SURFiN Program Lab Opportunities

Mentor: Krithika Mohan
Mentor Role: Postdoctoral Research Associate
Principal Investigator: Doris Tsao
Institution: University of California at Berkeley
Location: Berkeley, CA
Lab Website: https://tsaolab.berkeley.edu

Project Title: Understanding neural code for experience

Project Description: A major component of visual intelligence is the ability to understand new visual scenes we have never encountered before. We hypothesize that the key mechanism underlying this ability is representation of complex, dynamic visual scenes by a compositional, language-like representation. The goal of the project is to analyze neural data in response to videos to discover whether and how such a compositional, language-like representation is implemented by the brain.

Mentor Biography: Krithika Mohan is a neuroscientist, currently a postdoctoral scholar with Doris Tsao at the University of California, Berkeley. She has a doctorate in computational neuroscience from the University of Chicago where she focused on how the brain produces flexible behavior. In her postdoctoral work, her central goal is to discover the brain’s code for visual experience and memory, using large-scale neural recordings during naturalistic behavior combined with cutting-edge approaches in AI and machine learning.

Mentor: Nate Dolensek
Mentor Role: Postdoctoral Research Associate
Principal Investigator: Doris Tsao
Institution: University of California at Berkeley
Location: Berkeley, CA
Lab Website: https://tsaolab.berkeley.edu

Project Title: Understanding neural mechanisms for social cognition

Project Description: Primates exhibit remarkably sophisticated social cognitive abilities, navigating complex and ever-changing social situations by efficiently interpreting cues and producing appropriate responses. Consistent with the centrality of social cognition to primate brain function, many neuropsychiatric conditions are characterized by atypical social behavior, including autism, schizophrenia and depression. The project will exploit machine learning and neural data analysis to understand how the brain represents and predicts events in a social scene.

Mentor Biography: Nate Dolensek is a postdoctoral fellow at the University of California, Berkeley, working under the guidance of Prof. Doris Tsao. His research focuseNate Dolensek is a postdoctoral fellow at the University of California, Berkeley, working under the guidance of Doris Tsao. His research focuses on how the brain implements social cognition and produces social behavior, employing large-scale electrophysiology, fMRI and machine learning approaches. Dolensek earned his doctorate in systems neuroscience from the Max Planck Institute of Neurobiology in Munich, Germany, where he studied the neural encoding of emotion and discovered facial expressions of emotion states in mice using calcium imaging, optogenetics and computer vision techniques. Nate has been the recipient of the Long-Term Fellowship from the Human Frontier Science Program and the Young Scientist Award from the Max Planck Society. He also holds a bachelor’s degree in psychology from the University of Groningen in the Netherlands, with minors in mathematics and affective neuroscience.

Mentor: Janis Hesse
Mentor Role: Postdoctoral Research Associate
Principal Investigator: Doris Tsao
Institution: University of California at Berkeley
Location: Berkeley, CA
Lab Website: https://tsaolab.berkeley.edu

Project Title: Understanding neural mechanisms for consciousness

Project Description: How is activity in neurons able to generate conscious percepts? The project will analyze neural recordings during perception of ambiguous images (e.g., images like the rabbit duck illusion) to investigate the sequence of neural activity that leads an animal to see the same image one way or another.

Mentor Biography: Janis K. Hesse is a postdoctoral scholar at University of California, Berkeley. He completed his bachelor and master studies at Free University Berlin, Tsinghua University and University College London with a scholarship from the German National Academic Foundation, followed by completing a doctorate in computation and neural Systems at California Institute of Technology. His doctoral and postdoctoral research has focused on studying the neural mechanisms of conscious perception. For this purpose, he has helped develop a new recording technology that allows recording from over a thousand neurons in the primate brain to study how the brain generates new conscious percepts when the interpretation of an ambiguous image changes.

Mentor Name: Dyuthi Sristi
Mentor Role: PhD candidate
Principal Investigator: Gal Mishne
Institution: University of California, San Diego
Location: La Jolla, CA
Lab Website: http://mishne.ucsd.edu

Project Title: Multi-region analysis with coupled autoencoders

Project Description: Understanding the connectivity between brain regions is crucial for comprehending various cognitive functions and behaviors. However, the dynamics of information flow between these regions remain largely unknown. In this project, we aim to construct a computational model to analyze simultaneous recordings and uncover the intricate interconnections between brain regions. We will develop a multimodal dimensionality reduction technique to handle multi-region recordings effectively. Specifically, we will explore the utilization of a multi-region coupled autoencoder to encode neuronal activities into latent space representations. These representations will then be decoded to reconstruct the original activity, allowing us to investigate the functional roles of different brain regions. Moreover, we will examine the behavioral decoding capabilities of these regions by analyzing latent space representations. By utilizing machine learning techniques such as autoencoders, recurrent neural networks, and attention mechanisms, the undergraduate involved in this computational role will gain valuable skills and contribute to expanding our understanding of brain connectivity. This project offers an exciting opportunity for undergraduate students to engage in cutting-edge research at the intersection of neuroscience and machine learning while acquiring practical experience in Python programming and advanced data analysis techniques.

Applicants with a strong background in Python/matlab are highly encouraged.

Mentor Biography: Ram Dyuthi Sristi is a fifth-year doctoral student in Gal Mishne’s lab at the University of California, San Diego studying electrical engineering. Her primary focus revolves around the intersection of Machine Learning and the medical domain. She is particularly passionate about developing computational techniques to unravel the intricacies of brain connectivity. She enjoys teaching and believes that “One has a strong conceptual understanding of a subject only when one can explain it to someone completely unaware of that subject.” She has received exceptional feedback while working as a teaching assistant. Dyuthi completed her undergraduate studies at the Indian Institute of Technology Hyderabad. There she received an Institute Silver Medal for securing the highest overall cumulative grade point average in the Department of Electrical Engineering along with a Research Excellence Award and various recognitions and accolades in local and international competitions. Beyond her academic pursuits, Dyuthi finds joy in classical dance and cherishes moments spent in nature. Her dedication to both her studies and personal interests highlights her well-rounded approach to life and learning.

Mentor Name: Zhanqi (Victoria) Zhang
Mentor Role: PhD student
Principal Investigator: Gal Mishne
Institution: University of California, San Diego
Location: La Jolla, CA
Lab Website: http://mishne.ucsd.edu

Project Title: Unraveling Human Behavior: A Data-Driven Approach to Understanding Bipolar Disorder

Project Description: Undirected behavior reflects cognitive functions and provides insights for diagnosing psychiatric conditions such as bipolar disorder. Previous human action models cannot produce explicit action predictions to understand complex human behaviors in clinical settings.

This project aims to use a data-driven approach to discover and model subtle human behavioral motifs with minimum human involvement. It will combine statistical modeling involving computer vision and natural language processing, deep learning and probabilistic reasoning to model and cluster human actions from video.

The Mishne lab has shown that it is possible to differentiate behavioral motifs and quantify hallmark features related to bipolar disorder. SURFiN fellows will explore how to further improve the framework using models such as Gaussian Process Modeling and Graph Neural Networks. Fellows will also have the opportunity to explore natural language processing (NLP) generative models for human actions, and classification models to distinguish patient populations. A successful fellow will be able to make headway on machine learning problems using a combination of application domain knowledge, and state of the art machine learning techniques. In addition, they will be able to build a bridge between neuroscience and machine learning to address real research needs.

Mentor Biography: Zhanqi Zhang is a doctoral student in computer science at University of California, San Diego, supported by Halicioḡlu Data Science Institute Ph.D. fellowship. She is co-advised by Gal Mishne and Mikio Aoi. Previously, she studied Computer Science and Electrical Engineering at Washington University in St. Louis.
Zhanqi is broadly interested in how machine and biological intelligence complement each other to push forward the discoveries of the brain. Specifically, she is currently interested in how human behavior reflects complex neural and physiological processes such as learning, perception, and decision-making in the brain. Using tools in machine learning, computational neuroscience, optimization, and signal processing, she attempts to construct unsupervised animal and human action recognition and behavior classification models to understand disorders in clinical settings.

Zhanqi is originally from a small town in China. Outside the lab, she enjoys hiking, watercolor painting, bird watching, and cooking.

Mentor Name: Maxwell Melin
Mentor Role: Graduate Student Researcher
Principal Investigator: Anne Churchland
Institution: University of California Los Angeles (UCLA)
Location: Los Angeles, CA
Lab Website: https://churchlandlab.dgsom.ucla.edu/pages

Project Title: Understanding the causal role of corticostriatal circuits while learning to make visually-guided decisions

Project Description: The cortex and striatum are known to be topographically connected (ie. particular parts of the cortex are connected with particular parts of the striatum). This means that the cortex and striatum form many distinct subcircuits. These circuits are thought to transform incoming stimuli into goal-directed action. However, we do not know which specific corticostriatal circuits are most important for learning visually-guided decision making tasks. To tackle this question, we will selectively inhibit different corticostriatal circuits (via optogenetics) as mice learn a perceptual decision-making task. We will then quantify learning deficits that are induced by optogenetic inhibition. The fellow can expect to learn and use the following modalities over the course of the project:

Rodent handling and behavioral training: how to handle and care for laboratory mice. The fellow will also train mice to perform decision-making tasks.

Rodent surgery: the fellow will learn to perform optogenetics implantation surgery, allowing us to perform targeted manipulation of brain circuits.

Computation/data analysis: the fellow will learn to write custom Python scripts to analyze behavioral data and identify if learning deficits are present due to optogenetic stimulation.

Communication: the fellow will learn to craft clear, compelling scientific presentations in a low-stress environment.

Mentor Biography: Max Melin is a fifth year M.D.-Ph.D. student in the UCLA-Caltech Medical Scientist Training Program. He has worked in the lab of Dr. Anne Churchland for three years, studying the neural correlates of behavioral states across multiple timescales. Max received a bachelor’s degree in bioengineering from Stanford University. As an undergraduate, he worked in the lab of Thomas Sudhof, studying fear memory and essential tremor. As a graduate student, Max is interested in understanding how the brain solves decision-making problems across different behavioral states (e.g., active engagement vs. distracted or novice vs. expert). In addition to these areas, Max draws upon his engineering background to develop novel tools and software for systems neuroscience. While in the Churchland lab, he has worked extensively to improve experimental methods for chronic electrophysiology and has written multiple software packages to facilitate in-vivo electrophysiology experiments. Max also has multiple teaching experiences. He has worked as a teaching assistant in the UCLA Medical School and has taught computational bootcamps to fellow neuroscientists. He is very thankful for the scientific mentors who have supported him along his journey and is excited to mentor undergraduate students who are considering a career in neuroscience.

Mentor Name: Michael Coulter
Mentor Role: Postdoctoral Scholar
Principal Investigator: Loren Frank
Institution: University of California San Francisco
Location: San Francisco, CA
Lab Website: https://franklab.ucsf.edu

Project Title: Systems neuroscience in a rat model of autism

Project Description: This project will focus on a genetic rat model of autism. Specifically, we are studying heterozygous loss of function (loss of one copy) of the gene, Scn2a, which produces a voltage-gated sodium channel (a protein important for communication between neurons). Humans with this genetic variant are very likely to develop autism with intellectual disability. Recent work from our lab has shown that rats with heterozygous loss of function of Scn2a (Scn2a+/-) learn a spatial alternation task more slowly than wild type rats, and now we are using in-vivo physiology (brain recordings in freely moving rats) to characterize the systems-level differences that may be causing this learning impairment. We are using long-term physiology recording techniques to record the activity in awake rats from two brain regions that contribute to spatial alternation task learning: hippocampus and prefrontal cortex. This project would provide the student opportunities to learn rat handling and behavioral training, long-term in vivo physiology data collection, and subsequent analysis of the neural recording data. The primary questions we will address are (1) is neuronal activity different in the hippocampus and prefrontal cortex in Scn2a+/- rats compared to wild type rats, (2) is communication between these two brain regions different in Scn2a+/- rats, and (3) can any differences we find in neurophysiology explain the learning impairments we have observed in these rats?

Mentor Biography: Michael Coulter graduated from Harvard College with a degree in history of science in 2008. He then received a Ph.D. in neurobiology in 2018 from the M.D.-Ph.D. program at Harvard Medical School. During his Ph.D., Michael was in the lab of Chris A. Walsh at Boston Children’s Hospital, and his work focused on the genetics of neurodevelopmental and neurodegenerative disorders. He identified a new set of genes associated with a severe neurodevelopmental disorder, found a novel mechanism for growth factor secretion in the developing brain, and characterized single neuron somatic DNA mutations in early neurodegenerative disorders. With a long-term career goal of improving the lives of individuals with autism and intellectual disability Michael joined the lab of Loren Frank at UCSF to learn the experimental techniques and theoretical framework to approach the study of neurodevelopmental disorders from a systems neuroscience perspective to complement his genetic and molecular training during graduate school. In Dr. Frank’s lab, he has focused on developing a new system for neurofeedback in the hippocampus and begun to characterize the systems-level differences in a genetic rat model of autism. His postdoctoral research has been funded by individual fellowships from National Institute of Mental Health (F32) and the FamiliesScn2a foundation.

Mentor Name: Xulu Sun
Mentor Role: Postdoctoral Associate
Principal Investigator: Loren Frank
Institution: University of California San Francisco
Location: San Francisco, CA
Lab Website: https://franklab.ucsf.edu

Project Title: Cortical-hippocampal neural dynamics underlying model-based planning

Project Description: When dealing with novel situations or unexpected events, we often contemplate possible actions and imagine their outcomes using our knowledge of environmental contingencies. This flexible cognitive process is known as model-based planning and is typically impaired in many neuropsychiatric disorders. The hippocampus (HPC)—usually understood to represent past or present experience—has recently been implicated in the ability to imagine possible futures. Despite observing hippocampal future representations before decision-making, we understand little about how these representations are regulated and what functions they subserve. I hypothesize that, to find adaptive solutions in response to a changing environment, input from the prefrontal cortex (PFC) drives hippocampal future representations. I further hypothesize that these representations coordinate with PFC cost-benefit computations to chain imagined actions with predicted outcomes, thereby facilitating model-based decision-making. Employing a dynamic foraging task and multiregional electrophysiology, I will investigate how PFC and HPC interact when rats plan new routes toward rewards in the presence of novel barriers. I will leverage closed-loop optogenetic manipulations to determine the necessity of PFC-HPC interactions for model-based decision-making. This project will uncover the anatomical underpinnings, mechanistic control and functional significance of hippocampal future representations, which will ultimately illuminate the neural basis of mental simulation and flexible planning.

Mentor Biography: Xulu Sun graduated from Shandong University in 2013 with a bachelor’s degree in biology. As an undergraduate research assistant, she studied the molecular basis of synaptic trafficking and aging in mice hippocampus and cortex. For her Ph.D. work, Xulu joined Krishna Shenoy’s lab at Stanford University and investigated the neural dynamics underlying dexterous movement control and motor learning. There, she used behavioral tasks, large-scale neural recordings and computational models to show how the cortical motor system implements a behavior-organizing map in rhesus macaques. In Loren Frank’s lab at the University of California, San Francisco, she currently aims to explore the anatomical underpinnings, mechanistic control and functional significance of hippocampal future representations. Her project is funded by the Jane Coffin Childs fellowship and Howard Hughes Medical Institute.

Mentor Name: Erin Kunz
Mentor Role: Graduate Student
Principal Investigator: Jaimie Henderson
Institution: Stanford University
Location: Stanford, CA
Lab Website: nptl.stanford.edu

Project Title: Personalizing intracortical speech brain-computer interfaces

Project Description: Many neurological injuries and diseases, such as brainstem stroke and Amyotrophic Lateral Sclerosis (ALS), result in severe speech impairment or loss that drastically reduces quality of life. Recent progress in brain-computer interfaces (BCI) has allowed these individuals to communicate using a brain-to-text framework. Specifically, a neural network and language model is trained to decode neural signals of attempted speech into text of words and sentences in real-time. However, different users may have different preferences when it comes to their speech neuroprosthesis. In this project, we will brainstorm certain features to make the speech neuroprostheses more personalized to an individual user. Potential projects could involve incorporating the decoding of prosodic features into the decoder audio output, analyzing human neural data to understand the neural basis underlying various characteristics of speech, or analyzing error trends and incorporating linguistic or behavioral strategies to improve decoding accuracy. This project will be very interdisciplinary and may involve developing skills in systems and computational neuroscience, machine learning, software engineering or linguistics. The exact scope of the project will be catered to the fellow’s learning goals, experience and skill level.

Mentor Biography: Erin Kunz is currently an electrical engineering doctoral candidate in the Stanford Neural Prosthetics Translational Lab (NPTL) with Jaimie Henderson and Shaul Druckmann. Her research focuses on developing high-performance speech neuroprosthesis and understanding the neural representation and flow of speech and language in classically-defined ‘language‘ areas of the brain. Kunz received her bachelor’s degree in mechanical engineering, with a minor in electrical engineering and computer science from UC, Berkeley and a master’s degree in electrical engineering at Stanford. Prior to joining NPTL, part of the BrainGate consortium, she worked as a software engineer in autonomous vehicle development at General Motors. Kunz is a recipient of the Ketterer-Vorwald Neurosciences Interdisciplinary Graduate Fellowship and an Honorable Mention awardee for the 2021 Ford Foundation Fellowship. She has also been on the project team winning the first place BCI Award in 2023 and second place BCI Award in 2022 for work in the development of high-performance speech neuroprosthesis.

Mentor Name: Christopher Miranda
Mentor Role: Postdoctoral fellow
Principal Investigator: Mark Schnitzer
Institution: Stanford University
Location: Stanford, CA
Lab Website: pyramidal.stanford.edu

Project Title: High-speed voltage imaging of neural activity in behaving mice

Project Description: I plan to build the next-generation mini microscope for high-speed voltage imaging of neural action potentials in cell populations of two distinct neuron types concurrently in the brains of freely-behaving mice.

Mentor Biography: My graduate work in biomedical engineering chiefly focused on the development, characterization and application of new imaging technologies for biomedicine mainly based on the photoacoustic effect (ultrasound generation through optical absorption). To pursue my goal of transitioning from a biomedical engineer to a neuroengineer, I joined the Schnitzer lab at Stanford, one of the premier research labs for training neuroengineers that make a tangible impact in neuroscience, as a postdoctoral scholar.

