Ilya A. Rybak, Ph.D. - US grants

The brain integrates and coordinates neural processing across multiple levels of organization to produce behavior. This project takes the neural control of breathing as a system for computational modeling of cross-level integration of cellular, network and systems neural mechanisms. The overall objective is to build a united multi-level model of neural control of respiration, within a uniform framework to incorporate existing data and current hypotheses on respiratory control. It remains controversial whether respiratory oscillation is produced primarily by endogenous cellular 'pacemaker' activity, or instead by properties of excitation and inhibition within a network circuit. This project models membrane activity for single respiratory neurons to investigate bursting activity; models the whole circuitry of the central pattern generator (CPG) network to investigate how connectivity can result in a steady respiratory rhythm with realistic firing patterns and changes from external perturbations; and elaborates the CPG model to generate a pacemaker-driven rhythm under simulated conditions. Mechanisms and conditions for the transition between pacemaker-driven and network-based states for generating rhythms are investigated in computational models and directly compared to experimental biological data from other laboratories.
Results will clarify fundamental aspects of the important topic of respiratory control, may settle a current controversy, and will have an impact beyond basic neuroscience, eventually to biomedical work including control-systems analysis of physiology. The complex multi-scale approach is novel, and will provide valuable postdoctoral and student training.

DESCRIPTION (provided by applicant): Generation of the respiratory motor pattern is performed in the lower brainstem and involves complex cross-level interactions of cellular, network, and systems-level mechanisms. Because of these complex interactions, the system can operate in different functional states and engage different rhythmogenic mechanisms in each state. We hypothesize that the rhythmogenic mechanism operating in the respiratory network (i.e., network-based, pacemaker-driven or hybrid) is defined by the state of the pre-Botzinger complex, which in turn operates under control of other medullary and pontine circuits. We also suggest that the pons controls the state of the pre-Botzinger complex (and hence the rhythmogenic mechanism) directly and/or through other medullary circuits, such as the Botzinger complex. The overall goal of this multidisciplinary collaborative project is to investigate and understand these complex interactions and the state-dependency of respiratory rhythm generation by using experimental studies combined with computational modeling. The experimental studies will be performed by Dr. Smith (NINDS, NIH) and Dr. Paton (University of Bristol). The applied experimental methods will include (1) reduction of the operating respiratory network by sequential and highly precise transections applied to the pons and medulla and (2) using specific blockers of intrinsic neuronal properties (e.g., persistent sodium and other ionic channels) and network interactions (e.g., inhibitory synaptic transmission) applied to intact and reduced preparations. The computational model of the ponto-medullary respiratory network will be further developed by the group of Dr. Rybak (Drexel University) in close interactive collaboration with Drs. Smith and Paton using data accumulated in their laboratories. In turn, complementary experimental studies in these laboratories will be driven by modeling predictions. The resultant comprehensive computational model will be developed, tested and elaborated to reproduce the experimentally observed state-dependent changes in the firing patterns of respiratory neurons and in the discharge patterns of output motor nerves (phrenic, hypoglossal, central vagal and abdominal) under different experimental conditions. The proposed collaborative study will provide important insights into the complex neural mechanisms for control of breathing Ultimately, the model that will be developed in this project may be used for simulation of multiple respiratory disorders and diseases (e.g., sleep apnea, brainstem/spinal cord injury, CCHS), and for developing and investigations new methods for their treatment.

