Chandra Lab | Neuroscience and Cell Biology
Prerequisites: The student will not need to generate any new code, simply follow along from existing R scripts, with supervision. They do not need any preexisting skills.
General Lab Description: The Chandra lab studies the cellular and molecular of Parkinson’s disease and related neurodegenerative diseases. The lab uses mouse models of disease as well as induced pluripotent stem cells, primary neuronal cultures, and immortalized cell lines as our main experimental models.
Project Description: The student will investigate alpha-synuclein (Parkinson’s disease) pathology in the spinal cord of a mouse model treated with different gut microbiota. These tissues have already been collected, and the animals were shown to have motor dysfunction which may relate to spinal cord degeneration. The pathology in the brains of these animals has already been characterized, and the spinal cord may reveal an additional route by which the microbiome impacts motor function.
Day-to-day Activities: The student will spend the summer learning the techniques required for immunohistochemistry in mouse tissue. First, they will prepare slides from frozen spinal cords by cryosectioning. Next, they will stain these slides and use a microscope to take images of each spinal cord (with supervision). Finally, they will use image analysis software and basic R code to analyze the images.
Coughlan Lab | Ecology and Evolutionary Biology
Prerequisites: We will likely use R Studio to visualize the data collected so experience with R would be helpful but not necessary. Attention to detail, ability to take well written notes, able to keep data organized. Some lab experience (pipetting, etc.) would be beneficial but also not necessary.
General Lab Description: The Coughlan Lab is interested in how new species arise and how these species persist and adapt their local environments. We use a combination of molecular genetics computational genomics, as well as intensive greenhouse experimentation and fieldwork.
Project Description: This project focuses on understanding what keeps species distinct specifically, we are interested in identifying different barriers to reproduction between two closely related species. One type of barrier that can arise are developmental issues with hybrids that prevent them from reproducing or reduce their probability of survival. In plants, a common example of such developmental issues are a suite of traits that mimic an overactive immune system (i.e. yellowing/browning on the leaves and stunted growth). This project will involve growing hybrids from many different crosses to survey for how common such hybrid necrosis is and we plan to use these data to identify the genes that underlie such developmental problems.
Day-to-day Activities: Most of the project will primarily be in the greenhouse where we will survey the phenotype of the plants (is a plant a dwarf type yes/no), collect plant tissue, collect seeds/fruits and pollinate flowers on the plants. We may do a GA (gibberellic acid) treatment on seeds in the lab to improve germination if there is poor germination rate.
Prerequisites: Matlab experience preferred
General Lab Description: Our lab is focused on how energy usage informs structural and functional connections in the brain and how these networks change over time and in disease.
Project Description: You will work on a project to model the relationship between various signals in the brain (calcium signaling, cerebral blood volume, and glucose metabolism). This will help solidify our understanding of how these signals interact in the brain at rest, giving rise to a clearer picture of neurometabolic and neurovascular networks.
Day-to-day Activities: You will use Matlab to develop and refine a temporal transfer function that can take an input signal and recreate a desired output signal. If successful, you will also extend that function to the spatial realm.
Prerequisites: Bash, R
General Lab Description: Our lab is broadly interested in ancient DNA and human evolution.
Project Description: The project the intern will join to tries to understand the evolution of the human immune system, why some populations are more susceptible to specific pathogens, and if there are mutations in immune related genes that improve our cellular defense against pathogens.
Day-to-day Activities: Mostly computational work, may include some wet lab experience.
Natarajan Lab | Astronomy
Prerequisites: Some basic Python coding experience preferred (installing packages, running notebooks, basic command line). No astronomy knowledge required.
General Lab Description: A key interest of our lab is understanding how the supermassive black holes that are found in the hearts of galaxies have formed and grown over cosmic time.
Project Description: The goal is to measure the distances of the galaxies and the masses of their supermassive black holes using established methods. Mass is one of the fundamental properties of black holes that grow as they accrete matter. Once we know the black hole mass, we can compare this to the mass of the stars in the galaxy in order to determine how much the black hole has “grown” over time compared to the galaxy.
Day-to-day Activities: The student will calibrate and analyze spectroscopic data of galaxies with “actively accreting” supermassive black holes that we have obtained from the Palomar and/or Gemini Observatory using python scripts. Day to day tasks will involve downloading data files and Python packages, learning the principles of spectroscopy and calibration, and fitting models to the emission lines in the spectroscopic data.
Prerequisites: Experience with C/C++, Python, Matlab, or other programming languages is preferred but not required.
General Lab Description: The goal of this research project is to uncover the dominant deformation mechanisms of metallic glasses. Our current focus is the structural origin and the evolution of shear bands, i.e., plastic instabilities that localize shear strain inside a thin band of the material under deformation.