Mentor Name: Omar Jaidar
Mentor Role: Research Scientist
Principal Investigator: Mark Schnitzer
Institution: Stanford University
Location: Stanford, CA
Lab Website: pyramidal.stanford.edu

Project Title: Imaging of motor cortical and striatal neural activity underlying motor learning

Project Description: I am using advanced imaging techniques to track large-scale neural activity patterns that underlie motor learning in mice.

Mentor Biography: I earned my doctorate in biomedical science at the National Autonomous University of Mexico. My subsequent research in neuroscience as a postdoctoral scholar and research scientist was conducted in Japan and, recently, Stanford University.

Mentor Name: Yen-Wen Chen
Mentor Role: Postdoctoral Associate Postdoctoral Fellow
Principal Investigator: Gabriela Rosenblau
Institution: George Washington University
Location: Washington, D.C.
Lab Website: dsnlab.org

Project Title: The role of knowledge structures in social learning—from a computational, neural and psychiatric perspective

Project Description: The proposed project for the SURFiN fellow will be embedded in an international collaborative project between two labs: our lab in Washington, D.C. and Christoph Korn’s lab in Heidelberg, Germany. The overall aim of the larger project is to specify cognitive models of social learning across two psychiatric conditions with core social difficulties: autism and Borderline Personality Disorder (BPD). Under the mentorship of Yen-Wen Chen, the postdoctoral associate overseeing this broader project, and additional supervision of Gabriela Rosenblau, the principal investigator for both the hosting lab and project, the fellow will receive training in collecting in-person behavioral and functional magnetic resonance imaging (fMRI) data. The data collection will focus on social learning in young adults with autism and in a non-autistic comparison. Furthermore, the fellow will gain experience in conducting state-of-the-art neuroimaging analyses using both standardized processing pipelines and novel techniques. The fellow will also be exposed to the broader collaborative aspect of the project and be able to attend international workshops and meetings.

The fellow’s specific project will explore individual differences in rigidity and how they relate to social learning among autistic and non-autistic individuals. For this purpose, they will be able to leverage self-report measures of rigidity, personality structure and preferences collected in over 3,000 individuals. Using this rich data set will expose the fellow to efficient ‘big data’ computational tools and statistical models. Overall, the fellow will acquire technical skills through hands-on training in programming and statistical analysis with Python, MATLAB and R and have the opportunity to present their findings at both an organized student conference at George Washington University (GW) and an international conference.

Mentor Biography: Yen-Wen Chen received her doctorate in integrative neuroscience at Stony Brook University in 2023. Her doctoral work under the mentorship of Turhan Canli investigated the role of loneliness and personality structure in aging by comparing younger and older adults using MRI-based neuroimaging techniques. Her dissertation leveraged the Lifespan Human Connectome Project Aging dataset and graph theory to identify brain connectivity networks associated with loneliness and age. Yen-Wen has recently joined the Developmental Social Neuroscience Lab at GW to lead the above-mentioned project. She is interested in identifying phenotypes and biomarkers in developing brains among typically developing individuals and individuals with neurodevelopmental conditions and integrating behavioral, neuroimaging, and computational modeling approaches. With a solid background in experimental design and data analysis using Python and R, along with experiences in various neuroimaging data pipelines, she also possesses expertise in handling large datasets on High-Performance Computing clusters.

Mentor Name: Yumeng Xie
Mentor Role: Postdoctoral Fellow
Principal Investigator: Tingting Wang
Institution: George Washington University
Location: Washington, D.C.
Lab Website: https://www.wangtingtinglab.org/

Project Title: Elucidating the Signaling Networks Underpinning Homeostatic Synaptic Plasticity

Project Description: Numerous autism-associated genes are involved in epigenetic regulation and synaptic function. Our electrophysiology-based genetic screening in Drosophila has revealed the crucial role of epigenetic regulation genes in synaptic homeostatic plasticity. While epigenetic mechanisms are known to be essential for neural differentiation and learning and memory, their specific effects on brain function across different cell types remain largely unexplored. Preliminary findings from our electrophysiological and computational analyses have pinpointed potential signaling molecules that may act downstream of these epigenetic regulators in modulating homeostatic plasticity. In this project, we aim to dissect the signaling network governed by these epigenetic regulators, utilizing transcriptomic approaches and quantitative real-time PCR to examine their roles in synaptic homeostatic plasticity across various cell types in Drosophila. Furthermore, we will thoroughly investigate the expression patterns of these epigenetic regulators and their target genes during brain development within the mouse brain. This research will enhance our understanding of the mechanisms by which epigenetic regulators affect synaptic homeostatic plasticity during brain development, potentially uncovering new therapeutic avenues for neurodevelopmental conditions.

Mentor Biography: Yumeng Xie is a postdoctoral fellow in Tingting Wang’s laboratory at Georgetown University’s Department of Pharmacology and Physiology. Her academic journey began with an M.D.-Ph.D. from Wuhan University, where she focused on the molecular underpinnings of depression using mouse models to explore potential treatments for severe depression. This work ignited her passion for understanding the molecular and cellular bases of neurodevelopmental and psychiatric disorders, leading her to delve deeper into neuroscience with a particular focus on synaptic plasticity. Currently, Yumeng is part of the Wang lab, which employs Drosophila and rodent models to study the molecular and cellular mechanisms of homeostatic signaling in health and disease. The lab has pinpointed several critical genes involved in epigenetic regulation, necessary for homeostatic synaptic plasticity. These genes are associated with increased likelihood of epilepsy, intellectual disability and autism. Yumeng’s current research focuses on understanding the expression profiles and the transcriptomic networks regulated by these homeostatic genes. Her goal is to uncover their roles in neurological conditions, potentially leading to therapeutic strategies.

Mentor Name: Adhikansh Jain
Mentor Role: Graduate Student
Principal Investigator: Julia Dallman
Institution: University of Miami
Location: Coral Gables, FL
Lab Website: https://dallmanlab.weebly.com

Project Title: Gut as gatekeeper? Testing the role of serotonin in a zebrafish model of Phelan-McDermid Syndrome

Project Description: The aim of the study is to unravel the intricacies surrounding serotonin and its role in Phelan-McDermid syndrome (PMS), a form of autism linked to mutations in the SHANK3 gene. PMS is characterized by traits such as severe constipation, social interaction difficulties and repetitive behaviors, affecting both the gut and the brain in humans. We have shown that these traits are mirrored in zebrafish SHANK3 models. Serotonin acts as a neurotransmitter with diverse functions including gut motility, synaptic activity, mood regulation and social behaviors. Previous data has shown variations in serotonin levels in zebrafish wild type and SHANK3ab-mutated guts. Using anti-5HT staining, we will test the hypothesis that altered absorption of tryptophan, an essential amino acid and serotonin precursor, results in reduced levels of serotonin in SHANK3 mutant brains. In parallel, we will use bulk RNA sequencing to pinpoint affected serotonergic pathway components in both the gut and the brain. By scrutinizing RNA transcripts, specific genes causing serotonin variations can be identified and can discern if lower serotonin stems from gene inactivity or reduced expression. Subsequent investigations will probe these genes further to determine if they are inactive, diminished or undergoing differentiation. This research promises valuable insights into the interplay of serotonin, SHANK3ab and PMS in zebrafish to provide a foundation for understanding serotonin’s role in SHANK3 mutant phenotypes. Ultimately, this knowledge may pave the way for exploring serotonin administration as a means to alleviate PMS-linked traits.

Mentor Biography: Adhikansh Jain, a first-year graduate student at the University of Miami, completed his bachelor’s degree at the University of California, Davis. Starting his research journey in the Calisi lab, he explored the impact of hormones on pigeon biology and gained hands-on skills in DNA extraction and PCR. As an academic tutor at UC Davis, Adhikansh fostered inclusivity and refined his teaching abilities. Over the past two years, his contributions to research at the Wildlife Institute of India included significant work in leopard genomics and field skills, such as camera trapping and scat extraction. Collaborating with a doctoral scholar in bioacoustics, Adhikansh captured and studied Oriental Magpie Robins by analyzing vocalizations and constructing nest boxes. Additionally, his experience in the private sector involved working with companies such as Sphaerapharma and Color Genomics, providing real-world exposure to cancer research, cell culture, RNA extractions and testing for SARS-CoV-2. Since beginning graduate school at the University of Miami, along with research, Adhikansh has taken on a teaching role, instructing undergraduates in a general biology lab with approximately 25 students per class. In this capacity, he guides students in learning and practicing experimental design and laboratory skills. These diverse experiences collectively have given him the tools required to have an interdisciplinary approach in his academic career, and he hopes to be able to impart this insight onto future scientists, as well.

Mentor Name: Millie Rogers
Mentor Role: Graduate Student
Principal Investigator: Julia Dallman
Institution: University of Miami
Location: Coral Gables, FL
Lab Website: https://dallmanlab.weebly.com

Project Title: Zebrafish models of inherited human conditions

Project Description: This project will use CRISPR/CAS9 to attempt to uncover the genetic mechanisms underlying candidate genes for human disease phenotypes. Mutations are induced at a targeted gene locus, using designer IDT sgRNA, and the resulting phenotype is closely observed. Our lab uses zebrafish as our model organism, optimizing their fully sequenced genome, high fecundity, and transparency during larval development. Undergraduates accepted into our lab will learn a variety of practical lab skills including confocal microscopy, microinjection, genotyping and immunohistochemistry. Undergraduates will also be trained in working with zebrafish under IACUC protocols. No prior laboratory experience is needed, only a strong work ethic and a desire to learn!

Mentor Biography: Millie is a third-year graduate student at the University of Miami. She received her bachelor’s degree from the University of Florida, where she studied the genetics underlying cochlear detoxification in the mammalian inner ear. She continues her research in genetics at University of Miami, where she is currently investigating the role of candidate genes of influence in altered neurodevelopment. Since beginning graduate school, she has been teaching general biology labs to about thirty students per class. She is also the very proud mentor of two SURFiN fellows in her lab, from whom she learns as much as she teaches.

Mentor Name: Samuel Nason-Tomaszewski
Mentor Role: Postdoctoral Fellow
Principal Investigator: Chethan Pandarinath
Institution: Emory University
Location: Atlanta, GA
Lab Website: http://snel.ai

Project Title: Development of virtual tasks for a dexterous finger intracortical brain-computer interface

Project Description: People with paralysis have no avenues through which they can regain able-bodied function of their hands and fingers despite the circuits in the brain controlling movement often remaining intact. This project focuses on developing brain-computer interfaces to investigate how the brain generates dexterous hand and finger behaviors and restore such function to people with paralysis in a clinical trial. To do so, we implant sensors into the motor cortex (the part of the brain that controls movement) of a person with paralysis. Then, we use artificial neural networks to study how biological neuron populations generate behavior and use them to predict the movements a person is trying to make in real-time to control a variety of games. The SURFiN fellow joining our team will assist with developing the games and machine learning algorithms. This project is ideal training for someone interested in real-time brain-computer interfaces and cutting-edge machine learning.

Mentor Biography: Sam Nason-Tomaszewski is a postdoctoral fellow in the Systems Neural Engineering Lab advised by Chethan Pandarinath. His current research focuses on developing real-time brain-computer interfaces to recreate hand function in people with upper extremity paralysis. Specifically, he is using deep neural networks that predict high-fidelity arm, hand and finger movements in virtual environments using signals recorded by sensors implanted into the brain. Sam received his doctorate in biomedical engineering from Cindy Chestek’s lab at the University of Michigan where he investigated brain-controlled restoration of dexterous finger function in monkeys using functional electrical stimulation. He received the College of Engineering’s Towner Prize for Outstanding Ph.D. Research for his dissertation work.

Mentor Name: Anna Pritchard
Mentor Role: Graduate Student
Principal Investigator: Chethan Pandarinath
Institution: Emory University
Location: Atlanta, GA
Lab Website: http://snel.ai

Project Title: Development of virtual tasks for a discretely-controlled upper-limb iBCI

Project Description: In the US, about 180,000 people experience tetraplegia from spinal cord injury, in addition to cases resulting from Amyotrophic Lateral Sclerosis (ALS), stroke and other neurological injury or disease. Recovery of upper-limb and hand function is a top priority for people with tetraplegia. Intracortical brain-computer interfaces (iBCIs) have emerged as a method to decode motor intent from the brain to control prostheses like robotic arms. Electrodes are implanted in a participant’s cortex to collect neural data which are processed to infer a control signal for the effector (e.g., hand/arm kinematics). Functionality of these iBCI systems is assessed by reach-and-grasp clinical assessments or tasks, like feeding and drinking. The goal of this project is to develop a discretely-controlled virtual upper-limb iBCI for a participant with tetraplegia and test it with functionality and usability metrics. The hand will be the MuJoCo HAPTIX MPL, and the real-time iBCI system is mostly Python based. The SURFiN fellow will contribute to the development of virtual reach-and-grasp assessments and games, the analysis of intracortical neural data, and the development of our real-time upper-limb iBCI system. Relevant areas of interest include game/graphics development, machine learning, signal processing and neural data analysis.

Mentor Biography: Anna is a doctoral student in the Systems Neural Engineering Lab at Emory. She is part of the iBCI research team, conducting research as part of the BrainGate 2 clinical trial. Her current focus involves understanding how the brain controls upper-limb movements so that upper-limb functionality can be restored in people with tetraplegia. She is working to develop a discretely-controlled reach-and-grasp iBCI system that is more functional and user-friendly than current approaches. Anna’s undergraduate and master’s work was also in biomedical engineering, with a focus on signal processing and image analysis, developing analysis pipelines for understanding how spinal circuits change post-injury. Anna is a fellow of the National Institutes of Health Computational Neuroengineering Training Program at Georgia Tech/Emory and the National Science Foundation Graduate Research Fellowships Program. She has mentorship and teaching experience from teaching Senior Capstone at Georgia Tech and Texas A&M, mentoring undergraduate students, and STEM outreach programs.

Mentor Name: Mattia Rigotti
Mentor Role: Graduate Student
Principal Investigator: Chethan Pandarinath
Institution: Emory University
Location: Atlanta, GA
Lab Website: http://snel.ai

Project Title: Development of graphical tasks and user interfaces for characterization and practical use of intracortical brain-computer interfaces

Project Description: Intracortical brain-computer interfaces (iBCIs) are a promising avenue for allowing individuals with tetraplegia to regain movement capabilities through control of assistive devices, such as computer cursors or robotic arms. Despite significant advances over the years, iBCI control performance still falls short compared to that of able-bodied behavior. This project aims to gain a better understanding of how parameters of intended movement are encoded by neural activity recorded from the human motor cortex in order to inform the design of new iBCI control strategies. The SURFiN fellow joining our team will help pursue this goal through the design and coding of graphical motor tasks (e.g., controlling a cursor on the screen or through a virtual, 3D space) that will be performed by participants in an iBCI clinical trial. They will also aid in the analysis of intracortical neural data recorded during clinical sessions. Additionally, they may contribute to the development of user interfaces to assist participants in the practical use of brain-computer interfaces. Relevant areas of interest include brain-computer interfaces, game/graphics development and neural data analysis.

Mentor Biography: Mattia is a biomedical engineering doctoral student in the Systems Neural Engineering Lab at Emory and Georgia Tech, advised by Chethan Pandarinath. His research is part of the BrainGate 2 clinical trial and focuses on characterizing how neural activity within the human brain encodes intended movements with the goal of improving practical use of brain-computer interfaces to restore motor capabilities to people with upper-limb paralysis. Prior to starting his Ph.D., Mattia received master’s and bachelor’s degrees in electrical engineering at Pontificia Universidad Católica de Chile, where he worked on developing control strategies and hardware for robotic applications. Additionally, he worked on implementing control algorithms for commercial and research functional electrical stimulation (FES) devices for gait rehabilitation. Mattia is currently a J. William Fulbright Foreign Scholar and has received academic distinctions from institutions, including Pontificia Universidad Católica de Chile and the Institute of engineers of Chile.

Mentor Name: Mathew Rynes
Mentor Role: Postdoctoral Researcher
Principal Investigator: Lucas Pinto
Institution: Northwestern University
Location: Chicago, IL
Lab Website: https://www.pintolab.org

Project Title: Investigating cortex-wide dynamics underlying decision making using patterned optogenetics

Project Description: In neuroscience, understanding how the brain orchestrates decision-making processes remains a challenge. This project delves into cognitive functions in mice by employing a novel approach to spatially pattern light for optogenetics. Our objective is to unravel cortex-wide neural activity that influences cognitive processes during behavioral tasks.

As a participant in the SURFiN fellowship, your primary responsibility will involve conducting experimental trials with mice, leveraging a behavioral task tailored to unravel cognitive computations during decision-making junctures in a virtual reality environment.

Additionally, your role extends to the enhancement of our research methodologies. One focus will be the refinement of our software’s graphical user interface (GUI), aiming to democratize our technique within the neuroscience research community.

Your participation also encompasses a range of laboratory duties that are integral to the operation of a neuroscience research environment. These responsibilities provide a holistic view of laboratory dynamics in neuroscience research.

This project is tailored to accommodate undergraduates from diverse academic backgrounds, offering a stimulating yet accessible research experience. You will acquire practical skills in optogenetics, behavioral analysis, software development and general laboratory management, fostering a versatile skill set crucial in scientific research.

Mentor Biography: Mathew Rynes is a postdoctoral fellow at Northwestern University Feinberg School of Medicine. Before working at Northwestern University, he obtained a doctorate in biomedical engineering and a bachelor’s in neuroscience and biochemistry from the University of Minnesota. His research interests focus on developing techniques for neuroscience and uncovering brain-wide neural correlates of decision making and related cognitive processes. In his current research, he is developing a method for patterned illumination of the cortex for spatially patterned optogenetics in behaving mice aimed at investigating such brain-wide activity during decision making tasks.

Mentor Name: Renan Costa
Mentor Role: Postdoctoral Researcher
Principal Investigator: Lucas Pinto
Institution: Northwestern University
Location: Chicago, IL
Lab Website: https://www.pintolab.org

Project Title: Computation timescales as an organizing principle of large-scale cortical dynamics during decision making

Project Description: To generate cognitive behaviors, the brain needs to integrate information over multiple timescales. For example, reading a sign on a rainy evening requires integrating noisy visual information over the timescale of a few seconds, whereas deciding whether to make a turn requires combining that information with memories and plans that happened in the timescale of hours. Despite its ubiquity, our understanding of how neuronal circuits implement computations on flexible timescales remains very limited. We will tackle this open question by leveraging a virtual reality task for mice that dissociates computation identity and computation timescale. The task requires animals to accumulate visual evidence, retain that evidence in memory, and later use it to make a decision. The SURFiN fellow can expect opportunities to learn how to use widefield imaging to monitor neuronal activity in behaving animals, develop behavioral paradigms to probe cognition in virtual reality, use computational tools to analyze behavioral and neuronal data, perform surgery to enable optical access to the brain, and perform general wet lab techniques (e.g., immunohistochemistry).

