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Backyard Brains welcomes 2019 University of Santiago interns

Backyard Brains is now in its second year of interns from the University of Santiago de Chile (affectionately called Usach). Last year we had a project recording the ganglia of snails – and this we will continue our voyage in the world of invertebrates with an old favorite and a new favorite. Cockroaches and Clams.

The ElectrocardioCLAM

Hi, my name is Eduardo Isla, and I am in my final year as a student of biochemistry working at both USACH and UChile (Universidad de Chile). I am completing my undergraduate thesis right now as well as working for two months at the Backyard Brains Chile office. My thesis is in a quite different area (virology) working on epitranscriptomics of HIV-2. In my spare time I like to play MMORPG games as well as explore outdoor photography. 

A lot of high school students like Backyard Brains’ Neuropharmacology experiment, as you can indirectly study synaptic activity in crickets, but it is time for an upgrade. First, a little bit about neurotransmitters

Did you know that neurotransmitters were discovered working on frog hearts? Everything began in 1921, when an Austrian scientist named Otto Loewi discovered the first neurotransmitter. In his experiment, he used two frog hearts. Heart 1 was still connected to the vagus nerve, and Heart 1 was placed in a chamber that was filled with Ringers solution. This chamber was connected to a second chamber that contained Heart 2. So, fluid from chamber 1 could flow into chamber 2. Electrical stimulation of the vagus nerve (which was attached to Heart 1) caused Heart 1 to slow down its heart rate. Loewi observed that after a delay, Heart 2 also slowed down. From this experiment, Loewi hypothesized that electrical stimulation of the vagus nerve released a chemical into the fluid of chamber 1 that flowed into chamber 2. He called this chemical “Vagusstoff”. We now know this chemical as the neurotransmitter called acetylcholine. It is also interesting to know English scientist Henry Hallet Dale had previously isolated acetylcholine. So, they both shared the Nobel Prize in Physiology or Medicine in 1936.

For the Backyard Brains neuropharmacology upgrade I will use some Clams, yes Clams. We eat them, but they are animals too, and believe or not they have a heart. So, I’m trying to adapt Loewi’s experiments into much simpler animals, easier to access/buy and less traumatic to work on. These experiments consist of using the Backyard Brains Heart and Brain SpikerBox to make recordings of electrocardiograms on clam hearts and the effects of different compounds. For this, first of all I need to record an electrocardiogram of the heart of clams. Afterwards, I will then treat them with various compounds to attempt to alter the heart rate. I also need to ensure that the record that we actually obtain is EKG and not movement of the electrodes. In these first few days I am trying to optimize the preparation, opening the clam while keeping the cardiovascular system intact.

The Quantified RoboRoach

Hi, my name is Claudio Moreno, and I am also in my final year working at USach in the lab of Neuroscience. I am doing my thesis in ion channel physiology, studying TRPM8 channels. TRP channels are the body’s temperature transducers, and TRPM8 is responsible for the feeling of  coldness. In Chile we get cranky when the temperature gets below 40 degrees Fahrenheit (I know, nothing like Michigan), and we can thank our TRPM8 channels for that.

When not studying TRPM8 channels I enjoy going playing video games and guitar. I’ve being playing guitar for 13 years and it has been one of the best things I have done to get my mind distracted during moments of high stress. I also like to travel to different cities and countries. I have travelled to many cities here on Chile (my country), and it’s really beautiful, so if you have an opportunity to come here, trust me, you won’t regret it.

The RoboRoach is one of Backyard Brains’ original inventions where you can control cockroach locomotion by electrically stimulating the antenna, but, strangely, Backyard Brains has never systematically measured the adaptation rate. Until now. To do this experiment we are doing a bunch of RoboRoach surgeries, so we can have a high enough sample size to compare sensory adaptation rate.

Once a RoboRoach is recovered from the surgery, we can start to see if we can control our RoboRoach and measure turning responses with time! And for that we built a lego tower, which has a floating ball the cockroach walks on, along with an optical mouse to read the floating ball’s movements. When the antenna neurons are activated with electrical stimuli, they will send this electrical information (called spikes) to the cockroach brain, stimulating the neural-motor reactions. The cockroach will change direction, and we can measure this change.

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This contraption allows us to measure precisely the turning of the cockroach in response to stimulation of the antenna, so we can see how it adapts over time. Now it is time to collect the data and finally say with some degree of certainty the adaptation rates across cockroaches. Like all kinds of animals with a central neural system, you can expect that neurons can adapt to a stimulus (which Backyard Brains has anecdotally observed many times in the RoboRoach). Now it is time to quantify! I am starting to get skilled at the surgery, and below you can see my first successful antenna nerve recording!