Project Description: The student will investigate how shear bands form and evolve in CuZr metallic glasses under compression. Shear bands are the primary cause of sudden failure in metallic glasses. By studying the spatio-temporal evolution of shear bands, this project aims to uncover the atomic-scale mechanisms that govern plastic deformation, which will help guide ongoing efforts in the O’Hern research group to design metallic glasses with improved strength and ductility.
Day-to-day Activities: The student will perform molecular dynamics simulations on the Yale computing cluster to generate glassy samples of CuZr alloys and simulate their deformation under compression. The student will analyze the resulting data to track the formation of shear bands and learn computational techniques to identify “defect”-like weak regions in amorphous structures that act as precursors to deformation.
Perry Lab | Cell Biology
General Lab Description: The Perry lab studies metabolism, which is how our cells use nutrients and oxygen to make energy. Metabolism is necessary for all of our organs and cells to function properly so it is very important to understand. Each of our lab members studies metabolism in different contexts, either in different organs or in conditions like during exercise or disease.
Project Description: Our brain uses a lot of energy (almost 20% even though it only makes up 2% of our bodies!), and so I am interested in studying how brain metabolism works (or doesn’t) in diseases like cancer. We have found that mice with cancer are slower and more tired which is called “cancer-related fatigue” and is also found in cancer patients. We believe that decreased brain metabolism may contribute to fatigue. This is critical because fatigue is identified across many diseases and there are no effective fatigue treatments.
Day-to-day Activities: We will do a mix of computational work and bench science, which means the daily tasks will vary a lot. I will teach you to pipette, make solutions, work with cells, and perform data analysis for behavioral tests. So a typical day could look like a couple hours of cell work/bench work, lunch, then help me with another experiment or do some computer work. Importantly, while the student won’t handle animals, I do a lot of work with animals so the student should be aware/okay with animal work.
Peters Lab | Medical Imaging and Computational Biology
Prerequisites: Linear algebra, MATLAB (we will share learning materials, and mentor will be there for any questions)
General Lab Description: Improving medical diagnosis and discoveries with new imaging techniques, especially Cardiac Magnetic Resonance Imaging (MRI).
Project Description: We have developed new MRI techniques for measuring cardiac flow in a more robust way. The scan time, however, is pretty long for clinical applications.
Day-to-day Activities: We hope to accelerate this procedure, with better acquisition sampling and reconstruction algorithm. We have some ideas, using a method called CAIPI-cube. This project will include 1) Learning basics of MRI 2) read papers about cardiac flow measurement, understand phase-contrast and CAIPI 3) implement CAIPI-cube reconstruction with MATLAB and compare with alternative methods
Picciotto Lab | Psychiatry
General Lab Description: The Picciotto lab focuses on understanding the role of acetylcholine and its receptors in natural behaviors and those relevant to understanding psychiatric illness and addiction. We use molecular genetic, biochemical, pharmacological, neuroanatomical, circuit-level and behavioral techniques to manipulate and characterize neurons and circuits important for cholinergic signaling.
Project Description: This project aims to define the underlying molecular mechanisms involved in context-dependent fentanyl tolerance. With this we hope to discover how contextual information encoded in the brain prepares the body altering physiological responses to opioids.
Day-to-day Activities: While in the lab, the student will learn how to read scientific articles to build an understanding of molecular and addiction neuroscience. For the project, they will learn how to section mouse brains, do immunohistochemistry, prepare slides, image, and some statistical analysis.
Saxena Lab | Neuroscience and Computational Biology
Prerequisites: Experience with programming in any language would be beneficial, particularly Python.
General Lab Description: In this lab, we utilize computational methods such as machine learning and control in order to uncover the inner workings of the brain. We develop biologically inspired goal- and data- driven artificial intelligence methods to elucidate the neurodynamical basis of behavior, ranging from sensorimotor control to social behavior.
Project Description:
Project 1: We are studying how marmosets catch moths, a surprisingly complex task that requires the brain and body to rapidly coordinate multiple streams of sensory and motor signals. In collaboration with Nicho Hatsopoulos and Jason MacLean at the University of Chicago, we are building a virtual marmoset model and training it to replicate movements from real recordings to probe how sensorimotor processing is implemented across the brain and body. Data for this project was collected in the Hatsopoulos lab.
Project 2: Neurons in the brain belong to a variety of cell types, each of which constrain how neurons communicate with each other and perform computations. Implementing such cell types in modern recurrent neural networks (RNNs) can lead to training difficulties or instabilities during common tasks, however doing so is vital for modeling and interpreting how different brain areas and cell types perform behavior. In this project we will systematically analyze and benchmark methods for training RNNs with cell type constraints with the goal of endowing them with the learning capabilities of biological brains.
Day-to-day Activities:
Project 1: The student will likely perform programming tasks such as running training scripts for machine learning models and keeping track of their progress. Afterwards, analyses of the trained models will be beneficial, if time permits. Other activities would include meetings and general discussion with the Saxena lab, and reading/presenting papers.
Project 2: This project will only involve coding, primarily in python. Use of other tools such as git/GitHub and internal lab tools is also likely.