Mentor Biography: Renan M. Costa is a postdoctoral fellow in the Department of Neuroscience at Northwestern University. After obtaining an undergraduate degree in psychology at Universidade Federal do Paraná, Brazil, he moved to the U.S. to pursue a doctorate in neuroscience at the University of Texas Health Science Center at Houston (UTHealth). In Houston, he studied the neuronal population mechanisms underlying simple forms of learning. His current research aims at understanding how neurons across the cerebral cortex implement different cognitive computations, such as short-term memory, evidence accumulation and decision making. Ultimately, he hopes to uncover how complex nervous systems execute complex computations and how they learn to perform these computations. His graduate studies were supported by a Science Without Borders Fellowship (CNPq, Brazil) and a Larry Deaven Ph.D. Fellowship in Biomedical Sciences (UTHealth). His graduate research resulted in three first-author manuscripts and contributions to two other research papers. Moreover, he is a two-time recipient of the Dee S. and Patricia Osborne Endowed Scholarship, which acknowledges exceptional neuroscience research at UTHealth.

Mentor Name: Cheng Xue
Mentor Role: Staff Scientist
Principal Investigator: Marlene Cohen
Institution: University of Chicago
Location: Chicago, IL
Lab Website: http://www.cohenlab.com

Project Title: The ‘monkey home office’ to study flexible decision making

Project Description: How do we make choices? When do we make bad choices, and why? The Cohen lab studies perceptual decision making and its underlying neuronal basis. We will build a ‘game room’ for our experimental animals to interact with a touch screen and get treats for doing it, all at the ease of their home enclosure in our facility. We will record their behavior when they voluntarily engage with our decision-making game. The animal’s choices will be used to train artificial neural network models, which will tell us how these choices might be computed in the brain. We will also investigate the changes in the animal’s behavior under different states (e.g., drug use, menstrual cycles of females and neurodegenerative diseases) that will lead to important hypotheses about the neuronal changes that occur during these processes. The prospective student will help design and build the experiment system, collect and analyze data, use computational modeling to generate hypotheses about neuronal basis of this behavior, and work in tandem with ongoing, rig-based electrophysiology projects to test model predictions.

Mentor Biography: Cheng Xue is currently a staff scientist in Marlene Cohen’s lab in the Department of Neurobiology, University of Chicago. Cheng received his bachelor’s and master’s degree in physics at Nanjing University in China. He subsequently carried out his doctoral work at the German Primate Center before joining Marlene’s lab as a postdoctoral researcher. Cheng is interested in flexible decision-making behavior in the natural environment that are full of changes. He uses multi-faceted approaches, including behaving monkey electrophysiology, computational modeling, and human psychophysics to study decisions in various aspects. Through these research experiences, Cheng developed a keen interest in the pattern of mistakes in decision making across species. He believes that these patterns have a common biological basis and, therefore, can potentially become a window to reveal the neuronal mechanism for decision-making and cognitive flexibility or their malfunction. He is convinced that research in this direction will inspire new treatment for various neurological disorders, as well as better decision-making strategies for healthy individuals.

Mentor Name: Jaekyoon Kim
Mentor Role: Research Scientist
Principal Investigator: Edwin Abel
Institution: University of Iowa
Location: Iowa City, IA
Lab Website: https://tedabel.lab.uiowa.edu

Project Title: The role of striatal circuits on repetitive and stereotyped behaviors in 16p11.2 deletion mouse model

Project Description: The 16p11.2 hemi-deletion (16p11.2 del) is one of the most common genetic changes associated with autism. Because the human 16p11.2 region is highly conserved in mice, we can model and study this genetic risk factor in mice. Using this mouse model, we previously reported alterations in the structure and function of striatal circuits, which is consistent with recent studies reporting changes in striatal structure and function in study participants with autism. The striatum is the input structure of the basal ganglia, the key neural substrate for reward processing and motor control and these functions are often disrupted in individuals with autism. In this project, we will investigate how the genetic lesions lead to changes in molecular, cellular and circuit mechanisms that underlie repetitive and stereotyped behaviors in 16p11.2 del mice, applying a combination of genetically-modified mouse models and targeted intra-striatal virus injections with video tracking and fiber-photometry techniques. These findings will identify neuronal mechanisms specific to the striatal dysfunction in autism. We hope that our research will help to develop novel therapeutic approaches for autism.

Mentor Biography Jaekyoon Kim is a postdoctoral research scholar in the Department of Neuroscience and Pharmacology at Carver College of Medicine, Iowa Neuroscience Institute, University of Iowa. Jaekyoon received his bachelor’s in biochemistry from Yonsei University and his master’s in biotechnology from Seoul National University. Then he received a doctorate in psychology along another master’s at the University of Wisconsin, Milwaukee, working with Karyn Frick, widely considered a world expert on the effects of estrogens on the brain and cognition. This background has given him the important ability to assess neuroscience from both a biomedical science perspective and a psychology perspective. Throughout his Ph.D., his work focused on the effects of sex steroid hormones, especially estrogen, on memory consolidation and he has become interested in sex differences in neurological conditions. Autism is a neurodevelopment condition with sex differences. One of the most common genetic variations associated with autism is the deletion of the 16p11.2 chromosomal region, which can be faithfully modeled in mice. Using the 16p11.2 hemi-deletion mouse model, the Abel lab revealed male-specific impairments in the acquisition of reward-dependent goal-directed behaviors. Therefore, as a research scientist, Jaekyoon is working on elucidating the underlying mechanisms driving behavioral alterations in the 16p11.2 hemi-deletion mice.

Eligibility: Students not currently enrolled at the University of Iowa must enroll in the university for a minimum of one semester hour in order to receive funds through this program.

Mentor Name: Mollie Meffert
Mentor Role: Associate Professor
Principal Investigator: Mollie Meffert
Institution: Johns Hopkins University
Location: Baltimore, MD
Lab Website: https://neuroscience.jhu.edu/research/faculty/58

Project Title: Noncoding RNA dysregulation in Fragile X Syndrome

Project Description: The Meffert laboratory is interested in how gene programs are recruited and maintained to make long-lasting changes in the nervous system during development, experience-dependent plasticity (like learning and memories), and in injury or disease. The nervous system is a particularly interesting place to study gene expression because of the striking need for spatial as well as temporal control of gene expression to create and maintain accurate functional change at distinct sites of synaptic connection between neurons. While there is one site, the nucleus, for transcriptional control, post-transcriptional control of gene expression can take place in the cytoplasm and offers a mechanism for rapid differential gene expression across the complex space of the neuron with its thousands of synaptic connections. One major focus of our lab is to understand how gene expression is controlled at the RNA level and how misregulation of these processes contributes to complex conditions of the nervous system such as autism. Recently, we published our findings that a family of small RNAs, called ‘microRNAs,’ contributes to aberrant growth and behavioral phenotypes in a mouse model of Fragile X Syndrome which is the largest monogenic cause of autism. We now have exciting evidence that these microRNAs may be impacting the function of the mitochondria which fuels the intensive energy requirements of neurons. A project in our lab would investigate aspects of this project, working with myself and with other graduate students in the lab.

Mentor Biography: Mollie Meffert is an Associate Professor at the Johns Hopkins University School of Medicine in the Departments of Biological Chemistry and Neuroscience. She is also Vice Director of the Department of Biological Chemistry. Mollie completed her M.D.-Ph.D. in Neuroscience at Stanford University followed by postdoctoral training in the laboratory of David Baltimore at Caltech prior to joining the faculty at Johns Hopkins School of Medicine. Mollie has mentored 15 graduate students to successfully obtain their Ph.D.s from her lab to date and has also mentored numerous master’s and undergraduate trainees.

Mentor Name: Rebecca Andersen
Mentor Role: Postdoctoral Researcher
Principal Investigator: Christopher Walsh
Institution: Boston Children’s Hospital
Location: Boston, MA
Lab Website: https://walshlab.org

Project Title: Genetic convergence in autism

Project Description: This project focuses on understanding how individual genes can converge on shared molecular roles to coordinate crucial processes during human brain development. In particular, we are studying genes that have been associated with autism to understand how disruptions of these genes and their shared regulatory networks can contribute to autism. To uncover the roles of these genes, we are knocking them down using CRISPR-Cas13, which can specifically degrade the RNA transcripts of target genes. For these studies, we are primarily using human neural progenitor cell (NPC) cultures derived from induced pluripotent stem cells which have the capacity to self-renew as well as produce differentiated cell types like neurons. During the course of this project, you will gain extensive hands-on experience with cell culture techniques including expanding the NPCs as they proliferate, introducing the knockdown constructs through nucleofection, and inducing the NPCs to differentiate into neurons. You will also learn how to analyze the results of these experiments through immunocytochemistry. Furthermore, you will design and create CRISPR-Cas13 knockdown constructs to target new genes of interest. Throughout your training, we will emphasize critical aspects of experimental design and approach to enhance your scientific reasoning.

Mentor Biography: Rebecca Andersen is a postdoctoral research fellow in the lab of Christopher Walsh at Boston Children’s Hospital. She received her doctorate in developmental and stem cell biology from the University of California, San Francisco in 2019. Her doctoral thesis focused on the role of a novel long non-coding RNA in regulating brain development. This project was recognized and supported by a graduate research fellowship from the National Science Foundation, a National Research Service Award (F31) from the National Institutes of Health, and a graduate scholarship from Phi Beta Kappa. In the Walsh lab, her project seeks to understand how different autism -associated genes can converge on shared molecular and developmental effects. This work has been supported by a postdoctoral fellowship from Autism Speaks. As an aspiring academic principal investigator, she is dedicated to rigorously pursuing innovative research to generate long-lasting scientific contributions. Moreover, she is committed to actively promoting diversity and inclusion in order to create an equitable scientific research community. Her long-term goal is to become an independent principal investigator with a lab focused on cerebral cortical development and associated conditions such as autism.

Mentor Name: Paolo Capelli
Mentor Role: Postdoctoral Researcher
Principal Investigator: Bernardo Sabatini
Institution: Harvard University
Location: Boston, MA
Lab Website: https://sabatini.hms.harvard.edu

Project Title: Neuronal integration at the forebrain-brainstem interface

Project Description: The basal ganglia are important for the selection of goal-directed movements: active during complex motor actions and crucial for learning motor tasks. Alternatively, the brainstem is an evolutionary ancestral brain structure, and it contains key populations of neurons essential for the execution of several distinct actions. The project is focused on understanding the integration process at the interface of basal ganglia and brainstem motor control circuits. We hypothesize that integration and comparison of multiple inputs is a central mechanism of action switching. We use a wide variety of techniques (e.g., molecular biology, viral tracing, in vitro slice physiology, optogenetics and in vivo recordings) to address and test the biological hypotheses; we often develop new tools to be more rigorous in the experimental design.

Most of the experiments are performed in mice. The SURFiN student will have the chance to learn/explore the following aspects: 1) histology techniques: antibody fluorescent stainings and microscopy (fluorescence and confocal), analysis of viral tracing data; 2) handling and training mice in an action selection/motor task; 3) data analysis, MATLAB/Python; 4) discussing results and research articles will be essential, as the goal will be to understand some interesting biological questions on top of experiencing wet laboratory techniques.

Mentor Biography: Paolo Capelli is a postdoctoral fellow in the laboratory. Paolo studied molecular biology and neuroscience at the University of Pisa, Italy. He discovered molecules and mechanisms at the basis of the retina formation (bachelor’s degree) and neural stem cells differentiation (master’s degree). Paolo was selected to join Scuola Normale, a highly selective and competitive college in which students of different disciplines share lodging and follow supplementary courses. In this context, one to one mentorship from neurobiology professors shaped his approach to science: creativity, rigor in testing hypotheses and teamwork. Paolo performed his Ph.D. in Silvia Arber’s Laboratory in Basel. He discovered neuronal populations in the caudal brainstem essential for the performance of basic forms of movements. He supervised research associates, high school students approaching science for the first time, a master’s student and two graduate students. Paolo likes challenges. He moved to Boston to study how movements are regulated by neuronal integration at the forebrain-brainstem interface. He mentored four co-ops, one of which was awarded with the Horvitz Prize for outstanding undergraduate research. Paolo is currently supervising a master’s student from the Swiss Federal Institute of Technology in Lausanne and a research associate; each of them with a key role in pushing forward the discoveries on his project.

Mentor Name: Tomasz Kula
Mentor Role: Postdoctoral Fellow
Principal Investigator: Bernardo Sabatini
Institution: Harvard University
Location: Boston, MA
Lab Website: https://sabatini.hms.harvard.edu

Project Title: High-throughput genetic screening in the mouse brain

Project Description: Biomedical research has been revolutionized over the last two decades by stunning advances in DNA sequencing technology. Scientists have now mapped the complete set of genes, around 22,000 in all, which collectively give rise to the various cell types and functions in our body. Moreover, they have identified thousands of variants across patients that increase or decrease risk of various diseases. However, translating this genetic data into actionable biological understanding has proved difficult. This is largely due to the low throughput at which genes and variants can be studied, with model organisms such as mice typically allowing the study of only one gene at a time. We have developed approaches to generate mosaic mice to interrogate the function of hundreds of genes simultaneously. We are applying these tools to uncover novel pathways in the mouse brain and to identify therapeutic targets in a variety of contexts. In this project, the SURFiN fellow will apply pooled CRISPR screening to study the function of disease-related genes in the mouse brain in high-throughput.

Mentor Biography: Tomasz Kula is a postdoctoral fellow at Harvard Medical School working in the labs of Bernardo Sabatini and Beth Stevens. He is interested in developing and applying high-throughput genetic tools to understand complex disease and to identify therapeutic targets. Tomasz received his doctorate from Harvard University in the lab of Steve Elledge, where he developed two high-throughput tools to profile the immune system: VirScan, which maps the targets of antibodies against all viruses at once, and T-Scan, which identifies the targets of CD8 T cells at proteome scale. He is a co-founder of TScan Therapeutics, a company which is applying the T-Scan platform to develop cancer therapeutics that are currently in clinical trials. His work has been supported by the National Science Foundation Graduate Research Fellowship Program and the Harvard Society of Fellows.

Mentor Name: Shun Li
Mentor Role: Graduate Student
Principal Investigator: Bernardo Sabatini
Institution: Harvard University
Location: Boston, MA
Lab Website: https://sabatini.hms.harvard.edu

Project Title: Learning-dependent sign switching at pallid-habenular synapses

Project Description: Synaptic plasticity is widely considered as a critical component for learning. While various forms of synaptic plasticity have been characterized throughout the brain, most if not all of them can be summarized as activity-dependent changes in synaptic weight (i.e., connection strength). This is in contrast with neurons in artificial neural networks, in which both the sign and weights change during training. My projects focus on a unique synapse between entopeduncular nucleus (EP) and lateral habenula (LHb) that seems to violate this rule. Unlike most other synapses in the brain, somatostatin neurons in EP co-release opposing neurotransmitter glutamate and GABA within single vesicle; therefore, it both excites and inhibits downstream LHb neurons. My preliminary evidence suggests the possibility that this synapse can become either net excitatory or inhibitory through plasticity during learning. In this project, we will further characterize such novel bi-directional synaptic plasticity and examine the underlying molecular mechanism. Therefore, SURFiN fellows can get hands on experience with using cutting-edge neuroscience techniques including but not limited to optogenetics, fiber photometry, extracellular chronic/acute Neuropixel recording, in vivo pulse-chase labeling and in vitro whole-cell electrophysiology. SURFiN fellows can also expect to deeply participate in the design and analysis of experiments.

Mentor Biography: Shun Li is currently a doctoral candidate in Bernardo Sabatini’s lab at Harvard Medical School. Shun received his bachelor’s degree from Duke University, graduating with distinction (summa cum laude) in neuroscience with minor in computer science and psychology. During his time at Duke, Shun joined Fan Wang’s lab and studied neural mechanism behind generation and coordination of orofacial behaviors, like licking and swallowing. His first author review was published in eNeuro and received the Outstanding Thesis Award in Neuroscience. After graduation, Shun joined the Program in Neuroscience at Harvard University. Currently, Shun is broadly interested in various aspects of system neuroscience with a focus on understanding how neural circuits (biological or artificial) learn and how these mechanism might be disrupted in diseases like depression. Specifically, Shun’s thesis project concerns a unique synapse in the brain that co-releases opposing neurotransmitter glutamate and GABA. This property raised a novel possibility that the excitatory/inhibitory nature of this synapse can change depending on experience, which is analogous to artificial neural networks but drastically differs from the biological ones. Shun hopes to characterize potential synaptic plasticity mechanism of this circuit through cutting-edge techniques in system neuroscience.

Mentor Name: Shijia Liu
Mentor Role: Postdoctoral Fellow
Principal Investigator: Bernardo Sabatini
Institution: Harvard University
Location: Boston, MA
Lab Website: https://sabatini.hms.harvard.edu

Project Title: Time to stop: neural mechanisms of action termination

Project Description: The ability to stop an action is a critical aspect of executive control, the deficit of which is central to neuropsychiatric conditions like Obsessive-Compulsive Disorder (OCD) and Attention-Deficit/Hyperactivity Disorder (ADHD). Animals naturally stop their ongoing actions in the appropriate context, but how stop decisions are generated and executed remains unclear. My project aims to elucidate the neural mechanisms and pathways underlying the stop decisions by studying how mice voluntarily stop licking in response to the absence of water. I designed a ‘licking-for-water’ task that allows for precise temporal dissection of the stopping process in specific contexts. I observed task-related signals in the medulla that predict upcoming stop decisions and demonstrated a significant role of a prefrontal cortical region in initiating the stopping decision. The SURFiN student will work with me to dissect the neural pathway that relays the stop information from the cortex to the medulla. The SURFiN student will perform mouse behavioral training, brain histology and analysis of neural and behavioral data under my guidance with daily discussions.