The End of My Summer of Jellyfish (Or is it?)

Hello all! The summer fellowship is officially over, but it’s not quite the end of the line for the jellies and me! In this final(?) update to my blog series I’ll be recalling the findings I’ve made over this summer, showcasing the poster I presented at the UROP Symposium, sharing my road trip back home (with the jellies in tow!!!), and planning my post-fellowship jellyfish-based research!

Final Fellowship Findings:

I’ve learned a lot about clytia hemisphaerica over this fellowship. This ranges from their appearance and life stages (polyp, ephyrae, medusa) to their husbandry and maintenance needs (acceptable salt levels, daily and weekly water changes, feeding requirements). This newfound knowledge also includes their behaviors and abilities, like how they catch and eat prey or how they dart, zig-zag, and make circles in the water. I have collected a decent number of videos for my jellyfish dataset, and I’ve done some basic position tracking on most of that dataset, but unfortunately the fellowship was over before any rigorous analysis could be completed.

However, this is not the end! I will be dedicating time over the next few weeks to progressing my research by adding features to my jellyfish tracking/analysis software to get more usable stats on the videos, by analyzing jelly video stats using unsupervised machine learning for labeling behaviors, and by getting more raw footage of these wonderful jellies to add to the dataset! (But more on that later.)

Poster Presentation:

This first photo is of the poster I made for and presented at the UROP symposium. It gives a brief introduction on clytia hemisphaerica, explains how I created my dataset (video recordings), and shows what observations and findings were made.

This next photo shows the poster and me in action at the symposium!

I got to meet a lot of exciting people and shared endless amounts of unusual jellyfish facts with them. [Example fun fact: Did you know it’s been confirmed that some jellyfish (like the upside down jellyfish) sleep? This finding by researchers at Caltech (http://www.sciencemag.org/news/2017/09/you-don-t-need-brain-sleep-just-ask-jellyfish) was surprising since jellyfish don’t have brains or even a central nervous system, so sleep must be a more universal activity than previously thought.]

Jelly Road Trip:

The day came much too quickly – the day I had to leave Ann Arbor and go back home to Cincinnati. I spent 7 hours straight packing and loading the car with all the things I’d brought with me or accumulated during my stay.

There was a lot of stuff and it took up a lot of (hard to find) space in my compact-size sedan, but one spot remained clear: the passenger seat.

The passenger seat was reserved for the 2 remaining jellies! I got approval to take them home with me and continue my work in Cincinnati! After 220 miles of highway roads, the jellies finally got to see their new home (and I got to improvise a new DIY tank setup).

Now that the jellies are here, we can start on the post-fellowship jellyfish-based research plans!

Future Work:

Over the next few weeks, I plan to make more recordings of the jellyfish in a wider variety of situations. I’ll try changing environmental variables like lighting, current direction/intensity, salinity, and water temperature.

Some of the features I plan to add to the tracking/analysis software include optical flow options (to track the water current based on the dust particles visible in the videos), ellipse fitting options (to gauge when the jellyfish is actively pulsing), and multiple jelly support (for tracking 2 or more jellyfish at once).

Finally, the machine learning portion of this project will revolve around mostly unsupervised methods in the hopes that behaviors can be found with minimal bias and human error. Some options that were discussed include basic k means clustering as a start followed by other methods like compressing the layers of the neural network to force the algorithm to find patterns that effectively store the original data without losing any information.

This fellowship was a great experience and I’m very excited and grateful for the opportunity to bring my project home with me and continue my research.


Summer Summary

I didn’t write a lot of blog posts this summer because I didn’t have my own research project, but the other research projects kept me plenty busy. I converted over an old BYB library written in a pricy programming language called Matlab into a free open source language called Python. I also cleaned it up and commented out all of the code while I was at it.

I had the privilege of helping out the other fellows with their projects. I got to be a test subject for a couple studies and helped build a bee tunnel. Plus I wrote some code for graphing and analyzing the EAG of the moth experiment as well as some odd functions here and there. Not bad for a recent high school graduate!

I can’t believe it’s all over now. It was a wonderful way to spend a summer. Thank you to everyone who made it possible, especially Greg Gage, Sanja Gage, Etienne Serbe, and Stanislav Mircic. A special thanks to all of the 2018 fellows!