Call for Undergraduates in Biology or Engineering Fields
Do you have an interest in neuroscience? Do you like squids or dragonflies? Electrical, Mechanical or Computer engineering? Want to develop your own experiments and publish your results? Learn to communicate with the public? Maybe even all of the above? Then you’re in luck!
The Backyard Brains Summer Research Fellowship is an intensive 10 week program for undergraduates to participate in hands-on neuroscience research and experiment design with award winning neuroscientists. This is the 4th year of running our prestigious (and paid) summer program and this year it will run from May 22, 2017 to Aug 4, 2017 in Downtown Ann Arbor, MI. All applications must be received by noon eastern time on March 13, 2017 to be eligible. We will be notifying applicants status by March 21, 2017.
This is our 4th iteration of the program, which gets better each year. Our summer fellowship program is run much like a graduate school laboratory. All participants will be working on independent research projects, we will have journal clubs to go over key papers, and you will be trained how to develop your own experiments and to build your own devices to perform those experiments. You will be collecting data, analyzing and presenting your results.
The end result of your summer fellowship will be a publishable experiment and video for our website, as well as a poster to be delivered at Undergraduate Research Poster Session of the Society for Neuroscience. Last year, all of our participants presented their research at a Undergraduate Research conference and some were selected to be posters at the Society for Neuroscience. We also brought home the hardware to show for the hard work: Two of our students won awards for their poster presentations, and 2 others won the Hackaday’s Citizen Scientist Challenge! We will work with each student to prepare a 10 minute TED-style talk for a public event in Ann Arbor, with the possibility of presenting at our annual TEDx event. We have also worked with students to continue refining their experiment writeups into manuscripts to publish first-authored papers in peer-reviewed journals.
As interns, you will receive media coverage by the popular press. See below for previous examples:
Two Interns Win Hackaday’s Citizen Scientist Challenge
Arduino, EEG and Free Will by Patrick Glover “If the brain had already been preparing to perform the action for nearly half a second before the individual consciously “decides” to perform the action, did the individual actually… decide?” Read the full article here.
Neuroscience of Grasshopper Jumps by Dieu My Nyugen “Why are they hard to catch? Because they can quickly jump away when a person or another insect or object approaches it. How are they able to quickly hop away to escape a potential predator or avoid collision with an object? To address this specific question, I will look into the movement detector neurons in the grasshopper’s brain—the organ that fascinates me.” Read the full article here.
Optogenetics Featured In Hackaday
“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”. Read the full article here
RoboScorpion Featured in Popular Mechanics
“Backyard Brains, a small Michigan-based company dedicated to spreading the word about neuroscience, has been running surgical experiments on these deadly arachnids for the past two months, using electrical current to induce them to strike. Dylan Miller, a summer intern working the project, insists it’s the first time that an electrical current has ever been used to remotely induce a scorpion to strike with its pedipalps (claws) and tail”. Read the full article here.
This summer you will be trained by Ph.D. Neuroscientists, inventors, makers, seasoned engineers, and public speakers. With our team each intern will have a compelling demonstration that the public will be interested and delighted to see. For example, see our recent TED talk on some our recent work. Yours could be next!
Listen to a testimony from a former intern:
“It was fun and challenging, but extremely rewarding. Greg was a great mentor and I learned so much. More than any other experience I’ve had, this fellowship prepared me for graduate school and a career in research“-D. Miller, 2014 Intern
This year’s projects will be our most interesting and exciting ones yet.
Electric Fish – Amazon Mapping project The past 2 years, we have been slowly developing a fish recording device that will detect the Electric Organ Discharges (EODs) of weakly electric fish. We now have a project planned for next year where we need to make this device work! You will build new electrode arrays for detecting fish in our tanks and develop the bits and pieces to make our waterproof devices run for months on batteries. Our goal is to deploy 500 of these into 2 estuaries in the Amazon in 2018. Skills required: EE, ME.
