Talks

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ICTP-ICTS Winter School on Quantitative Systems Biology (ONLINE)
Monday, 06 December 2021
Time Speaker Title Resources
16:45 to 16:55 Rajesh Gopakumar (ICTS, India) Welcome remarks

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17:00 to 20:30 VENKATESH MURTHY (Harvard University, USA) SESSION CHAIR
17:00 to 18:30 Suhita Nadkarni (IISER - Pune, India) Membrane Excitability and Synaptic Plasticity (Lecture 1)

Neurons stand apart from other cells in their ability to communicate via electrical and chemical signaling. This signaling is the basis of all brain functions. Scholars in the field have proposed that complex behavior can be understood by how cells respond to stimuli from their environment and that membrane excitability (the ability of neurons to fire action potentials) is the “lowest candidate mechanism” for consciousness. Despite the vast diversity of neuronal and synaptic morphologies and the currency neurons use to communicate, the physical laws governing communication are conserved throughout the nervous system. Transmembrane currents that lead to changes in membrane voltage are primarily carried by the movement of sodium, potassium, calcium, and chloride ions across the cell membrane, both passively (down concentration gradients) and actively (by ion pumps that use up energy). I will discuss the framework developed by Hodgkin and Huxley (H and H) to understand the mechanisms involved in the passage of ions across the membrane. This Nobel prize-winning work by H and H forms the foundation of our understanding of the sophisticated dynamical repertoire of neurons. I will discuss the biophysics of some important ion channels that allow neurons to adapt their firing rate, that is, fire rapidly or at a sluggish pace, or in sudden quick bursts of ‘excitement.’ I will also talk about the complex dynamics of ion channels in a single neuron that lead to robust rhythmic activity. These rhythms play an important role in several brain functions, in particular, movement. In the second part of my lectures, I will discuss different forms of synaptic plasticity – mechanisms that modulate the strength of inter-neuronal communication. Synaptic plasticity serves as the basis of learning and memory. There are thousands of morphologically distinct synapses across brain areas suggesting that the structure of a synapse is likely to have evolved to serve specific functions. Using some of the work from my lab as an example, I will discuss how details of synaptic design impact behavior.
     
19:00 to 20:30 Adrienne Fairhall (University of Washington, USA) Neural Coding and Adaptation (Lecture 1)
   
Tuesday, 07 December 2021
Time Speaker Title Resources
14:00 to 16:00 - Python bootcamp
17:00 to 20:30 VENKATESH MURTHY (Harvard University, USA) SESSION CHAIR
17:00 to 18:30 Suhita Nadkarni (IISER - Pune, India) Membrane Excitability and Synaptic Plasticity (Lecture 2)

Neurons stand apart from other cells in their ability to communicate via electrical and chemical signaling. This signaling is the basis of all brain functions. Scholars in the field have proposed that complex behavior can be understood by how cells respond to stimuli from their environment and that membrane excitability (the ability of neurons to fire action potentials) is the “lowest candidate mechanism” for consciousness. Despite the vast diversity of neuronal and synaptic morphologies and the currency neurons use to communicate, the physical laws governing communication are conserved throughout the nervous system. Transmembrane currents that lead to changes in membrane voltage are primarily carried by the movement of sodium, potassium, calcium, and chloride ions across the cell membrane, both passively (down concentration gradients) and actively (by ion pumps that use up energy). I will discuss the framework developed by Hodgkin and Huxley (H and H) to understand the mechanisms involved in the passage of ions across the membrane. This Nobel prize-winning work by H and H forms the foundation of our understanding of the sophisticated dynamical repertoire of neurons. I will discuss the biophysics of some important ion channels that allow neurons to adapt their firing rate, that is, fire rapidly or at a sluggish pace, or in sudden quick bursts of ‘excitement.’ I will also talk about the complex dynamics of ion channels in a single neuron that lead to robust rhythmic activity. These rhythms play an important role in several brain functions, in particular, movement. In the second part of my lectures, I will discuss different forms of synaptic plasticity – mechanisms that modulate the strength of inter-neuronal communication. Synaptic plasticity serves as the basis of learning and memory. There are thousands of morphologically distinct synapses across brain areas suggesting that the structure of a synapse is likely to have evolved to serve specific functions. Using some of the work from my lab as an example, I will discuss how details of synaptic design impact behavior.
     
