Carlos D. Brody - US grants

? DESCRIPTION (provided by applicant): Working memory, the ability to temporarily hold multiple pieces of information for mental manipulation, is central to virtually all cognitive abiliies. Working memory has been closely associated with multiple kinds of neural activity dynamics, such as persistent neural activity, activity ramps, and activity sequences. The neural circuit mechanisms of these dynamics remain unclear. This proposal will apply advanced technologies such as virtual reality, automated monitoring of behavior, in vivo microscopy, ontogenetic, and neural circuit reconstruction to solve fundamental problems in the understanding of working memory. The accumulation of evidence over time scales of seconds, a type of working memory critical for decision-making, will be used as a test bed for studying working memory. The proposal will build upon a rodent evidence-accumulation paradigm that allows quantitative, temporally precise parameterization of working memory and decision-making. The paradigm will be implemented with head-fixed rodents behaving in a virtual reality system (Aim 1), providing mechanical stability that enables the use of two-photon calcium imaging to observe neural activity related to working memory in the neocortex, basal ganglia, and cerebellum (Aim 3). Brain activity will also be perturbed using ontogenetic to probe the roles of brain regions and specific cell types in the formation and stabilization of memory (Aim 2). Finally, we will develop methods for probing the roles of cell types and connectivity in working memory through correlative serial electron microscopy and light microscopy as well as imaging of population responses to ontogenetic stimulation of single cells or groups of cells (Aim 4). This three-year project will produce a catalog of the types of neural circuit dynamics that are related to working memory across many brain regions. In subsequent years, this catalog will be mechanistically investigated by the anatomical and physiological methods developed in Aim 4. The long-term goal of this project is to arrive at a complete, brain-wide understanding of the cellular and circut mechanisms of activity dynamics related to working memory. The understanding is expected to take the form of a new generation of models containing cognitive variables distributed across brain regions, as well as models that explicitly represent neural circuit dynamics. This achievement will be a crucial step towards a mechanistic understanding of the neural basis of cognition.

? DESCRIPTION (provided by applicant): Many types of decisions that are important in everyday life are driven by the gradual accumulation of evidence favoring one possible outcome over another. The long-term goal of this line of research is to understand how individual brain areas and their interactions process information related to evidence accumulation to reach decisions. Previous work from this laboratory has determined how regions in the brain's cortex encode such information and has determined their temporally precise causal role in a rat model of perceptual decisions. The proposed experiments will study the specific contributions of two subcortical brain areas, the striatum and the superior colliculus, to decision-making. The overall objective of this application is to understand how decision- related information is encoded in each of these areas, whether each representation is required for decision-making, and exactly when during a task trial this information is needed. In addition, we will distinguish the causal roles of neural connections from frontal cortex to each area individually. We will achieve this objective by recording neural activity to examine the moment-by-moment electrophysiological signatures of evidence accumulation in these subcortical areas and compare them directly to decision variables from behavioral data. Then we will inactivate each of these areas or the projections to them to define whether, and when, such neural activity is required for accumulation of evidence. The contribution is significant because it will resolve several important questions about the flow of information across time and space in this circuit. The approach is innovative because this laboratory has developed tools that allow continuous, single-trial estimates of decision behavior variables along with precisely timed interference with task-relevant signals within and between brain regions. The work proposed in this application will therefore advance knowledge of how the encoding of information and interactions among brain regions lead to decisions. In the long run, we expect this research to produce a detailed understanding of how information flows through this brain circuit to produce decisions.

  Project Summary: Core 1, Administration    The Administrative Core will support the Team Director and the Internal Advisory Committee of this  multi-component research project as they supervise budgets and scientific activities to enable the project to  achieve its goal of determining how the brain produces working memory and decisions. The investigators in  this proposal have a strong history of collaboration over the past three years. The research projects that they  have developed are tightly integrated around shared conceptual questions and a closely related set of  behavioral tasks. To ensure that the project continues as a well-coordinated collaboration, the team will hold  monthly meetings that include all research personnel and weekly meetings of all project leaders to review  results and plan upcoming experiments. Six of the project leaders are based at Princeton University and are  part of a cohesive academic community that regularly interacts in scheduled meetings and spontaneous  discussions. The seventh project leader (located at the University of California, Davis) participates in weekly  team meetings via video link and will travel to Princeton as needed for formal meetings. The full team is  already sharing documents, drafts, figures, talks, and posters and conducting frequent informal discussions  on one dedicated Slack channel that is used by all research personnel and another channel for PIs only. The  team will hold one formal meeting per year of all personnel. The Annual Meeting will include the project  leaders, students, and postdocs, along with an External Advisory Board, to be appointed by the Team  Director. The purpose of this meeting will be to document and evaluate the previous year?s progress. The  administrator will coordinate the Annual Meeting and produce a monthly budget report for the Team Director  to review. The administrator will also assist all investigators in scheduling interviews for job candidates,  meeting reporting requirements, booking travel, and acquiring major supplies and equipment. Results from  the proposed research will be disseminated through formal and informal mechanisms, and the administrator  will assist in these efforts whenever possible. In addition, the Administrative Core will assist the Data Science  Core in managing the dissemination and ongoing support of the prototype data science framework for the use  of other researchers. The administrator will also design and implement public outreach activities. By managing  these resources and activities, the Administrative Core will help the Team Director to coordinate the five  Projects and the four Cores, while allowing the project leaders and other research personnel to concentrate on  their strengths in research by spending less time and energy on administrative tasks. 