Mentor Biography: As a postdoctoral fellow in Bernardo Sabatini’s laboratory, Shijia’s research focuses on the neural underpinnings of context-dependent decision-making and the modulation of actions by internal states. Shijia obtained a doctorate at the Salk Institute with Sung Han, where she discovered neural circuits that orchestrate pain and breathing and identified potential targets to mitigate opioid overdose deaths. Her expertise lies in systems neuroscience and neural circuits dissection, through techniques like brain-wide activity monitoring, single-cell in vivo calcium imaging, optogenetics, chemogenetics, and the analysis of mouse behavior. Shijia is deeply committed to mentorship, having guided over ten students towards successful careers in graduate and medical programs. Furthermore, she is an advocate for equity, diversity and inclusion, exemplified by her co-founding of an affinity group dedicated to supporting scientists from Asian, Pacific Islander and Desi backgrounds during her time at the Salk Institute.

Mentor Name: Kevin Mastro
Mentor Role: Postdoctoral Fellow
Principal Investigator: Bernardo Sabatini
Institution: Harvard University
Location: Boston, MA
Lab Website: https://sabatini.hms.harvard.edu

Project Title: Uncovering mechanisms of cognitive decline vs. resilience

Project Description: Aging is an evitable process where changes in both brain structure and behavior are observed, and its impact on each individual can vary widely. We hypothesize that these differences in cognitive trajectory are due to changes in underlying brain structure. First, we will use a combination of neuronal recordings in freely moving animals paired to define how the brain contributes to behaviorally-relevant events. Second, we will use viral tools (e.g., optogenetics and chemogenetics) to manipulate brain activity and identify what pathways are necessary and sufficient to drive age-related changes in behavior. Mentees will acquire skills in mouse behavior, in vivo physiology, immunohistochemistry and data analysis. To achieve these goals, we will spend approximately half of our time on data collection and the other half on both data analysis and a critical review of the literature. We will work within the context of research team that includes both research assistants and other undergraduates. In doing so, we will learn how to apply cutting-edge neuroscience techniques and unravel how changes in brain structure drive changes in behavior across the lifespan.

Mentor Biography: Kevin Mastro is a postdoc jointly mentored by two Simon’s investigators, Beth Stevens and Bernardo Sabatini. Before starting his postdoc, Kevin earned a doctorate at University of Pittsburgh with Aryn Gittis. His interest in neuroscience is focused on understanding how our genes and environment contribute to cognitive changes across the lifespan. Utilizing both ex vivo electrophysiology, optogenetics and behavior, they have uncovered a prolonged period of cognitive maturation that extends across the first six months of the mouse lifespan. Specifically, the prefrontal cortex, a critical hub for cognitive function, changes dramatically across this period of time, but how the changes in prefrontal cortex contribute the behavioral changes is an active area of exploration. More recently, the lab has been able to track the same mouse across many developmental stages and have opened up a whole new area that they are excited to pursue with your help! As a mentor, Kevin would describe his mentorship style as highly collaborative where the focus will be on building a project that will both advance our understanding of cognitive aging and provide tractable means for your progress. Outside of the lab, they are an artist and ceramicist!

Mentor Name: Jason B. Alipio
Mentor Role: Postdoctoral Fellow
Principal Investigator: Amar Sahay
Institution: Massachusetts General Hospital
Location: Boston, MA
Lab Website: www.sahaylab.com

Project Title: Experience-dependent regulation of GABAergic inhibition in aging

Project Description: Hippocampal inhibitory interneurons orchestrate circuit and network activity important for memory processing and cognitive function. In Alzheimer’s disease and in the normal aging brain, memory deficits are associated with reduced inhibitory circuit functions in the hippocampus. Our lab recently demonstrated a unique form of experience-dependent structural plasticity exhibited by hippocampal parvalbumin interneurons that enables these neurons to reorganize inhibitory inputs onto pyramidal neurons to restore circuit function and cognition. We performed a gain-of-function screen to identify candidate gene regulators of this experience-dependent plasticity. Our research project involves harnessing these cell-type targeted gene regulators to restore inhibitory circuit function in aging and aging-sensitive models of Alzheimer’s disease. This project will employ inducible mouse and viral genetics, pharmaco- and optogenetics, ex vivo patch-clamp and in vivo electrophysiology, machine learning software (SLEAPai), and memory-related behavioral paradigms to test our hypotheses. Mentees will have the opportunity to acquire a conceptual framework for thinking about mechanisms of cognition in aging, build a solid foundation in circuit neuroscience, and learn new techniques to probe circuit functions in vivo.

Mentor Biography: Jason B. Alipio is currently a postdoctoral fellow in Amar Sahay’s lab at Massachusetts General Hospital, Harvard Medical School studying neural circuit mechanisms of cognitive decline in aging. Jason is a Filipino American, born and raised in California, and is a U.S. Marine Corps veteran of the Global War on Terrorism military campaign. Jason received his doctorate at the University of Maryland School of Medicine as a Meyerhoff Graduate Fellow, Graduate Program in Life Sciences Thesis awardee and received the National Research Service Award from the National Institute on Drug Abuse . His doctoral publications advanced our understanding of how opioids reshape somatosensory cortical circuit functions across the lifespan and led to creation of University of Maryland School of Medicine Center for Substance Use in Pregnancy. His postdoctoral studies, funded in part by a National Institute on Aging diversity supplement, integrate molecular, electrophysiological (ex vivo and in vivo) and behavioral approaches to understand how enhancing inhibitory circuit functions in aging reverses cognitive impairments. Jason has been involved in training and mentoring programs since the beginning of his academic journey and takes pride in mentoring trainees to achieve their own career goals.

Mentor Name: Anne Billot
Mentor Role: Postdoctoral Fellow
Principal Investigator: Randy Buckner
Institution: Harvard University
Location: Cambridge, MA
Lab Website: https://bucknerlab.fas.harvard.edu

Project Title: Precision brain circuit modulation in people with major depressive disorder

Project Description: Transcranial Magnetic Stimulation (TMS) is an established therapy for treatment resistant Major Depressive Disorder. Recently, FDA-approved TMS protocols using personalized targets derived from functional connectivity measures have shown improved clinical efficacy. However, the degree to which TMS engages canonical large-scale networks, as defined through precision estimates of network organization in the individual, remains unclear. This project aims to understand and enhance TMS precision by integrating within-individual network estimates to modulate specific brain networks related to distinct behavioral domains and symptoms. In this study, we will recruit both healthy individuals and individuals with treatment-resistant depression to undergo network-specific stimulation, followed by functional MRI (fMRI) and behavioral measures, to evaluate the neural and behavioral effects of targeted neuromodulation. The prospective student will learn about personalized TMS, brain network organization, and have hands-on experience collecting and analyzing fMRI and behavioral data.

Mentor Biography: Before working at Harvard University and the Massachusetts General Hospital, Anne Billot received a bachelor’s and a master’s degrees in speech and language pathology from the Sorbonne University, France and a doctorate in behavioral neuroscience from Boston University. Her work in the Buckner Lab focuses on characterizing the functional and behavioral consequences of precision circuit modulation in patients with depression. She is particularly interested in understanding neuroplasticity mechanisms in clinical populations with neurological or psychiatric disorders and developing personalized treatments for these individuals.

Mentor Name: Sara Matias
Mentor Role: Postdoctoral Fellow
Principal Investigator: Naoshige Uchida
Institution: Harvard University
Location: Cambridge, MA
Lab Website: https://projects.iq.harvard.edu/uchidalab/home

Project Title: Distributional value coding in the brain

Project Description: Recent studies in our laboratory have suggested that the brain implements a new reinforcement learning (RL) algorithm called distributional RL (Dabney et al., 2020; Lowet et al. 2024). While traditional RL algorithms learn the average future rewards, distributional RL learns the entire distribution of rewards. In this project, we have performed Neuropixels recording from dopamine neurons projecting to different regions of the striatum as well as multi-fiber photometry of dopamine signals using 14 fibers covering wide regions in the striatum. We have included various behavioral paradigms to probe how encoding properties of dopamine neurons differ, such as odor-reward association tasks with different reward distributions, delay discounting, novel object exploration and threat learning. The student will learn how to perform analyses on the neural data obtained in these experiments, fit computational models, including RL models, and analyze the behavior and dopamine data to test whether dopamine signals across striatal regions differ systematically in their coding properties. If the time allows, the student will further perform multi-fiber photometry experiments during behavior to further test specific hypotheses derived by earlier analyses.

Mentor Biography: Sara Matias is a postdoctoral fellow with Naoshige Uchida studying the functional organization of the basal ganglia-dopamine circuits in mice. In particular, she studies how specific algorithms for reinforcement learning (RL), such as distributional RL are implemented in the brain. Sara majored in biomedical engineering in Instituto Superior Técnico (IST) in Portugal. She received her graduate training in Zachary F. Mainen’s lab in Champalimaud Neuroscience Programme, Portugal, where she was involved in the development of fiber photometry techniques and studied the role of serotonin in learning and behavior. In the Uchida lab, taking advantage of her strong background in engineering, Sara has implemented new techniques for the lab, including GRIN lens-based two-photon calcium imaging from dopamine neurons as well as multi-fiber photometry using 14 fibers. She has also mastered Neuropixels recording of dopamine neurons with optogenetic identification from their projection sites.

Mentor Name: Lyle Kingsbury
Mentor Role: Postdoctoral Fellow
Principal Investigator: Naoshige Uchida
Institution: Harvard University
Location: Cambridge, MA
Lab Website: https://projects.iq.harvard.edu/uchidalab/home

Project Title: Neuronal mechanisms of decision-making in foraging mice

Project Description: Most animals must learn from their environment how to make efficient choices about where, when and how to gather resources, such as food and water, to secure their survival. We can use this foraging context as a natural window into the neurobiological processes in the brain that instantiate flexible cognition and decision making. In this project, the student will expand upon ongoing work in the lab to characterize how mice learn about rewards in complex environments, how they make economic decisions, and how they develop strategies to forage effectively in different environments. The student will run experiments and analyze behavioral data to gain insight into how animals make decisions. Building on this foundation, we will then incorporate state-of-the-art circuit manipulation tools, such as optogenetics, to interrogate the functional role of different neural circuits in reward learning and decision making. Through this research experience, the student will learn basic wet lab skills, how to work with laboratory mice, how to rigorously analyze neuroscience data, and how to carefully design behavior experiments for neuroscience research.

Mentor Biography: Lyle Kingsbury is a postdoctoral fellow with Naoshige Uchida studying the biology of cognition in the brain. How do neural circuits process information from the world and perform computations that enable flexible cognition and decision making? To address this, he records neural activity from the brains of mice while they make economic decisions to forage for resources. He uses a variety of neural recording and manipulation tools, such as electrophysiology and optogenetics, to dissect the computational functions of neural circuitry.

Before coming to Harvard, Lyle completed a doctorate in neuroscience at UCLA, where he worked with Weizhe Hong on the neural mechanisms of social behavior. There, he studied how neurons in the frontal cortex represent social information and shape behavior, as well as how neural activity across individuals becomes synchronized during social interaction. As an undergraduate at Hunter College (CUNY), Lyle studied biology and bioinformatics and worked on research with Carmen Melendez on cell signaling pathways in brain glial cells.

In addition to neuroscience expertise, Lyle has extensive mentoring and teaching experience. He has taught in several undergraduate and graduate neuroscience courses at UCLA, and has mentored eight students, including one high school student, four undergraduates, and three doctoral students.

Mentor Name: Kevin Charland
Mentor Role: Graduate Student
Principal Investigator: Catherine Kaczorowski
Institution: University of Michigan
Location: Ann Arbor, MI
Lab Website: https://kaczorowski.lab.medicine.umich.edu

Project Title: Generation of mouse and human tri-cultures to test genes influencing the observed sex differences in pathology

Project Description: I will be generating in vitro tri-cultures with neurons, astrocytes and microglia derived from both genetically-diverse mouse embryonic stem cells (mESCs) and human-induced pluripotent stem cells (hiPSCs) isolated from Alzheimer’s disease (AD) patients. Male and female mESCs will be utilized to investigate the influence of sex on various outcomes. hiPSCs will also be used to make organoids to model AD pathology in a 3D system. Cultures will be treated with beta amyloid 1-42 (Aβ42) and used to probe the influences of candidate genes that modify sex-specific differences in Aβ42 pathology. Cellular phenotypes of interest include inflammation, protein homeostasis, cellular senescence, mitochondrial functioning, cellular energetics (NAD+/NADH) and lysosomal functioning. Techniques used in this project will include various molecular assays, viral transfections, live cell imaging, immunocytochemical staining, neuronal functioning, gene expression, protein expression, computational biology, developing/optimizing derivation protocols from stem cells and general cell culturing practices. The ultimate goal of the project is to refine candidate genes identified from analyzing cortical Aβ42 abundance in AD-BXD mice and investigate the mechanisms through which they modify cellular response to Aβ42 pathology in a sex-specific and genetic background-dependent manner.

Qianying Wu Biography: Kevin Charland is a second-year predoctoral candidate in the neuroscience program at Tufts University. He received a bachelor’s degree in integrative neuroscience from SUNY Binghamton then a master’s degree in neuroscience from University of Hartford. While he started in the Tufts neuroscience program at The Jackson Laboratory in Bar Harbor, Maine, he will be transitioning to the University of Michigan at Ann Arbor with the Kaczorowski lab but will remain in the Tufts program as a visiting scholar. His current research interests include the influences of sex and genetic background in Alzheimer’s disease pathology with a current focus on cortical beta-amyloid 1-42 (Aβ42) pathology. He is also interested in the gut microbiome and its influence on the brain as well as using dietary interventions to help ameliorate various diseases. At Hartford, he received teaching assistantships for biology and anatomy/physiology labs and has experience mentoring undergraduate researchers in the lab. He received his master’s degree studying the influences of a ketogenic diet on Alzheimer’s pathology. Additionally, he was awarded the William S. and Dorothy G. Wallace Memorial Award for Academic Achievement in Neuroscience twice during his time at the University of Hartford.

Mentor Name: Stephanie Boas
Mentor Role: Postdoctoral Research Associate
Principal Investigator: Catherine Kaczorowski
Institution: University of Michigan
Location: Ann Arbor, MI
Lab Website: https://kaczorowski.lab.medicine.umich.edu

Project Title: Genetic Mechanisms Controlling Resilience to Huntington’s Disease

Project Description: The project I envision as the best fit for a SURFiN scholar in the Kaczorowski lab (under my mentorship) is the NIH-funded project focusing on identifying drivers of resilience to Huntington’s disease (HD). For this project, we have generated a novel mouse panel, crossing an HD mouse line to the genetically-diverse BXD panel for a systems genetic approach to identify modifiers that contribute to HD resilience in a ‘humanized’ mouse population. To quantify resilience across this panel, we are evaluating BXD substrains carrying the HD transgene on various cognitive and motor tasks. The BXD panel allows for quantitative trait loci mapping to correlate genetic variants to a given phenotypic outcome. We will investigate targets identified through trait mapping to inform follow-up genetic knockout/CRISPR editing strategies using both in vitro and in vivo models. The Kaczorowski lab, and this project in particular, are ideal for a student in this program, because there is an opportunity for exposure to diverse techniques depending on the proclivities of the student. A SURFiN student could focus on: 1) behavioral phenotyping, learning to run mice on behavioral tasks; 2) genetic and behavioral characterization of novel HD resilience mouse model; and/or 3) computational analyses (trait mapping, pathway modeling).

Mentor Biography: Stephanie Boas is a postdoctoral research associate in the lab of Catherine Kaczorowski at the University of Michigan. Her research interests focus on understanding cell-type-specific pathogenic mechanisms across neurodegenerative diseases, and how genetic risk factors differentially impact diverse cell types and regions of the brain. Stephanie has a strong background in molecular techniques and neurodegenerative disease processes. In her graduate work at the University of Alabama at Birmingham, she studied how heterogeneous neuronal subtypes are differentially affected in rodent models of Parkinson’s in the lab of Rita Cowell. She also took advantage of several informal and formal mentorship opportunities. She trained several Cowell lab undergraduates in molecular techniques and science communication. Stephanie also mentored several summer students through the SPIN program. Additionally, she served as a teaching assistant for two semesters of biostatistics. She finds mentorship opportunities to be really energizing, both to her individually, and to the lab as a whole. While she has had incredible opportunities throughout her education, Stephanie is originally from a rural town in Illinois. She understands what it’s like to have limited exposure to academic opportunities, and how much this exposure can influence young scientists. She’s excited to be a part of programs like these that create such opportunities.

Mentor Name: Apoorva Arora
Mentor Role: Graduate Student
Principal Investigator: Adam Kepecs
Institution: Washington University in St. Louis
Location: St. Louis, MO
Lab Website: https://sites.wustl.edu/kepecslab/research

Project Title: Study of behavioral strategies supporting few-shot learning in rats using a LEGO-maze paradigm

Project Description: We have devised a LEGO-maze to ask questions related to rapid learning, inferential reasoning and cognitive maps in rats. Our maze task is a naturalistic paradigm for rodents that are adept at exploring and remembering physical spaces. In this setting, a thirsty rat’s objective is to swiftly and correctly solve the maze to receive a water reward. One of the key questions we are after is a century-old one asked by Tolman: In a maze they know well, will rats take a newly revealed shortcut? This question underlies a key feature of biological intelligence that is lacking in modern day AI — inferential reasoning (i.e., recognition of connections between entities without directly experiencing it). Shortcuts in the maze represent such connections that can be inferred, if the maze is known well. Then, preferentially taking shortcuts — over other revealed paths that are either longer or lead to dead-ends — will reflect the rats’ inferential reasoning. In this project, you will learn how to design behavioral experiments with appropriate controls, use machine learning-based tools, like DeepLabCut, to analyze videos, learn some python programming to analyze rat’s position data, and think and talk about what is meant by intelligence.

