Alan Michael Litke - US grants

The primary objective of this U.S.-Poland cooperative research project between Dr. Alan Litke of the University of California at Santa Cruz and Dr. Michal Turala of the Institute of Nuclear Physics, Krakow, is to develop a means for detecting and identifying short-lived particles, including charm hadrones, bottom hadrons and tau leptons, which emerge from high energy collisions. In addition to contributing to progress on a prototype vertex detector, the results of the project are expected to produce measurements of the decays of the Zo into heavy quark-anti-quark final states. The researchers also anticipate that their efforts will contribute to the fundamental search for the top quark. This project in particle physics fulfills the program objective of advancing scientific knowledge by enabling leading experts in the United States and Eastern Europe to combine complementary talents and pool research resources in areas of strong mutual interest and competence.

This proposal requests support for automated equipment for use in assembling and testing state-of-the-art silicon detectors and custom designed VLSI electronics to be used in several high priority experiments in the EPP program. This in-house facility will replace contractual work which cannot now meet the custom requirements of these detectors. Students and post-doctoral researchers will receive valuable training in the advanced techniques that are necessary in this project.

*** 9713365 Litke This grant will support the initial development of a system to study how the retina process and encodes a visual image. This "Retinal Readout System" will allow the simultaneous detection of signals from thousands of output cells in live retinal tissue as a visual image is focused on the cells. The signals from the output neurons will be detected in real- time, in a single retinal preparation, with all spatial and temporal correlations recorded. This system will be based, in large part, on technology developed in the field of high energy physics for the study of short-lived particles: the technology of silicon microstrip detectors. The silicon detector techniques to implement the Retinal Readout System include: high-density wire-bonding, custom-designed analog VLSI readout chips, and fast data acquisition. The specific items to be developed include a variety of electrode arrays for the detection of the retinal signals, a prototype VLSI chip (the "Neurochip") for reading out the electrode arrays, and a fast data acquisition system based on an analog-to-digital converter module installed in a PC. ***

This is a project to develop a "Retinal Readout System" that will allow the simultaneous detection of signals from hundreds to thousands of retinal output neurons while the retina is stimulated by dynamic visual images focused on the input neutrons. The signals from the output neurons will be detected in real time, from a single living retinal preparation, with all spatial and temporal correlations among the signals recorded. The Retinal Readout System will be based in part on the silicon microstrip detector technology and expertise developed to study short-lived particles in high energy physics experiments. The work will be carried out by an interdisciplinary team with expertise in high energy physics, neurobiology, nanofabrication, and VLSI design.

[unreadable] DESCRIPTION (provided by applicant): The goal of this research is to develop new technology that would allow neuroscientists to investigate emergent properties in networks of hundreds of synaptically connected cortical neurons. Although many of the most important emergent properties of brains are predicted to arise in "local" networks involving a few hundred neurons, limitations in technology have largely prevented experiments in this regime. Work at the local network level is difficult because it requires high temporal and spatial resolution at hundreds of recording sites over durations of hours. Most approaches used today fail to meet all of these requirements because of long distances between recording sites, short recording durations, or low temporal resolution. Without new approaches to study activity at the local network level, we will be limited in our ability to determine the mechanisms that allow networks to produce important emergent properties, and in our ability to understand disorders like epilepsy and schizophrenia that have been hypothesized to involve disruptions at the local network level. The specific objective of this proposal is the development of a 512 microelectrode array system that can detect and manipulate emergent properties in cortical slice networks. We propose to accomplish this goal by pursuing three specific aims: (1) develop the existing software for a 60 electrode array so that it will identify neuronal avalanches and repeating activity patterns in data from the 512 electrode array; (2) develop a sterile recording chamber compatible with the 512 electrode array so that cortical slice cultures can be monitored for up to two weeks; and (3) develop the hardware and software necessary to deliver complex patterned stimulation through the 512 electrode array. Many scientists think that disorders such as epilepsy and schizophrenia are caused by disruptions in networks of cortical neurons. The proposed studies are expected to increase our understanding of how networks of neurons interact, and may therefore lead to new information that could help treat these and other disorders. [unreadable] [unreadable]

