stanford university phd neuroscience

Andrew D. Huberman

Associate professor of neurobiology and, by courtesy, of psychiatry and behavioral sciences.

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Academic Appointments

• Associate Professor, Neurobiology
• Associate Professor (By courtesy), Psychiatry and Behavioral Sciences
• Member, Bio-X
• Member, Wu Tsai Human Performance Alliance
• Member, Wu Tsai Neurosciences Institute

Administrative Appointments

• Associate Professor, Stanford School of Medicine (2016 - Present)
• Assistant Professor, University of California, San Diego (2011 - 2015)

Honors & Awards

• Cogan Award for Contributions to Vision Science and Ophthalmology, ARVO (2017)
• Pew Biomedical Scholar Award, Pew Charitable Trusts (2013-2017)
• McKnight Neuroscience Scholar Award, McKnight Endowment Fund (2013-2016)
• Catalyst for a Cure Investigator, Glaucoma Research Foundation (2012- present)
• Helen Hay Whitney Postdoctoral Fellow, HHWF Foundation (2006-2009)
• Allan G. Marr Prize for Best Ph.D. Dissertation, University of California, Davis (2005)
• ARCS Foundation Graduate Fellowship Award, ARCS Foundation (2003)
• Graduation with Honors and Distinction in Major, University of California, Santa Barbara (1998)

Boards, Advisory Committees, Professional Organizations

• Wu-Tsai Neurosciences Seminar Committee Chair, Stanford University (2021 - 2022)
• Faculty Search Committee, Neurobiology/Molecular Neuroscience, Stanford School of Medicine (2019 - 2020)
• Faculty Search Committee, Neurosurgery Chair, Stanford School of Medicine (2019 - 2020)
• Within-Department Tenure Review Committee, Neurobiology, Stanford School of Medicine (2019 - 2019)
• Editorial Board, Faculty of 1000 (2018 - Present)
• Faculty Search Committee, Neurobiology/Molecular Neuroscience, Stanford School of Medicine (2018 - 2019)
• Editorial Board, Neural Development (2016 - Present)
• Editorial Board, Cell Reports (2016 - 2022)
• Editorial Board, Current Opinion in Neurobiology (2016 - 2018)
• Within-Department Tenure Review Committee, Neurobiology, Stanford School of Medicine (2016 - 2016)
• Editorial Board, The Journal of Comparative Neurology (2015 - Present)
• Research Committee Co-chair, Neurosciences, University of California, San Diego (2014 - 2015)
• Associate Editor: Systems/Circuits, The Journal of Neuroscience (2013 - 2018)
• Editorial Board, Current Biology (2011 - Present)
• Faculty Recruitment Committee, Neurobiology, University of California, San Diego (2011 - 2014)
• Seminar Committee, Neurobiology Section Chair, University of California, San Diego (2011 - 2013)
• Neuroscience Graduate Program Admissions Committee, University of California, San Diego (2011 - 2012)

Professional Education

• Postdoc, Stanford University, Neuroscience (2010)
• PhD, University of California, Davis, Neuroscience (2004)
• MA, University of California, Berkeley, Psychology (2000)
• BA, University of California, Santa Barbara, Psychology (1998)
• Huberman Lab Website

Current Research and Scholarly Interests

In 2017, we developed a virtual reality platform to investigate the neural and autonomic mechanisms contributing to fear and anxiety. That involved capturing 360-degree videos of various fear-provoking situations in real life for in-lab VR movies, such as heights and claustrophobia, as well as unusual scenarios like swimming in open water with great white sharks. The primary objective of our VR platform is to develop new tools to help people better manage stress, anxiety and phobias in real-time, as an augment to in-clinic therapies. In May 2018, we reported the discovery of two novel mammalian brain circuits as a Research Article published in Nature. One circuit promotes fear and anxiety-induced paralysis, while the other fosters confrontational reactions to threats. This led to ongoing research into the involvement of these brain regions in anxiety-related disorders such as phobias and generalized anxiety in humans. In 2020, we embarked on a collaborative effort with Dr. David Spiegel's laboratory in the Stanford Department of Psychiatry and Behavioral Sciences, aimed to explore how specific respiration patterns synergize with the visual system to influence autonomic arousal and stress, and other brain states, including sleep. In 2023, the first results of that collaboration were published as a randomized controlled trial in Cell Reports Medicine, demonstrating that specific brief patterns of deliberate respiration are particularly effective in alleviating stress and enhancing mood, and improving sleep. In a 2021, our collaboration with Dr. Edward Chang, professor and chair of the Department of Neurological Surgery at the University of California, San Francisco (UCSF), was published in Current Biology, revealing that specific patterns of insular cortex neural activity may be linked to, and potentially predict, anxiety responses.