DESCRIPTION (provided by applicant): This Bioengineering Partnership brings together a multidisciplinary team of neuroscientists and engineers with complementary expertise in neural organization of the spinal cord (Dr. David McCrea, University of Manitoba), biomedical engineering and neuromuscular stimulations (Dr. Michel Lemay, Drexel University), physiology and biomechanics of locomotion (Dr. Boris Prilutsky, Georgia Institute of Technology), and computational neuroscience and neural control (Dr. llya Rybak, Drexel University). The goals of this project are (1) to perform a comprehensive multidisciplinary study of neural mechanisms in the mammalian spinal cord responsible for generation of the locomotor pattern and control of locomotion and (2) to find optimal strategies for restoring locomotor function after spinal cord injuries. In this project, two comprehensive databases will be created based on experimental studies of fictive locomotion in the decerebrate cat and on biomechanical studies of freely moving uninjured cats and spinal cats. These databases will be used for the development of (1) a computational model of neural circuitry of the spinal cord responsible for generation and control of the locomotor pattern and (2) a neuro-musculo-skeletal model of cat's locomotion. Special quantitative biomechanical criteria will be developed for evaluation of locomotor capabilities of spinal cats during and after implementation of different treatments for restoring the locomotor function. The computational models and biomechanical criteria developed will provide guidance for the applied treatments and evaluation of their results. Different strategies for the restoration of locomotor capabilities based on the combination of locomotor training on a treadmill with phase-dependent electrical stimulation of the selected sensory afferents will be implemented and investigated. The results of this project will provide significant insights into spinal mechanisms responsible for control of locomotion and will represent an important step toward the development of optimal and effective methods for restoration of locomotor function after various spinal cord injuries.

DESCRIPTION (provided by applicant): Ventilatory arrhythmia plays a pathogenic role in many common respiratory disorders ranging from sleep apnea, and acute lung injury to ventilatory support in the setting of chronic lung disease. Brainstem neural circuits that control cardiopulmonary functions generate oscillatory patterns that drive respiratory as well as sympathetic motor activities. These patterns exhibit highly structured variability and patients with various chronic diseases exhibit aberrations of these patterns and their variabilities. Analytic tools for quantifying ventilatory arrhythmia and for stratification of severity or prognosis are unavailable, representing a major barrier to defining its pathogenic contribution to disease, or to developing novel non-invasive or therapeutic markers. The long-term objectives of this exploratory project are these targets by determining the neurophysiologic mechanisms for ventilatory arrhythmia, specifically the physiological balance between central (pontomedullary) and afferent (pulmonary and baro) feedback mechanisms in the control of respiratory phase switching and pattern stabilization. The applicants hypothesize that alterations in this balance are evident in the pathology of the pulmonary conditions, but lie dormant due to lack of quantitative understanding of the dynamic properties of the respiratory control system. This hypothesis will be tested by analyzing breathing patterns in: 1) a mouse model of Rett syndrome, in which ventilatory arrhythmia originates primarily from central deficits and 2) in humans with lung disease and a rat model of lung injury, in which ventilatory arrhythmia originates primarily from altered afferent feedback. The central aim is to develop analytical methods that incorporate new characteristics of breathing pattern variability, and a computational model that accurately predicts respiratory rhythm variability resulting from internal (e.g. network modulation of feedback gain, neuromodulator interactions etc.) and external factors (peripheral chemoreceptor function, lung mechanics). An interdisciplinary research team that includes four experienced groups at different Universities will collaborate closely to perform this project. The specific aims are: 1) to expand a computational model of the brainstem respiratory network to include not only the ponto-medullary circuits but pulmonary and baro-feedback and their interactions (Rybak);2) to test novel tools permitting the identification of disturbed breathing patterns (Loparo/Wilson);3) to elucidate the cellular mechanisms involved in reciprocal ponto-vagal interactions by synaptic inputs to pontine and medullary respiratory neurons elicited by vagal afferent activation, including an influence of brain derived neurotrophic factor on the balance of pontine-vagal control of phase duration (Dutschmann);4) to determine how the network interactions are altered by activation of vagal or dorsolateral pontine neurons in normal and disease states (Dick/Jacono);and 5) to describe the relative role of heritable vagal mechanisms in generating breathing pattern variability in adult twins;and the impact of ventilatory coupling to cardiac activation (cardioventilatory coupling) on breathing variability in twins and patients with lung disease (Strohl/ Jacono). The quantitative tools and insights created from this unique collaboration will permit insight into new diagnostic, prognostic and therapeutic avenues to promote stable breathing and improve patient outcomes in acute and chronic lung injury. (End of Abstract)