Project Summary: Core 3, Behavior Automation Working memory, the ability to temporarily hold multiple pieces of information in mind for manipulation, is central to virtually all cognitive abilities. This multi-component research project aims to comprehensively dissect the neural circuit mechanisms of this ability across multiple brain areas. The individual parts of the project cohere conceptually, in part, because they all involve rodents trained to perform a type of decision-making task that is based on the gradual accumulation of sensory evidence and thus relies on working memory. To produce enough subjects for these experiments, this Core will scale up an existing high-throughput rat training facility run by technicians and adapt it for mice. This expansion will quintuple the project?s capacity for rodent training. To do so, we will take advantage of the expertise of the project leader in developing and managing such a training facility for sophisticated cognitive tasks in an existing virtual reality infrastructure, software, and hardware. Once this facility is operational, the Core will manage it and troubleshoot problems as needed. It will develop new hardware and software components for training rigs to make technician interventions as reproducible and error-free as possible. Because the most crucial and time-consuming aspect of mouse virtual training is ensuring that the head-fixed animal is properly aligned to the ball and the projection system, the Core will develop an automated alignment system based on image registration and actuators to replace the current manual alignment. It will develop software tools and standardized technician procedures to ensure consistency in rodent training, prevent training errors, detect hardware failures, and monitor the health of the animals. This centralized facility will promote rigor and reproducibility by reducing variability in animal training across labs, increase the rate of data acquisition, and free personnel to focus on designing and carrying out creative experiments. In the long run, the entire neuroscience community will benefit from this effort, as the software and hardware tools and management protocols produced will be made freely available, along with their documentation. These tools will enable other researchers to introduce automated training for well-controlled cognitive tasks in their own laboratories, leading to improved efficiency, rigor, and reproducibility in behavioral research across the field of neuroscience.

Project Summary Working memory, the ability to temporarily hold multiple pieces of information in mind for manipulation, is central to virtually all cognitive abilities. R? ecent technical advances have opened an unprecedented opportunity to comprehensively dissect the neural circuit mechanisms of this ability across multiple brain areas. The task to be studied is a common form of decision-making that is based on the gradual accumulation of sensory evidence and thus relies on working memory. ?A team of leading experts propose to investigate the neural basis of this behavior using the latest techniques, including virtual reality, high-throughput automated behavioral training, l? arge-scale cellular-resolution imaging ?in behaving rodents, manipulation of neural activity in specific brain areas and cell types, and a? utomated anatomical reconstruction?. In particular, the researchers will i? dentify key brain regions that are required for this decision task through systematic, temporally specific inactivations via optogenetics technology, across all of dorsal cortex and in key subcortical areas, and use quantitative model-fitting to evaluate the effects. They will use state-of-the-art ?two-photon calcium imaging? methods and electrophysiology to characterize the information flow in many individual neurons within these brain areas during the task. In addition, they will use cutting-edge anatomical reconstructions and new functional connectivity methods, within and across brain regions, to evaluate the interactions of these physiologically characterized neurons. ?The long-term goal of this project is to arrive at a complete, brain-wide understanding of the cellular and circuit mechanisms of activity dynamics related to working memory. ?Finally, they will use sophisticated computational methods to incorporate this new understanding into a realistic circuit model that will support a tightly integrated process of model-guided experimental design, in which the model suggests the most informative experiments and their results are then fed back to improve the model?s fidelity. ?This process is expected to produce? the most accurate and detailed multi-brain-region biophysical circuit model of a cognitive process in existence?. ?In addition, the proposed research will enable researchers to generate and test a variety of hypotheses about the neural basis of evidence accumulation, working memory, and decision-making. Taken together, these achievements will represent a crucial step toward a mechanistic understanding of how the brain works with information.