Clinical Trials

The investigators aim to understand the effectiveness of 3 types of breathwork exercises and a mindfulness meditation control on improving psychological and physiological measures of wellbeing. The interventions will be delivered remotely and effects are monitored through daily surveys and physiological monitoring with WHOOP wristband through a 28-day period. The information gained will help develop the most effective remote interventions for lowering stress and improving wellbeing. The study will be run on a healthy general population. The three breathing conditions were 1) Cyclic Sighing, which emphasizes relatively prolonged exhalations, 2) Box Breathing, which is equal duration of inhalations, breath retentions, exhalations and breath retentions, and 3) Cyclic Hyperventilation with Retention, with longer, more intense inhalations and shorter, passive exhalations. Mindfulness Meditation practice involved passive attention to breath.

Stanford is currently not accepting patients for this trial.

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2023-24 Courses

• Directed Reading in Neurobiology NBIO 198 (Aut, Spr, Sum)
• Directed Reading in Neurobiology NBIO 299 (Aut, Win, Spr, Sum)
• Directed Reading in Neurosciences NEPR 299 (Aut, Win, Spr)
• Graduate Research NBIO 399 (Aut, Win, Spr, Sum)
• Graduate Research NEPR 399 (Aut, Win, Spr, Sum)
• Medical Scholars Research NBIO 370 (Spr, Sum)
• Undergraduate Research NBIO 199 (Aut, Win, Spr, Sum)

2022-23 Courses

• The Nervous System NBIO 206 (Win)

2021-22 Courses

2020-21 courses, all publications.

The wiring of visual circuits requires that retinal neurons functionally connect to specific brain targets, a process that involves activity-dependent signaling between retinal axons and their postsynaptic targets. Vision loss in various ophthalmological and neurological diseases is caused by damage to the connections from the eye to the brain. How postsynaptic brain targets influence retinal ganglion cell (RGC) axon regeneration and functional reconnection with the brain targets remains poorly understood. Here, we established a paradigm in which the enhancement of neural activity in the distal optic pathway, where the postsynaptic visual target neurons reside, promotes RGC axon regeneration and target reinnervation and leads to the rescue of optomotor function. Furthermore, selective activation of retinorecipient neuron subsets is sufficient to promote RGC axon regeneration. Our findings reveal a key role for postsynaptic neuronal activity in the repair of neural circuits and highlight the potential to restore damaged sensory inputs via proper brain stimulation.

View details for DOI 10.1016/j.celrep.2023.112476

View details for PubMedID 37141093

Controlled breathwork practices have emerged as potential tools for stress management and well-being. Here, we report a remote, randomized, controlled study (NCT05304000) of three different daily 5-min breathwork exercises compared with an equivalent period of mindfulness meditation over 1 month. The breathing conditions are (1) cyclic sighing, which emphasizes prolonged exhalations; (2) box breathing, which is equal duration of inhalations, breath retentions, and exhalations; and (3) cyclic hyperventilation with retention, with longer inhalations and shorter exhalations. The primary endpoints are improvement in mood and anxiety as well as reduced physiological arousal (respiratory rate, heart rate, and heart rate variability). Using a mixed-effects model, we show that breathwork, especially the exhale-focused cyclic sighing, produces greater improvement in mood (p < 0.05) and reduction in respiratory rate (p < 0.05) compared with mindfulness meditation. Daily 5-min cyclic sighing has promise as an effective stress management exercise.