Mentor Biography: Apoorva Arora is a senior graduate student in the Neuroscience Ph.D. program at Washington University in St. Louis doing her thesis project in the Kepecs Lab. She received a bachelor’s degree in biochemistry from the University of Delhi, India, a master’s degree in biotechnology from Amity University, India, and a master’s degree in neuroscience from Brandeis University, MA, U.S. During this time, she worked on research related to gene cloning, radiation biology and human speech processing. She then worked as a research technician for the late John Lisman to study the molecular mechanisms of long-term memory storage. In her doctoral research, she is studying value-guided decision making in rats using fiber photometry to record mesolimbic dopamine. She has set up a LEGO maze to study rapid learning in rats. In the future, she wants to study mechanisms of brain-wide coordination of activity. Apoorva is trained on the CIMER curriculum for bench-mentoring undergraduate students in biological sciences. Since 2021, she has been mentoring undergraduates in her lab and high school students as part of the Young Scientist Program. She is also the director of St. Louis Neuroscience Outreach and regularly organizes brain carnivals for the public at the St. Louis Science Center.

Mentor Name: Jiayi Zhang
Mentor Role: Graduate Student
Principal Investigator: Tatiana Engel
Institution: Princeton University
Location: Princeton, NJ
Lab Website: https://pni.princeton.edu/people/tatiana-engel

Project Title: Representations of learning in RNNs

Project Description: Recurrent neural networks (RNNs) are often used for modeling complex neurobiological activity. Neuroscientists typically train these networks to perform tasks (like decision making) and/or to reproduce activities recorded from animal brains. We can then probe the trained networks to see what gives rise to their behavior. Despite their popularity and the existence of analytical tools, many fundamental and interesting questions about RNNs remain open. For example, where is ’learning’ represented in these ’black-box’ models? An RNN is defined by its input, output and recurrent connectivity matrices, which are the (only) parameters iteratively updated during training. Therefore, if a network ’learns’ to perform some task, it must be instantiated on the changes that occur in the connectivity matrices. Which of these matrices have to change (the most)? Does a randomly initialized network have to rewire dramatically or only a little (e.g., following the ’lottery ticket hypothesis’)? How would biologically plausible constraints change learning? In this project, we will train RNNs to execute various, well-established cognitive tasks in neuroscience literature and compare their connectivity from initialization to the end-of-training to explore the questions above. Basic coding skills (e.g., Python) will be helpful; no prior experience with RNN is required.

Mentor Biography: Jiayi Zhang is a graduate student in the Quantitative and Computational Biology program at Princeton University. She obtained a bachelor’s in computational biology with a minor in linguistics from Carnegie Mellon University (CMU) in 2022. During her undergraduate training, Jiayi focused on applying techniques in signal processing and machine learning to solve problems spanning several disciplines, including automatic detection of Amyotrophic Lateral Sclerosis (with Rita Singh, CMU), semantic segmentation of oceanographic field images (with Lisa Gilbert, Williams College, now at Cabrillo College), and analysis of hyper-resolution spectrogram (with Marcelo Magnasco, Rockefeller University). She was also interested in science pedagogy, which motivated her to develop content for CMU Computer Science Academy (online Python programming curricula for high school students) and to serve as a teaching assistant for various courses. At Princeton, Jiayi plans to apply quantitative and computational methods she has learned to understand information encoding and computation in biological systems. Specifically, with supervision from Tatiana Engel, she now seeks to uncover circuit mechanisms driving cognitive behavior, such as perceptual decision making. She is currently working on extending a dimensionality reduction method for neural dynamics (Latent Circuit Inference, by Langdon and Engel, 2022) and applying it to large-scale neural recordings.

Mentor Name: Erik Toraason
Mentor Role: Postdoctoral Fellow
Principal Investigator: Coleen Murphy
Institution: Princeton University
Location: Princeton, NJ
Lab Website: https://murphylab.princeton.edu

Project Title: Identifying neuronal receptors that detect ‘todstoff’ (‘death substance’)

Project Description: Organisms use multipronged strategies to navigate and survive in hazardous environments. Many species display warning signals when injured or threatened, allowing conspecifics to enact defense strategies and avoid a similar fate. For example, zebrafish exhibit panic behaviors when they smell schreckstoff (‘fright substance’); a mixture of glycosaminoglycans released by other injured fish. Warning and avoidance behaviors are therefore vital social interactions that promote the survival and propagation of species. Caenorhabditis elegans is a nematode that serves as a powerful model system to understand the molecular underpinnings of social behavior. C. elegans avoids the lysed remains of other C. elegans worms (‘negative necrotaxis’ behavior), indicating that they recognize a yet unknown signal present in other injured or deceased worms. The molecular identity of this necrotaxis cue (which we have termed ‘todstoff’ or ‘death substance’) and the receptors that sense it remain unknown.

In this project, the SURFiN fellow will employ a combination of classical genetics, behavioral assays and genome editing technologies to identify which of the over 1,300 chemoreceptor genes encoded in the C. elegans genome detect the necrotaxis cue. The fellow will work with researchers in the Murphy lab to perform a forward genetic screen to generate mutants that cannot sense the remains of other dead worms. They will then sequence the genomes of these worms to identify which genes are disrupted in these mutants. Finally, they will use CRISPR/Cas9 genome editing to create fluorescent reporter lines and identify the neuronal expression of these genes. Taken together, the fellow will learn classical and cutting-edge genetic and molecular biology skills and will isolate the neuronal receptors that mediate critical survival behaviors.

Mentor Biography: Erik Toraason completed his doctorate at the University of Oregon, where he developed genetic and computational tools in the nematode Caenorhabditis elegans to study mechanisms that preserve the genome integrity of developing sperm and egg cells. As a postdoctoral fellow in the Murphy lab, he employs C. elegans to illuminate inter-cellular and inter-organism signaling pathways that promote survival and longevity.

Mentor Name: Abigail Brown
Mentor Role: Postdoctoral Fellow
Principal Investigator: Coleen Murphy
Institution: Princeton University
Location: Princeton, NJ
Lab Website: https://murphylab.princeton.edu

Project Title: Deciphering the molecular mechanisms underlying learned pathogenic avoidance

Project Description: The inheritance of complex traits and behaviors has largely been thought to be governed thoroughly by genes. However, there has been increasing evidence of the role that non-genetic materials play in transmitting information to their progeny. Recently, work done by our lab and others have found that the nematode Caenorhabditis elegans (C. elegans) can learn to avoid the pathogen Pseudomonas aeruginosa (PA14) through small RNA training. This learned avoidance behavior is passed to their progeny, enabling them to avoid PA14 for four generations. This inherited behavior was shown to be facilitated through epigenetic means. However, how the small RNA which is ingested affects the host neurons at the molecular level to drive this aversive behavior and its inheritance remains unclear. This proposal will examine this by: 1) determining the chromatin accessibility and gene expression changes that occur in neurons, 2) determine germline and neuron-specific proteins needed for learned avoidance, and 3) determine why this inherited behavior halts after four generations. Our findings will give critical insight to the molecular mechanisms that underly complex behaviors, including those that are transgenerational.

Mentor Biography: Abigail Brown conducted her doctoral research in the laboratory of Ashley Webb at Brown University. The Webb laboratory seeks to understand the molecular and cellular mechanisms that underly mammalian brain aging. During this time, she made the exciting discovery that the pro-longevity transcription factor FOXO3 functions at the chromatin level in distinct mechanisms in healthy proliferating cells and senescent cells. Presently, she is conducting her postdoctoral work in the laboratory of Coleen Murphy at Princeton University. Abigail’s current research aims to answer two main questions: 1) how animals process external stimuli that leads to behavioral changes and 2) how they pass this learned behavior to future generations.

Mentor Name: Xinping Li
Mentor Role: Postdoctoral Researcher
Principal Investigator: Mala Murthy
Institution: Princeton University
Location: Princeton, NJ
Lab Website: https://murthylab.princeton.edu

Project Title: Integrating sensory cues and metabolic costs in fruit fly courtship behavior

Project Description: All animals perform precise movements for critical tasks such as foraging, escaping and mating. On one hand, the central nervous system processes sensory information from the external environment to pattern motor commands. On the other hand, executing these motor commands is constrained by the metabolic costs of generating muscle force. Insects, for instance, need to warm their muscles to fly, achieving this by moving their wings. Yet, how the brain integrates sensory input with energy costs to control complex movements remains unclear.

The Murthy lab uses fruit fly courtship behavior to investigate how the brain integrates sensory information to pattern complex behavior. During courtship, males and females engage in complex interactions influenced by sensory cues. In particular, male flies produce a diverse range of wing movements. We do not know to what extent their movements are constrained by the energy cost requirement to produce an optimum muscle temperature. This project leverages the lab’s expertise in quantitative behavioral methods, aiming to develop a high-resolution assay to simultaneously track behavior and body temperature during courtship and build models that describe these dynamics. The SURFiN fellow will gain hands-on experience in experimental setup, behavioral experiment design, computational modeling, data analysis and presentation skills.

Mentor Biography: Xinping Li is a postdoctoral researcher in Mala Murthy’s lab. She received a doctorate from the Federated Department of Biological Sciences at Rutgers and NJIT prior to joining Princeton. Xinping’s research interests center on the emergence of flexibility in neural processing and its impact on adaptive behaviors. Her current work integrates high-resolution behavioral assays, functional imaging and electrophysiology. Xinping brings a wealth of teaching and mentoring experience; over the past few years, she has guided three undergraduate and postbaccalaureate trainees, all of whom have successfully moved on to doctoral programs.

Mentor Name: Dean Pospisil
Mentor Role: Postdoctoral Fellow
Principal Investigator: Jonathan Pillow
Institution: Princeton University
Location: Princeton, NJ
Lab Website: https://pillowlab.princeton.edu

Project Title: Extracting structure from neural data

Project Description: This project will involve developing statistical models of neural population activity and applying them to new datasets. Applicants with a strong background in linear algebra, probability/statistics and programming are highly encouraged.

Mentor Biography: Dean received his doctorate in neuroscience from the University of Washington and is now a postdoctoral fellow in the Pillow lab at Princeton University.

Mentor Name: Maria Clara Selles Japas
Mentor Role: Postdoctoral Fellow
Principal Investigator: Moses Chao
Institution: New York University School of Medicine
Location: New York, NY
Lab Website: https://chaolabnyu.com

Project Title: Interplay between social interactions and oxytocin

Project Description: Oxytocin was first recognized as a regulator of the reproductive system but has gained attention for its ability to modulate social behaviors. We are interested in understanding how social context (e.g., social housing vs. social isolation) shapes the oxytocin system and consequently affects subsequent social interactions. To do so, we will combine long-term behavioral monitoring approaches with molecular techniques to assess oxytocin levels in male and female adult mice. The SURFiN fellow can expect to learn how to acquire, analyze and present data regarding social behaviors; the fellow will also learn to process tissue to quantify peptide levels using molecular approaches, such as qPCR and whole brain immunostaining. The lab has extensive expertise in social behaviors and cell biology and has made significant contributions in the field of oxytocin signaling.

Mentor Biography: Maria Clara Selles is a postdoctoral fellow in the Chao and Froemke Labs at New York University (NYU). Clara is originally from Argentina, where she received her bachelor’s in biochemistry from the University of Buenos Aires. She then moved to Brazil to pursue her master’s degree and Ph.D. from the Federal University of Rio de Janeiro. During her graduate work, she studied the therapeutic potential of oxytocin for Alzheimer’s disease in collaboration with the Chao and Froemke labs. After spending the last months of her doctoral training at NYU, she became a postdoctoral fellow funded by the PEW Charitable Trusts. Currently, she is interested in understanding how social context impacts the oxytocin system at molecular and cellular levels and the behavioral implications of these changes for subsequent social interactions in male and female mice. This is particularly relevant to diseases that present social dysfunction as a risk factor and/or symptom, including anxiety, depression and autism.

Mentor Name: Melissa Cooper
Mentor Role: Postdoctoral Fellow
Principal Investigator: Moses Chao
Institution: New York University School of Medicine
Location: New York, NY
Lab Website: https://chaolabnyu.com

Project Title: Astrocyte networks

Project Description: A major question in neuroscience is to identify intrinsic mechanisms that respond after injury and neurodegeneration. Traditionally, astrocytes were thought to support neurons and occupy a passive niche. However, recent discoveries have revealed that astrocytes constitute a network of cells that process information in parallel with neurons. We have found specific astrocyte networks of communication are present in the brain. To this end, trophic factors such as BDNF, a potent survival and plasticity factor, has a widespread role as a mediator of metabolic responses of the brain and body to fluctuations in energy expenditure. We have identified a novel metabolite, D-β-hydroxybutyrate, that is elevated in the hippocampus after exercise and results in an increase in BDNF. This small molecule is an example for how physical activity may boost the endogenous protection by astrocyte metabolic networks. Proposed experiments are to define discrete networks that connect different brain regions by tissue clearing imaging and to identify small molecules by mass spectrometry made by astrocytes for their function in neurons from peripheral neurons and hippocampal neurons.

Mentor Biography: After her doctoral thesis work at Vanderbilt University with David Calkins, Melissa Cooper started postdoctoral work at NYU in the Neuroscience Institute, where she pursued her interests in mechanisms of astrocyte connectivity and how astrocytes alter in response to neurodegenerative stress. Melissa has displayed many interests in advocacy. The efforts to increase recruitment and diversity on campus have benefited highly from Melissa’s leadership and guidance. Melissa has participated in workshops and seminars in a R25 Diversity and Mentoring Grant (R25 NS107178, Diverse Neuroscientists: Doctoral Training Series) and has been elected to the leadership board for the Women in Science in STEM organization. Melissa has gained valuable experience in mentoring junior trainees, who are interns in the laboratory.

Mentor Name: Lucas Tian
Mentor Role: Postdoctoral Associate
Principal Investigator: Winrich Freiwald
Institution: Rockefeller University
Location: New York, NY
Lab Website: https://lab.rockefeller.edu/freiwald

Project Title: Neural mechanisms of compositional planning in a macaque drawing task

Project Description: How can networks of neurons create intelligence? This is the central question of cognitive science. A key to answering this question is understanding compositionality or the fundamental ability for the brain to generate complex thoughts and actions by systematically recombining simpler components (e.g., like in language). We aim to uncover the neural basis of compositionality with a novel approach combining a new macaque drawing task, large-scale neural recordings and computational modeling. In this SURFiN project, we will explore the relationship between neural activity and action planning. The SURFiN fellow will analyze neural and behavioral data collected from macaques making a variety of drawings. The fellow will build computational models to decode cognitive drawing plans directly from neural activity. The fellow can expect to gain experience analyzing neural activity and macaque behavior and in building a variety of computational models, from linear classifiers to neural nets. Moreover, because this is an interdisciplinary project collaborating with Xiao-Jing Wang (theoretical neuroscientist at NYU) and Josh Tenenbaum (cognitive scientist at MIT), there will be opportunities to gain experience across neuroscience and artificial intelligence. The findings may have broad implications, including for brain-machine interfaces, and in understanding how cognition works in the brain.

Mentor Biography: Lucas Tian is a postdoctoral fellow in the Laboratory of Neural Systems at The Rockefeller University. He received a bachelor’s in biology from the University of Chicago in 2011, and a doctorate in neuroscience from the University of California, San Francisco in 2019 studying neural mechanisms of vocal learning in songbirds (advised by Michael Brainard). He then decided to focus his research on neural and computational mechanisms of primate cognition, and to do so he first completed a visiting postdoctoral fellowship in computational cognitive science with Josh Tenenbaum at MIT in 2019. He moved to Rockefeller in late 2019, where he is currently advised by Winrich Freiwald and co-advised by Xiao-Jing Wang (NYU) and Josh Tenenbaum (MIT). His research focuses on the neural mechanisms of high-level cognition and intelligence in primates. His approach is to study behavior of non-human primates in complex cognitive tasks, combined with large-scale neural recordings and computational modeling. His ongoing work focuses on mechanisms of compositional action planning in a novel drawing task. During his postdoctoral research, he has been awarded the NIH Ruth L. Kirschstein NRSA F32 Fellowship and the NINDS K99/R00 Pathway to Independence Award.

Mentor Name: Juliana Rhee
Mentor Role: Postdoctoral Research Associate
Principal Investigator: Vanessa Ruta
Institution: Rockefeller University
Location: New York, NY
Lab Website: https://www.rockefeller.edu/our-scientists/heads-of-laboratories/989-vanessa-ruta

Project Title: The evolution of social behaviors

Project Description: Many of the most dramatic behaviors displayed across the animal kingdom have evolved for social contexts, from attracting a mate with elaborate courtship rituals to repelling rivals with acts of aggression. Though driven by instinct, these social behaviors are not fixed sequences but reflect the dynamic interplay between an individual’s internal drives and the external world. While courtship and aggression are typically studied in the lab with single animal pairs, most species face far more complex social landscapes in which the concurrent demands of courtship and competition jointly sculpt an individual’s interactions within larger groups. This project explores how different Drosophila (fruit fly) species have evolved distinct strategies to contend with complex group dynamics to win a mate or defeat a rival. The SURFiN fellow will learn computational approaches to dissect behavior, including using deep networks for animal pose-tracking and machine learning to predict how sensory signals drive behavior. They will gain expertise in the wealth of neurogenetic tools available in Drosophila, enabling them to combine behavioral analyses with neural activation or silencing to identify underlying circuit mechanisms. This interdisciplinary project will offer insights into the nuanced interplay of innate drives, social dynamics and environmental cues that shape animal behavior.

Mentor Biography: Juliana Rhee is a postdoctoral researcher in the lab of Vanessa Ruta at Rockefeller University. She is interested in how nervous systems evolve to support diverse behaviors and is currently using the Drosophila clade as a model to study the evolution of courtship behavior. She received her bachelor’s degree in philosophy and germanic languages and literature at Harvard University, where she became interested in how animals perceive the world. During her graduate research at Harvard University, she developed a system for cellular resolution imaging and high-throughput behavior in a rodent model for complex visual behaviors that are typically studied in primates. After completing her graduate work, she was awarded an independent Grass Fellowship in Neuroscience at the Marine Biological Laboratories to study the visual behaviors of octopuses and cuttlefish in social contexts. Juliana has mentored high school, undergraduate and graduate students in the lab and has been the recipient of several grants and awards for teaching. She is also actively involved in efforts to make science a more diverse and inclusive space and is excited about programs that create paid opportunities for students from historically-marginalized backgrounds or underrepresented in academic spaces.