It’s like Tinder, but for Mosquitos. Ever hear that annoying sound of a mosquito in your ear? That, dear friends, is actually a mating call. Awwwww. In this project, you will record the frequency of Michigan Mosquitos as they flap their wings while glued to sticks. Eavesdrop in on Male/Female, Male/Male and Female/Female interactions. Their wing patterns should sync if there is a love connection. Dr. Ron Hoy (Cornell, see: http://www.cornell.edu/video/mosquito-hearing) will help you support this project. Skills: Neuroscience, Psychology, EE
Pygmy Squid Behavioural analysis. Off the coast of the Japanese islands live a wonderful and strange tiny species of squid called “Pygmy Squid” (Idiosepius paradoxus). These squid attach to the bottom of surfaces with a sticky part of their mantle to eat. Their behaviors are not well understood… that’s where you come in! We want to use a mobile phone to collect video data on these squid, and use machine learning techniques to identify new behaviours. Some videos of freely behaving attached adults are here [https://vimeo.com/133217986] and here [https://vimeo.com/133212253] Dr. Eric Edsinger (MBL) will assist you on this project. Skills: CS, EE, Psychology.
Sleep and learn (better) with EEGs. Wouldn’t it be cool if you could improve your memory while sleeping? Studies have shown that cuing memories with sounds during sleep can lead to a robust improvement in recall of memories. Really? We’d like to make a DIY version of this project to see for ourselves. Sound cues are said to be most effective if they are played during a particular phase of sleep (slow-wave sleep, which has previously been linked to memory consolidation). Thus to run these experiments & get memory benefits, you will need to automatically detect slow waves and trigger the cue! You will be working with Dr. Ken Norman (Princeton) and one of his high school students. Skills: Neuroscience, CS.
Diel migration in squid hatchlings. Newly-born squid move up and down the water column of the ocean, possibly in seek of food, currents, or protection from predators. This is not well understood. We would like to detect the depth behaviour of these tiny hatchling by detecting where they are in a large cylinder of water. We will be using freshly hatched Longfin inshore squid babies. (Editor’s note: This is the famous species used by Huxley and Hodgkin in their 1963 Nobel Prize for understanding the Action Potential of neurons). You will be working with Dr. Eric Edsinger from the Marine Biological Labs in Woods Hole, MA. Skills: ME, EE, Neuroscience, CS.
EEG visual decoding: I can see that you’re seeing faces. In this study, you will peer inside the thoughts of another human being… not really. But you will be able to record electroencephalogram (EEG) from a human scalp to determine if you can detect if a person is looking at pictures of scenery or of human faces. This is collaboration with Dr. Ken Norman at Princeton University. Here is the reference paper. Skills: Neuroscience, CS.
Killer Dragonfly neural recording: Dragonflies-the perfect flying predators, living up to their namesake! Dragonfly eyes are incredibly complex and achieve near all-around vision, as well as extremely accurate in determining the position and velocity of a flying target. Neurons in their eyes are directly connected to their flight muscles (rather than going through their brain first), so they can change their flight path or speed near instantly. Last year we were able to get some early recordings that shows this may be possible to do! Your project will be to build on that work and carefully map the dragonflies descending flight neurons by recording while controlling a “fake fly” (prey) using a laser. Skills: EE, CS, ME, Neuroscience.
What’s on the Fly Menu tonight? Fruit flies can be annoying, seeming to appear out of nowhere to invade your fruit basket. What are they looking to eat? We will find out! We will use a new device called the “FlyPAD” to zoom in on the tiny flies’ tiny sips of food. Once we get it working, we can start to ask interesting questions: do flies change their appetites based on what’s lacking in their diet? What neurons control these behaviours? We will use some cutting-edge genetic tools (themo and optogenetics) to turn on neurons that could affect their feeding behaviour. Dr. Pavel Itskov (Champalimaud) invented the FlyPAD and will support this project. Skills: EE, Neuroscience, genetics.