View details for DOI 10.1016/j.xcrm.2022.100895

View details for PubMedID 36630953

View details for DOI 10.1016/j.expneurol.2022.114256

View details for PubMedID 36457222

Visual impairment caused by retinal ganglion cell (RGC) axon damage or degeneration affects millions of individuals throughout the world. While some progress has been made in promoting long-distance RGC axon regrowth following injury, it remains unclear whether RGC axons can properly reconnect with their central targets to restore visual function. Additionally, the regenerative capacity of many RGC subtypes remains unknown in part due to a lack of available genetic tools. Here, we use a new mouse line that labels On direction-selective RGCs (oDSGCs) and characterize the survival and regenerative potential of these cells following optic nerve crush (ONC). In parallel, we use a previously characterized mouse line to answer these same questions for M1 intrinsically photosensitive RGCs (ipRGCs). We find that both M1 ipRGCs and oDSGCs are resilient to injury but do not display long-distance axon regrowth following Lin28a overexpression. Unexpectedly, we found that M1 ipRGC, but not oDSGC, intraretinal axons exhibit ectopic branching and are misaligned near the optic disc between one- and three-weeks following injury. Additionally, we observe that numerous ectopic presynaptic specializations associate with misguided ipRGC intraretinal axons. Taken together, these results reveal insights into the injury response of M1 ipRGCs and oDSGCs, providing a foundation for future efforts seeking to restore visual system function following injury.

View details for DOI 10.1016/j.expneurol.2022.114176

View details for PubMedID 35870522

View details for Web of Science ID 000844437003268

Neurons of the mammalian central nervous system fail to regenerate. Substantial progress has been made toward identifying the cellular and molecular mechanisms that underlie regenerative failure and how altering those pathways can promote cell survival and/or axon regeneration. Here, we summarize those findings while comparing the regenerative process in the central versus the peripheral nervous system. We also highlight studies that advance our understanding of the mechanisms underlying neural degeneration in response to injury, as many of these mechanisms represent primary targets for restoring functional neural circuits.

View details for DOI 10.1016/j.cell.2021.10.029

View details for PubMedID 34995518

Introduction to the special issue on thalamus This article is protected by copyright. All rights reserved.

View details for DOI 10.1002/cne.25288

View details for PubMedID 34897681

Rapid alternations between exploration and defensive reactions require ongoing risk assessment. How visual cues and internal states flexibly modulate the selection of behaviors remains incompletely understood. Here, we show that the ventral lateral geniculate nucleus (vLGN)-a major retinorecipient structure-is a critical node in the network controlling defensive behaviors to visual threats. We find that vLGNGABA neuron activity scales with the intensity of environmental illumination and is modulated by behavioral state. Chemogenetic activation of vLGNGABA neurons reduces freezing, whereas inactivation dramatically extends the duration of freezing to visual threats. Perturbations of vLGN activity disrupt exploration in brightly illuminated environments. We describe both a vLGNnucleus reuniens (Re) circuit and a vLGNsuperior colliculus (SC) circuit, which exert opposite influences on defensive responses. These findings reveal roles for genetic- and projection-defined vLGN subpopulations in modulating the expression of behavioral threat responses according to internal state.

View details for DOI 10.1016/j.celrep.2021.109792

View details for PubMedID 34610302

Vision is the primary sense humans use to evaluate and respond to threats. Understanding the biological underpinnings of the human threat response has been hindered by lack of realistic in-lab threat paradigms. We established an immersive virtual reality (VR) platform to simultaneously measure behavior, physiological state, and neural activity from the human brain using chronically implanted electrodes. Subjects with high anxiety showed increased visual scanning in response to threats as compared to healthy controls. In both healthy and anxious subjects, the amount of scanning behavior correlated with the magnitude of physiological arousal, suggesting that visual scanning behavior is directly linked to internal state. Intracranial electroencephalography (iEEG) recordings from three subjects suggested that high-frequency gamma activity in the insula positively correlates with physiological arousal induced by visual threats and that low-frequency theta activity in the orbitofrontal cortex (OFC) negatively correlates with physiological arousal induced by visual threats. These findings reveal a key role of eye movements and suggest that distinct insula and OFC activation dynamics may be important for detecting and adjusting human stress in response to visually perceived threats.