Mentor Name: Stefan Lemke
Mentor Role: Postdoctoral Fellow
Principal Investigator: Adam Hantman
Institution: University of North Carolina, Chapel Hill
Location: Chapel Hill, NC
Lab Website: https://www.med.unc.edu/neuroscience/hantmanlab

Project Title: Examining behavioral flexibility in mouse models of neurodevelopmental conditions

Project Description: In this project, we examine behavioral flexibility in mouse models of several single-gene neurodevelopmental conditions. Behavioral flexibility is our ability to adapt our behavior when required by changes in the environment. We use this flexibility everyday as we adjust to small changes, such as delayed bus routes, or big changes, such as new jobs. A central feature among many neurodevelopmental conditions is behavioral inflexibility. Behavioral inflexibility can be thought of as being ‘stuck’ in a repetitive set of behaviors that disrupts daily living, opportunities to learn and social interactions. To measure this in mice, we train them to perform a skilled action in which they reach out and grab a food pellet. Once mastered, we move the food pellet and see how they adjust. Are the mice quickly able to adjust to the new location, or do they have trouble changing their learned behavior? We will carefully measure this behavior in several different sets of mice which have disruptions to specific genes that we know are closely related to neurodevelopmental conditions. Then, we use in vivo electrophysiology to find abnormal neural dynamics that provide insights into the neural basis of behavioral inflexibility.

Mentor Biography: Stefan Lemke grew up in rural Minnesota and went to St. Olaf College, where he spent his time running on the cross country and track teams, swimming on the swim team, and learning about what neuroscience was. Stefan then headed to the University of California, San Francisco, where he got a doctorate in neuroscience and developed an interest in how the distributed networks in the brain control complex behaviors. After a year-long postdoctoral fellowship at the Italian Institute of Technology where he worked in computational neuroscience, Stefan joined the University of North Carolina, Chapel Hill to start a project where he uses the latest tools from systems neuroscience to advance our understanding of neurodevelopmental conditions.

Mentor Name: Kevin Cross
Mentor Role: Postdoctoral Fellow
Principal Investigator: Adam Hantman
Institution: University of North Carolina, Chapel Hill
Location: Chapel Hill, NC
Lab Website: https://www.med.unc.edu/neuroscience/hantmanlab

Project Title: Investigating the role of primary somatosensory cortex in a skilled motor action

Project Description: In this project, we will explore the primary somatosensory cortex, a region that plays a critical role that supports sensorimotor integration. The aim is to uncover how sensory inputs are processed by this region during a motor action, how this region communicates with areas involved with motor execution, and how this region may be disrupted in autism. Trainees will be exposed to a comprehensive experience that will combine both theoretical and experimental approaches to investigate brain activity. Trainees will be responsible for handling and training mice in a task where mice reach for food pellets in the environment. Trainees will learn how to handle and implant high-density silicon electrode arrays to record neural activity and how to analyze neural signals using modern data analysis methods.

Mentor Biography: Kevin Cross is a postdoctoral fellow at the University of North Carolina at Chapel Hill in the laboratory of Adam Hantman. He has a bachelor’s degree in biophysics from York University and completed his doctorate under the supervision of Stephen Scott at Queen’s University. His thesis focused on how sensory feedback from the body and external world influenced corrective motor actions to unexpected disturbances. He gained experience in neurophysiological recordings in macaques, computational methods in neuroscience and modeling. Since joining the Hantman lab in 2021 his projects have encompassed how the motor cortex processes inputs to generate motor commands for skilled behavior. His work is supported by a fellowship from the Human Frontiers Science Program.

Mentor Name: Scott Albert
Mentor Role: Postdoctoral Fellow
Principal Investigator: Adam Hantman
Institution: University of North Carolina, Chapel Hill
Location: Chapel Hill, NC
Lab Website: https://www.med.unc.edu/neuroscience/hantmanlab

Project Title: Mapping whole-brain neuromotor resilience across the lifespan

Project Description: Motor control declines with aging, reducing our quality of life and increasing risk of injury and mortality. This deterioration in motor function is in part due to a decrease in the resilience of neural circuitry. Young brains can flexibly adapt to damage and dysfunction, but this fluidity dissipates as we age. For example, a child with a hemispherectomy can re-learn to walk with only half their brain, but a focal stroke can render an elderly individual to the use of a wheelchair indefinitely. What network supports recovery following damage to motor control circuitry, and why does its resilience weaken as we age? In this project, we will train mice to perform a reach-to-grasp task, and then use a technology called optogenetics to inactivate motor circuits in young and old mice. Like a stroke, losing the motor cortex causes paralysis, but, remarkably, animals regain the ability to use their limb over time. We will use fMRI to monitor the entire brain during this motor recovery process to search for the source of neural recovery and repair. Our goal is to understand why rehabilitation worsens with age and if we can augment the aged nervous system to increase recovery potential.

Mentor Biography: Scott Albert attended Lafayette College where he learned about mathematics and chemical engineering, played soccer, trumpet and acted a bit on the side. A summer research experience at the National Institutes of Health opened his eyes to biological research. In graduate school, Scott studied biomedical engineering at Johns Hopkins University, where he became fascinated by neural adaptation; the flexibility built into our brain to ensure that we can endure perturbations to our environments and within ourselves. His research centered on human motor control and how individuals adapt to visual and physical disturbances to skilled reaching actions. Working with stroke and Parkinson’s disease patients showed him the immense toll that motor disorders can have on life. After earning his doctorate, Scott decided that he wanted to uncover processes of neural resilience and recovery inside the brain. As a postdoctoral fellow at HHMI Janelia, and now UNC Chapel Hill, he started working with state-of-the-art techniques, such as electrophysiology, optogenetics and fMRI, that allow us to perform reversible inactivation of the mouse motor cortex across the lifespan. With this approach, Scott studies how the brain recovers from losing its center of motor control and how neural resilience is deteriorated by aging.

Mentor Name: Elena Tenenbaum
Mentor Role: Assistant Professor
Principal Investigator: Elena Tenenbaum
Institution: Duke University
Location: Durham, NC
Lab Website: https://sites.duke.edu/risebattery/

Project Title: Remote Infant Studies of Early Learning (RISE) Battery

Project Description: This project will examine early markers of autism in infancy, before a clinical diagnosis can be made, using an innovative battery of scalable, clinically-accessible, remote assessment tools called the Remote Infant Studies of Early Learning (RISE) Battery. We are interested in exploring how mechanisms of learning, including attention, memory, numeracy, language, prediction and social evaluation, develop in infants who will later receive a diagnosis of autism. Infants enroll from home and are shown videos of tasks that were traditionally used in laboratory studies of infant cognitive development. We record their response to those videos and use computer vision software to detect gaze direction in response to the stimuli. We also gather parent-report measures of infant development to assess risk for developmental conditions. With early identification of signs of atypical development, we can improve early monitoring and targeted early interventions for infants who stand to benefit most from them.

Mentor Biography: Elena Tenenbaum is an early career faculty member in the Department of Psychiatry and Behavioral Sciences at Duke. She has mentored over a dozen students and is very interested in supporting future trainees who are interested in learning about the cognitive and behavioral research techniques used in the study of neurodevelopmental conditions.

Mentor Name: Jessica A. Herstine
Mentor Role: Doctoral Candidate
Principal Investigator: Allison Bradbury
Institution: Research Institute at Nationwide Children’s Hospital
Location: Columbus, OH
Lab Website: https://www.nationwidechildrens.org/research/areas-of-research/center-for-gene-therapy/bradbury-lab

Project Title: Uncovering disease mechanisms and executing a translational gene therapy for Vanishing White Matter disease

Project Description: One of the focuses of the Bradbury Lab at Nationwide Children’s Hospital is development of a gene therapy for a rare, genetic, neurological disease called Vanishing White Matter disease (VWM). VWM is an autosomal recessive disorder that leads to ataxia, spasticity, seizures, neurodegeneration and premature death in patients. Jessica Herstine serves as the project lead, and her thesis work has included the establishment of novel in vitro models, such as patient-derived astrocytes, to understand disease etiology. Furthermore, her NIH TL1 Training Grant includes the use of the I98M Toy mouse model to both characterize disease pathology and to evaluate gene therapy efficacy. Currently, neonatal mice are being treated via intra-cerebrospinal fluid (intra-CSF) administration of numerous potential gene therapy constructs. Continual analysis of therapeutic efficacy is evaluated through behavior assays and magnetic resonance imaging (MRI) to visualize disease progression and myelin loss. Additional experiments include post-mortem analysis to analyze histology, molecular disease markers and vector biodistribution. Future studies include dose ranging studies and toxicology testing of the lead candidate gene therapy. Our SURFiN fellow will assist in molecular assays related to disease pathogenesis and attenuation with therapy with additional insight to all aspects of this highly translational and transformative project.

Mentor Biography: Jessica A. Herstine received her bachelor’s in molecular genetics with a minor in neuroscience from The Ohio State University (OSU) in 2020. That same year, Jessica matriculated as a doctoral student in OSU’s Molecular, Cellular and Developmental Biology (MCDB) graduate program where she joined the lab of Allison Bradbury at Nationwide Children’s Hospital. Jessica is now a doctoral candidate with active NIH TL1 Training Grant funding to investigate gene replacement therapy for a rare, genetic leukodystrophy called Vanishing White Matter disease. In her current role, she has become adept in numerous techniques such as direct fibroblast to neuron and astrocyte conversions, viral vector cloning, gene therapy application, mouse colony management, behavioral testing and preclinical study design and execution. In addition, she has exploited ample opportunities for mentorship and teaching as a teaching assistant through a leadership role in the MCDB Graduate Student Organization and Vice Chair of the Research Institute’s Trainee Association at Nationwide Children’s. Jessica thoroughly enjoys teaching and inspiring others through science and mentorship. She aspires to have a fulfilling career in academics as a professor and principal investigator, so that she can help train the next generation of scientists.

Mentor Name: Sara Caldas Martinez
Mentor Role: Doctoral Candidate
Principal Investigator: Kate Hong
Institution: Carnegie Mellon University
Location: Pittsburgh, PA
Lab Website: thehonglab.com

Project Title: Circuit mechanisms of tactile discrimination

Project Description: This project aims to determine how the brain mediates the discrimination between different tactile patterns to guide behavior. Mice are trained to perform various tactile discrimination behavioral tasks, and neurons from various areas in the brain are recorded to determine how tactile information from periphery are processed to mediate discrimination.

Mentor Biography: Sara Caldas Martinez is a doctoral candidate in biological sciences at Carnegie Mellon University. She holds a bachelor’s in biochemistry and master’s in neuroscience from the Autonomous University of Barcelona, Spain. Prior to graduate school, Sara worked as a research assistant in the Department of Electrical and Computer Engineering at Carnegie Mellon University.

Mentor Name: Seo-Jun Kang
Mentor Role: Postdoctoral Fellow
Principal Investigator: Hye Young Lee
Institution: University of Texas Health Science Center, San Antonio
Location: San Antonio, TX
Lab Website: https://lsom.uthscsa.edu/physiology/team-member/hye-young-lee-ph-d

Project Title: Pathophysiological mechanism underlying FXS and gene therapy development using nonviral delivery vectors

Project Descriptions: Gene therapeutics have great potential for treating neurological disorders. However, challenges with delivery have limited their clinical potential. CRISPR/Cas9 is one of the most widely used gene editing tools due to the target specificity and simple design of sgRNA lending it both precision and ease of use. The Lee lab has demonstrated that gene editing with Cas9 RNPs (Cas9 protein/sgRNA complexes) using non-viral delivery is possible in adult mouse brain (Lee et al 2018, Nature Biomedical Engineering). Our current project aims to deliver Cas9 in a form of mRNA/sgRNA using non-viral vector in brain disorder mouse models given the promising features of mRNA delivery. To achieve this goal, aim 1 will focus on identifying the most efficient delivery vehicle by using reporter mice which can detect tdTomato expression as a result of gene editing. Aim 2 will focus on optimizing a dose, brain region, delivery efficiency, injection method and duration conditions. Aim 3 will focus on testing delivery vehicle in the preclinical model for brain disorders. We will use molecular, cellular and behavioral assessments to test Aim 3.

Mentor Biography: Seo-Jun’s long-term research interests involve the development of a comprehensive understanding of the connection between neurodevelopmental conditions and neurodegenerative diseases and how alterations in gene expression contribute to human disease. His academic training and research experience has provided him with an excellent background in multiple biological disciplines, including molecular biology, genetics, neuronal physiology and cell biology. As an undergraduate at Ajou University, Seo-Jun studied diverse fields of biological science, including genetics, immunology, neurology, physiology and molecular biology. For his graduate training at Ajou University, he focused on neurodegenerative disease and cell biology fields by studying the molecular mechanism of propagation of α-synuclein in neuronal cells. He demonstrated that ApoE regulates the propagation of α-synuclein under Sang Myun Park. This resulted in multiple publications including two first authorship publications. Dr. Park gave him new conceptual and technical training such as literature analysis, diverse bench work and presentation skills. After graduating, Seo-Jun moved into the fields of neurobiology and development to expand his knowledge for understanding neurodevelopmental disorders and primary cilia under Hye Young Lee. As a postdoctoral fellow, he focuses on fragile X syndrome (FXS) and primary cilia by studying the regulation of primary cilia in FXS patient-derived fibroblast cells under Dr. Lee. More recently, Seo-Jun also started projects on nonviral delivery of CRISPR to develop gene therapy for brain disorders. Overall, he feels that his choice of sponsor, research project and training gave him a solid foundation for his long-term goal to become an independent academic researcher.

Mentor Name: Bruno Cruz
Mentor Role: Scientist 1
Principal Investigator: Cindy Poo
Institution: Allen Institute
Location: Seattle, WA
Lab Website: https://alleninstitute.org/division/neural-dynamics/behavior

Project Title: Developing open-source tools for experimental behavior neuroscience

Project Description: Understanding how the brain gives rise to behavior relies on measuring and manipulating the animal’s environment. As behavior becomes more sophisticated, bespoke software and hardware solutions that match experimental needs are necessary.

This project will integrate the SURFiN fellow into a dynamic team of developers at the Allen Institute for Neural Dynamics. We will design, integrate, characterize and curate open-source tools with a strong focus on experimental neuroscience and behavior applications. These tools will be developed in close collaboration with scientists and are expected to be integrated into existing experimental pipelines. Consistent with the institute’s vision, the end goal will be to disseminate all output through open-source platforms and publications. The fellow will gain valuable hands-on experience in hardware and software design, DevOps practices and communication skills.

The project is well suited for an applicant with previous programming and/or hardware design experience interested in developing tools for the neuroscience community. We will tailor the details of the project to the candidate’s background, goals and expectations.

Mentor Biography: Bruno Cruz received his bachelor’s degree in biochemistry and a master’s degree in molecular biology from the University of Coimbra, Portugal. He moved to the Champalimaud Foundation, in Lisbon, where he received his doctorate under the supervision of Joe Paton. During his graduate work, he combined complex behavior tasks with electrophysiological recordings, closed-loop optogenetic experiments, and modeling to study the role of striatal circuits for the production and suppression of action.

After completing his doctorate he moved to London, UK, where he joined NeuroGEARS as a research scientist and software engineer. He worked with academic laboratories all over the world helping set up bespoke hardware and software infrastructure solutions for neuroscience experiments.

He has recently joined the Allen Institute for Neural Dynamics as a scientist, where he is part of a team developing new behavior tasks to study animal foraging behavior and navigation by using multi-sensorial experimentally-controlled environments. In parallel, he keeps developing open-source hardware and software tools for the neuroscience community.

Mentor Name: Tiffany Ona
Mentor Role: Scientist 1
Principal Investigator: Cindy Poo
Institution: Allen Institute
Location: Seattle, WA
Lab Website: https://alleninstitute.org/division/neural-dynamics/behavior

Project Title: Behavioral flexibility during decision making

Project Description: Adapting to an ever-changing world is key to success for all animals. To do this, animals infer causal structures of the world from varying sensory experiences and use this knowledge to make flexible behavioral choices. How these flexible decisions are implemented by interconnected neural circuits is unknown. In this project, we will study decision making in head-fixed mice performing an olfactory patch foraging task in close-looped, multi-sensory virtual reality, where mice are incentivized to collect resources in patchy environments. The SURFiN fellow would work with their mentor in designing and deploying these behavioral tasks in the context of high throughput, standardized and modular software and hardware platforms tailored for quantitative behavior. The fellow will also analyze behavioral datasets by applying and modifying existing analytical tools and pipelines. This project will serve as the foundation to study multi-regional, cell-type specific neural dynamics for flexible computations and behavior.

Mentor Biography: Tiffany Ona-Jodar is originally from Barcelona, Spain, where she studied biomedical sciences at the Autonomous University of Barcelona. To pursue her master’s degree, she moved to Regensburg, Germany, where she worked under the supervision of Veronica Egger. She characterized the dynamics of granule cells in the olfactory bulb using sodium imaging combined with patch-clamp electrophysiology in brain slices. For her doctorate studies, she was awarded a La Caixa Fellowship and conducted her research at the Brain Circuits and Behavior Lab, supervised by Jaime de la Rocha and Albert Compte in Barcelona. During these studies, she developed a behavioral paradigm in mice to characterize short-term maintenance memory errors and their corresponding neural profiles. By combining carefully quantified behavior with electrophysiological recordings and modeling, she gained insights into the various behavioral strategies that animals use to solve the task and their distinct dynamics during errors. In her postdoctoral work at the Allen Institute, she aims to explore flexible foraging behavior during an odor navigation task and describe which neural circuits allow mice to optimally harvest their environment.

Mentor Name: Camilo Laiton
Mentor Role: Software Engineer 3
Principal Investigator: Karel Svoboda
Institution: Allen Institute
Location: Seattle, WA
Lab Website: https://alleninstitute.org/division/neural-dynamics

Project Title: Enhancing large scale lightsheet brain data analysis with automated fault detection

Project Description: Lightsheet microscopy is a technology that enables imaging of tissue without the need for physical sectioning. At the Allen Institute for Neural Dynamics, we are interested in using this technology to image whole mouse brains to understand the organization and connectivity of the brain, as well as for spatial transcriptomics experiments to profile gene activity. For this, we need to collect hundreds of samples, image them under the microscope and generate digital volumes of these data by ‘stitching’ the images together. There are several steps in this stitching process, many of which are susceptible to errors. If these errors are not corrected, the data could be misrepresented, and the quality of data for analysis would be greatly degraded. Several previous studies have relied on manual inspection to address this problem. However, due to the scale of the data we are interested in studying, manual inspection is not a feasible solution for error detection.