Snell Lab | Neuroscience and Cell Biology
Prerequisites: Must be comfortable handling laboratory mice and strictly following ethical research protocols. Prior experience is not required. Successful completion of at least one high school biology or introductory life sciences course
General Lab Description: The Snell Lab investigates how the cerebellum (a brain region traditionally associated with movement) contributes to complex cognitive functions like attention and decision-making. We use mouse models to understand how the brain processes prediction errors (when expectations fail to match reality). This mechanism is a core feature of neurodevelopmental conditions like autism and ADHD.
Project Description:
Project 1: Imagine playing a game where you must press a lit button to get a prize. The room is visually noisy and the target lights are dim. If you press the correct button and get your prize, but the light unexpectedly stays on, what do you do? Do you ignore it, or do you double-check the button to see if the rules changed? This project uses a behavioral task called the 5-Choice Serial Reaction Time Task (5CSRTT) to study how mice handle uncertainty.
Project 2: Some changes (mutations) in a specific calcium channel, that is highly expressed in the cerebellum, can lead to very different symptoms in people, ranging from movement problems to cognitive conditions like autism. This project asks: how can changes in the same protein cause such different effects? As an intern, you will work with a lab mentor to study different versions of this calcium channel by growing DNA and using imaging tools to compare how these changes affect cell function.
Day-to-day Activities:
Project 1: The student will help us identify “”epistemic actions”” (curious movements like re-checking a light after receiving a reward) to measure exactly when a mouse seeks information to resolve its confusion. Activities include:
Psychometric Calibration: The student will start the summer by running specialized training sessions to map the visual threshold of each mouse
Mapping Epistemic Curiosity: Analyzing behavioral data to find information-seeking behaviors. Neuro-Engineering: Assisting with the maintenance of custom sound-attenuated chambers and learning how to manage the hardware-software interfaces that run the behavioral experiments
Project 2: Daily tasks would include:
a. Growing and copying DNA that contains specific mutations
a. Growing and copying DNA that contains specific mutations
b. Taking care of cells and adding DNA to them so they produce the calcium channel (called transfection)
c. Assist in preparing and imaging cells using advanced microscopes
d. Analyzing images and data to look for patterns and differences
e. Working closely with a lab member to interpret your results
Taylor Lab | Neuroscience
Prerequisites: This experience will involve on-the-job learning, so while no specific skills are required, we are looking for students who are highly motivated, organized, responsible, curious, and proactive. Coding skills (in Matlab and/or Python) are a plus (but not required), and interest in working with rodents (rats) is a necessity.
General Lab Description: How do individual differences in play behavior as juveniles (playing a lot or a little) predict social behavior as adults (cooperating with others)? The SNaP Team within the Taylor Lab is a neuroscience lab that looks into the brain regions underlying social behaviors throughout development and into adulthood.
Project Description: The project uses a translational approach, which means we use an animal model (in our case, rats) to understand behaviors that are relevant in humans, specifically social behaviors. Even when raised in identical environments, individual animals differ in subtle ways, and we’re interested in whether these early behavioral differences predict how they act as adults. Specifically, students will score videos of rats playing (much like dogs play) to capture individual differences and see if they predict willingness to work together (cooperate) with a partner for a reward (sugar pellets). Beyond video scoring, students may also get to count active brain cells (neurons) captured in images, and potentially get hands-on experience handling rats.
Day-to-day Activities: The primary responsibility for this internship is scoring behavioral videos; students will spend most of their time becoming proficient in examining and coding rat play behavior from video recordings. Beyond that, students might get exposure to shadowing behavioral experiments with rats and wet lab skills like mounting sliced brain tissue and performing microscopy.
Prerequisites: Previous coursework in Geometry and Trigonometry and a class in chemistry and/or physics (preferably physics)
General Lab Description: Our research explores some of the most fundamental questions in physics, such as what matter is made of and what forces hold it together. Using powerful particle accelerators, scientists collide particles at extremely high energies in order to study the smallest building blocks of matter. By measuring the particles produced in these collisions, we investigate the strong nuclear force, the interaction that binds quarks together to form protons and neutrons, and ultimately the atoms that make up everything around us.
Project Description: Our group is helping develop a detector for a future particle accelerator called the Electron-Ion Collider (EIC), which will be built at Brookhaven National Laboratory on Long Island, NY. One subsystem of this detector, called pfRICH, helps scientists identify different types of particles by measuring tiny flashes of light they produce when traveling through the detector. In this project, the intern will help improve and test an optical setup used to evaluate very sensitive light sensors that will eventually be used in the detector.
Day-to-day Activities: This project involves hands-on work with a laboratory testing setup used to study how sensitive light sensors respond to very small signals. The intern will help operate and improve the testing setup inside a light-tight enclosure and assist with preparing and running tests of the sensors. They will also use computer software to record and organize measurement data and learn how scientists evaluate the performance of detector components.