Become a BYB Research Fellow in 2017, and help start the neuro-revolution!
You will be located at the Backyard Brains headquarters in downtown Ann Arbor (map). You will also be working out of our MakerSpace lab called “All Hands Active”.
How much are the interns paid?
The weekly payment is $404/wk.
How much is housing and can you help us find it?
While we do not pay for your housing, we are happy to inform you that summer housing is notoriously easy to find in Ann Arbor, as students leave for the summer and make available sublets. The price varies, but you can find sublet housing on craigslist for under $400. We recommend that you stay close to downtown/central campus.
I am not out of class until June. Can I start a bit later?
We feel that our interns need a full 10w to make significant progress on their projects. If you have a compelling reason on how this will not affect your project, we are willing to evaluate it on a case by case basis.
I am not an undergrad, can I still apply?
While our program is designed for undergraduates… If you are a college graduate, or a super smart High Schooler, we will accept your application.
Is there time off for vacations?
While you will have ample free time in Ann Arbor, we ask that you make the commitment to stay on project for the entire length of the internship.
Are projects assigned to interns or do the interns get some autonomy in deciding the course of their research?
The summer projects are described above and in the fellowship application. Each student will submit the project that they are interested during this process, or can suggest their own ideas. We take the applicant’s preferences in mind, and we pair a student with a project early on so that the intern will have some time to do some background reading and familiarize themselves with the organism/methods. While we have some idea of the direction or end result of a project, we encourage independent thought throughout the process-some of our most successful projects have come from slight deviations from the original goals. We will send out some suggested papers a few weeks before the program starts.
I aim to study the neuroscience behind this question by replicating past studies on grasshopper vision. Grasshoppers can sense an approaching object and quickly hop away to avoid collision with the object because their visual system includes a type of neurons (descending contralateral movement detector, DCMD) that underlies the animal’s visual and motor sensitivity to approaching objects, such as predators. I use Backyard Brains’ open source SpikerBox and the SpikeRecorder iPad app to record and visualize the activity of the DCMDs in the form of electrochemical action potentials, or spikes.
Throughout this project, I aim to bring neuroscience research out of the far, far away university labs and design and perform a low-cost and reproducible project using open source and DIY tools, to explore and learn from the neural basis of the grasshopper’s escape mechanism.
Somewhere in Portland, there’s a restaurant that serves grasshopper sushi rolls. Is it safe? Is it good? I don’t know!
Because I am a grasshopper researcher this summer in Ann Arbor, Michigan, I have other questions in mind: How do people catch these bugs? If you’ve ever tried to catch one, you know that it is nearly uncatchable when its skeletal muscles get to work as you approach with silent steps, trying to capture it for an afternoon snack.
Catching grasshoppers in Ann Arbor is my exciting challenge this summer. Finding out why they are hard to catch is my neuroscience project.
Why are they hard to catch? Because they can quickly jump away when a person or another insect or object approaches it. How are they able to quickly hop away to escape a potential predator or avoid collision with an object? To address this specific question, I will look into the movement detector neurons in the grasshopper’s brain—the organ that fascinates me.
Just as I can see it with my eyes, the grasshopper can see me if I come to it. Or if I show it scenes from Star Wars when spaceships are flying toward the viewer, the grasshopper can see them too and would hop, hop away. That is what researchers Rind and Simmons found in 1992 in their research on the vision of the locust, or a kind of grasshoppers that form swarms. The grasshopper’s nervous system includes a type of visual neurons, called descending contralateral movement detector (DCMD), that receives visual info from the eyes and sends that info to the legs, and underlies the grasshoppers’ ability to visually detect and react to an approaching object, be it a spider looking for a crunch or an astronomically speedy spaceship.