View details for DOI 10.1016/j.cub.2020.11.035

View details for PubMedID 33242389

A new study reveals the retinal circuit for encoding the types of light prominent at sunrise and sunset. The output of that circuit is conveyed to the brain's master circadian clock. Subconscious processing of sky color changes may therefore be the key stimulus for conveying morning and evening information to the circadian timing system in the brain.

View details for DOI 10.1016/j.cub.2020.02.090

View details for PubMedID 32259506

Glaucoma is a neurodegenerative disease that features the death of retinal ganglion cells (RGCs) in the retina, often as a result of prolonged increases in intraocular pressure. We show that preventing the formation of neuroinflammatory reactive astrocytes prevents the death of RGCs normally seen in a mouse model of glaucoma. Furthermore, we show that these spared RGCs are electrophysiologically functional and thus still have potential value for the function and regeneration of the retina. Finally, we demonstrate that the death of RGCs depends on a combination of both an injury to the neurons and the presence of reactive astrocytes, suggesting a model that may explain why reactive astrocytes are toxic only in some circumstances. Altogether, these findings highlight reactive astrocytes as drivers of RGC death in a chronic neurodegenerative disease of the eye.

View details for DOI 10.1016/j.celrep.2020.107776

View details for PubMedID 32579912

View details for DOI 10.1038/d41586-020-03119-1

View details for PubMedID 33268872

View details for DOI 10.1523/JNEUROSCI.1784-18.2018

View details for Web of Science ID 000454689500008

The brain circuits that create our sense of fear rely on ancient 'hard-wired' components of the limbic system, but also use sensory processing to determine what we become afraid of. A new study shows that, when viewing of simple oriented line stimuli is coupled with aversive experiences, neurons in primary visual cortex rapidly alter their responses in a manner that indicates the line stimuli become a source of fear.

View details for DOI 10.1016/j.cub.2019.10.008

View details for PubMedID 31794754

View details for DOI 10.1002/cne.24457

View details for Web of Science ID 000457345800018

View details for DOI 10.1002/cne.24599

View details for PubMedID 30597554

View details for DOI 10.1002/cne.24601

View details for Web of Science ID 000457345800003

View details for PubMedID 30597552

View details for DOI 10.1016/j.neuron.2018.11.038

View details for Web of Science ID 000452295400006

In this issue of Neuron, Macé et al. (2018) use whole-brain functional ultrasound imaging in mice to unveil the circuits involved reflexive eye movements. They separated the sensory and motor networks and discovered that certain eye movements robustly suppress the amygdala.

View details for PubMedID 30521775

View details for DOI 10.1016/j.conb.2018.10.001

View details for Web of Science ID 000451938500027

Sensory processing can be tuned by a neuron's integration area, the types of inputs, and the proportion and number of connections with those inputs. Integration areas often vary topographically to sample space differentially across regions. Here, we highlight two visual circuits in which topographic changes in the postsynaptic retinal ganglion cell (RGC) dendritic territories and their presynaptic bipolar cell (BC) axonal territories are either matched or unmatched. Despite this difference, in both circuits, the proportion of inputs from each BC type, i.e., synaptic convergence between specific BCs and RGCs, remained constant across varying dendritic territory sizes. Furthermore, synapse density between BCs and RGCs was invariant across topography. Our results demonstrate a wiring design, likely engaging homotypic axonal tiling of BCs, that ensures consistency in synaptic convergence between specific BC types onto their target RGCs while enabling independent regulation of pre- and postsynaptic territory sizes and synapse number between cell pairs.