19:00 to 20:30 Adrienne Fairhall (University of Washington, USA) From Neurons to Behavior in Hydra (Lecture 2)
 
Wednesday, 08 December 2021
Time Speaker Title Resources
14:00 to 16:00 - Python bootcamp
17:00 to 20:30 VIJAYKUMAR KRISHNAMURTHY (ICTS, India) SESSION CHAIR
17:01 to 18:30 Antonio Celani (ICTP Trieste, Italy) Olfactory Search and Navigation (Lecture 1)

I will be discussing examples of olfactory navigation in different organisms, with emphasis on the physics of the olfactory signal and emergent behavioral patterns.
 
19:00 to 20:30 Dima Rinberg (NYU Neuroscience Insititute, USA) Introduction to Olfaction (Lecture 1)

Olfaction is the main sense used by most animals to interact with the environment. It is probably the oldest evolutionary senses. From bacteria to humans, life organisms extract information from chemical world around them. An anatomical organization of olfactory system is similar from insect to mammals. Here I will describe the basic olfactory biology and information processing in the mammalian olfactory system: from receptors to perception. I will discuss unsolved fundamental questions in the field.
   
Thursday, 09 December 2021
Time Speaker Title Resources
14:00 to 16:00 - Python bootcamp
17:00 to 20:30 VIJAYKUMAR KRISHNAMURTHY (ICTS, India) SESSION CHAIR
17:01 to 18:30 Antonio Celani (ICTP Trieste, Italy) Olfactory Search and Navigation (Lecture 2)

I will give a short introduction to Reinforcement Learning as a theoretical framework for decision-making problems and specifically discuss olfactory navigation algorithms in that context.
 
19:00 to 20:30 Dima Rinberg (NYU Neuroscience Institute, USA) Sensory (olfactory) Coding from Behavioral Perspective (Lecture 2)

Two of the most fundamental questions of sensory neuroscience are: 1) how is stimulus information represented by neuronal activity? and 2) what features of this activity are read out to guide behavior? The first question has been the subject of a large body of work across different sensory modalities. The second question remains a significant challenge, since one needs to establish a causal link between neuronal activity and behavior.

In olfaction, it has been proposed that information about odors is encoded in spatial distribution of receptor activation and the next level mitral/tufted cells, as well as in their relative timing and synchrony. However, the role of different features of neural activity in guiding behavior remains unknown. Using mouse olfaction as a model system, I will present our work on developing both technological and conceptual approaches to study sensory coding by perturbing neural activity at different levels of information processing during sensory driven behavioral tasks. We will first ask the questions about psychophysical limits of the readability of different features of the neural code, and, second, how to quantify their behavioral relevance.

 
   
Friday, 10 December 2021
Time Speaker Title Resources
17:00 to 20:30 SANJAY SANE (NCBS, India) SESSION CHAIR
17:01 to 18:30 Katherine Nagel (NYU Langone Health, USA) An Introduction to Drosophila Neuroscience (Lecture 1)

In this pair of lectures I will introduce students to using Drosophila as a model to dissect neural circuits supporting a complex ethological behavior.  In the first lecture I will provide an introduction to the Drosophila toolkit, including public repositories of driver lines, tools for refining driver expression, tools for monitoring and manipulating neural activity and neuronal function, and new connectomic resources.  I will also provide an overview of Drosophila brain anatomy, and discuss how the fly has contributed to our understanding of memory formation and the generation of internal representations.   In the second lecture, I will describe our lab’s ongoing work seeking to understand the neural circuit basis of olfactory navigation behavior.  I will describe the physics of odor transport, tools for measuring olfactory navigation in high throughput, and algorithmic models of navigation.  I will then describe our progress in using genetic tools to elucidate the structure of neural circuits that support olfactory navigation behavior.  Our current data suggest that this behavior may be supported by parallel pathways from sensory input to motor output of different lengths and complexities.  I will end by discussing some possible hypotheses for why olfactory-motor neural circuits may be organized in this way and present current computational/theoretical problems in neural circuit design that may be of interest to the students.
 