This project involves investigation and development of a tool for automated error detection in lightsheet volumes with computer vision and machine-learning techniques. Such a tool would have an impact not only in reducing manual inspection work but really provide a stepping-stone into the ability to perform reliable large-scale lightsheet volume studies.

Mentor Biography: Camilo Laiton is a computer vision engineer working at the Allen Institute for Neural Dynamics. He received his master’s in computer science from the National University of Colombia, where he focused on developing artificial intelligence algorithms based on attention models for whole human brain segmentation. Before this, he completed his bachelor’s in computer science from the University of Magdalena, where he conducted research focusing on multi-objective algorithms for optimizing waiting times, pollution and noise in road intersection systems.

At Neural Dynamics, he is a member of the scientific computing team, focusing on building large-scale microscopic image processing pipelines in the cloud. Some of the image processing steps he has been working on include image noise removal using wavelet decomposition, image stitching, image brain registration to the Common Coordinate Framework (CCF) and evaluation of stitching errors using No-Reference Image Quality Assessment metrics (NR-IQA).

Currently, Camilo is working on projects related to cell segmentation and RNA detection. His research interests include computer vision, digital image processing and machine-learning techniques. Outside of work, he enjoys engaging in outdoor activities like running, skiing and soccer, finding balance between his professional pursuits and personal interests.

Mentor Name: Ulises Pereira-Obilinovic
Mentor Role: Scientist 2
Principal Investigator: Karel Svoboda
Institution: Allen Institute
Location: Seattle, WA
Lab Website: https://alleninstitute.org/division/neural-dynamics/behavior

Project Title: Understanding the mechanisms underlying foraging behavior using deep reinforcement learning

Project Description: Animals and artificial agents learn the causal structure of their environment to survive and thrive. An important part of the learning happens online by continuously using sensory experiences, rewards and punishments to update internal representations of the environments that drive future actions. Recently, artificial agents trained using deep reinforcement learning (Deep RL) have been remarkably successful in learning the causal structure of complex environments, such as the streets of a modern city or the Go play. What can we learn about the neural mechanisms underlying foraging from artificial neural networks (ANN) trained using Deep RL? In this project, we will study decision making of an agent performing a multi-sensory patch foraging task which has been recently implemented for mice. In this task, the mice and the artificial agent must collect resources in patchy environments. The SURFiN fellow would work with their mentor in implementing the environment for an artificial agent and then training an ANN to forage in this environment using Deep RL. The fellow will also analyze the behavior of the ANN and compare it with the behavior of mice performing the same task. This project will serve as a foundation computational model for understanding the neural dynamics and computations during foraging behavior.

Mentor Biography: Ulises Pereira-Obilinovic was born and raised in Chile. He studied physics and engineering at the University of Chile and graduated in 2013. The same year, he started a doctorate in statistics at the University of Chicago under the guidance of Nicolas Brunel. At Chicago, he developed theories for connecting learning and neural dynamics in cortical circuits. In 2019, after his doctoral training, he joined NYU as an independent Swartz Fellow in theoretical neurobiology, where he explored several theoretical neuroscience problems ranging from neural mechanisms of naturalistic behavior to building theories for multi-regional interactions. At AIND, he plans to focus on understanding foraging from a multi-scale standpoint (multi-regional and across time scales). His modeling approach investigates neural computations through the lens of recurrent networks’ (RNNs) latent dynamics. He uses biologically-constrained RNNs and tools from statistical physics to derive interpretable and low-dimensional models of the multi-regional latent dynamics and look for computational principles. Critically, he collaborates in a close iterative loop with systems neuroscientists, usually from early experimental design stages.

Mentor Name: Vardan Arutiunian
Mentor Role: Postdoctoral Fellow
Principal Investigator: Sara Webb
Institution: Seattle Children’s Hospital
Location: Seattle, WA
Lab Website: http://depts.washington.edu/pbslab/wordpress

Project Title: Excitation/inhibition imbalance, it’s neural correlates and relation to clinical phenotypes in youth with autism

Project Description: Neurophysiological studies of the past decade have suggested that the imbalance between neural excitation (E) and inhibition (I) is one of the core pathophysiological mechanisms contributing to autism. Cortical gamma-band oscillations (30-80Hz) measured with electroencephalography (EEG) can be a non-invasive measure of E/I balance and, thus, they are of particular interest in autism research. However, little is known about 1) how this measure derived from resting-state EEG is associated with other measures of E/I balance (aperiodic exponent and alpha peak); and 2) how a heterogeneous group of youth with autism can be divided and grouped based on the measures of E/I balance in relation to clinical phenotype.

The aim of the project is to provide a secondary data analysis of a large sample of youth with and without autism (n = 400) from the Autism Biomarkers Consortium for Clinical Trials (ABC-CT). For each participant, resting-state EEG as well as behavioral clinical measures (e.g., language/communication skills, non-verbal IQ and the profoundness of autistic traits) were collected. In this project, we address between-group differences (youth with vs. without autism) in measures of E/I balance and subgrouping of autistic groups based on the measures of E/I balance and clinical phenotype.

Mentor Biography: Vardan Arutiunian is currently a postdoctoral fellow at Seattle Children’s Research Institute, Sara Jane Webb’s Lab (Seattle, WA, USA). He received a doctorate in linguistics at the Center for Language and Brain (HSE University, Moscow, Russia) in the field of language and communication in autism (dissertation topic: “Language Impairment in Children with Autism: Linguistic Aspects”). In his research, Vardan uses behavioral assessment, genetic approaches and neurobiological methods (e.g., magnetoencephalography, electroencephalography, brain morphometry) to investigate variability of language skills, as well as structural and functional brain mechanisms of language impairment in children with autism. He received a number of research and teaching awards from several organizations, including the European Union, and has published eight articles in international peer-reviewed journals.

Mentor Name: Siyue (Brenda) Qiu
Mentor Role: Graduate Student
Principal Investigator: Scott Murray
Institution: University of Washington
Location: Seattle, WA
Lab Website: https://www.murraybrainlab.com

Project Title: Altered attention allocation in individuals with autism

Project Description: Visual attention is a cognitive process during which the brain selectively focuses on specific visual information while ignoring others. It is conceivable that visual attention is crucial for navigating the everyday world, and differences in visual attention could significantly affect visual perception. Emerging research suggests that autistic individuals allocate attention in a fundamentally different way from neurotypical individuals, leading to differences in their sensory and perceptual processing.

This project aims to measure the quantitative differences in attention allocation in autistic individuals and investigate whether these differences correspond to variations in sensory and perceptual neural responses. In terms of behavioral measurements, we will assess the spatial attention profile of autistic vs. neurotypical individuals through psychophysics experiments. To understand potential differences in neural responses, we will measure the attention field size of different visual cortical regions through single-voxel population receptive field modeling. This project consists of a series of experiments using a variety of methodologies, and the SURFiN mentee would have the opportunity to be involved in many aspects of it, including the collection of behavioral and fMRI data and the subsequent data analysis using programming languages (including Python, R, and MATLAB; no prior experience required). In addition, the mentee would also receive support on skills generally applicable to their later careers, including scientific reading, writing and presentation skills.

Mentor Biography: Siyue (Brenda) Qiu is a doctoral student in the Department of Psychology at the University of Washington. Siyue received her bachelor’s degree with honors in psychology from New York University (NYU) in 2023, after which she joined the Murray lab as a psychology graduate student in the area of cognition and perception. Her current research focuses on the neural and computational mechanisms of visual attention in both neurotypical and neurodivergent populations using neuroimaging techniques. Before joining the Murray Lab, Siyue was an undergraduate researcher in the Winawer lab at NYU, where she studied the retinotopic organization of the human visual cortex. During her time there, she gained experience in conducting fMRI experiments and analyzing retinotopic data. She is enthusiastic about mentoring aspiring researchers and is dedicated to fostering their growth and passion for research.

Mentor Name: Daniela Seczon
Mentor Role: Graduate Student
Principal Investigator: Scott Murray
Institution: University of Washington
Location: Seattle, WA
Lab Website: https://www.murraybrainlab.com

Project Title: Alpha-band oscillations and their role in attention modulation

Project Description: Alpha oscillations are naturally occurring brain oscillations that happen in the 8-13 Hz frequency range. These are often observed in posterior regions of the brain, and they tend to increase when an individual is relaxing with their eyes closed and decrease when an individual is engaged in active cognitive tasks. These observations have led to the hypothesis that these oscillations serve an inhibitory influence over neural activity, potentially aiding in filtering out irrelevant information. This brings about their potential implication in cognitive functions, such as attention and perception.

This project aims to investigate the roles that alpha oscillations play in attention modulation and explore potential differences in autism. The project will involve the designing and implementation of attentional tasks. The SURFiN fellow can expect to gain experience in the science of brain oscillations and become familiar with electrophysiological methods (e.g., EEG). They can also expect to develop a variety of skills, including, data analysis (which will include programming, although no prior experience is required!), scientific reading, conducting literature reviews and sharing of scientific progress.

Mentor Biography: Daniela (Dani) Seczon is a clinical psychology graduate student in the Murray lab at the University of Washington. Her work focuses on understanding the neural mechanisms that underlie individual differences in perceptual processes in autism. Daniela’s current research project involves examining the role that alpha-band power plays in shaping these perceptual differences. Daniela received her bachelor’s degree in psychology from the University of Tulsa, where she explored the association between eye-tracking responses and psychoticism. She also received a master’s degree in neuroscience from Teachers College, Columbia University, where she studied eye-tracking and EEG responses in perceptual organization tasks among individuals with schizophrenia and schizotypal personality disorder.

Mentor Name: Ryan Canfield
Mentor Role: Graduate Student
Principal Investigator: Amy Orsborn
Institution: University of Washington
Location: Seattle, WA
Lab Website: https://faculty.washington.edu/aorsborn

Project Title: Laminar-specific coordination of activity across motor cortices during reaching

Project Description: Performing a goal-directed movement is largely the result of two steps: planning and execution. To pick your keys up from the table, your brain first plans how far and how fast to reach, then sends the signals to your arm muscles to correctly execute the movement. Evidence shows that different parts of motor cortices are primarily associated with planning and execution. Generally, planning-related neural activity is first seen in the pre-motor cortex (PMd) followed by execution-related activity in the primary motor cortex (M1). This project asks how information is transferred and transformed from planning through execution across motor cortical regions by comparing the computations performed in the output layer of PMd, the input layer of M1, and the output layer of M1. As part of our team, you will assist with designing the necessary hardware to successfully conduct these experiments then assist experiments where this hardware is implemented. You will also use machine-learning methods to identify shared neural activity patterns in cortical layers across areas in motor cortices. The project will provide training in both experimental and computational approaches in systems neuroscience and novel ways to study motor control.

Mentor Biography: Ryan Canfield is a Bioengineering doctoral student in the Orsborn lab. His current work focuses on improving the accessibility of neuroprosthetic devices by investigating how the brain learns new motor skills. He conducts experiments that leverage high-density neural recordings, optogenetics and brain-machine interfaces (BMI) in monkeys to study how neuronal networks both constrain learning and adapt during learning. His doctoral research and training have been partly supported by the Institute of Translational Health Sciences (ITHS) TL1 training program. Before joining the Orsborn lab, Canfield received his master’s degree in mechanical engineering from the University of Washington where he implemented automated material property tests and data analysis for composite aircraft parts.

Mentor Name: Anna Li
Mentor Role: Doctoral Candidate
Principal Investigator: Nicholas Steinmetz
Institution: University of Washington
Location: Seattle, WA
Lab Website: steinmetzlab.net

Project Title: Simultaneous imaging and control of cortical activity in the mouse brain

Project Description: Join an interdisciplinary team from neuroscience, applied math and engineering backgrounds working toward a new understanding of brain dynamics. In this project, we have the goal of testing our models of brain activity by manipulating aspects of the activity patterns to determine whether we can correctly predict the way these perturbations affect other aspects of the patterns and, eventually, the way the perturbations affect the perception and behavior of the subjects. This project will involve work developing experimental techniques for performing simultaneous manipulation and recording, data collection and data analysis. The experimental subjects are mice, so this position involves performing experiments with live animals and will include training on the proper performance of these techniques.

Mentor Biography: Anna Li is a fourth-year neuroscience doctoral candidate in the Steinmetz lab at the University of Washington. She earned her undergraduate degree in behavioral neuroscience at Northeastern University. Before starting her graduate studies, she was a post-baccalaureate fellow in the Histed lab at the National Institutes of Health. In the Steinmetz lab, she studies how interactions between different brain areas impact visual coding in the mouse brain.

Mentor Name: Zhiyan Xu
Mentor Role: Graduate Student
Principal Investigator: Xinyu Zhao
Institution: University of Wisconsin, Madison
Location: Madison, WI
Lab Website: https://zhao-lab.com

Project Title: To determine the critical periods of FMPP restoration for correcting cellular deficits in FXS mice

Project Descriptions: The Fragile X Messenger Ribonucleoprotein (FMR1) encodes FMRP, a brain-enriched RNA-binding protein. FMRP deficiency causes Fragile X Syndrome (FXS), a neurodevelopmental condition with cognitive and behavioral difficulties. Individuals with FXS exhibit hyperactivity, impaired learning, reduced social interaction and repetitive behaviors. While FXS mice serve as valuable models for studying the syndrome, a crucial question remains unanswered: What are the critical periods for effective treatment to induce correct cellular changes in FXS mouse models? In this project, we aim to determine the critical periods of FMPP restoration for correcting cellular deficits in FXS mice. We will use various cell type-specific markers and utilize high-resolution fluorescent images to generate three-dimensional reconstructions with innovative software for subsequent quantitative analyses. This approach will help identify specific brain regions and analyze cell populations within each region after restoring FMRP at different ages. The SURFiN fellow will gain background knowledge in neuroscience and neurodevelopment and lean skills and techniques, including genotyping, mouse brain sectioning, immunofluorescence staining, image capture using microscopes and three-dimensional brain structural analysis. The outcome of this project will yield important information for treatment for FXS.

Mentor Biography: Zhiyan Xu is a second-year doctoral student in the Cellular and Molecular Biology Graduate Program at the University of Wisconsin-Madison (UW-Madison). He earned his bachelor’s degree and master’s degree in pharmaceutical science at Nanjing Medical University and Rutgers University, respectively. He then worked as a research assistant at Rutgers University to study the role of the sonic hedgehog signaling pathway in regulating the plasticity of the adult central nervous system in mouse models,using genetic, surgical, pharmacological, histological and transcriptomic approaches. He became interested in neurodevelopment after enrolling as a doctoral student at UW-Madison, where he joined Xinyu Zhao’s laboratory in 2022. His research focuses on determining the developmental timing for treating fragile X syndrome using mouse models. His work has yielded several publications, including one co-first author publication in Proceedings of the National Academy of Sciences of the United States of America and one coauthor paper in Neurons. He has been mentoring undergraduate students since his master’s training and he is currently mentoring three undergraduate students in the Zhao laboratory.

Mentor Name: Soraya Sandoval
Mentor Role: Graduate Student
Principal Investigator: Xinyu Zhao
Institution: University of Wisconsin, Madison
Location: Madison, WI
Lab Website: https://zhao-lab.com

Project Title: To investigate the mechanism underlying fragile X syndrome using brain organoids

Project Descriptions: Fragile X syndrome (FXS) is the most common form of inherited intellectual disability and autism. FXS is typically caused by the loss of X-linked fragile X messenger ribonucleoprotein (FMRP), an RNA binding protein that controls many aspects of gene expression important for neuronal function. Our laboratory uses human-induced pluripotent stem cells (iPSCs) derived from FXS patients to study the functions of FMRP in human neurons. However, human neurons can only be maintained for a short period of time, whereas cortical brain organoids can be maintained for at least a year and provide a three-dimensional structure that is closer to the developing brain. For my doctoral thesis, I am generating FXS cortical organoids and using immunohistochemical, functional and genetic techniques to test the hypothesis that FMRP deficiency leads to dysregulation of FMRP targets important for neuronal maturation resulting in disrupted development. The SURFiN fellow will help to test this hypothesis by performing immunohistochemistry to quantitatively analyze the cell composition of FXS and control organoids at multiple developmental time points, as well as becoming well-versed in molecular techniques, like quantitative polymerase chain reaction (qPCR) and western blot to identify dysregulated molecular mechanisms in FXS.

Mentor Biography: Soraya Sandoval is a fourth-year graduate student in the Neuroscience Training Program at the University of Wisconsin-Madison. Her first research experience was through the Keep Engaging Youth in Science internship at the University of Arizona where she later obtained her bachelor’s degree in biochemistry and molecular and cellular biology. As an undergraduate student, Soraya worked in the laboratory of Brett Colson studying the function of myosin binding protein-C in muscle contractility. She was a Ronald E. McNair Achievement Scholar and earned the Galileo Circle Scholarship award for her research. Her keen interest in mentorship led her to mentor two students, earning her the Biochemistry Outstanding Peer Mentor Award. After graduation, Soraya decided to pursue a doctorate in neuroscience to follow her research interests in neurodevelopment. She currently receives her doctoral training in the laboratory of Xinyu Zhao where she investigates the mechanism underlying fragile X syndrome using brain organoids derived from human-induced pluripotent stem cells. She has been awarded the Science and Medicine Graduate Research Scholars fellowship and an NIH diversity supplement for her research. She has been mentoring three undergraduate students and hopes to continue to enhance her graduate training through mentorship.

Mentor Name: Natasha Mendez Abelo
Mentor Role: Graduate Student
Principal Investigator: Xinyu Zhao
Institution: University of Wisconsin, Madison
Location: Madison, WI
Lab Website: https://zhao-lab.com

Project Title: To interrogate the functions of RNA binding protein fragile X autosomal homolog 1 in the development of human excitatory neurons

Project Descriptions: Our project will focus on studying the brain-enriched RNA binding protein fragile X autosomal homolog 1 (FXR1) in the development of human excitatory neurons. FXR1 is crucial for development, because its loss of function is intolerant in humans and causes neonatal death in mice. Despite a lack of direct evidence linking FXR1 to many neurodevelopmental conditions, FXR1 has been associated with a number of brain conditions, including autism, bipolar disorder and schizophrenia. However, the functional role of FXR1 in human neurons has not been investigated. This project aims to determine the role of FXR1 in the development of human forebrain excitatory neurons. To achieve these goals, I use human-induced pluripotent stem cells (iPSCs) that have either FXR1 knockdown or knockout and study how the absence of FXR1 affects neuronal morphology, survival and gene expression. The SURFiN fellow will be able to learn various quantitative techniques like immunohistochemistry, stereology quantification, qPCR and western blot as well as gain basic knowledge in stem cells and neurodevelopment. The outcome of this study will provide insight into the functions and mechanisms of FXR1 in human brain development.