DESCRIPTION (provided by applicant): Respiration in mammals is a primal homeostatic process, regulating levels of oxygen (O2) and carbon dioxide (CO2) in blood and tissues and is crucial for life. Rhythmic respiratory movements must occur continuously throughout life and originate from neural activity generated by specially organized circuits in the brain stem constituting the respiratory central pattern generator (CPG). The respiratory CPG generates rhythmic patterns of motor activity that produce coordinated movements of the respiratory pump (diaphragm, thorax, and abdomen), controlling lung inflation and deflation, and upper airway muscles, controlling airflow. These coordinated rhythmic movements drive exchange and transport of O2 and CO2 that maintain physiological homeostasis of the brain and body. Uncovering complex multilevel and multiscale mechanisms operating in the respiratory system, leading to mechanistic understanding of breathing, including breathing in different disease states requires a Physiome-type approach that relies on the development and explicit implementation of multiscale computational models of particular organs and physiological functions. The specific aims of this multi-institutional project are: (1) develop a Physiome-type, predictive, multiscale computational model of neural control of breathing that links multiple physiological mechanisms and processes involved in the vital function of breathing but operating at different scales of functional and structural organization, (2) validate this model in a series of complementary experimental investigations and (3) use the model as a computational framework for formulating predictions about possible sources and mechanisms of respiratory pattern alteration associated with heart failure. The project brings together a multidisciplinary team of scientists with long standing collaboration and complementary expertise in respiration physiology, neuroscience and translational medical studies (Thomas E. Dick, Case Western Reserve University;Julian F.R. Paton, University of Bristol, UK;Robert F. Rogers, Drexel University;Jeffrey C. Smith, NINDS, NIH, intramural), mathematics, system analysis and bioengineering (Alona Ben-Tal, Massey University, NZ), and computational neuroscience and neural control (Ilya A. Rybak, Drexel University). The end result of our proposed cross-disciplinary modeling and experimental studies will be the development and implementation of a new, fully operational, multiscale model of the integrated neurophysiological control system for breathing based on the current state of physiological knowledge. This model can then be used as a computational framework for formulating predictions about possible neural mechanisms of respiratory diseases and suggesting possible treatments.

DESCRIPTION (provided by applicant): This project combines electrophysiological and modeling approaches to study the organization and neuronal composition of the Central Pattern Generator (CPG) neural circuits in the mammalian spinal cord that coordinate rhythmic neural activity driving locomotion. This study will take a general approach that utilizes various spontaneous and evoked perturbations in the locomotor pattern (including deletions of motoneuron activity, spinal cord lesions and pharmacological manipulations) as probes to understand CPG organization and function. It is proposed that analysis of the influences of these perturbations on the rhythmic motor pattern and the activity of identified spinal interneurons will provide important insights on the spinal CPG organization and operation. These data will be used to develop a comprehensive computational model of the spinal locomotor CPG, and to refine and validate this model, so that it can reproduce both normal locomotor activity and the consequences of experimental perturbations. In turn, the model will serve as a computational framework to formulate predictions to guide subsequent experimental investigations. The project brings together two senior scientists with complementary and overlapping expertise in experimental (Dr. Harris-Warrick at Cornell University) and computational (Dr. Rybak at Drexel University) neuroscience. It has three interlocking objectives: 1) Explore alterations in behavior of, and synaptic drive to, motoneurons and genetically defined interneurons during spontaneous and evoked deletions in flexor and/or extensor rhythmic motor activity, to define the possible function of these interneurons in the locomotor CPG. 2) Explore the consequences of reducing CPG complexity by spinal cord hemisection and removal of spinal segments, and compare the behavior of identified interneurons in the reduced cord during deletions and after pharmacological blockade of synaptic inhibition. 3) Develop a comprehensive computational model of the neural circuits forming the locomotor CPG in the neonatal mouse spinal cord that includes genetically identified interneurons and suggests their roles in the generation of the locomotor pattern. Validate this model in simulations reproducing the specific transformations in motoneuron and interneuron activity and the entire locomotor pattern during experimental perturbations proposed in objectives 1 and 2.The model will be progressively developed by continuous interaction with the experimental studies, and will serve both as a testbed for working concepts on spinal cord organization and as a source of predictions for subsequent experimental validation. Intellectual Merit: This proposal represents an important step toward a mechanistic understanding of the organization of the neural circuits forming the spinal locomotor CPG in mammals. The proposed experimental and modeling studies will also provide novel insights into the general principles of neural control of rhythmic motor behaviors. Broader Impacts: (1) Integration of research and education: At Cornell and Drexel, this work will be included in several courses on basic neuroscience and neuroengineering for students at many levels, from undergraduate to graduate and medical students. Undergraduate and graduate students will participate in this project at both institutions. At Cornell, Dr. Harris-Warrick will invite an underrepresented minority student to work on this project each year, and the project will support two female scientists who will be given careful mentoring for a future career in science. (2) Enhance infrastructure for research and education: Two laboratories with mostly nonoverlapping technical expertise will collaborate to understand the neural circuitry for locomotion. This collaboration will help both laboratories to combine computational and electrophysiological approaches to the study of neural circuits. The simulation package NSM 3.0, developed at Drexel, and all models developed in this project will be shared between project participants and made available to other research groups via a specially developed website at Drexel. (3) Medical Impact: It is now clear that all vertebrates, including humans, have spinal CPGs that drive and coordinate locomotor movements. These CPGs survive upper spinal cord injuries, and are in principle capable of restoring locomotion after injury, as demonstrated in rodents and cats. Better understanding of the organization and function of such CPGs will provide essential insights into future clinical strategies for restoration of locomotor function after spinal cord injury.