In human language, the brains of these bugs are capable of serious mathematics. In a paper published in 1995, researcher Hatsopoulos and colleagues came up with an equation that describe how the DCMD neurons sense and respond to approaching and receding objects: velocity, or speed, of the approaching image:
multiplied by an exponential function of size of object’s image on the retina: On a high-level consideration of the computational way the brain of the grasshopper functions, the activity of the DCMD neuron is related to how fast the image is coming toward the eye of the grasshopper and the image size on the eye that changes with decreasing distance between object and the eye. The peak in firing is reached before the collision of the object and the grasshopper, and the bug can leap away using their legs to avoid being hit or eaten.
In the world of scientific research, disagreements founded upon experimental evidence and thoughtful arguments give rise to scientific progress. In the two above-cited papers, I see several discrepancies between the two groups of researchers. While Rind and Simmons concluded that there was good correlation between the neuron’s activity and the object’s acceleration during the exposure of the grasshopper to approaching objects, Hatsopoulos and colleagues used both their computation and experiment to conclude that the correlation was poor. The two papers generally agree that the DCMD neuron’s responses depend on the size and speed of the object. Keeping these ideas in mind, I will see what results my project will yield and I look forward to contributing to the discussion.
Art by Tanner @ All Hands Active, Ann Arbor, MI
I hope to demonstrate that a fun and educational neuroscience project can be done outside of the far far away university labs! I use Backyard Brains’ Neuron SpikerBox that amplifies and visualizes the activity of the DCMDs in the form of electrochemical action potentials, or spikes. I also have an iPad with the SpikeRecorder app, which provides visual stimuli (growing or receding black dots on a white background) in front of the grasshopper’s eye as well as records the DCMD activity.
Hop, hop away. This is how the grasshopper stays alive. This is how it continues to exist and eats plants and destroys our crops. But it is also our food and art and stories. And it is my friend (euphemism for “study organism”) this summer. Please check out how I chase, catch, maybe eat, and perform electrophysiology on the grasshoppers to record the activity of the DCMD neurons in an open-source and DIY style.
iPad: ~$400 or if already have – As screen for visual stimuli and recording and visualizing spikes, in a cumulative SpikeRecorder app
Microscope: $200 or ask around or use a phone app! – 20X magnification is sufficient; For surgery on grasshopper and electrode placement
Magnetic stirrer: $100 or be creative! -To heat, melt and mix the wax and rosin mixture
RadioShack mini speaker/amplifier: $15 – To hear the spikes when the grasshopper sees the balls being thrown at it
Backyard Brains Neuron SpikerBox: $100 or DIY – A bioamplifier that allows us to hear and see spikes in living neurons; has cork board piece on top for mounting animal
Backyard Brains Micromanipulator: $100 or DIY – For precise placement of electrodes
1-Channel Electrodes: Reference and Recordingincluded with manipulator or DIY – Hook electrode around neck connective of grasshopper and reference electrode in abdomen, both connected to SpikerBox
Painter’s Tape$2 – To restrain grasshopper and tape it down to corkboard piece on the SpikerBox
Thread: $2 – To pull grasshopper’s neck up to expose neck where recording electrode is placed
Wax and violin rosin mixture: $6 – Heated to be mixed together; for placing on thread around grasshopper’s neck to keep it in place
Build the SpikerBox, micromanipulator, and electrodes. Build instructions for these items are in the files section! Gather the materials:
Anesthetize the grasshopper by placing it in a plastic container (also its home in the lab) and keeping in the fridge (not freezer) for 15-20 minutes or until it is inactive. This keeps the animal still and painless (if insects indeed feel pain) during the upcoming surgery. (Dragonflies are also our faves.)
After anesthesia, tape the grasshopper belly up on the cork board piece on the BYB SpikerBox. Tape all the legs and the abdomen. Leave the head and a little of the thorax exposed—these areas are where electrodes will be placed. (I find masking/painter’s tape to be the easiest to work with.)
Then, use a piece of black thread to pull the head back until the neck connectives (two white strips under the neck skin) are visible. This step is tricky, so be patient. Also, the thread must not block the eye opposite of the side of the neck that the recording electrode will be placed. In the picture above, I plan to put the recording hook electrode (where needle is pointing in photo) around the left neck connective of the grasshopper. So the right side of the grasshopper (our left) must not be blocked by anything.