19:00 to 20:30 Larry Abbott (Columbia University, USA) How Flies Navigate (Lecture 1)

Flies have a “compass” system in which a bump-like pattern of activity keeps track of the fly’s heading relative to visual objects in the world. This system is well described by a classic neuroscience model - the ring attractor. I will introduce the fly compass system, go over the construction and analysis of the ring attractor model, and show how they relate.
   
Monday, 13 December 2021
Time Speaker Title Resources
17:00 to 20:30 SANJAY SANE (NCBS, India) SESSION CHAIR
17:01 to 18:30 Larry Abbott (Columbia University, USA) How do Flies Navigate (Lecture 2)

Navigation requires the manipulation of vectors.  I will go over basic vector operations as humans do them, and then show how the fly performs the same calculations.  This will end in a model for how fly’s determine where they are going and where they have been.
 
   
19:00 to 20:30 Katherine Nagel (NYU Langone Health, USA) Algorithms and Circuits for Olfactory Navigation in Drosophila (Lecture 2)

In this pair of lectures I will introduce students to using Drosophila as a model to dissect neural circuits supporting a complex ethological behavior.  In the first lecture I will provide an introduction to the Drosophila toolkit, including public repositories of driver lines, tools for refining driver expression, tools for monitoring and manipulating neural activity and neuronal function, and new connectomic resources.  I will also provide an overview of Drosophila brain anatomy, and discuss how the fly has contributed to our understanding of memory formation and the generation of internal representations.   In the second lecture, I will describe our lab’s ongoing work seeking to understand the neural circuit basis of olfactory navigation behavior.  I will describe the physics of odor transport, tools for measuring olfactory navigation in high throughput, and algorithmic models of navigation.  I will then describe our progress in using genetic tools to elucidate the structure of neural circuits that support olfactory navigation behavior.  Our current data suggest that this behavior may be supported by parallel pathways from sensory input to motor output of different lengths and complexities.  I will end by discussing some possible hypotheses for why olfactory-motor neural circuits may be organized in this way and present current computational/theoretical problems in neural circuit design that may be of interest to the students.
 
Tuesday, 14 December 2021
Time Speaker Title Resources
17:00 to 20:30 VATSALA THIRUMALAI (NCBS, India) SESSION CHAIR
17:01 to 18:30 Claire Wyart (Brain and Spine Institute (ICM), France) Optogenetic Dissection of Sensorimotor Circuits Shaping, Locomotion

Sensory feedback is intrinsic to all animal species, but how this information impacts movement execution as a whole is not known. Larval zebrafish is an interesting genetic model organism to tackle this question using optical techniques for monitoring and manipulating neuronal activity during active locomotion. First, we will investigate how activity of neurons in the motor neurons is affected by sensory feedback, and how sensory feedback impacts speed of execution. Second, we will show how the content of the cerebrospinal fluid (CSF), a complex solution circulating around the brain and spinal cord, can influence motor functions. We will focus on a ciliated cell type conserved throughout vertebrate species and located at the interface between the CSF and the nervous system that are in ideal position to sense CSF cues, to relay information to local networks and to regulate CSF content by secretion. Our approach combines electrophysiology, optogenetics and calcium imaging in vivo in larval zebrafish. Our work first sheds light on the cellular and network mechanisms enabling sensorimotor integration of mechanical and chemical cues from the CSF onto motor circuits controlling locomotion and posture in the spinal cord. We will present converging evidence that the interoceptive sensory pathway we discovered is involved in guiding a straight body axis throughout life, as well as innate immunity via the detection and combat of pathogens invading the CSF.
   