DESCRIPTION (provided by applicant): Neuronal networks within the spinal cord organize and drive rhythmic movements like walking and swimming. These circuits represent the central pattern generator (CPG) that controls both the rhythm and the pattern of the locomotor activity. The organization of these circuits has recently begun to be revealed due to the state-of- art combination of complementary genetic, molecular and physiological methods. The overall goal of this project is to dissect the organization of the spinal CPG with focus on the organization of flexor-extensor alternating and left-right coordinating circuits. All work will be done on identifiable classes of spinal interneurons labeled by genetic markers in transgenic mice and/or classified by anatomic or electrophysiological labeling needed to obtain a unified picture of the CPG organization. We propose to identify the functional connectome and the interactions between these fundamental components of the CPG. The experiments performed will use a combination of electrophysiological, imaging, and molecular biology techniques complemented with advanced computer modeling. The three PIs involved in this project have strong background and experience in spinal cord studies and unique expertise in physiological, genetic and molecular methods (Martyn Goulding and Ole Kiehn) and computational modeling (Ilya Rybak). The Specific Aims of the project include: investigation of activity patterns and connectivity of the genetically identified spinal interneurons responsible for left-right coordinaton during locomotion (Aim 1), investigation of the genetically identified spinal interneurons and thei connectivity responsible for flexor-extensor alternation and their interactions with the circuits providing left-right coordination (Aim 2), development of a comprehensive computational model of spinal cord circuits (Aim 3). The proposed multidisciplinary approach based on the state-of-art methods and close collaboration between the three leading labs will investigate and analyze the specific contributions of left-right and flexor-extensor coordinating neuronal circuits and their interactions to the generation and control of the locomotor pattern and provide important insights into the neural organization of the mammalian spinal cord, leading to new strategies to treat spinal cord injury and degeneration spinal cord disorders.

