms I grew to operate this setup
This setup allowed me to access the programmable real time units (PRUs) on the BeagleBone. PRUs are essentially microprocessors within a microprocessor that sit around eagerly awaiting a program to execute. Unlike the main CPU, the PRUs do not run Linux, allowing them to collect the data in real time. Now that I had my setup I was only missing one thing-the fish! A quick trip to the Electric Fish Lab at MSU and the newest additions to the Backyard Brains Petting Zoo, Tina and Taco, were ready for some data collection.
The one on the right with the goatee is Taco. Tina is on the left
I started recording by using the example code from chapter 13 on the Exploring BeagleBone website. The code filled up the PRU memory with data from the recording, and then used another program to read the data from the memory. Although this worked well, it was not what I wanted in terms of a final product. Using the example code as a basis, Stanislav Mircic, Backyard Brains’ ultra-programmer, and I modified it to continuously write the data to a circular buffer as well as simultaneously read the buffer and check if an EOD has occurred.
Now the program will record only the EODs, which is what we are ultimately interested in, instead of all of the raw data. Here’s an example of the output:
Now that I’ve verified what the circuit needs to be, I have to draw out the schematic so that a board can be printed in a form that can snap onto the BeagleBone.
My drawing of the circuit
And finally the actual board.
Goodbye Shiva! Only two arms needed for this one.
For the rest of the summer I will be modifying the circuit design to better suit the goal, such as altering the gain to match the type of recordings we’ll be getting, and preparing the device for field work by building a portable power source and a case that it can float in. Soon we hope for the device to be picking up lots of fish conversations from around the world! Stay tuned!
Name: Katelyn Rowley
School: University of Michigan (Go Blue!)
Major: Biomedical Engineering
Hobbies: Running (I’ve run a half marathon and I hope to run a full one someday!), journaling, trying new restaurants in Ann Arbor, being outdoors, finding new music to listen to (Florence and the Machines, Bon Iver, classic rock, you name it)
What’s up interwebz? When I think of things that terrify me here is a brief list of things that come to mind: White Walkers (shout out to Game of Thrones fans), the killer bunny rabbit from Monty Python and the Holy Grail, Physics 240 (electricity and magnetism), liking Kayne West’s music, history classes, and a Moose Tracks ice cream cone melting all over my hand before I can enjoy it. Digressing, this summer I get to face two of my fears and get a good understanding of the electricity, magnetism, and the history of neuroscience.
The origins of my project began with a paper describing the life of Julius Bernstein (1839–1917) and his process of developing Membrane Theory—the prediction that the concentrations and charge of electrolytes (charged atoms) inside and outside of a nerve cell is responsible for a nerve firing and thus pretty much the ability to move, sense, feel, and survive. The differing concentrations of charged particles, such as K+ (potassium), is obtained through the cells selecting which particles are allowed inside and outside of the cell, thus creating an electrical potential across the membrane, as described by the Nernst equation below.
This equation tells us that the greater the temperature and the bigger the concentration difference, the more electrical potential a cell has. As the difference in concentration between inside and outside of the cell increases, the more the thermodynamic system craves to return everything to a perfect balance and expel the consequent stored electrical energy used to invoke motion or transmit signals.
To develop this Membrane Theory, he had spent time developing what became known as a time slicer to measure the current our bodies use to signal muscles and adjacent cells. It had been shown by this time that jolts of electricity can be conducted and cause a muscle to spasm (first shown by a frog leg twitching when an electrical charge touched its nerve by Galvani), but Bernstein took it upon himself to assign a speed and direction of this supposed current that could exist while being entrapped inside of the human body. Thus, from the depths of his scientific and electrical genius, he made the time slicer (below).
…I was confused at first, too. Bernstein’s original paper was in German so that also made it difficult to find anything more in depth about the mysterious time slicer.
After many hours of research and study, I eventually learned what all of these parts were. Basically speaking, this wheel spins and alternates between stimulating the muscle/nerve (left half of wheel) and recording the current from this stimulation (right half of wheel). By changing positions of the different circuits, Bernstein was able to measure the current precisely at differing parts in time…hence the imposed name, time slicer. He eventually collected enough information about the currents at different parts in time and produced this:
Which, remarkably, shows that the current is negative. This publication was the first accurate description of the action potential in the nerve.
Further, my job this summer is to recreate this machine that sliced through current and time (which makes me sound more like a supervillain than an intern) and defined a key moment in the development of what we know about neuroscience today. If we think about my project in two key parts, it involves the wheel pictured above to manipulate the different circuits and the device called a galvanometer to measure the currents at different points in time. And so, my journey into science begins by recreating the ancient galvanometer to measure these small currents. A galvanometer I would like to redesign is pictured below.
This is where I will begin, and I will be sure to update this blog as I continue my summer.
Thanks for reading!