View details for PubMedID 30463000

View details for DOI 10.1016/j.celrep.2018.10.089

View details for Web of Science ID 000450794200003

The ability to detect moving objects is an ethologically salient function. Direction selective neurons have been identified in the retina, thalamus, and cortex of many species, but their homology has remained opaque. For instance, it is unknown whether direction-selective retinal ganglion cells (DSGCs) exist in primates, and if so, whether they are the equivalent to mouse and rabbit DSGCs. Here, we used a molecular/circuit approach in both sexes to address these issues. In mice, we identify the transcription factor Satb2 (Special AT-rich sequence-binding protein 2) as a selective marker for three RGC types: On-Off DSGCs encoding motion in either the anterior or posterior direction, a newly identified type of Off-DSGC and an Off-sustained RGC type. In rabbits, we find that expression of Satb2 is conserved in On-Off DSGCs; however, has evolved to include On-Off DSGCs encoding upward and downward motion, in addition to anterior and posterior motion. Next, we show that macaque RGCs express Satb2 most likely in a single type. We used rabies-virus based circuit mapping tools to reveal the identity of macaque Satb2-RGCs and discovered their dendritic arbors are relatively large and monostratified. Together, these data indicate Satb2-expressing On-Off DSGCs are likely not present in the primate retina. Moreover, if DSGCs are present in the primate retina, it is unlikely that they express Satb2.SIGNIFICANCE STATEMENTThe ability to detect object-motion is a fundamental feature of almost all visual systems. Here we identify a novel marker for retinal ganglion cells encoding directional motion that is evolutionarily conserved in mice and rabbits, but not in primates. We show that in macaque monkeys the retinal ganglion cells that express this marker comprise a single type and are morphologically distinct from mouse and rabbit direction-selective retinal ganglion cells. Our findings indicate that On-Off direction-selective retinal neurons may have evolutionarily diverged in primates and more generally provide novel insight into the identity and organization of primate parallel visual pathways.

View details for PubMedID 30377226

Vision is the sense humans rely on most to navigate the world and survive. A tremendous amount of research has focused on understanding the neural circuits for vision and the developmental mechanisms that establish them. The eye-to-brain, or 'retinofugal' pathway remains a particularly important model in these contexts because it is essential for sight, its overt anatomical features relate to distinct functional attributes and those features develop in a tractable sequence. Much progress has been made in understanding the growth of retinal axons out of the eye, their selection of targets in the brain, the development of laminar and cell type-specific connectivity within those targets, and also dendritic connectivity within the retina itself. Moreover, because the retinofugal pathway is prone to degeneration in many common blinding diseases, understanding the cellular and molecular mechanisms that establish connectivity early in life stands to provide valuable insights into approaches that re-wire this pathway after damage or loss. Here we review recent progress in understanding the development of retinofugal pathways and how this information is important for improving visual circuit regeneration.

View details for PubMedID 30339988

In many species, neurons are unevenly distributed across the retina, leading to nonuniform analysis of specific visual features at certain locations in visual space. In recent years, the mouse has emerged as a premiere model for probing visual system function, development and disease. Thus, achieving a detailed understanding of mouse visual circuit architecture is of paramount importance. The general belief is that mice possess a relatively even topographic distribution of retinal ganglion cells (RGCs)- the output neurons of the eye. However, mouse RGCs include 30 subtypes; each responds best to a specific feature in the visual scene and conveys that information to central targets. Given the crucial role of RGCs and the prominence of the mouse as a model, we asked how different RGC subtypes are distributed across the retina. We targeted and filled individual fluorescently tagged RGC subtypes from across the retinal surface and evaluated the dendritic arbor extent and soma size of each cell according to its specific retinotopic position. Three prominent RGC subtypes: On-Off direction selective RGCs, object-motion-sensitive RGCs, and a specialized subclass of non-image-forming RGCs each had marked topographic variations in their dendritic arbor sizes. Moreover, the pattern of variation was distinct for each RGC subtype. Thus, there is increasing evidence that the mouse retina encodes visual space in a region-specific manner. As a consequence, some visual features are sampled far more densely at certain retinal locations than others. These findings have implications for central visual processing, perception and behavior in this prominent model species. This article is protected by copyright. All rights reserved.

View details for PubMedID 29675855

View details for Web of Science ID 000423475100035

View details for PubMedID 29345654

How our internal state is merged with our visual perception of an impending threat to drive an adaptive behavioural response is not known. Mice respond to visual threats by either freezing or seeking shelter. Here we show that nuclei of the ventral midline thalamus (vMT), the xiphoid nucleus (Xi) and nucleus reuniens (Re), represent crucial hubs in the network controlling behavioural responses to visual threats. The Xi projects to the basolateral amygdala to promote saliency-reducing responses to threats, such as freezing, whereas the Re projects to the medial prefrontal cortex (Re→mPFC) to promote saliency-enhancing, even confrontational responses to threats, such as tail rattling. Activation of the Re→mPFC pathway also increases autonomic arousal in a manner that is rewarding. The vMT is therefore important for biasing how internal states are translated into opposing categories of behavioural responses to perceived threats. These findings may have implications for understanding disorders of arousal and adaptive decision-making, such as phobias, post-traumatic stress and addictions.