Project Summary: Project 1, Perturbations and Behavior Working memory, the ability to temporarily hold multiple pieces of information in mind for manipulation, is central to virtually all cognitive abilities. This multi-component research project aims to comprehensively dissect the neural circuit mechanisms of this ability across multiple brain areas. The individual parts of the project cohere conceptually, in part, because they all involve rodents trained to perform a type of decision-making task that is based on the gradual accumulation of sensory evidence and thus relies on working memory. Neural correlates of working memory and decision-making are distributed across a very wide range of cortical and subcortical regions, but a complete listing of which of these regions actually cause these processes?and most importantly, what the nature of their contribution might be?remains out of reach. A significant obstacle has been that these processes can evolve rapidly (for example, going from loading an item into working memory, to holding it in memory, to retrieving it) and it is only recently that inactivation tools, such as inhibitory optogenetic molecules, could be turned on and off fast enough to distinguish between different phases. This project will use optogenetic inactivation in combination with this set of closely related working memory and decision-making tasks for the head-fixed rodent. The tasks are amenable to highly quantitative behavioral analysis. These features will allow a systematic and comprehensive quantitative probe of the causal contribution to working memory and decision-making of a very large set of regions across the dorsal cortex, deeper cortices, and targeted subcortical regions, including the cerebellum, the ventral tegmental area, the hippocampus, and the striatum. Other experiments will study the causal contributions of different genetically defined cell types, in targeted brain regions. Taken together, these experiments are expected to provide detailed information about how the interaction of particular neurons in the brain produces working memory and decisions, increasing knowledge about the brain basis of cognition.

Project Summary: Understanding the mechanistic underpinnings of cognition is highly dependent on technologies that allow monitoring brain activity in behaving animals. The recent progress in functional ultrasonic imaging (fUSi) provides this ability by enabling imaging both cortical and subcortical brain structures simultaneously in freely moving animals. The long term goal of this line of research is to unravel the brain wide networks underlying cognitive tasks such as decision making and working memory. This lab has succeeded in training rats on sophisticated cognitive tasks with a special focus on evidence accumulation. Moreover, work from this lab has focused on studying one brain area at a time during evidence accumulation finding that frontal orbital field (FOF), posterior parietal cortex (PPC) and dorsal striatum are part of an integration circuit. The remaining nodes of this circuit are largely unknown and how activity is flowing from one brain area to another, in the context of evidence accumulation, remains to be elucidated. The proposed experiments will study the contribution of cortical and sub-cortical areas in the evidence accumulation process and pave the way for obtaining a circuit diagram for the neural mechanisms underlying this behavior. The overall objective of this project is to advance functional ultrasound imaging (fUSi) technology to measure cortical and subcortical brain activity during cognitive tasks and apply it to an evidence accumulation task as a test case. In the evidence accumulation context, fUSi will help us understand how decision related information is routed in the brain and which specific brains areas are involved in multiple aspects of the task. The contribution is significant because it will resolve several important questions about the flow of information across time and space in the brain during decision making. The approach is innovative because this laboratory has advanced tools that allow imaging both cortical and subcortical brain areas in a freely moving animal preforming cognitive tasks. The work proposed in this application will therefore advance our knowledge of how the encoding of information and interactions among brain regions lead to cognition with a special emphasis on decision making. In the long run, we expect this research to produce mechanistic models of cognition.

Project Summary Our ability to flexibly select, based on context, the relevant information to form decisions is a fundamental cognitive process, yet its underlying neural mechanisms are still largely unknown. Most of our knowledge at single-neuron resolution is derived from a few recent studies in macaque monkeys, where animals were trained to perform tasks requiring context-dependent selection and integration of sensory information. In these tasks, feature selection is performed within a sensory modality, and the strength of the evidence can be precisely titrated by the experimenter. Despite the groundbreaking impact of these studies, so far only a handful of brain areas have been studied, and no perturbation experiments have yet been performed. To address these issues, we will train rats to perform context-dependent selection and integration of sensory information, and we will leverage the powerful experimental tools available in rodents to dissect the neural circuits responsible for this behavior. First, we will develop a new pulse-based task requiring context-dependent selection and integration of sensory evidence. In our task, rats will be presented with a train of randomly-timed auditory pulses, where each pulse varies in its location (right or left) and its tone frequency (high or low). In separate blocks of trials, rats will be cued to report either the prevalent location of the pulses, or their prevalent frequency. Because in this task information will be presented to subjects in highly random but precisely known pulses, over the course of hundreds of thousands of trials we will have access to a highly varied sample of stimuli allowing us to fully characterize temporal dynamics of the processes involved. Second, we will develop an automated, high- throughput training pipeline to efficiently train rats to perform the task. Third, we will develop a complementary automated high-throughput setup for the collection of electrophysiology and optogenetics data during behavior. Fourth, we will develop a series of novel modeling and statistical analyses to leverage this rich dataset to probe the underlying computational mechanisms. The proposed approach aims to provide an unprecedented platform to probe the neural mechanisms underlying flexible decision-making.