Posts classified under: Computational and Systems Neuroscience

Avishek Adhikari, Ph.D.

Biography

Dr. Adhikari joined UCLA’s Psychology Department in 2016, following postdoctoral training at Stanford University with Prof. Karl Deisseroth and Ph.D. studies at Columbia University with Prof. Joshua A. Gordon and Prof. Rene Hen.

Dr. Adhikari’s lab investigates how the brain coordinates the constellation of changes related to emotional behaviors, with a focus on fear and anxiety. These multi-faceted changes involve complex and dynamic adaptations in hormonal, physiological and behavioral realms. Dr. Adhikari dissects how interactions between different brain structures control these processes, seeking insights that shed light on the neural basis of pathological anxiety disorders and adaptive aversion to danger. To do so we use a combination of powerful techniques, including electrophysiology, behavioral assays, optogenetics and calcium imaging to monitor and control neural activity and behavior.

Learn more about our research at our lab website

Publications

A selected list of publications:

Ye Li, Allen William E, Thompson Kimberly R, Tian Qiyuan, Hsueh Brian, Ramakrishnan Charu, Wang Ai-Chi, Jennings Joshua H, Adhikari Avishek, Halpern Casey H, Witten Ilana B, Barth Alison L, Luo Liqun, McNab Jennifer A, Deisseroth Karl   Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences Cell, 2016; 165(7): 1776-88.
Adhikari Avishek, Lerner Talia N, Finkelstein Joel, Pak Sally, Jennings Joshua H, Davidson Thomas J, Ferenczi Emily, Gunaydin Lisa A, Mirzabekov Julie J, Ye Li, Kim Sung-Yon, Lei Anna, Deisseroth Karl   Basomedial amygdala mediates top-down control of anxiety and fear Nature, 2015; 527(7577): 179-85.
Adhikari Avishek   Distributed circuits underlying anxiety Frontiers in behavioral neuroscience, 2014; 8(7): 112.
Gunaydin Lisa A, Grosenick Logan, Finkelstein Joel C, Kauvar Isaac V, Fenno Lief E, Adhikari Avishek, Lammel Stephan, Mirzabekov Julie J, Airan Raag D, Zalocusky Kelly A, Tye Kay M, Anikeeva Polina, Malenka Robert C, Deisseroth Karl   Natural neural projection dynamics underlying social behavior Cell, 2014; 157(7): 1535-51.
Kim Sung-Yon, Adhikari Avishek, Lee Soo Yeun, Marshel James H, Kim Christina K, Mallory Caitlin S, Lo Maisie, Pak Sally, Mattis Joanna, Lim Byung Kook, Malenka Robert C, Warden Melissa R, Neve Rachael, Tye Kay M, Deisseroth Karl   Diverging neural pathways assemble a behavioural state from separable features in anxiety Nature, 2013; 496(7444): 219-23.
Tye Kay M, Mirzabekov Julie J, Warden Melissa R, Ferenczi Emily A, Tsai Hsing-Chen, Finkelstein Joel, Kim Sung-Yon, Adhikari Avishek, Thompson Kimberly R, Andalman Aaron S, Gunaydin Lisa A, Witten Ilana B, Deisseroth Karl   Dopamine neurons modulate neural encoding and expression of depression-related behaviour Nature, 2013; 493(7433): 537-41.
Warden Melissa R, Selimbeyoglu Aslihan, Mirzabekov Julie J, Lo Maisie, Thompson Kimberly R, Kim Sung-Yon, Adhikari Avishek, Tye Kay M, Frank Loren M, Deisseroth Karl   A prefrontal cortex-brainstem neuronal projection that controls response to behavioural challenge Nature, 2012; 492(7429): 428-32.
Nason Malcolm W, Adhikari Avishek, Bozinoski Marjan, Gordon Joshua A, Role Lorna W   Disrupted activity in the hippocampal-accumbens circuit of type III neuregulin 1 mutant mice Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology, 2011; 36(2): 488-96.
Adhikari Avishek, Sigurdsson Torfi, Topiwala Mihir A, Gordon Joshua A   Cross-correlation of instantaneous amplitudes of field potential oscillations: a straightforward method to estimate the directionality and lag between brain areas Journal of neuroscience methods, 2010; 191(2): 191-200.
Resende Rodrigo R, da Costa José L, Kihara Alexandre H, Adhikari Avishek, Lorençon Eudes   Intracellular Ca2+ regulation during neuronal differentiation of murine embryonal carcinoma and mesenchymal stem cells Stem cells and development, 2010; 19(3): 379-94.
Adhikari Avishek, Topiwala Mihir A, Gordon Joshua A   Synchronized activity between the ventral hippocampus and the medial prefrontal cortex during anxiety Neuron, 2010; 65(2): 257-69.
Resende Rodrigo R, Adhikari Avishek   Cholinergic receptor pathways involved in apoptosis, cell proliferation and neuronal differentiation Cell communication and signaling : CCS, 2009; 7(2): 20.
Resende Rodrigo R, Gomes Katia N, Adhikari Avishek, Britto Luiz R G, Ulrich Henning   Mechanism of acetylcholine-induced calcium signaling during neuronal differentiation of P19 embryonal carcinoma cells in vitro Cell calcium, 2008; 43(2): 107-21.
Bechara Etelvino J H, Dutra Fernando, Cardoso Vanessa E S, Sartori Adriano, Olympio Kelly P K, Penatti Carlos A A, Adhikari Avishek, Assunção Nilson A   The dual face of endogenous alpha-aminoketones: pro-oxidizing metabolic weapons Comparative biochemistry and physiology. Toxicology & pharmacology : CBP, 2008; 146(1-2): 88-110.
Adhikari Avishek, Penatti Carlos A A, Resende Rodrigo R, Ulrich Henning, Britto Luiz R G, Bechara Etelvino J H   5-Aminolevulinate and 4, 5-dioxovalerate ions decrease GABA(A) receptor density in neuronal cells, synaptosomes and rat brain Brain research, 2006; 1093(1): 95-104.

Michele Basso, Ph.D.

Biography

Dr. Michele A. Basso is a Professor in the Departments of Psychiatry and Biobehavioral Sciences and Neurobiology. She studied Neuroscience at Stony Brook University in NY and was a post-doctoral fellow at the National Eye Institute, NIH. After serving as a faculty member at the University of Wisconsin Madison, she moved to UCLA to join the faculty and direct the Fuster Laboratory of Cognitive Neuroscience. The work performed in her laboratory is aimed at unravelling the neuronal circuits of decision-making in health and disease. Her work spans multiple species and employs multiple technologies designed to understand how memory and sensory information are combined to give rise to our decisions.

Publications

A selected list of publications:

Perugini Alessandra, Basso Michele A   Perceptual decisions based on previously learned information are independent of dopaminergic tone Journal of neurophysiology, 2018; 119(3): 849-861.
Odegaard Brian, Grimaldi Piercesare, Cho Seong Hah, Peters Megan A K, Lau Hakwan, Basso Michele A   Superior colliculus neuronal ensemble activity signals optimal rather than subjective confidence Proceedings of the National Academy of Sciences of the United States of America, 2018; 115(7): E1588-E1597.
Crapse Trinity B, Lau Hakwan, Basso Michele A   A Role for the Superior Colliculus in Decision Criteria Neuron, 2018; 97(1): 181-194.e6.
May Paul J, Basso Michele A   Connections between the zona incerta and superior colliculus in the monkey and squirrel Brain structure & function, 2018; 223(1): 371-390.
Basso Michele A, May Paul J   Circuits for Action and Cognition: A View from the Superior Colliculus Annual review of vision science, 2017; 3(1): 197-226.
Ghitani Nima, Bayguinov Peter O, Basso Michele A, Jackson Meyer B   A sodium afterdepolarization in rat superior colliculus neurons and its contribution to population activity Journal of neurophysiology, 2016; 116(1): 191-200.
Perugini Alessandra, Ditterich Jochen, Basso Michele A   Patients with Parkinson’s Disease Show Impaired Use of Priors in Conditions of Sensory Uncertainty Current biology : CB, 2016; 26(14): 1902-10.
Basso Michele A   Monkey neurophysiology to clinical neuroscience and back again Proceedings of the National Academy of Sciences of the United States of America, 2016; 113(24): 6591-3.
Crapse Trinity B, Basso Michele A   Insights into decision making using choice probability Journal of neurophysiology, 2015; 114(6): 3039-49.
Grimaldi Piercesare, Lau Hakwan, Basso Michele A   There are things that we know that we know, and there are things that we do not know we do not know: Confidence in decision-making Neuroscience and biobehavioral reviews, 2015; 55: 88-97.
Bayguinov Peter O, Ghitani Nima, Jackson Meyer B, Basso Michele A   A hard-wired priority map in the superior colliculus shaped by asymmetric inhibitory circuitry Journal of neurophysiology, 2015; 114(1): 662-76.
Vokoun Corinne R, Huang Xin, Jackson Meyer B, Basso Michele A   Response normalization in the superficial layers of the superior colliculus as a possible mechanism for saccadic averaging The Journal of neuroscience : the official journal of the Society for Neuroscience, 2014; 34(23): 7976-87.
Ghitani Nima, Bayguinov Peter O, Vokoun Corinne R, McMahon Shane, Jackson Meyer B, Basso Michele A   Excitatory synaptic feedback from the motor layer to the sensory layers of the superior colliculus The Journal of neuroscience : the official journal of the Society for Neuroscience, 2014; 34(20): 6822-33.
Mahamed Safraaz, Garrison Tiffany J, Shires Joel, Basso Michele A   Stimulation of the Substantia Nigra Influences the Specification of Memory-Guided Saccades Journal of neurophysiology, 2013; 39(1): .
Powers Alice S, Basso Michele A, Evinger Craig   Blinks slow memory-guided saccades Journal of neurophysiology, 2013; 109(3): 734-41.
Vokoun Corinne R, Jackson Meyer B, Basso Michele A   Circuit dynamics of the superior colliculus revealed by in vitro voltage imaging Annals of the New York Academy of Sciences, 2011; 1233(2): 41-7.
Li Xiaobing, Basso Michele A   Cues to move increased information in superior colliculus tuning curves Journal of neurophysiology, 2011; 106(2): 690-703.
Shires Joel, Joshi Siddhartha, Basso Michele A   Shedding new light on the role of the basal ganglia-superior colliculus pathway in eye movements Current opinion in neurobiology, 2010; 20(6): 717-25.
Vokoun Corinne R, Jackson Meyer B, Basso Michele A   Intralaminar and interlaminar activity within the rodent superior colliculus visualized with voltage imaging The Journal of neuroscience : the official journal of the Society for Neuroscience, 2010; 30(32): 10667-82.
Kim Byounghoon, Basso Michele A   A probabilistic strategy for understanding action selection The Journal of neuroscience : the official journal of the Society for Neuroscience, 2010; 30(6): 2340-55.
Gooding Diane C, Basso Michele A   The tell-tale tasks: a review of saccadic research in psychiatric patient populations Brain and cognition, 2008; 68(3): 371-90.
Liu Ping, Basso Michele A   Substantia nigra stimulation influences monkey superior colliculus neuronal activity bilaterally Journal of neurophysiology, 2008; 100(2): 1098-112.
Basso Michele A   Electrical stimulation of nervous system tissue. Introduction Neuroscience and biobehavioral reviews, 2008; 32(3): 331.
Li Xiaobing, Basso Michele A   Preparing to move increases the sensitivity of superior colliculus neurons The Journal of neuroscience : the official journal of the Society for Neuroscience, 2008; 28(17): 4561-77.
Kim Byounghoon, Basso Michele A   Saccade target selection in the superior colliculus: a signal detection theory approach The Journal of neuroscience : the official journal of the Society for Neuroscience, 2008; 28(12): 2991-3007.
Utter Amy A, Basso Michele A   The basal ganglia: an overview of circuits and function Neuroscience and biobehavioral reviews, 2008; 32(3): 333-42.
Basso Michele A, Liu Ping   Context-dependent effects of substantia nigra stimulation on eye movements Journal of neurophysiology, 2007; 97(6): 4129-42.
Smith Joshua J, Hadzic Vezira, Li Xiaobing, Liu Ping, Day Tiffany, Utter Amy, Kim Byounghoon, Washington Ida M, Basso Michele A   Objective measures of health and well-being in laboratory rhesus monkeys (Macaca mulatta) Journal of medical primatology, 2006; 35(6): 388-96.
Li Xiaobing, Kim Byounghoon, Basso Michele A   Transient pauses in delay-period activity of superior colliculus neurons Journal of neurophysiology, 2006; 95(4): 2252-64.
Li Xiaobing, Basso Michele A   Competitive stimulus interactions within single response fields of superior colliculus neurons The Journal of neuroscience : the official journal of the Society for Neuroscience, 2005; 25(49): 11357-73.
Basso Michele A, Pokorny Jennifer J, Liu Ping   Activity of substantia nigra pars reticulata neurons during smooth pursuit eye movements in monkeys The European journal of neuroscience, 2005; 22(2): 448-64.
Basso Michele A, Uhlrich Daniel, Bickford Martha E   Cortical function: a view from the thalamus Neuron, 2005; 45(4): 485-8.
Williamson Shawn S, Zivotofsky Ari Z, Basso Michele A   Modulation of gaze-evoked blinks depends primarily on extraretinal factors Journal of neurophysiology, 2005; 93(1): 627-32.
Basso Michele A, Wurtz Robert H   Neuronal activity in substantia nigra pars reticulata during target selection The Journal of neuroscience : the official journal of the Society for Neuroscience, 2002; 22(5): 1883-94.

Steve Cannon, M.D., Ph.D.

Biography

The primary research interests of our laboratory are how ion channels regulate the electrical excitability of cells and how defects in these channels lead to human disease. In the past two decades, mutations of ion channel genes have been found to be the primary cause for over 100 human diseases. Our research program is focused on the mechanistic basis for a group of inherited conditions that alter the electrical excitability of skeletal muscle, including periodic paralysis and myotonia. We have characterized the gating defects of mutant channels, generated computational models of muscle excitability, and produced genetically-engineered mice to gain insights on the pathomechanisms of these disorders and to explore therapeutic interventions.

Dean Buonomano, Ph.D.

Biography

NEURAL DYNAMICS: THE NEURAL BASIS OF LEARNING AND MEMORY AND TEMPORAL PROCESSING Behavior and cognition are not the product of isolated neurons, but rather emerge from the dynamics of interconnected neurons embedded in complex recurrent networks. Significant progress has been made towards understanding cellular and synaptic properties in isolation, as well as in establishing which areas of the brain are active during specific tasks. However, elucidating how the activity of hundreds of thousands of neurons within local cortical circuits underlie computations remains an elusive and fundamental goal in neuroscience. The primary goal of my laboratory is to understand how functional computations emerge from networks of neurons. One computation we are particularly interested in is how the brain tells time. Temporal processing refers to your ability to distinguish the interval and duration of sensory stimuli, and is a fundamental component of speech and music perception. To answer these questions the main approaches in my laboratory involve: (1) In Vitro Electrophysiology: Using acute and chronic brain slices we study the spatio-temporal dynamics of cortical circuits, as well as the learning rules that allow networks to develop, organize and perform computations ??? that is, to learn. (2) Computer Simulations: Computer models are used to simulate how networks perform computations, as well as test and generate predictions in parallel with our experimental research. (3) Human Psychophysics: We also use human pyschophysical experiments to characterize learning and generalization of temporal tasks, such as interval discrimination.

Publications

A selected list of publications:

Goel Anubhuti, Buonomano Dean V   Timing as an intrinsic property of neural networks: evidence from in vivo and in vitro experiments Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2014; 369(1637): 20120460.
Laje Rodrigo, Buonomano Dean V   Robust timing and motor patterns by taming chaos in recurrent neural networks Nature neuroscience, 2013; 16(7): 925-33.
Buonomano Dean V, Laje Rodrigo   Population clocks: motor timing with neural dynamics Trends in cognitive sciences, 2010; 14(12): 520-7.
Johnson Hope A, Goel Anubhuthi, Buonomano Dean V   Neural dynamics of in vitro cortical networks reflects experienced temporal patterns Nature neuroscience, 2010; 13(8): 917-9.
Liu Jian K, Buonomano Dean V   Embedding multiple trajectories in simulated recurrent neural networks in a self-organizing manner The Journal of neuroscience : the official journal of the Society for Neuroscience, 2009; 29(42): 13172-81.
Buonomano Dean V   Harnessing chaos in recurrent neural networks Neuron, 2009; 63(4): 423-5.
Buonomano Dean V, Bramen Jennifer, Khodadadifar Mahsa   Influence of the interstimulus interval on temporal processing and learning: testing the state-dependent network model Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2009; 364(1525): 1865-73.
Buonomano Dean V, Maass Wolfgang   State-dependent computations: spatiotemporal processing in cortical networks Nature reviews. Neuroscience, 2009; 10(2): 113-25.
Johnson Hope A, Buonomano Dean V   A method for chronic stimulation of cortical organotypic cultures using implanted electrodes Journal of neuroscience methods, 2009; 176(2): 136-43.
van Wassenhove V, Buonomano DV, Shimojo S, Shams L.   Distortions of subjective time perception within and across senses, PLoS ONE, 2008; 3(1): e1437.
Johnson, Hope A. Buonomano, Dean V.   Development and Plasticity of Spontaneous Activity and Up States in Cortical Organotypic Slices J. Neurosci, 2007; 27(22): 5915-5925.
Buonomano, D. V.   The biology of time across different scales Nat Chem Biol, 2007; 3(10): 594-7.
Karmarkar, U. R. Buonomano, D. V.   Timing in the absence of clocks: encoding time in neural network states Neuron, 2007; 53(3): 427-38.
Karmarkar, U. R. Buonomano, D. V.   Different forms of homeostatic plasticity are engaged with distinct temporal profiles, Eur J Neurosci, 2006; 23(6): 1575-84.
Eagleman, D. M. Tse, P. U. Buonomano, D. Janssen, P. Nobre, A. C. Holcombe, A. O.   Time and the brain: how subjective time relates to neural time, J Neurosci, 2005; 25(45): 10369-71.
Dong, H. W. Buonomano, D. V.   A technique for repeated recordings in cortical organotypic slices, J Neurosci Methods, 2005; 146(1): 69-75.
Buonomano, D. V.   A learning rule for the emergence of stable dynamics and timing in recurrent networks, J Neurophysiol, 2005; 94(4): 2275-83.
Marder, C. P. Buonomano, D. V.   Timing and balance of inhibition enhance the effect of long-term potentiation on cell firing, J Neurosci, 2004; 24(40): 8873-84.
Mauk, M. D. Buonomano, D. V.   The Neural Basis of Temporal Processing, Annual Rev. Neuroscience, 2004; 27: 304-340.
Karmarkar, U. R. Buonomano, D. V.   Temporal specificity of perceptual learning in an auditory discrimination task, Learn Mem, 2003; 10(2): 141-7.
Buonomano, D. V.   Timing of Neural Responses in Cortical Organotypic Slices, Proc. Natl. Acad. Sci. USA, 2003; 100: 4897-4902.
Marder, C. P. Buonomano, D. V.   Differential effects of short- and long-term potentiation on cell firing in the CA1 region of the hippocampus, J Neurosci, 2003; 23(1): 112-21.
Karmarkar, U. R. Buonomano, D. V.   A model of spike-timing dependent plasticity: one or two coincidence detectors?, J Neurophysiol, 2002; 88(1): 507-13.
Buonomano, D. V. Karmarkar, U. R.   How do we tell time?, Neuroscientist, 2002; 8(1): 42-51.
Karmarkar, U. R. Najarian, M. T. Buonomano, D. V.   Mechanisms and significance of spike-timing dependent plasticity, Biol Cybern, 2002; 87(5-6): 373-82.
Buonomano, D. V.   Decoding temporal information: a model based on short-term synaptic plasticity, J Neurosci, 2000; 20: 1129-1141.
Buonomano, D. V.   Distinct functional types of associative long-term potentiation in neocortical and hippocampal pyramidal neurons, J Neurosci, 1999; 19: 6748-6754.
Buonomano, D. V. Merzenich, M.   A neural network model of temporal code generation and position-invariant pattern recognition, Neural Comput, 1999; 11(1): 103-16.
Buonomano, D. V. Merzenich, M. M.   Cortical plasticity: from synapses to maps, Annual Rev. Neuroscience, 1998; 21: 149-186.
Buonomano, D. V. Merzenich, M. M.   Temporal information transformed into a spatial code by a neural network with realistic properties, Science, 1995; 267: 1028-30.
Buonomano, D. V. Byrne, J. H.   Long-term synaptic changes produced by a cellular analog of classical conditioning in Aplysia, Science, 1990; 249(4967): 420-3.