View details for PubMedID 29720647

The brightness of our visual environment varies tremendously from day to night. In this issue of Cell, Milner and Do describe how the population of retinal neurons responsible for entrainment of the brain's circadian clock cooperate to encode irradiance across a wide range of ambient-light intensities.

View details for PubMedID 29100070

View details for Web of Science ID 000432170304131

View details for Web of Science ID 000432170306309

The brain uses sensory information from the periphery to create percepts. In this issue of Neuron, Rompani et al. (2017) show that visual signals are combined in unexpected ways that vastly expand the possible representations of the outside world.

View details for DOI 10.1016/j.neuron.2017.02.020

View details for PubMedID 28231456

Humans are highly visual. Retinal ganglion cells (RGCs), the neurons that connect the eyes to the brain, fail to regenerate after damage, eventually leading to blindness. Here, we review research on regeneration and repair of the optic system. Intrinsic developmental growth programs can be reactivated in RGCs, neural activity can enhance RGC regeneration, and functional reformation of eye-to-brain connections is possible, even in the adult brain. Transplantation and gene therapy may serve to replace or resurrect dead or injured retinal neurons. Retinal prosthetics that can restore vision in animal models may too have practical power in the clinical setting. Functional restoration of sight in certain forms of blindness is likely to occur in human patients in the near future.

View details for PubMedID 28596336

Vision is the sense humans rely on most to navigate the world, make decisions, and perform complex tasks. Understanding how humans see thus represents one of the most fundamental and important goals of neuroscience. The use of the mouse as a model for parsing how vision works at a fundamental level started approximately a decade ago, ushered in by the mouse's convenient size, relatively low cost, and, above all, amenability to genetic perturbations. In the course of that effort, a large cadre of new and powerful tools for in vivo labeling, monitoring, and manipulation of neurons were applied to this species. As a consequence, a significant body of work now exists on the architecture, function, and development of mouse central visual pathways. Excitingly, much of that work includes causal testing of the role of specific cell types and circuits in visual perception and behavior-something rare to find in studies of the visual system of other species. Indeed, one could argue that more information is now available about the mouse visual system than any other sensory system, in any species, including humans. As such, the mouse visual system has become a platform for multilevel analysis of the mammalian central nervous system generally. Here we review the mouse visual system structure, function, and development literature and comment on the similarities and differences between the visual system of this and other model species. We also make it a point to highlight the aspects of mouse visual circuitry that remain opaque and that are in need of additional experimentation to enrich our understanding of how vision works on a broad scale.

View details for PubMedID 28772103

The use of sensory information to drive specific behaviors relies on circuits spanning long distances that wire up through a range of axon-target recognition events. Mechanisms assembling poly-synaptic circuits and the extent to which parallel pathways can "cross-wire" to compensate for loss of one another remain unclear and are crucial to our understanding of brain development and models of regeneration. In the visual system, specific retinal ganglion cells (RGCs) project to designated midbrain targets connected to downstream circuits driving visuomotor reflexes. Here, we deleted RGCs connecting to pupillary light reflex (PLR) midbrain targets and discovered that axon-target matching is tightly regulated. RGC axons of the eye-reflex pathway avoided vacated PLR targets. Moreover, downstream PLR circuitry is maintained; hindbrain and peripheral components retained their proper connectivity and function. These findings point to a model in which poly-synaptic circuit development reflects independent, highly stringent wiring of each parallel pathway and downstream station.