In this project the PI will study how the primate retina processes and encodes visual images. The retina is an extraordinarily sophisticated optical image detector, converting a light image into a set of electrical signals, filtering these signals both spatially and temporally, and sending the output up the optic nerve to the brain. The output signals consist of multiple trains of electrical spikes organized in an exquisite and complex way, with more than 20 separate parallel pathways carrying visual information from the retina to the brain. In pilot experiments, a number of previously unknown, or poorly known, functional types of retinal neurons have been uncovered and in this research project the PI will answer the following questions: What roles do these cell types play in retinal processing? How do these neurons respond to different kinds of visual images? What information about the outside visual world do these cells communicate to the brain, and how is this information encoded? To answer these questions, a movie will be focused on the retinal input neurons (the rod and cone photoreceptors) and the electrical spikes generated by the retinal output neurons (including the new and poorly-known cell types) will be imaged and recorded by a dense two-dimensional array of over 500 microscopic electrodes. The output signals will then be correlated in space and time among themselves and with the input visual images to probe the neural code at the retina/brain interface. This research project will aid the development of future retinal prosthetic devices that are intended to restore some visual function in blind human patients with retinas damaged by photoreceptor disease. The project will also provide interdisciplinary research opportunities for undergraduate students, graduate students in both physics and biology.

DESCRIPTION (provided by applicant): The goal of this co-principal investigator, interdisciplinary proposal is to develop techniques for the comprehensive functional characterization of retinal ganglion cell (RGC) types in the mouse retina, and to combine this characterization with mouse transgenic technology in order to determine the relationships between the morphology and physiology of RGC types. Our experiments take advantage of novel multi- electrode array (MEA) recording systems built in the Litke lab. These systems contain over 500 electrodes and can simultaneously record the activity from hundreds of neurons in an intact retina;this represents a 10 fold better yield over currently available technology. We find that this increase in yield is critical for unambiguous functional classification and reliable characterization of the many RGC types in the retina. Furthermore, we hypothesize that the detailed information provided by these MEA systems will make it possible to match the physiologically identified neurons to optically imaged RGCs. Such a match will create a link between function and structure in an unprecedented manner. We have two main aims to accomplish our goals. In the first aim we propose to use two types of large- scale MEAs, a 512-electrode array with 605m interelectrode spacing, and a high density 519-electrode array with 305m spacing, to characterize the receptive field and mosaic properties of RGC types of wild type mice. We have chosen to use these arrays to characterize RGC types in mice because the mouse retina has become an important model to study the role various genes/molecules play in the development of retinal circuitry. The mouse also serves as a model for studying the progression of retinal-degenerative diseases such as glaucoma. In the second aim we plan to use the large-scale MEA technology to correlate the morphological RGC types to their functional counterparts. In addition to being classified using physiological criteria, RGCs are classified using morphological criteria. However, only in rare circumstances can cells be classified by both morphological and physiological properties. Experiments proposed in this aim are designed to correlate morphologically labeled cells with their physiological properties. We will do this by matching the morphological images of GFP marked RGCs with their electrophysiological images and receptive fields. (As described in section c, the electrophysiological image is a technique, developed by the Litke lab, for imaging the spatiotemporal pattern of electrical activity generated by individual neurons.). The purpose of this grant is to obtain a comprehensive characterization of retinal ganglion cell (RGC) types in the mouse retina. This knowledge is essential in order to understand how various molecular and environmental perturbations affect the retina's development and function. Vision is a crucial component of human perception and blindness is a devastating affliction. Understanding what the retinal circuits are is the first step toward understanding how they develop and is also essential to better understand the progression of retinal degenerative diseases (Are specific circuits differentially affected in disease?). In the last 10-20 years, modern molecular techniques, in combination with powerful advances in imaging and electrophysiology, have led to an increase in the use of the mouse as a model system for studying retinal circuitry. It is likely that the knowledge obtained from experiments proposed here will be essential to all who use the mouse visual system as a model. PUBLIC HEALTH RELEVANCE: The first aim of this project is to develop techniques for the classification and functional characterization of retinal ganglion cell (RGC) types in the mouse retina. The second aim is to combine this characterization with mouse transgenic technology in order to determine the relationship between the morphology and physiology of RGC types. Upon completion of the proposed aims, we will be in a strong position to use these techniques to determine how various genetic, activity-related, and disease perturbations affect and control the development of neural circuits. This will build a solid foundation for future work aimed at developing therapies for treating retinal damage due to injury or disease.