Mentor Biography: Natasha Méndez-Albelo is in her fourth year of her doctoral training at the Molecular and Cellular Pharmacology program (MCP) at the University of Wisconsin-Madison. She earned her bachelor’s degree in cell and molecular biology at Ana G. Mendez University (UAGM), Cupey campus in Puerto Rico. During her time at UAGM, she studied how specific leukemia drugs affected cellular morphology and protein expression. She was accepted twice by the NINDS-funded ENDURE program and performed research two consecutive summers at Michigan State University. She presented her data at the SACNAS and SfN conferences. Her interest lies in studying the signaling pathways that regulate neurodevelopment for developing novel therapeutics for brain diseases. This interest led her to enroll in the MCP program and join Xinyu Zhao’s laboratory. She has been awarded the Science and Medicine Graduate Research Scholars fellowship, an NIH pre-doctoral trainee fellowship, and a predoctoral fellowship from Wisconsin Stem Cell and Regeneration Medicine Center. Her thesis project aims to understand the role of a brain-enriched RNA binding protein in the development of human excitatory neurons. She has been mentoring undergraduate students for over two years, and she is excited to assist new students in discovering their enthusiasm for neuroscience.

Mentor Name: Yu Gao
Mentor Role: Research Scientist
Principal Investigator: Xinyu Zhao
Institution: University of Wisconsin, Madison
Location: Madison, WI
Lab Website: https://zhao-lab.com

Project Title: Epigenetic regulation of neurodevelopment by methyl-CpG binding protein 1

Project Description: This project aims to investigate the regulatory mechanism by methyl-CpG binding protein 1 (MBD1), a gene associated with autism, and evaluate the roles of genes targeted by MBD1 in brain development. We will use several experimental models created in our laboratory, including MBD1 knockout mice, mouse lines with mutations found in human individuals with autism, and human pluripotent stem cell lines with human MBD1 mutations for this study. The SURFiN fellow can anticipate the following experiences: (1) actively participating in the mentor’s research and acquiring fundamental knowledge in areas such as transgenic mouse models and epigenetics; (2) learning techniques, including genotyping, gene manipulation (gene knockdown and activation), and neuron morphological analyses; (3) conducting sample preparations and data collections from MBD1 deficient neurons; (5) engaging in research discussions, attending research seminars/presentations and presenting findings at lab meetings; (6) contributing to manuscript(s) that we plan to submit in the coming year.

Mentor Biography:
Yu Gao is a research scientist of molecular neuroscience at the University of Wisconsin-Madison. He received a doctoral degree in developmental biology specializing in epigenetic regulations of embryonic development from the University of Copenhagen (Denmark). As a postdoctoral fellow, and now research scientist in Xinyu Zhao’s laboratory at the University of Wisconsin-Madison, he investigates the genetic and epigenetic mechanism underlying brain development and plasticity. His research has unveiled the critical roles played by epigenetic regulators, such as MeCP2, associated with Rett syndrome, and MBD1, linked to autism, in complex regulation of brain development. In addition, he is using single cell genetics to explore the molecular mechanisms underlying neuronal maturation during the prenatal development when neurons undergo significant changes in morphology, physiology and gene expression. His research has yielded eight first author or co-first author publications and 16 collaborative publications. He has trained more than 15 undergraduate students with five students receiving competitive awards and graduate school admission.

Mentor Name: Itamar Lev
Mentor Role: Postdoctoral Fellow
Principal Investigator: Manuel Zimmer
Institution: University of Vienna
Location: Vienna, Austria
Lab Website: https://neurodevbio.univie.ac.at/zimmer-research/

Project Title: Analysis of dominant re-afferent oxygen signals in whole brain activity of freely-moving C. elegans

Project Description: The ability to distinguish between external sensory stimuli and self-generated signals is fundamental for animals to effectively navigate and interact with their environment. Recently, our lab has developed a method for recording whole-brain neuronal activity in freely-moving animals. Utilizing this method, we have discovered that a significant portion of neural activity in freely-moving animals is associated with intrinsic activity of forward-backward motor commands. Importantly, our recent investigations have unveiled an additional layer of complexity in the neural dynamics of freely-moving animals. Specifically, we have identified sensory neurons exhibiting forward and reversal activity patterns, distinct from intrinsic motor-related signals. Remarkably, we gathered evidence suggesting that these sensory neurons respond to oxygen (O2) signals originating from the animal itself. In this proposed project, we aim to further characterize the oxygen-responsive neurons and elucidate their activity in response to shifts in oxygen levels and movement. Finally, we will validate that movement-related activity is O2-driven by using a mutant background that lacks the ability to sense O2.

Mentor Biography: Itamar Lev is currently a postdoctoral fellow in the Zimmer lab at the University of Vienna investigating C. elegans neuroscience. He completed his Ph.D. at Tel Aviv University, where he worked on transgenerational inheritance via heritable small-RNAs in C. elegans. Currently, he studies how distributed brain states convey feedback on behavior execution and how these behaviors are flexibly adjusted in varying environments. His research leverages novel and unique techniques such as functional whole-brain imaging in freely behaving animals. A special interest of his work is to study neuronal responses in natural, ecologically relevant settings such as when the worms interact with their predator, a nematophagic fungus. His research is funded by the VIP2, EMBO and now HFSP postdoctoral fellowships.

Mentor Name: Benjamin Schaar
Mentor Role: Doctoral Student
Principal Investigator: Manuel Zimmer
Institution: University of Vienna
Location: Vienna, Austria
Lab Website: https://neurodevbio.univie.ac.at/zimmer-research/

Project Title: Odor induced neural activity and behavior in C. elegans

Project Description: In this project, we will explore the dynamics between the brain, body and environment in the nematode C. elegans while it moves through a sensory-enriched environment. C. elegans’s navigation highly depends on its ability to sense chemical stimuli in the environment through chemosensory neurons. Importantly, when navigating static landscapes of food borne odorants, much of the animal’s perception must be directly coupled to its locomotion. Little is known so far how animals integrate both their ongoing behavior with movement-induced perception of the environment to make navigational decisions.

During this SURFiN internship, we will (1) use state of the art high-speed cameras to image the worm’s behavior while it crawls through defined odorant landscapes to characterize its navigational behaviors with unprecedented detail; and (2) image the worm’s whole brain activity while it is exposed to different olfactory stimuli to assess how external sensory information is perceived and processed.

Both parts, (1) and (2), will include extensive training in both wet lab skills (e.g., animal maintenance and recording of behavior and neuronal activity using advanced microscopy techniques) as well as in computational skills to analyze high-content behavioral and neuronal datasets. Since we are using Python for data analysis, some prior programming knowledge is beneficial but not strictly required.

Mentor Biography: Benjamin Schaar is a doctoral student in the Zimmer lab, which is situated in the UBB, the University of Vienna’s new Bio-Center in the third district of Vienna. He studied molecular neuroscience at the University of Vienna and did his master’s thesis at the Medical University in the field of neuropharmacology. His current research interests include understanding the dynamics between the brain, the body and the environment in the nematode C. elegans during food chemotaxis.

Mentor Name: Mai Ahmed
Mentor Role: Research Fellow
Principal Investigator: Yun Li
Institution: SickKids Hospital
Location: Toronto, Ontario, Canada
Lab Website: https://lab.research.sickkids.ca/li

Project Title: Studying the role of autism-linked genes in human neural stem cells using functional genomics

Project Description: To date, over 1000 genes are linked to autism, suggesting its strong genetic contribution. However, how perturbations in these genes contribute to autism pathology at the cellular and molecular levels remains largely elusive. Several studies have reported that mutations in autism-linked genes led to disrupted neurogenesis and altered brain size. In this project, we aim to utilize large-scale functional genomics approaches to examine how perturbations of autism-linked genes will impact human neural stem cell (NSC) behavior at the transcriptomic and functional levels. This study will shed light on the different gene networks that converge on NSCs for autism pathology, which will provide novel therapeutic targets that can improve condition outcomes in people with autism. To conduct this project, we will perform molecular cloning experiments to generate a CRISPR knockout library of autism-linked genes. Furthermore, we will generate hPSC-derived 2D neural stem cell cultures to test the library and 3D brain organoids to validate our findings. We will also perform different molecular biology techniques, imaging, viral infections and bioinformatics analyses. The SURFiN student will be involved in the design and implementation of many of these approaches.

Mentor Biography: Mai Ahmed is a postdoctoral research fellow in Yun Li’s lab at the Hospital for Sick Children (SickKids) in Toronto. Mai received her doctorate in developmental neurobiology from the Okinawa Institute of Science and Technology Graduate University (OIST) in Japan. During her graduate research in Ichiro Masai’s lab, Mai examined the molecular mechanisms that underlie retinal neural circuit development using the zebrafish model. In her postdoctoral research, Mai is interested in applying functional genomics approaches using human pluripotent stem cell-derived neural cultures to study the mechanisms that underlie human-specific brain development and neurodevelopmental conditions, such as autism. In 2023, Mai received a Human Frontier Science Program Long-Term fellowship to support her postdoctoral research. Mai is passionate about teaching and mentorship. During her training, she has served as a teaching assistant in different undergraduate and graduate courses and mentored several undergraduate students toward their thesis projects.

Eligibility: SickKids is fully affiliated with the University of Toronto, which is a credit-granting institution, but SickKids itself does not grant any academic credit.

Mentor Name: Ourania Semelidou
Mentor Role: Postdoctoral Fellow
Principal Investigator: Andreas Frick
Institution: Institut National de la Sante et de la Recherche Medicale, ADR-Bordeaux
Location: Bordeaux, France
Lab Website: https://neurocentre-magendie.fr/recherche/Frick/descriptionTeam.php

Project Title: Exploration of altered tactile perception in a mouse model of autism using a translational approach

Project Description: Altered sensory experience is one of the core features of autism, a neurodevelopmental condition also characterized by alterations in social communication and repetitive behaviors. Altered sensitivity and reactivity to sensory stimulation affect 90% of autistic individuals, having a strong impact on their day-to-day life and contributing to the development of higher cognitive traits and repetitive behaviors. Importantly, these simple sensory alterations can be exploited to identify the neurobiological mechanisms of autism.

In this project, our lab aims to explore the neurobiological mechanisms that underlie altered tactile perception in autism. To this end, we use a sophisticated toolset by combining a novel behavioral task with in vivo two-photon microscopy in a genetic mouse model of autism. To assess tactile sensitivity, we developed a perceptual decision-making task where the animal discriminates vibrotactile stimuli of different intensities to receive a water reward. In parallel, we measure neuronal activity at cellular resolution, focusing on the excitatory and inhibitory neurons of the somatosensory cortex. The results of this project will help us understand how tactile responses are changed in autism and identify their neocortical underpinnings, aiming to establish preclinical biomarkers to test treatments for autism.

Mentor Biography: Ourania Semelidou is a postdoctoral researcher in neuroscience at the Neurocentre Magendie, in Bordeaux, France. Following a bachelor’s degree in molecular biology and genetics and a master’s degree in molecular medicine, she obtained a doctorate in neuroscience from the University of Crete. Her work has yielded novel and influential insights into the neuronal and molecular underpinnings of perception, learning and memory, and how changes in these features contribute to neurodevelopmental and psychiatric conditions (autism, schizophrenia). In her current project, she focuses on better understanding altered sensory experience in autism by characterizing perceptual measures of tactile and multisensory information processing and uncovering their neural underpinnings in genetic mouse models of autism. Throughout her research career, she has received numerous honors and awards, including a postdoctoral fellowship for three years from the Fondation pour la Recherche Médicale (FRM) and in a mobility project funding from the GIS Autisme et TND, the autism and neurodevelopmental disorders scientific interest group that is supported by the French National Strategy for Autism. In 2018, she was selected as one of the young scientists representing the next generation of leading scientists and researchers to participate in the 68th Lindau Nobel Laureate Meeting, dedicated to physiology and medicine.

Mentor Name: Senka Hadzibegovic
Mentor Role: Postdoctoral Fellow
Principal Investigator: Andreas Frick
Institution: Institut National de la Sante et de la Recherche Medicale, ADR-Bordeaux
Location: Bordeaux, France
Lab Website: https://neurocentre-magendie.fr/recherche/Frick/descriptionTeam.php

Project Title: Changes in neuronal excitability contribute to the early cognitive decline in Alzheimer’s disease

Project Description: Rapid forgetting emerges as an early indicator of Alzheimer’s disease (AD), correlating with amyloid-ß accumulation in the prefrontal cortex (PFC). Our research data demonstrates that associative learning tasks engage specific neuron populations in the PFC, inducing plasticity in their intrinsic excitability through different ion channels which is crucial for long-term memory storage. Furthermore, amyloid-ß disrupts the function of these ion channels in PFC neurons. We hypothesize that this abnormal excitability leads to PFC network dysfunction and impairs cellular memory mechanisms, resulting in accelerated forgetting. Our proposal aims to address how amyloid-ß impacts PFC neuronal ensemble activity at the cellular level across memory formation phases. Additionally, we seek to investigate the effects of modulating PFC engram neuron excitability on memory deficits and network activity. These measures could lead to development of therapeutic strategies targeting ion channels as potential interventions in early-stage AD. Our approach integrates associative memory tasks with innovative viral tool-based methods, mouse models of AD, electrophysiology and qPCR techniques.

Mentor Biography: After obtaining a diploma in biological pharmacy from Belgrade University in Serbia, Senka Hadzibegovic was awarded an Erasmus Mundus fellowship to pursue her doctorate in neuroscience at the University of Bordeaux, France. Her research utilized various approaches, including behavioral and molecular analyses in a mouse model of Alzheimer’s disease (AD), to discover novel markers of AD. Her findings highlighted the significant role of hippocampal oscillations, known as sharp-wave ripples, in spatial memory formation. Additionally, she identified amyloid-β-induced disruptions in the dynamics of these ripples as a mechanism contributing to spatial memory deficits in AD. Senka presented her work at international conferences where she received awards for best poster and presentation. Currently, as a postdoctoral researcher in the Frick lab at Bordeaux, she investigates neuronal allocation mechanisms of remote memories under physiological conditions and in two AD mouse models. Her research aims to comprehend the molecular and cellular processes underlying memory formation and to pinpoint changes that may elucidate memory deficits associated with AD. Senka has also mentored several graduate student projects, guiding them through complex neuroscientific techniques and providing scientific and intellectual support to foster their development into independent and confident young scientists.

Mentor Name: Melanie Ginger
Mentor Role: Permanent Scientist
Principal Investigator: Andreas Frick
Institution: Institut National de la Sante et de la Recherche Medicale, ADR-Bordeaux
Location: Bordeaux, France
Lab Website: https://neurocentre-magendie.fr/recherche/Frick/descriptionTeam.php

Project Title: Probing the role of thalamo-cortical loop dysfunction in genetic mouse models of autism

Project Description: Melanie Ginger is interested in how neocortical circuits are modified in genetic mouse models of autism. She is particularly interested in the role of prefrontal cortex circuit alterations in sensory filtering and attention. Numerous evidence points to a role for the prefrontal cortex circuit alterations in autism, but this brain area has, to date, been poorly explored. The prefrontal cortex has reciprocal connections with the cognitive thalamus, which is itself a hub for modulatory signals, through its diverse connections with cortical and non-cortical areas. The project will explore alterations in these circuits using a novel circuit tracing approach based on set-tagging. We will also use behaviors and other approaches to measure or modify circuit activity.

Mentor Biography: Melanie is a tenured research associate in the team of Andreas Frick. After a doctorate in biochemistry and a postdoctoral fellowship in cell biology/cancer biology, she converted to neuroscience research. After second postdoctoral fellowship, she joined the team of Andreas Frick where she is interested in neocortical circuits and their plastic or pathophysiological modification in memory or neurodevelopmental conditions, such as autism. To address these questions, she uses behavior and a range of techniques for circuit tracing or manipulation. She is currently preparing for the French Professorial exam (or ‘Habilitation’). She supervises two doctoral students and has supervised numerous master’s students in the past.

Mentor Name: Firdaouss Zemmouri
Mentor Role: Predoctoral Fellow
Principal Investigator: Hiroki Asari
Institution: European Molecular Biology Laboratory
Location: Rome, Italy
Lab Website: https://www.embl.org/groups/asari/

Project Title: Characterization of retinal signal transformation in the mouse superior colliculus

Project Description: The visual system consists of a hierarchy of distinct brain areas, each responsible for processing different aspects of visual features. To better understand how signals from an upstream area contribute to visual processing in the downstream area, this project will focus on a specific type of computation broadly found in the visual system (i.e., selectivity to motion direction). Many neurons in the mouse superior colliculus, a direct target of the retina, preferentially respond to stimuli moving in one direction but not the opposite, with diverse direction preferences across populations. Such direction-selective responses can be found already in the retina but biased to the four cardinal directions: up, down, left and right. This raises a question: Is direction selectivity in the superior colliculus fully dependent on the retinal inputs or (re-)computed de novo? To address this question, we will take interdisciplinary approaches — including in vivo two-photon calcium imaging, genetic manipulations and statistical data analysis and modelling — and study how direction-selective retinal signals are integrated and processed in the mouse superior colliculus. Candidates can have a background from either natural science, such as biology and physics, or computer science, and the project involvement will be tailored to their specific interests and expertise.

Mentor Biography: Firdaouss Zemmouri is a predoctoral fellow in Hiroki Asari’s group at the European Molecular Biology Laboratory (EMBL Rome, Italy) since September 2021. She received a bachelor’s degree in biomedical sciences in 2018 and a master’s degree in neurosciences in 2020, both from the University of Antwerp, Belgium. As a predoctoral fellow, Firdaouss’ scientific interests are in the wiring principles that guide the specific organization of different neuronal cell types, enabling them to perform specific neuronal functions in the early visual system. More specifically, she aims to unravel how the topographic relationship of motion sensitive cell types in the visual pathway. To address this, Firdaouss takes an interdisciplinary approach, including in vivo two-photon calcium imaging, genetic manipulations and statistical data analysis and modelling.