Project Summary The ability to coordinate movements of the limbs is one of the main features of locomotion in mammals. Interlimb coordination is essential for maintaining balance when navigating in complex and/or changing environments. It involves complex dynamic interactions between neural circuits at different levels of the nervous system and biomechanical properties of the musculoskeletal system to allow animals to adjust locomotor speed and gait for goal-oriented behaviors. Interactions within the nervous system include those between the spinal circuits controlling each limb, supraspinal inputs and sensory feedback from the limbs. Neurological disorders resulting from spinal cord injury (SCI) and other diseases disrupt limb coordination in humans and animal models, thus impairing locomotion. Despite their obvious importance, the mechanisms that control interlimb coordination and contribute to locomotor recovery following SCI and other neurological disorders remain poorly understood. To address this gap in knowledge, we will integrate multiple experimental and modeling approaches to investigate the neural and biomechanical mechanisms controlling interlimb coordination in a feline model before and after SCI disrupting neural communication between the brain and spinal cord and/or between the circuits controlling fore- and hindlimb movements. The project will be performed in close interactive collaboration between three groups of investigators with strong and complementary expertise in the experimental study of cat locomotion, including SCI models (Alain Frigon, Université de Sherbrooke), biomechanics of cat locomotion (Boris Prilutsky, Georgia Tech) and neural control of locomotion (Ilya Rybak, Drexel University). The project has the following Specific Aims: (1) Characterize muscle synergies and limb kinematics in intact and spinal cats during locomotion on regular and split-belt treadmills; (2) Extend and refine the current computational model of neural circuits and spinal central pattern generators involved in the control of locomotion; (3) Develop an integrated quadrupedal neuromechanical model of cat locomotion Develop an integrated quadrupedal neuromechanical model of cat locomotion; (4) Investigate the neural and biomechanical control of interlimb coordination during locomotion using interrelated and complementary experimental and modeling studies. Results obtained from these studies will have an important theoretical impact on our understanding of how the limbs are coordinated during locomotion and how this coordination is altered and adjusted after disruption of spinal pathways between left-right or cervical-lumbar circuits. The results will identify neural pathways and biomechanical mechanisms that could be targeted to improve interlimb coordination in people with various movement disorders, such as SCI, stroke, and Parkinson's disease.

The ability to move within the environment is essential for the survival of all animals, including humans. In mammals, the neurons that generate and drive locomotor movements reside in the spinal cord, and these spinal networks are controlled by upstream signals from the brainstem. Most studies of neural control of locomotion in mammals have focused on straight-trajectory forward locomotion. However, how brainstem and spinal neural networks control turning movements remains poorly understood. This study will investigate this question, using a combination of experimental and computational approaches. The results of this study will provide important insights into the neural control of turning and, more broadly, the neural control of locomotion. The models developed in this project can serve as test-beds for simulating different aspects of motor disorders and treatment approaches. Study outcomes can help in the development of novel strategies to restore locomotor function after spinal cord injury, neurodegenerative pathologies, and other motor disorders.

This multidisciplinary project will investigate the neural control of locomotion in mice with a focus on mechanisms of turning movements. A recently uncovered population of reticulospinal neurons in the gigantocellular reticular nucleus (Gi) of the brainstem projects to all segments of the spinal cord and is defined by the expression of the transcription factor Chx10 (V2a neurons). Experimentally activating these neurons in the mouse induces robust turning movements that seem to be mostly driven by an asymmetric control of the motor circuits of the neck, upper trunk, and forelimbs. This study will test the hypothesis that these pathways represent a major orchestrator of locomotor turning maneuvers. This study combines state-of-the-art physiological, genetic, pharmacological, and motion tracking approaches with computational modeling of the brainstem and spinal cord circuits and animal biomechanics. The results of in vitro and in vivo studies will be incorporated in a neuro-biomechanical data-driven model of quadrupedal mammalian (mouse) locomotion. The model will provide mechanistic explanations, and generate testable predictions that will then be verified experimentally. The project has the following three objectives. (1) Study the influence of reticulospinal V2a Gi neuron activation on spinal circuits potentially involved in locomotor steering behaviors and computational modeling of these brainstem-spinal pathways and circuits; (2) Characterize kinematics of mouse locomotion during changes of locomotor direction and develop a full-body neuro-biomechanical model of mouse locomotion; (3) Study the role of different populations of reticulospinal V2a Gi neurons in locomotor steering and test model predictions, challenge model assumptions, and investigate general mechanisms. This study will provide a functional connectome linking brainstem structures that initiate and support turning behaviors to the corresponding executive circuits in the spinal cord and effector muscle groups. Studies will also shed light on more general mechanisms of motor control like the coordination of multiple rhythmic motor systems and will be useful for the development of effective methods for recovery of locomotion after various motor disorders and injuries affecting the brainstem and spinal cord.

A companion project is being funded by the French National Research Agency (ANR). This project is jointly funded by the following NSF programs: Disability and Rehabilitation Engineering, Collaborative Research in Computational Neuroscience, Robust Intelligence, Engineering of Biomedical Systems, and Directorate for Biological Sciences Emerging Frontiers.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.