View details for PubMedID 29241535

The mammalian visual cortex massively innervates the brainstem, a phylogenetically older structure, via cortico-fugal axonal projections. Many cortico-fugal projections target brainstem nuclei that mediate innate motor behaviours, but the function of these projections remains poorly understood. A prime example of such behaviours is the optokinetic reflex (OKR), an innate eye movement mediated by the brainstem accessory optic system, that stabilizes images on the retina as the animal moves through the environment and is thus crucial for vision. The OKR is plastic, allowing the amplitude of this reflex to be adaptively adjusted relative to other oculomotor reflexes and thereby ensuring image stability throughout life. Although the plasticity of the OKR is thought to involve subcortical structures such as the cerebellum and vestibular nuclei, cortical lesions have suggested that the visual cortex might also be involved. Here we show that projections from the mouse visual cortex to the accessory optic system promote the adaptive plasticity of the OKR. OKR potentiation, a compensatory plastic increase in the amplitude of the OKR in response to vestibular impairment, is diminished by silencing visual cortex. Furthermore, targeted ablation of a sparse population of cortico-fugal neurons that specifically project to the accessory optic system severely impairs OKR potentiation. Finally, OKR potentiation results from an enhanced drive exerted by the visual cortex onto the accessory optic system. Thus, cortico-fugal projections to the brainstem enable the visual cortex, an area that has been principally studied for its sensory processing function, to plastically adapt the execution of innate motor behaviours.

View details for DOI 10.1038/nature19818

View details for PubMedID 27732573

Axons in the mammalian CNS fail to regenerate after injury. Here we show that if the activity of mouse retinal ganglion cells (RGCs) is increased by visual stimulation or using chemogenetics, their axons regenerate. We also show that if enhancement of neural activity is combined with elevation of the cell-growth-promoting pathway involving mammalian target of rapamycin (mTOR), RGC axons regenerate long distances and re-innervate the brain. Analysis of genetically labeled RGCs revealed that this regrowth can be target specific: RGC axons navigated back to their correct visual targets and avoided targets incorrect for their function. Moreover, these regenerated connections were successful in partially rescuing a subset of visual behaviors. Our findings indicate that combining neural activity with activation of mTOR can serve as powerful tool for enhancing axon regeneration, and they highlight the remarkable capacity of CNS neurons to re-establish accurate circuit connections in adulthood.

View details for DOI 10.1038/nn.4340

View details for PubMedID 27399843

The National Eye Institute (NEI) hosted a workshop on November 19, 2014, as part of the Audacious Goals Initiative (AGI), an NEI-led effort to rapidly expand therapies for eye diseases through coordinated research funding. The central audacious goal aims to demonstrate by 2025 the restoration of usable vision in humans through the regeneration of neurons and neural connections in the eye and visual system. This workshop focused on identifying promising strategies for optic nerve regeneration. Its principal objective was to solicit input on future AGI-related funding announcements, and specifically to ask, where are we now in our scientific progress, and what progress should we reach for in the coming years? A full report was generated as a white paper posted on the NEI Web site; this report summarizes the discussion and outcomes from the meeting and serves as guidance for future funding of research that focuses on optic nerve regeneration.

View details for DOI 10.1167/iovs.15-18500

View details for PubMedID 26990163

View details for DOI 10.1038/nn.4233

View details for Web of Science ID 000369172600003

View details for PubMedID 26814584

View details for Web of Science ID 000365352500034

View details for PubMedID 26607542

There are many transgenic GFP reporter lines that allow the visualization of specific populations of cells. Using such lines for functional studies requires a method that transforms GFP into a molecule that enables genetic manipulation. We developed a method that exploits GFP for gene manipulation, Cre recombinase dependent on GFP (CRE-DOG), a split component system that uses GFP and its derivatives to directly induce Cre/loxP recombination. Using plasmid electroporation and AAV viral vectors, we delivered CRE-DOG to multiple GFP mouse lines, which led to effective recombination selectively in GFP-labeled cells. Furthermore, CRE-DOG enabled optogenetic control of these neurons. Beyond providing a new set of tools for manipulation of gene expression selectively in GFP(+) cells, we found that GFP can be used to reconstitute the activity of a protein not known to have a modular structure, suggesting that this strategy might be applicable to a wide range of proteins.