A central task in understanding how neurons collectively process information is to map how neurons influence each other in local cortical networks. As defined here, local cortical networks will consist of tens to hundreds of neurons. Influence will be defined as how well knowledge of activity in one neuron will allow the activity in another neuron to be predicted. Three methods for measuring influence between neurons will be explored. To assess these methods, they will be used on data from simple, and then realistic, models of cortical networks where the underlying connectivity structure is known. After refinement, the methods will be applied to recordings from hundreds of cortical neurons in small slice cultures of brain tissue. Over 100 cortical neurons at a time will be recorded through the use of an advanced, 512 electrode array. In addition, measures of influence will be applied to data taken from 16 wire electrodes placed in behaving rats. These in vivo recordings will serve as a first step toward linking influence maps in cortical networks to behavior. This research is expected to provide new knowledge that could aid the design of brain-like computing devices. In addition, it could ultimately be used as a tool to identify differences in influence patterns between healthy and pathological brains.

The three methods for measuring influence will include directed information, transfer entropy, and Granger causality. Special care will be taken to identify situations where these measurements may produce false positive connections. These include cases where two neurons are driven by a common source at different delays, and cases where one neuron influences another neuron indirectly through an intercalated neuron. Such false positive connections will be identified and corrected, to the extent possible, by comparing raw pairwise measures of influence with conditional measures of influence. Simulations will also provide an estimate of how often neurons outside the recorded population can contribute to false positive connections. These estimates will be used to place confidence limits on the influence maps extracted from actual data. In neurons where influences converge, synergistic interactions between influences will be measured. The map of influence will serve to identify locations within the network where synergistic transformations of information, or computations, occur.

Project Summary Here we propose to develop and integrate a suite of experimental and computational tools to measure the visual response and network properties of a large population of neurons in the mouse superior colliculus (SC), to determine how these properties change during locomotion, and the contribution of cortical and specific retinal inputs to these properties. The mouse SC is a subcortical area that integrates vision with touch and hearing to initiate orienting movements of the eyes and head, and is an attractive model to study how specific circuits form during development. Our development of high-density, high-channel count silicon probes to record neural activity has several significant advantages compared to alternative methods: (1) high efficiency for recording neuron spatial and temporal visual response properties; (2) the ability to rapidly study the topological/functional organization in a large neuron population over a wide field of view in a uniform way in a single animal; (3) the possibility to study correlated activity and connectivity among neurons as well as network rhythms; (4) the ability to ascertain differences in visual responses associated with behavioral state such as locomotion. Experiments proposed in Aim 1 will measure the functional and topological properties of visually- responsive neurons in the SC of mice that are awake and head-fixed on a freely-floating Styrofoam ball used as a spherical treadmill. For each neuron, the spatial receptive field (RF), the temporal filtering spike-triggered average (STA), direction and orientation selectivity, and the non-linearity of spatial summation will be determined and correlated with its location in the SC and correlated with locomotion. Aim 2 will apply the recording and data analysis tools developed in Aim 1 toward understanding the changes in circuitry in mutant mice that lack cortical inputs to the SC or lack On-Off direction selecive retinal ganglion cells (DS RGCs). This will allow us to determine the contribution of the cortex and DS RGCs toward the receptive field properties of SC neurons. Upon completion, a comprehensive classification of SC neurons, their topological organization, and their coding properties will be in hand. We will then take advantage of the ever-expanding availability of genetic tools (including optogenetics) that alter visual function, and mouse models of complex neurological disease that have altered activity patterns such as autism and schizophrenia. These same techniques will be useful to understand the circuitry of brain areas of animals with more complex visual systems and brain circuitry such as cat, ferret, and non-human primates.