Create a 50/50 mixture of rosin and bee wax in a glass petri dish. Put the dish on magnetic stirrer, on very low heat (I’ve broken several dishes due to ignorance of kitchen basics). After a few minutes, the solid mixture is melted into a liquid.
Use a needle to pick up the warm rosin-wax liquid and place it around the thread holding back the head of the grasshopper. When the liquid cools and molds into a wax texture, the thread is secured to the neck of the grasshopper.
Now, another step as tricky as pulling back the grasshopper’s head: Placing the hook silver wire electrode around the neck connective to pick up the activity of the DCMD neurons. The BYB manipulator electrode comes as a simple straight wire. For this experiment, I modify it by using tweezers to bend the tip into a small hook, to place around the connective.
Then, under the microscope, use a tiny needle to pierce a hole on the left side of the grasshopper’s neck, next to the connective. Then, carefully place the hook electrode into the hole and use the BYB Micromanipulator to adjust so the electrode is deep enough to hook around the connective.
Depending on the grasshopper and the spot in the neck where the hole is made, there might be green blood oozing out from the hole (top photo). If there is no blood coming out, I immediately put a drop of Vaseline on the recording electrode and nerve cords to isolate them from the rest of the body and keep the pierced hole from drying out (which would otherwise happen within minutes).
Connect the BYB manipulator electrodes to the SpikerBox. Then, place the reference electrode (needle) either on the mid-thorax or abdomen. I find that the reference electrode grounded in the thorax yields better signals.
The prep is now finished! It looks something like this:
Almost done! On the iPad SpikeRecorder app, set the parameters for a new experiment. Here, I am testing the response of the DCMD neurons to an approaching black ball on a white screen. The balls of different sizes will approach the grasshopper’s eye at different speeds. Between each trial (each trial is a pair of an approach velocity and an object size) is an intertrial interval of 45 seconds for the neuron to fire again, based on literature and my own experiments.
The black balls originate from the center of the iPad screen and fill up the screen to simulate approach and collision with the grasshopper’s eye.
After the iPad is ready, tape it upright to the wall so the angle between the center of the screen/ball and the center of the grasshopper’s eye is minimal. Use a level and ruler to measure. Then, connect the iPad to the SpikerBox (green cable) and also connect a RadioShack mini speaker to the SpikerBox (blue cable) to hear the spikes. Then, turn off the lights and close the doors to the experimental room for good contrast of the black ball on the white screen.
Otherwise, make a portable experimental room! I use a card board box from the recycle bin of a restaurant. I turn on the iPad and close the flaps, and the ball begins to come at the grasshopper’s eye. And the grasshopper’s DCMD neuron will activate. And I will get experimental data!
Note: You might know that electrophysiology recording is troubled by lots of noise,including body and other electronic sources. Choose a spot without many electronics being used, and minimize body movement. I stay at least 5 feet away and sit as still as possible while the experiment is going on.
Finally, when the experiment is over, thank the grasshopper. Unhook the electrodes, untape it from the cork board, and bring it back to the field where it can feel most at home.
With the ideal ITI determined, I can move on to the set of core experiments: testing to see how the DCMD neuron behaves when simulated black balls of different sizes and velocities approach the grasshopper’s exposed eye. So my little friends spend about 2 hours on top of the SpikerBox for these experiments.
I continue to process the data in MatLab for better visualization. Here are the results for balls approaching from a constant initial distant of 10cm, 6cm in size, and with various velocities (-2, -4, -6, -8m/s).
Perievent histogram: showing DCMD firing frequency 2s before and 2s after the simulated collision between the eye and the object:
Raster plot: showing DCMD spiking pattern across each pair of S and v over time. DCMD firing peaks around collision for objects approaching at -2m/s, and after collision for objects approaching faster: