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Dunlop K, Grosenick L, Downar J, Vila-Rodriguez F, Gunning FM, Daskalakis ZJ, Blumberger DM, Liston C. Dimensional and Categorical Solutions to Parsing Depression Heterogeneity in a Large Single-Site Sample. Biol Psychiatry 2024:S0006-3223(24)00055-6. [PMID: 38280408 DOI: 10.1016/j.biopsych.2024.01.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 12/21/2023] [Accepted: 01/13/2024] [Indexed: 01/29/2024]
Abstract
BACKGROUND Recent studies have reported significant advances in modeling the biological basis of heterogeneity in major depressive disorder, but investigators have also identified important technical challenges, including scanner-related artifacts, a propensity for multivariate models to overfit, and a need for larger samples with more extensive clinical phenotyping. The goals of the current study were to evaluate dimensional and categorical solutions to parsing heterogeneity in depression that are stable and generalizable in a large, single-site sample. METHODS We used regularized canonical correlation analysis to identify data-driven brain-behavior dimensions that explain individual differences in depression symptom domains in a large, single-site dataset comprising clinical assessments and resting-state functional magnetic resonance imaging data for 328 patients with major depressive disorder and 461 healthy control participants. We examined the stability of clinical loadings and model performance in held-out data. Finally, hierarchical clustering on these dimensions was used to identify categorical depression subtypes. RESULTS The optimal regularized canonical correlation analysis model yielded 3 robust and generalizable brain-behavior dimensions that explained individual differences in depressed mood and anxiety, anhedonia, and insomnia. Hierarchical clustering identified 4 depression subtypes, each with distinct clinical symptom profiles, abnormal resting-state functional connectivity patterns, and antidepressant responsiveness to repetitive transcranial magnetic stimulation. CONCLUSIONS Our results define dimensional and categorical solutions to parsing neurobiological heterogeneity in major depressive disorder that are stable, generalizable, and capable of predicting treatment outcomes, each with distinct advantages in different contexts. They also provide additional evidence that regularized canonical correlation analysis and hierarchical clustering are effective tools for investigating associations between functional connectivity and clinical symptoms.
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Affiliation(s)
- Katharine Dunlop
- Centre for Depression and Suicide Studies, St Michael's Hospital, Toronto, Ontario, Canada; Keenan Research Centre for Biomedical Science, St. Michael's Hospital, Toronto, Ontario, Canada; Department of Psychiatry and Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Logan Grosenick
- Department of Psychiatry, Weill Cornell Medicine, New York, New York
| | - Jonathan Downar
- Department of Psychiatry and Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada
| | - Fidel Vila-Rodriguez
- Non-Invasive Neurostimulation Therapies Laboratory, Department of Psychiatry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Faith M Gunning
- Institute of Geriatric Psychiatry, Weill Cornell Medicine, White Plains, New York
| | - Zafiris J Daskalakis
- Department of Psychiatry, University of California San Diego, San Diego, California
| | - Daniel M Blumberger
- Department of Psychiatry and Institute of Medical Sciences, University of Toronto, Toronto, Ontario, Canada; Department of Psychiatry, Weill Cornell Medicine, New York, New York; Temerty Centre for Therapeutic Brain Intervention and Campbell Family Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Conor Liston
- Department of Psychiatry, Weill Cornell Medicine, New York, New York; Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York.
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2
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Lynch CJ, Elbau I, Ng T, Ayaz A, Zhu S, Manfredi N, Johnson M, Wolk D, Power JD, Gordon EM, Kay K, Aloysi A, Moia S, Caballero-Gaudes C, Victoria LW, Solomonov N, Goldwaser E, Zebley B, Grosenick L, Downar J, Vila-Rodriguez F, Daskalakis ZJ, Blumberger DM, Williams N, Gunning FM, Liston C. Expansion of a frontostriatal salience network in individuals with depression. bioRxiv 2023:2023.08.09.551651. [PMID: 37645792 PMCID: PMC10461904 DOI: 10.1101/2023.08.09.551651] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Hundreds of neuroimaging studies spanning two decades have revealed differences in brain structure and functional connectivity in depression, but with modest effect sizes, complicating efforts to derive mechanistic pathophysiologic insights or develop biomarkers. 1 Furthermore, although depression is a fundamentally episodic condition, few neuroimaging studies have taken a longitudinal approach, which is critical for understanding cause and effect and delineating mechanisms that drive mood state transitions over time. The emerging field of precision functional mapping using densely-sampled longitudinal neuroimaging data has revealed unexpected, functionally meaningful individual differences in brain network topology in healthy individuals, 2-5 but these approaches have never been applied to individuals with depression. Here, using precision functional mapping techniques and 11 datasets comprising n=187 repeatedly sampled individuals and >21,000 minutes of fMRI data, we show that the frontostriatal salience network is expanded two-fold in most individuals with depression. This effect was replicable in multiple samples, including large-scale, group-average data (N=1,231 subjects), and caused primarily by network border shifts affecting specific functional systems, with three distinct modes of encroachment occurring in different individuals. Salience network expansion was unexpectedly stable over time, unaffected by changes in mood state, and detectable in children before the subsequent onset of depressive symptoms in adolescence. Longitudinal analyses of individuals scanned up to 62 times over 1.5 years identified connectivity changes in specific frontostriatal circuits that tracked fluctuations in specific symptom domains and predicted future anhedonia symptoms before they emerged. Together, these findings identify a stable trait-like brain network topology that may confer risk for depression and mood-state dependent connectivity changes in frontostriatal circuits that predict the emergence and remission of depressive symptoms over time.
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Unda SR, Marongiu R, Pomeranz LE, Dyke JP, Fung EK, Grosenick L, Zirkel R, Antoniazzi AM, Norman S, Liston CM, Schaffer C, Nishimura N, Stanley SA, Friedman JM, Kaplitt MG. Bidirectional Regulation of Motor Circuits Using Magnetogenetic Gene Therapy. bioRxiv 2023:2023.07.13.548699. [PMID: 37503198 PMCID: PMC10369996 DOI: 10.1101/2023.07.13.548699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Regulating the activity of discrete neuronal populations in living mammals after delivery of modified ion channels can be used to map functional circuits and potentially treat neurological diseases. Here we report a novel suite of magnetogenetic tools, based on a single anti-ferritin nanobody-TRPV1 receptor fusion protein, which regulated neuronal activity in motor circuits when exposed to magnetic fields. AAV-mediated delivery of a cre-dependent nanobody-TRPV1 calcium channel into the striatum of adenosine 2a (A2a) receptor-cre driver mice led to restricted expression within D2 neurons, resulting in motor freezing when placed in a 3T MRI or adjacent to a transcranial magnetic stimulation (TMS) device. Functional imaging and fiber photometry both confirmed focal activation of the target region in response to the magnetic fields. Expression of the same construct in the striatum of wild-type mice along with a second injection of an AAVretro expressing cre into the globus pallidus led to similar circuit specificity and motor responses. Finally, a mutation was generated to gate chloride and inhibit neuronal activity. Expression of this variant in subthalamic nucleus (STN) projection neurons in PitX2-cre parkinsonian mice resulted in reduced local c-fos expression and a corresponding improvement in motor rotational behavior during magnetic field exposure. These data demonstrate that AAV delivery of magnetogenetic constructs can bidirectionally regulate activity of specific neuronal circuits non-invasively in vivo using clinically available devices for both preclinical analysis of circuit effects on behavior and potential human clinical translation.
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4
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Fetcho RN, Hall BS, Estrin DJ, Walsh AP, Schuette PJ, Kaminsky J, Singh A, Roshgodal J, Bavley CC, Nadkarni V, Antigua S, Huynh TN, Grosenick L, Carthy C, Komer L, Adhikari A, Lee FS, Rajadhyaksha AM, Liston C. Regulation of social interaction in mice by a frontostriatal circuit modulated by established hierarchical relationships. Nat Commun 2023; 14:2487. [PMID: 37120443 PMCID: PMC10148889 DOI: 10.1038/s41467-023-37460-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 03/17/2023] [Indexed: 05/01/2023] Open
Abstract
Social hierarchies exert a powerful influence on behavior, but the neurobiological mechanisms that detect and regulate hierarchical interactions are not well understood, especially at the level of neural circuits. Here, we use fiber photometry and chemogenetic tools to record and manipulate the activity of nucleus accumbens-projecting cells in the ventromedial prefrontal cortex (vmPFC-NAcSh) during tube test social competitions. We show that vmPFC-NAcSh projections signal learned hierarchical relationships, and are selectively recruited by subordinate mice when they initiate effortful social dominance behavior during encounters with a dominant competitor from an established hierarchy. After repeated bouts of social defeat stress, this circuit is preferentially activated during social interactions initiated by stress resilient individuals, and plays a necessary role in supporting social approach behavior in subordinated mice. These results define a necessary role for vmPFC-NAcSh cells in the adaptive regulation of social interaction behavior based on prior hierarchical interactions.
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Affiliation(s)
- Robert N Fetcho
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA
| | - Baila S Hall
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - David J Estrin
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Alexander P Walsh
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Peter J Schuette
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Jesse Kaminsky
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Ashna Singh
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Jacob Roshgodal
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Charlotte C Bavley
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Viraj Nadkarni
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Susan Antigua
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Thu N Huynh
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Logan Grosenick
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Camille Carthy
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA
| | - Lauren Komer
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Avishek Adhikari
- Department of Psychology, University of California, Los Angeles, Los Angeles, CA, USA
| | - Francis S Lee
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Anjali M Rajadhyaksha
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Department of Pediatrics, Division of Pediatric Neurology, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Autism Research Program, New York, NY, USA.
| | - Conor Liston
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA.
- Weill Cornell Autism Research Program, New York, NY, USA.
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5
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Buch AM, Vértes PE, Seidlitz J, Kim SH, Grosenick L, Liston C. Molecular and network-level mechanisms explaining individual differences in autism spectrum disorder. Nat Neurosci 2023; 26:650-663. [PMID: 36894656 DOI: 10.1038/s41593-023-01259-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/17/2023] [Indexed: 03/11/2023]
Abstract
The mechanisms underlying phenotypic heterogeneity in autism spectrum disorder (ASD) are not well understood. Using a large neuroimaging dataset, we identified three latent dimensions of functional brain network connectivity that predicted individual differences in ASD behaviors and were stable in cross-validation. Clustering along these three dimensions revealed four reproducible ASD subgroups with distinct functional connectivity alterations in ASD-related networks and clinical symptom profiles that were reproducible in an independent sample. By integrating neuroimaging data with normative gene expression data from two independent transcriptomic atlases, we found that within each subgroup, ASD-related functional connectivity was explained by regional differences in the expression of distinct ASD-related gene sets. These gene sets were differentially associated with distinct molecular signaling pathways involving immune and synapse function, G-protein-coupled receptor signaling, protein synthesis and other processes. Collectively, our findings delineate atypical connectivity patterns underlying different forms of ASD that implicate distinct molecular signaling mechanisms.
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Affiliation(s)
- Amanda M Buch
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
| | - Petra E Vértes
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Jakob Seidlitz
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA, USA
- Department of Child and Adolescent Psychiatry and Behavioral Science, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - So Hyun Kim
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA
- Center for Autism and the Developing Brain, Weill Cornell Medicine, White Plains, NY, USA
- School of Psychology, Korea University, Seoul, South Korea
| | - Logan Grosenick
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
| | - Conor Liston
- Department of Psychiatry and Brain and Mind Research Institute, Weill Cornell Medicine, New York, NY, USA.
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6
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Solomonov N, Kanellopoulos D, Grosenick L, Wilkins V, Goldman R, Ritholtz S, Falk A, Gunning FM. CopeNYP: a brief remote psychological intervention reduces health care workers' depression and anxiety symptoms during COVID-19 pandemic. World Psychiatry 2022; 21:155-156. [PMID: 35015344 PMCID: PMC8751568 DOI: 10.1002/wps.20946] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Affiliation(s)
- Nili Solomonov
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | | | - Logan Grosenick
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Victoria Wilkins
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Rachel Goldman
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Shira Ritholtz
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Avital Falk
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
| | - Faith M Gunning
- Department of Psychiatry, Weill Cornell Medicine, New York, NY, USA
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7
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Grosenick L, Liston C. Reply to: A Closer Look at Depression Biotypes: Correspondence Relating to Grosenick et al. (2019). Biol Psychiatry Cogn Neurosci Neuroimaging 2020; 5:556. [PMID: 31926903 DOI: 10.1016/j.bpsc.2019.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 11/07/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Logan Grosenick
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York; Department of Psychiatry, Weill Cornell Medicine, New York, New York; Simons Foundation, Columbia University, New York, New York; Department of Statistics, Columbia University, New York, New York
| | - Conor Liston
- Feil Family Brain and Mind Research Institute, Weill Cornell Medicine, New York, New York; Department of Psychiatry, Weill Cornell Medicine, New York, New York.
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8
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Grosenick L, Shi TC, Gunning FM, Dubin MJ, Downar J, Liston C. Functional and Optogenetic Approaches to Discovering Stable Subtype-Specific Circuit Mechanisms in Depression. Biol Psychiatry Cogn Neurosci Neuroimaging 2019; 4:554-566. [PMID: 31176387 PMCID: PMC6788795 DOI: 10.1016/j.bpsc.2019.04.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Revised: 04/29/2019] [Accepted: 04/29/2019] [Indexed: 12/18/2022]
Abstract
BACKGROUND Previously, we identified four depression subtypes defined by distinct functional connectivity alterations in depression-related brain networks, which in turn predicted clinical symptoms and treatment response. Optogenetic functional magnetic resonance imaging offers a promising approach for testing how dysfunction in specific circuits gives rise to subtype-specific, depression-related behaviors. However, this approach assumes that there are robust, reproducible correlations between functional connectivity and depressive symptoms-an assumption that was not extensively tested in previous work. METHODS First, we comprehensively reevaluated the stability of canonical correlations between functional connectivity and symptoms (N = 220 subjects) using optimized approaches for large-scale statistical hypothesis testing, and we validated methods for improving estimation of latent variables driving brain-behavior correlations. Having confirmed this necessary condition, we reviewed recent advances in optogenetic functional magnetic resonance imaging and illustrated one approach to formulating hypotheses regarding latent subtype-specific circuit mechanisms and testing them in animal models. RESULTS Correlations between connectivity features and clinical symptoms were robustly significant, and canonical correlation analysis solutions tested repeatedly on held-out data generalized. However, they were sensitive to data quality, preprocessing, and clinical heterogeneity, which can reduce effect sizes. Generalization could be markedly improved by adding L2 regularization, which decreased estimator variance, increased canonical correlations in left-out data, and stabilized feature selection. These improvements were useful for identifying candidate circuits for optogenetic interrogation in animal models. CONCLUSIONS Multiview, latent-variable approaches such as canonical correlation analysis offer a conceptually useful framework for discovering stable patient subtypes by synthesizing multiple clinical and functional measures. Optogenetic functional magnetic resonance imaging holds promise for testing hypotheses regarding latent, subtype-specific mechanisms driving depressive symptoms and behaviors.
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Affiliation(s)
- Logan Grosenick
- Feil Family Brain and Mind Research Institute and Department of Psychiatry, Weill Cornell Medicine, New York, New York; Department of Statistics, Columbia University, New York, New York; Simons Foundation, New York, New York
| | - Tracey C Shi
- Feil Family Brain and Mind Research Institute and Department of Psychiatry, Weill Cornell Medicine, New York, New York
| | - Faith M Gunning
- Feil Family Brain and Mind Research Institute and Department of Psychiatry, Weill Cornell Medicine, New York, New York
| | - Marc J Dubin
- Feil Family Brain and Mind Research Institute and Department of Psychiatry, Weill Cornell Medicine, New York, New York
| | - Jonathan Downar
- Department of Psychiatry, Toronto Western Hospital, Toronto, Ontario, Canada
| | - Conor Liston
- Feil Family Brain and Mind Research Institute and Department of Psychiatry, Weill Cornell Medicine, New York, New York.
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9
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Moda-Sava RN, Murdock MH, Parekh PK, Fetcho RN, Huang BS, Huynh TN, Witztum J, Shaver DC, Rosenthal DL, Alway EJ, Lopez K, Meng Y, Nellissen L, Grosenick L, Milner TA, Deisseroth K, Bito H, Kasai H, Liston C. Sustained rescue of prefrontal circuit dysfunction by antidepressant-induced spine formation. Science 2019; 364:364/6436/eaat8078. [PMID: 30975859 DOI: 10.1126/science.aat8078] [Citation(s) in RCA: 315] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 02/18/2019] [Indexed: 12/11/2022]
Abstract
The neurobiological mechanisms underlying the induction and remission of depressive episodes over time are not well understood. Through repeated longitudinal imaging of medial prefrontal microcircuits in the living brain, we found that prefrontal spinogenesis plays a critical role in sustaining specific antidepressant behavioral effects and maintaining long-term behavioral remission. Depression-related behavior was associated with targeted, branch-specific elimination of postsynaptic dendritic spines on prefrontal projection neurons. Antidepressant-dose ketamine reversed these effects by selectively rescuing eliminated spines and restoring coordinated activity in multicellular ensembles that predict motivated escape behavior. Prefrontal spinogenesis was required for the long-term maintenance of antidepressant effects on motivated escape behavior but not for their initial induction.
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Affiliation(s)
- R N Moda-Sava
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - M H Murdock
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - P K Parekh
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - R N Fetcho
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - B S Huang
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - T N Huynh
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - J Witztum
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - D C Shaver
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - D L Rosenthal
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - E J Alway
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - K Lopez
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - Y Meng
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - L Nellissen
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - L Grosenick
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA.,Departments of Bioengineering and of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - T A Milner
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA
| | - K Deisseroth
- Departments of Bioengineering and of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - H Bito
- Department of Neurochemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - H Kasai
- Laboratory of Structural Physiology, Center for Disease Biology and Integrative Medicine, Faculty of Medicine, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan.,International Research Center for Neurointelligence (WPI-IRCN), UTIAS, The University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - C Liston
- Brain and Mind Research Institute, Department of Psychiatry, and Sackler Institute for Developmental Psychobiology, Weill Cornell Medicine, New York, NY 10021, USA.
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10
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Andalman AS, Burns VM, Lovett-Barron M, Broxton M, Poole B, Yang SJ, Grosenick L, Lerner TN, Chen R, Benster T, Mourrain P, Levoy M, Rajan K, Deisseroth K. Neuronal Dynamics Regulating Brain and Behavioral State Transitions. Cell 2019; 177:970-985.e20. [PMID: 31031000 PMCID: PMC6726130 DOI: 10.1016/j.cell.2019.02.037] [Citation(s) in RCA: 123] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 02/02/2019] [Accepted: 02/20/2019] [Indexed: 12/11/2022]
Abstract
Prolonged behavioral challenges can cause animals to switch from active to passive coping strategies to manage effort-expenditure during stress; such normally adaptive behavioral state transitions can become maladaptive in psychiatric disorders such as depression. The underlying neuronal dynamics and brainwide interactions important for passive coping have remained unclear. Here, we develop a paradigm to study these behavioral state transitions at cellular-resolution across the entire vertebrate brain. Using brainwide imaging in zebrafish, we observed that the transition to passive coping is manifested by progressive activation of neurons in the ventral (lateral) habenula. Activation of these ventral-habenula neurons suppressed downstream neurons in the serotonergic raphe nucleus and caused behavioral passivity, whereas inhibition of these neurons prevented passivity. Data-driven recurrent neural network modeling pointed to altered intra-habenula interactions as a contributory mechanism. These results demonstrate ongoing encoding of experience features in the habenula, which guides recruitment of downstream networks and imposes a passive coping behavioral strategy.
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Affiliation(s)
- Aaron S Andalman
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Vanessa M Burns
- Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | - Matthew Lovett-Barron
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Michael Broxton
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Ben Poole
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Samuel J Yang
- Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Logan Grosenick
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Talia N Lerner
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Ritchie Chen
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Tyler Benster
- Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Philippe Mourrain
- Stanford Center for Sleep Sciences and Medicine, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; INSERM U1024, Ecole Normale Supérieure Paris, Paris 75005, France
| | - Marc Levoy
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Kanaka Rajan
- Department of Neuroscience and Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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11
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Aimon S, Katsuki T, Jia T, Grosenick L, Broxton M, Deisseroth K, Sejnowski TJ, Greenspan RJ. Fast near-whole-brain imaging in adult Drosophila during responses to stimuli and behavior. PLoS Biol 2019; 17:e2006732. [PMID: 30768592 PMCID: PMC6395010 DOI: 10.1371/journal.pbio.2006732] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 02/28/2019] [Accepted: 01/28/2019] [Indexed: 11/18/2022] Open
Abstract
Whole-brain recordings give us a global perspective of the brain in action. In this study, we describe a method using light field microscopy to record near-whole brain calcium and voltage activity at high speed in behaving adult flies. We first obtained global activity maps for various stimuli and behaviors. Notably, we found that brain activity increased on a global scale when the fly walked but not when it groomed. This global increase with walking was particularly strong in dopamine neurons. Second, we extracted maps of spatially distinct sources of activity as well as their time series using principal component analysis and independent component analysis. The characteristic shapes in the maps matched the anatomy of subneuropil regions and, in some cases, a specific neuron type. Brain structures that responded to light and odor were consistent with previous reports, confirming the new technique's validity. We also observed previously uncharacterized behavior-related activity as well as patterns of spontaneous voltage activity.
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Affiliation(s)
- Sophie Aimon
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
- Neurobiology Section, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Takeo Katsuki
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
| | - Tongqiu Jia
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
| | - Logan Grosenick
- Departments of Computer Science and Bioengineering, Stanford University, Stanford, California, United States of America
| | - Michael Broxton
- Departments of Computer Science and Bioengineering, Stanford University, Stanford, California, United States of America
| | - Karl Deisseroth
- Departments of Bioengineering and Psychiatry, Stanford University, Stanford, California, United States of America
- Howard Hughes Medical Institute, Stanford University, Stanford, Stanford, California, United States of America
| | - Terrence J. Sejnowski
- Computational Neurobiology Laboratory, Salk Institute for Biological Studies, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ralph J. Greenspan
- Kavli Institute for Brain and Mind, UCSD, La Jolla, California, United States of America
- Neurobiology Section, University of California, San Diego, La Jolla, California, United States of America
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
- Department of Cognitive Science, University of California, San Diego, La Jolla, California, United States of America
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12
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Reed SJ, Lafferty CK, Mendoza JA, Yang AK, Davidson TJ, Grosenick L, Deisseroth K, Britt JP. Coordinated Reductions in Excitatory Input to the Nucleus Accumbens Underlie Food Consumption. Neuron 2018; 99:1260-1273.e4. [DOI: 10.1016/j.neuron.2018.07.051] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 06/14/2018] [Accepted: 07/27/2018] [Indexed: 12/21/2022]
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13
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Tomer R, Lovett-Barron M, Kauvar I, Andalman A, Burns VM, Sankaran S, Grosenick L, Broxton M, Yang S, Deisseroth K. SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function. Cell 2016; 163:1796-806. [PMID: 26687363 PMCID: PMC4775738 DOI: 10.1016/j.cell.2015.11.061] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/01/2015] [Accepted: 11/23/2015] [Indexed: 12/11/2022]
Abstract
The goal of understanding living nervous systems has driven interest in high-speed and large field-of-view volumetric imaging at cellular resolution. Light sheet microscopy approaches have emerged for cellular-resolution functional brain imaging in small organisms such as larval zebrafish, but remain fundamentally limited in speed. Here, we have developed SPED light sheet microscopy, which combines large volumetric field-of-view via an extended depth of field with the optical sectioning of light sheet microscopy, thereby eliminating the need to physically scan detection objectives for volumetric imaging. SPED enables scanning of thousands of volumes-per-second, limited only by camera acquisition rate, through the harnessing of optical mechanisms that normally result in unwanted spherical aberrations. We demonstrate capabilities of SPED microscopy by performing fast sub-cellular resolution imaging of CLARITY mouse brains and cellular-resolution volumetric Ca(2+) imaging of entire zebrafish nervous systems. Together, SPED light sheet methods enable high-speed cellular-resolution volumetric mapping of biological system structure and function.
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Affiliation(s)
- Raju Tomer
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Matthew Lovett-Barron
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Isaac Kauvar
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Aaron Andalman
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA
| | - Vanessa M Burns
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA
| | | | | | - Michael Broxton
- Department of Computer Science, Stanford University, Stanford, CA 94305, USA
| | - Samuel Yang
- CNC Program, Stanford University, Stanford, CA 94305, USA; Department of Electrical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; CNC Program, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA.
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14
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Ferenczi EA, Zalocusky KA, Liston C, Grosenick L, Warden MR, Amatya D, Katovich K, Mehta H, Patenaude B, Ramakrishnan C, Kalanithi P, Etkin A, Knutson B, Glover GH, Deisseroth K. Prefrontal cortical regulation of brainwide circuit dynamics and reward-related behavior. Science 2016; 351:aac9698. [PMID: 26722001 DOI: 10.1126/science.aac9698] [Citation(s) in RCA: 351] [Impact Index Per Article: 43.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Motivation for reward drives adaptive behaviors, whereas impairment of reward perception and experience (anhedonia) can contribute to psychiatric diseases, including depression and schizophrenia. We sought to test the hypothesis that the medial prefrontal cortex (mPFC) controls interactions among specific subcortical regions that govern hedonic responses. By using optogenetic functional magnetic resonance imaging to locally manipulate but globally visualize neural activity in rats, we found that dopamine neuron stimulation drives striatal activity, whereas locally increased mPFC excitability reduces this striatal response and inhibits the behavioral drive for dopaminergic stimulation. This chronic mPFC overactivity also stably suppresses natural reward-motivated behaviors and induces specific new brainwide functional interactions, which predict the degree of anhedonia in individuals. These findings describe a mechanism by which mPFC modulates expression of reward-seeking behavior, by regulating the dynamical interactions between specific distant subcortical regions.
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Affiliation(s)
- Emily A Ferenczi
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Kelly A Zalocusky
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Conor Liston
- Brain Mind Research Institute, Weill Cornell Medical College, New York, NY 10065, USA
| | - Logan Grosenick
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Neurosciences Program, Stanford University, Stanford, CA 94305, USA
| | - Melissa R Warden
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Debha Amatya
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kiefer Katovich
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Hershel Mehta
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Brian Patenaude
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Charu Ramakrishnan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Paul Kalanithi
- Department of Neurosurgery, Stanford University, Stanford, CA 94305, USA
| | - Amit Etkin
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Brian Knutson
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Gary H Glover
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
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15
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Montgomery KL, Yeh AJ, Ho JS, Tsao V, Mohan Iyer S, Grosenick L, Ferenczi EA, Tanabe Y, Deisseroth K, Delp SL, Poon ASY. Wirelessly powered, fully internal optogenetics for brain, spinal and peripheral circuits in mice. Nat Methods 2015; 12:969-74. [PMID: 26280330 DOI: 10.1038/nmeth.3536] [Citation(s) in RCA: 303] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 07/06/2015] [Indexed: 01/22/2023]
Abstract
To enable sophisticated optogenetic manipulation of neural circuits throughout the nervous system with limited disruption of animal behavior, light-delivery systems beyond fiber optic tethering and large, head-mounted wireless receivers are desirable. We report the development of an easy-to-construct, implantable wireless optogenetic device. Our smallest version (20 mg, 10 mm(3)) is two orders of magnitude smaller than previously reported wireless optogenetic systems, allowing the entire device to be implanted subcutaneously. With a radio-frequency (RF) power source and controller, this implant produces sufficient light power for optogenetic stimulation with minimal tissue heating (<1 °C). We show how three adaptations of the implant allow for untethered optogenetic control throughout the nervous system (brain, spinal cord and peripheral nerve endings) of behaving mice. This technology opens the door for optogenetic experiments in which animals are able to behave naturally with optogenetic manipulation of both central and peripheral targets.
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Affiliation(s)
- Kate L Montgomery
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Alexander J Yeh
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - John S Ho
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Vivien Tsao
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Shrivats Mohan Iyer
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Logan Grosenick
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Neurosciences Program, Stanford University, Stanford, California, USA
| | - Emily A Ferenczi
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Neurosciences Program, Stanford University, Stanford, California, USA
| | - Yuji Tanabe
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Neurosciences Program, Stanford University, Stanford, California, USA.,Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA.,Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
| | - Scott L Delp
- Department of Bioengineering, Stanford University, Stanford, California, USA.,Department of Mechanical Engineering, Stanford University, Stanford, California, USA
| | - Ada S Y Poon
- Department of Electrical Engineering, Stanford University, Stanford, California, USA
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16
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Abstract
Advances in optical manipulation and observation of neural activity have set the stage for widespread implementation of closed-loop and activity-guided optical control of neural circuit dynamics. Closing the loop optogenetically (i.e., basing optogenetic stimulation on simultaneously observed dynamics in a principled way) is a powerful strategy for causal investigation of neural circuitry. In particular, observing and feeding back the effects of circuit interventions on physiologically relevant timescales is valuable for directly testing whether inferred models of dynamics, connectivity, and causation are accurate in vivo. Here we highlight technical and theoretical foundations as well as recent advances and opportunities in this area, and we review in detail the known caveats and limitations of optogenetic experimentation in the context of addressing these challenges with closed-loop optogenetic control in behaving animals.
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Affiliation(s)
- Logan Grosenick
- Department of Bioengineering, Stanford University, Stanford, CA 94305 USA; CNC Program, Stanford University, Stanford, CA 94305 USA; Neurosciences Program, Stanford University, Stanford, CA 94305 USA
| | - James H Marshel
- Department of Bioengineering, Stanford University, Stanford, CA 94305 USA; CNC Program, Stanford University, Stanford, CA 94305 USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305 USA; CNC Program, Stanford University, Stanford, CA 94305 USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305 USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305 USA.
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17
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Cohen N, Yang S, Andalman A, Broxton M, Grosenick L, Deisseroth K, Horowitz M, Levoy M. Enhancing the performance of the light field microscope using wavefront coding. Opt Express 2014; 22:727-36. [PMID: 25322056 DOI: 10.1364/oe.22.000727] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.
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18
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Cohen N, Yang S, Andalman A, Broxton M, Grosenick L, Deisseroth K, Horowitz M, Levoy M. Enhancing the performance of the light field microscope using wavefront coding. Opt Express 2014; 22:24817-39. [PMID: 25322056 PMCID: PMC4247191 DOI: 10.1364/oe.22.024817] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2014] [Revised: 09/18/2014] [Accepted: 09/21/2014] [Indexed: 05/04/2023]
Abstract
Light field microscopy has been proposed as a new high-speed volumetric computational imaging method that enables reconstruction of 3-D volumes from captured projections of the 4-D light field. Recently, a detailed physical optics model of the light field microscope has been derived, which led to the development of a deconvolution algorithm that reconstructs 3-D volumes with high spatial resolution. However, the spatial resolution of the reconstructions has been shown to be non-uniform across depth, with some z planes showing high resolution and others, particularly at the center of the imaged volume, showing very low resolution. In this paper, we enhance the performance of the light field microscope using wavefront coding techniques. By including phase masks in the optical path of the microscope we are able to address this non-uniform resolution limitation. We have also found that superior control over the performance of the light field microscope can be achieved by using two phase masks rather than one, placed at the objective's back focal plane and at the microscope's native image plane. We present an extended optical model for our wavefront coded light field microscope and develop a performance metric based on Fisher information, which we use to choose adequate phase masks parameters. We validate our approach using both simulated data and experimental resolution measurements of a USAF 1951 resolution target; and demonstrate the utility for biological applications with in vivo volumetric calcium imaging of larval zebrafish brain.
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Affiliation(s)
- Noy Cohen
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Samuel Yang
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Aaron Andalman
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Michael Broxton
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Logan Grosenick
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Karl Deisseroth
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Mark Horowitz
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
| | - Marc Levoy
- Departments of Electrical Engineering, Computer Science and Bioengineering, Stanford University, Stanford, CA 94305,
USA
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19
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Gunaydin LA, Grosenick L, Finkelstein JC, Kauvar IV, Fenno LE, Adhikari A, Lammel S, Mirzabekov JJ, Airan RD, Zalocusky KA, Tye KM, Anikeeva P, Malenka RC, Deisseroth K. Natural neural projection dynamics underlying social behavior. Cell 2014; 157:1535-51. [PMID: 24949967 DOI: 10.1016/j.cell.2014.05.017] [Citation(s) in RCA: 871] [Impact Index Per Article: 87.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/30/2014] [Accepted: 05/12/2014] [Indexed: 01/11/2023]
Abstract
Social interaction is a complex behavior essential for many species and is impaired in major neuropsychiatric disorders. Pharmacological studies have implicated certain neurotransmitter systems in social behavior, but circuit-level understanding of endogenous neural activity during social interaction is lacking. We therefore developed and applied a new methodology, termed fiber photometry, to optically record natural neural activity in genetically and connectivity-defined projections to elucidate the real-time role of specified pathways in mammalian behavior. Fiber photometry revealed that activity dynamics of a ventral tegmental area (VTA)-to-nucleus accumbens (NAc) projection could encode and predict key features of social, but not novel object, interaction. Consistent with this observation, optogenetic control of cells specifically contributing to this projection was sufficient to modulate social behavior, which was mediated by type 1 dopamine receptor signaling downstream in the NAc. Direct observation of deep projection-specific activity in this way captures a fundamental and previously inaccessible dimension of mammalian circuit dynamics.
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Affiliation(s)
- Lisa A Gunaydin
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Logan Grosenick
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Neuroscience Program, Stanford University, Stanford, CA 94305, USA
| | - Joel C Finkelstein
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Isaac V Kauvar
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lief E Fenno
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Neuroscience Program, Stanford University, Stanford, CA 94305, USA
| | - Avishek Adhikari
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Stephan Lammel
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Julie J Mirzabekov
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Raag D Airan
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Kelly A Zalocusky
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Neuroscience Program, Stanford University, Stanford, CA 94305, USA
| | - Kay M Tye
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Polina Anikeeva
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Robert C Malenka
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA
| | - Karl Deisseroth
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA.
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20
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Fenno LE, Mattis J, Ramakrishnan C, Hyun M, Lee SY, He M, Tucciarone J, Selimbeyoglu A, Berndt A, Grosenick L, Zalocusky KA, Bernstein H, Swanson H, Perry C, Diester I, Boyce FM, Bass CE, Neve R, Huang ZJ, Deisseroth K. Targeting cells with single vectors using multiple-feature Boolean logic. Nat Methods 2014; 11:763-72. [PMID: 24908100 DOI: 10.1038/nmeth.2996] [Citation(s) in RCA: 335] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 05/01/2014] [Indexed: 01/20/2023]
Abstract
Precisely defining the roles of specific cell types is an intriguing frontier in the study of intact biological systems and has stimulated the rapid development of genetically encoded tools for observation and control. However, targeting these tools with adequate specificity remains challenging: most cell types are best defined by the intersection of two or more features such as active promoter elements, location and connectivity. Here we have combined engineered introns with specific recombinases to achieve expression of genetically encoded tools that is conditional upon multiple cell-type features, using Boolean logical operations all governed by a single versatile vector. We used this approach to target intersectionally specified populations of inhibitory interneurons in mammalian hippocampus and neurons of the ventral tegmental area defined by both genetic and wiring properties. This flexible and modular approach may expand the application of genetically encoded interventional and observational tools for intact-systems biology.
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Affiliation(s)
- Lief E Fenno
- 1] Department of Neuroscience, Stanford University, Stanford, California, USA. [2] Department of Bioengineering, Stanford University, Stanford, California, USA. [3]
| | - Joanna Mattis
- 1] Department of Neuroscience, Stanford University, Stanford, California, USA. [2] Department of Bioengineering, Stanford University, Stanford, California, USA. [3]
| | - Charu Ramakrishnan
- 1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2]
| | - Minsuk Hyun
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Soo Yeun Lee
- 1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] CNC Program, Stanford University, Stanford, California, USA
| | - Miao He
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Jason Tucciarone
- 1] Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA. [2] Program in Neuroscience, Stony Brook University, Stony Brook, New York, USA
| | | | - Andre Berndt
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Logan Grosenick
- 1] Department of Neuroscience, Stanford University, Stanford, California, USA. [2] Department of Bioengineering, Stanford University, Stanford, California, USA. [3] CNC Program, Stanford University, Stanford, California, USA
| | - Kelly A Zalocusky
- 1] Department of Neuroscience, Stanford University, Stanford, California, USA. [2] CNC Program, Stanford University, Stanford, California, USA
| | - Hannah Bernstein
- Department of Neuroscience and Physiology, New York University School of Medicine, New York, New York, USA
| | - Haley Swanson
- CNC Program, Stanford University, Stanford, California, USA
| | - Chelsey Perry
- CNC Program, Stanford University, Stanford, California, USA
| | - Ilka Diester
- 1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] Ernst Struengmann Institute for Neuroscience, Frankfurt, Germany
| | - Frederick M Boyce
- Department of Neurology, Massachusetts General Hospital, Cambridge, Massachusetts, USA
| | - Caroline E Bass
- Department of Pharmacology and Toxicology, School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York, USA
| | - Rachael Neve
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Z Josh Huang
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Karl Deisseroth
- 1] Department of Bioengineering, Stanford University, Stanford, California, USA. [2] CNC Program, Stanford University, Stanford, California, USA. [3] Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, California, USA. [4] Howard Hughes Medical Institute, Stanford University, Stanford, California, USA
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21
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22
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Broxton M, Grosenick L, Yang S, Cohen N, Andalman A, Deisseroth K, Levoy M. Wave optics theory and 3-D deconvolution for the light field microscope. Opt Express 2013; 21:25418-39. [PMID: 24150383 PMCID: PMC3867103 DOI: 10.1364/oe.21.025418] [Citation(s) in RCA: 186] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Revised: 09/30/2013] [Accepted: 10/04/2013] [Indexed: 05/18/2023]
Abstract
Light field microscopy is a new technique for high-speed volumetric imaging of weakly scattering or fluorescent specimens. It employs an array of microlenses to trade off spatial resolution against angular resolution, thereby allowing a 4-D light field to be captured using a single photographic exposure without the need for scanning. The recorded light field can then be used to computationally reconstruct a full volume. In this paper, we present an optical model for light field microscopy based on wave optics, instead of previously reported ray optics models. We also present a 3-D deconvolution method for light field microscopy that is able to reconstruct volumes at higher spatial resolution, and with better optical sectioning, than previously reported. To accomplish this, we take advantage of the dense spatio-angular sampling provided by a microlens array at axial positions away from the native object plane. This dense sampling permits us to decode aliasing present in the light field to reconstruct high-frequency information. We formulate our method as an inverse problem for reconstructing the 3-D volume, which we solve using a GPU-accelerated iterative algorithm. Theoretical limits on the depth-dependent lateral resolution of the reconstructed volumes are derived. We show that these limits are in good agreement with experimental results on a standard USAF 1951 resolution target. Finally, we present 3-D reconstructions of pollen grains that demonstrate the improvements in fidelity made possible by our method.
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23
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Grosenick L, Klingenberg B, Katovich K, Knutson B, Taylor JE. Interpretable whole-brain prediction analysis with GraphNet. Neuroimage 2013; 72:304-21. [PMID: 23298747 DOI: 10.1016/j.neuroimage.2012.12.062] [Citation(s) in RCA: 121] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2011] [Revised: 12/06/2012] [Accepted: 12/26/2012] [Indexed: 10/27/2022] Open
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Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K. Structural and molecular interrogation of intact biological systems. Nature 2013; 497:332-7. [PMID: 23575631 DOI: 10.1038/nature12107] [Citation(s) in RCA: 1299] [Impact Index Per Article: 118.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2012] [Accepted: 03/20/2013] [Indexed: 12/15/2022]
Abstract
Obtaining high-resolution information from a complex system, while maintaining the global perspective needed to understand system function, represents a key challenge in biology. Here we address this challenge with a method (termed CLARITY) for the transformation of intact tissue into a nanoporous hydrogel-hybridized form (crosslinked to a three-dimensional network of hydrophilic polymers) that is fully assembled but optically transparent and macromolecule-permeable. Using mouse brains, we show intact-tissue imaging of long-range projections, local circuit wiring, cellular relationships, subcellular structures, protein complexes, nucleic acids and neurotransmitters. CLARITY also enables intact-tissue in situ hybridization, immunohistochemistry with multiple rounds of staining and de-staining in non-sectioned tissue, and antibody labelling throughout the intact adult mouse brain. Finally, we show that CLARITY enables fine structural analysis of clinical samples, including non-sectioned human tissue from a neuropsychiatric-disease setting, establishing a path for the transmutation of human tissue into a stable, intact and accessible form suitable for probing structural and molecular underpinnings of physiological function and disease.
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Affiliation(s)
- Kwanghun Chung
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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25
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Burns R, Roncal WG, Kleissas D, Lillaney K, Manavalan P, Perlman E, Berger DR, Bock DD, Chung K, Grosenick L, Kasthuri N, Weiler NC, Deisseroth K, Kazhdan M, Lichtman J, Reid RC, Smith SJ, Szalay AS, Vogelstein JT, Vogelstein RJ. The Open Connectome Project Data Cluster: Scalable Analysis and Vision for High-Throughput Neuroscience. Sci Stat Database Manag 2013:10.1145/2484838.2484870. [PMID: 24401992 PMCID: PMC3881956 DOI: 10.1145/2484838.2484870] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
We describe a scalable database cluster for the spatial analysis and annotation of high-throughput brain imaging data, initially for 3-d electron microscopy image stacks, but for time-series and multi-channel data as well. The system was designed primarily for workloads that build connectomes- neural connectivity maps of the brain-using the parallel execution of computer vision algorithms on high-performance compute clusters. These services and open-science data sets are publicly available at openconnecto.me. The system design inherits much from NoSQL scale-out and data-intensive computing architectures. We distribute data to cluster nodes by partitioning a spatial index. We direct I/O to different systems-reads to parallel disk arrays and writes to solid-state storage-to avoid I/O interference and maximize throughput. All programming interfaces are RESTful Web services, which are simple and stateless, improving scalability and usability. We include a performance evaluation of the production system, highlighting the effec-tiveness of spatial data organization.
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Affiliation(s)
- Randal Burns
- Department of Computer Science and the Institute for Data Intensive Engineering and Science, Johns Hopkins University
| | | | - Dean Kleissas
- Department of Statistical Science and Mathematics and the Institute for Brain Science, Duke University
| | - Kunal Lillaney
- Janelia Farm Research Campus, Howard Hughes Medical Institute
| | - Priya Manavalan
- Department of Molecular and Cellular Biology, Harvard University
| | - Eric Perlman
- Department of Computational Neuroscience, Massachusetts Institute of Technology
| | | | - Davi D Bock
- Department of Physics and Astronomy and the Institute for Data Intensive Engineering and Science, Johns Hopkins University
| | | | - Logan Grosenick
- Department of Molecular and Cellular Physiology, Stanford University
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26
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Tye KM, Prakash R, Kim SY, Fenno LE, Grosenick L, Zarabi H, Thompson KR, Gradinaru V, Ramakrishnan C, Deisseroth K. Amygdala circuitry mediating reversible and bidirectional control of anxiety. Nature 2011; 471:358-62. [PMID: 21389985 DOI: 10.1038/nature09820] [Citation(s) in RCA: 856] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2010] [Accepted: 01/14/2011] [Indexed: 11/09/2022]
Abstract
Anxiety--a sustained state of heightened apprehension in the absence of immediate threat--becomes severely debilitating in disease states. Anxiety disorders represent the most common of psychiatric diseases (28% lifetime prevalence) and contribute to the aetiology of major depression and substance abuse. Although it has been proposed that the amygdala, a brain region important for emotional processing, has a role in anxiety, the neural mechanisms that control anxiety remain unclear. Here we explore the neural circuits underlying anxiety-related behaviours by using optogenetics with two-photon microscopy, anxiety assays in freely moving mice, and electrophysiology. With the capability of optogenetics to control not only cell types but also specific connections between cells, we observed that temporally precise optogenetic stimulation of basolateral amygdala (BLA) terminals in the central nucleus of the amygdala (CeA)--achieved by viral transduction of the BLA with a codon-optimized channelrhodopsin followed by restricted illumination in the downstream CeA--exerted an acute, reversible anxiolytic effect. Conversely, selective optogenetic inhibition of the same projection with a third-generation halorhodopsin (eNpHR3.0) increased anxiety-related behaviours. Importantly, these effects were not observed with direct optogenetic control of BLA somata, possibly owing to recruitment of antagonistic downstream structures. Together, these results implicate specific BLA-CeA projections as critical circuit elements for acute anxiety control in the mammalian brain, and demonstrate the importance of optogenetically targeting defined projections, beyond simply targeting cell types, in the study of circuit function relevant to neuropsychiatric disease.
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Affiliation(s)
- Kay M Tye
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA
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27
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Abstract
Despite growing interest in applying machine learning to neuroimaging analyses, few studies have gone beyond classifying sensory input to directly predicting behavioral output. With spatial resolution on the order of millimeters and temporal resolution on the order of seconds, functional magnetic resonance imaging (fMRI) is a promising technology for such applications. However, fMRI data's low signal-to-noise ratio, high dimensionality, and extensive spatiotemporal correlations present formidable analytic challenges. Here, we apply different machine-learning algorithms to previously acquired data to examine the ability of fMRI activation in three regions-the nucleus accumbens (NAcc), medial prefrontal cortex (MPFC), and insula-to predict purchasing. Our goal was to improve spatiotemporal interpretability as well as classification accuracy. To this end, sparse penalized discriminant analysis (SPDA) enabled automatic selection of correlated variables, yielding interpretable models that generalized well to new data. Relative to logistic regression, linear discriminant analysis, and linear support vector machines, SPDA not only increased interpretability but also improved classification accuracy. SPDA promises to allow more precise inferences about when specific brain regions contribute to purchasing decisions. More broadly, this approach provides a general framework for using neuroimaging data to build interpretable models, including those that predict choice.
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Affiliation(s)
- Logan Grosenick
- Neuroscience Institute at Stanford, Stanford University, Stanford, CA 94305 USA
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28
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Abstract
While magnetoencephalography (MEG) is widely used to identify spatial locations of brain activations associated with various tasks, classification of single trials in stimulus-locked experiments remains an open subject. Very significant single-trial classification results have been published using electroencephalogram (EEG) data, but in the MEG case, the weakness of the magnetic fields originating from the relevant sources relative to external noise, and the high dimensionality of the data are difficult obstacles to overcome. We present here very significant MEG single-trial mean classification rates of words. The number of words classified varied from seven to nine and both visual and auditory modalities were studied. These results were obtained by using a variety of blind sources separation methods: spatial principal components analysis (PCA), Infomax independent components analysis (Infomax ICA) and second-order blind identification (SOBI). The sources obtained were classified using two methods, linear discriminant classification (LDC) and v-support vector machine (v-SVM). The data used here, auditory and visual presentations of words, presented nontrivial classification problems, but with Infomax ICA associated with LDC we obtained high classification rates. Our best single-trial mean classification rate was 60.1% for classification of 900 single trials of nine auditory words. On two-class problems rates were as high as 97.5%.
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Affiliation(s)
- Marcos Perreau Guimaraes
- Center for Study of Language and Information, CSLI 220 Panama Street, Stanford University, Stanford, CA 94305, USA.
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29
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Flanagan CA, Chen CC, Coetsee M, Mamputha S, Whitlock KE, Bredenkamp N, Grosenick L, Fernald RD, Illing N. Expression, structure, function, and evolution of gonadotropin-releasing hormone (GnRH) receptors GnRH-R1SHS and GnRH-R2PEY in the teleost, Astatotilapia burtoni. Endocrinology 2007; 148:5060-71. [PMID: 17595228 DOI: 10.1210/en.2006-1400] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Multiple GnRH receptors are known to exist in nonmammalian species, but it is uncertain which receptor type regulates reproduction via the hypothalamic-pituitary-gonadal axis. The teleost fish, Astatotilapia burtoni, is useful for identifying the GnRH receptor responsible for reproduction, because only territorial males reproduce. We have cloned a second GnRH receptor in A. burtoni, GnRH-R1(SHS) (SHS is a peptide motif in extracellular loop 3), which is up-regulated in pituitaries of territorial males. We have shown that GnRH-R1(SHS) is expressed in many tissues and specifically colocalizes with LH in the pituitary. In A. burtoni brain, mRNA levels of both GnRH-R1(SHS) and a previously identified receptor, GnRH-R2(PEY), are highly correlated with mRNA levels of all three GnRH ligands. Despite its likely role in reproduction, we found that GnRH-R1(SHS) has the highest affinity for GnRH2 in vitro and low responsivity to GnRH1. Our phylogenetic analysis shows that GnRH-R1(SHS) is less closely related to mammalian reproductive GnRH receptors than GnRH-R2(PEY). We correlated vertebrate GnRH receptor amino acid sequences with receptor function and tissue distribution in many species and found that GnRH receptor sequences predict ligand responsiveness but not colocalization with pituitary gonadotropes. Based on sequence analysis, tissue localization, and physiological response we propose that the GnRH-R1(SHS) receptor controls reproduction in teleosts, including A. burtoni. We propose a GnRH receptor classification based on gene sequence that correlates with ligand selectivity but not with reproductive control. Our results suggest that different duplicated GnRH receptor genes have been selected to regulate reproduction in different vertebrate lineages.
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Affiliation(s)
- Colleen A Flanagan
- Department of Biological Sciences and Program in Neuroscience, Stanford University, Stanford, CA 94305-2130, USA
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30
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Wong DK, Grosenick L, Uy ET, Perreau Guimaraes M, Carvalhaes CG, Desain P, Suppes P. Quantifying inter-subject agreement in brain-imaging analyses. Neuroimage 2007; 39:1051-63. [PMID: 18023210 DOI: 10.1016/j.neuroimage.2007.07.064] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 06/29/2007] [Accepted: 07/27/2007] [Indexed: 11/19/2022] Open
Abstract
In brain-imaging research, we are often interested in making quantitative claims about effects across subjects. Given that most imaging data consist of tens to thousands of spatially correlated time series, inter-subject comparisons are typically accomplished with simple combinations of inter-subject data, for example methods relying on group means. Further, these data are frequently taken from reduced channel subsets defined either a priori using anatomical considerations, or functionally using p-value thresholding to choose cluster boundaries. While such methods are effective for data reduction, means are sensitive to outliers, and current methods for subset selection can be somewhat arbitrary. Here, we introduce a novel "partial-ranking" approach to test for inter-subject agreement at the channel level. This non-parametric method effectively tests whether channel concordance is present across subjects, how many channels are necessary for maximum concordance, and which channels are responsible for this agreement. We validate the method on two previously published and two simulated EEG data sets.
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Affiliation(s)
- Dik Kin Wong
- Center for the Study of Language and Information, Ventura Hall, 200 Panama St., Stanford University, CA, USA.
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31
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Abstract
Transitive inference (TI) involves using known relationships to deduce unknown ones (for example, using A > B and B > C to infer A > C), and is thus essential to logical reasoning. First described as a developmental milestone in children, TI has since been reported in nonhuman primates, rats and birds. Still, how animals acquire and represent transitive relationships and why such abilities might have evolved remain open problems. Here we show that male fish (Astatotilapia burtoni) can successfully make inferences on a hierarchy implied by pairwise fights between rival males. These fish learned the implied hierarchy vicariously (as 'bystanders'), by watching fights between rivals arranged around them in separate tank units. Our findings show that fish use TI when trained on socially relevant stimuli, and that they can make such inferences by using indirect information alone. Further, these bystanders seem to have both spatial and featural representations related to rival abilities, which they can use to make correct inferences depending on what kind of information is available to them. Beyond extending TI to fish and experimentally demonstrating indirect TI learning in animals, these results indicate that a universal mechanism underlying TI is unlikely. Rather, animals probably use multiple domain-specific representations adapted to different social and ecological pressures that they encounter during the course of their natural lives.
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Affiliation(s)
- Logan Grosenick
- Department of Biological Sciences, Stanford University, Stanford, California, 94305, USA.
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