19:00 to 20:30 Misha Ahrens (Janelia Research Campus, USA) Optical Imaging and Analysis of Neuronal and Astrocyte Activity Across the Whole Brain (Lecture 1)
       
Wednesday, 15 December 2021
Time Speaker Title Resources
17:00 to 20:30 VATSALA THIRUMALAI (NCBS, India) SESSION CHAIR
17:01 to 18:30 Misha Ahrens (Janelia Research Campus, USA) Neuron-Glia Computation for Behavioral States and Navigation (Lecture 2)
       
19:00 to 20:30 Claire Wyart and Gautam Reddy Nallamala (Brain and Spine Institute (ICM), France) Identifying Patterns in Animal Behavior (Lecture 2)

Animals display characteristic behavioral patterns when performing a task, such as the spiraling of a soaring bird or the surge-and-cast of a male moth searching for a female. Identifying such recurring sequences occurring rarely in noisy behavioral data is key to understanding the behavioral response to a distributed stimulus in unrestrained animals. Existing models seek to describe the dynamics of behavior or segment individual locomotor episodes, or bouts, rather than to identify the rare and transient sequences of bouts that make up the behavioral response. To fill this gap, we develop a lexical, hierarchical model of behavior. We designed an unsupervised algorithm called "BASS" to effectively identify and segment recurring behavioral action sequences transiently occurring in long behavioral recordings. When applied to navigating larval zebrafish, BASS extracts a dictionary of remarkably long, non-Markovian sequences consisting of repeats and mixtures of slow forward and turn bouts. Applied to a pH taxis assay, BASS uncovers chemotactic strategies deployed by zebrafish to avoid aversive cues consisting of sequences of fast large-angle turns and burst swims. In a simulated dataset of soaring gliders climbing thermals, BASS finds the spiraling patterns characteristic of soaring behavior. In both cases, BASS succeeds in identifying rare action sequences in the behavior deployed by freely moving animals. BASS can be easily incorporated into the pipelines of existing behavioral analyses across diverse species, and even more broadly used as a generic algorithm for pattern recognition in low-dimensional sequential data.
   
Thursday, 16 December 2021
Time Speaker Title Resources
17:00 to 20:30 VATSALA THIRUMALAI (NCBS, India) SESSION CHAIR
17:01 to 18:30 Konrad Kording (University of Pennsylvania, USA) Bayesian Modeling of Behavior (Tutorial)
           
19:00 to 20:30 Daniel Wolpert (Columbia's Zuckerman Institute, USA) Computational Principles of Sensorimotor Control (Lecture 1)

The effortless ease with which humans move our arms, our eyes, even our lips when we speak masks the true complexity of the control processes involved. This is evident when we try to build machines to perform human control tasks. I will review models of human motor planning, state estimation, prediction and learning. I attach two review papers which are related but don't exactly cover this but are useful I hope Chapter 30 of Principle of Neural Sciences 6th edition
       
Friday, 17 December 2021
Time Speaker Title Resources
17:00 to 20:30 VATSALA THIRUMALAI (NCBS, India) SESSION CHAIR
17:01 to 18:30 Daniel Wolpert (Columbia's Zuckerman Institute, USA) Computational Principles Underlying the Learning of Sensorimotor repertoires (Lecture 2)

Humans spend a lifetime learning, storing and refining a repertoire of motor memories appropriate for the multitude of tasks we perform. However, it is unknown what principle underlies the way our continuous stream of sensorimotor experience is segmented into separate memories and how we adapt and use this growing repertoire. I will review our work on how humans learn to make skilled movements focussing on the role role of context in activating motor memories and how statistical learning can lead to multimodal object representations. I will then present a principled theory of motor learning based on the key insight that memory creation, updating, and expression are all controlled by a single computation – contextual inference. Unlike dominant theories of single-context learning, our repertoire-learning model accounts for key features of motor learning that had no unified explanation and predicts novel phenomena, which we confirm experimentally. These results suggest that contextual inference is the key principle underlying how a diverse set of experiences is reflected in motor behavior.
       
19:00 to 20:30 Konrad Kording (University of Pennsylvania, USA) Uncertainty in Visuomotor Behavior