View details for DOI 10.1038/nn.4081

View details for Web of Science ID 000360292600024

View details for PubMedID 26258682

How is sensory information transformed by each station of a synaptic circuit as it flows progressively deeper into the brain? In this issue of Cell, Mauss et al. describe a set of connections in the fly brain that combines opposing directional signals, and they hypothesize that this motif limits global motion noise as the fly moves through space.

View details for DOI 10.1016/j.cell.2015.06.051

View details for PubMedID 26186184

Adjustments in neural activity can drive cortical plasticity, but the underlying circuit components remain unclear. In this issue of Neuron, Barnes et al. (2015) show that visual deprivation-induced homeostatic plasticity invokes specific changes among select categories of V1 neurons.

View details for DOI 10.1016/j.neuron.2015.05.039

View details for Web of Science ID 000355666400002

View details for PubMedID 26050030

The mammalian eye-to-brain pathway includes more than 20 parallel circuits, each consisting of precise long-range connections between specific sets of retinal ganglion cells (RGCs) and target structures in the brain. The mechanisms that drive assembly of these parallel connections and the functional implications of their specificity remain unresolved. Here we show that in the absence of contactin 4 (CNTN4) or one of its binding partners, amyloid precursor protein (APP), a subset of direction-selective RGCs fail to target the nucleus of the optic tract (NOT)--the accessory optic system (AOS) target controlling horizontal image stabilization. Conversely, ectopic expression of CNTN4 biases RGCs to arborize in the NOT, and that process also requires APP. Our data reveal critical and novel roles for CNTN4/APP in promoting target-specific axon arborization, and they highlight the importance of this process for functional development of a behaviorally relevant parallel visual pathway.

View details for DOI 10.1016/j.neuron.2015.04.005

View details for Web of Science ID 000354878400013

View details for PubMedID 25959733

View details for PubMedCentralID PMC4706364

Accurate motion detection requires neural circuitry that compensates for global visual field motion. Select subtypes of retinal ganglion cells perceive image motion and connect to the accessory optic system (AOS) in the brain, which generates compensatory eye movements that stabilize images during slow visual field motion. Here, we show that the murine transmembrane semaphorin 6A (Sema6A) is expressed in a subset of On direction-selective ganglion cells (On DSGCs) and is required for retinorecipient axonal targeting to the medial terminal nucleus (MTN) of the AOS. Plexin A2 and A4, two Sema6A binding partners, are expressed in MTN cells, attract Sema6A(+) On DSGC axons, and mediate MTN targeting of Sema6A(+) RGC projections. Furthermore, Sema6A/Plexin-A2/A4 signaling is required for the functional output of the AOS. These data reveal molecular mechanisms underlying the assembly of AOS circuits critical for moving image perception.

View details for DOI 10.1016/j.neuron.2015.03.064

View details for PubMedID 25959730

Retinal ganglion cell (RGC) loss is a hallmark of glaucoma and the second leading cause of blindness worldwide. The type and timing of cellular changes leading to RGC loss in glaucoma remain incompletely understood, including whether specific RGC subtypes are preferentially impacted at early stages of this disease. Here we applied the microbead occlusion model of glaucoma to different transgenic mouse lines, each expressing green fluorescent protein in 1-2 specific RGC subtypes. Targeted filling, reconstruction, and subsequent comparison of the genetically identified RGCs in control and bead-injected eyes revealed that some subtypes undergo significant dendritic rearrangements as early as 7 d following induction of elevated intraocular pressure (IOP). By comparing specific On-type, On-Off-type and Off-type RGCs, we found that RGCs that target the majority of their dendritic arbors to the scleral half or "Off" sublamina of the inner plexiform layer (IPL) undergo the greatest changes, whereas RGCs with the majority of their dendrites in the On sublamina did not alter their structure at this time point. Moreover, M1 intrinsically photosensitive RGCs, which functionally are On RGCs but structurally stratify their dendrites in the Off sublamina of the IPL, also underwent significant changes in dendritic structure 1 week after elevated IOP. Thus, our findings reveal that certain RGC subtypes manifest significant changes in dendritic structure after very brief exposure to elevated IOP. The observation that RGCs stratifying most of their dendrites in the Off sublamina are first to alter their structure may inform the development of new strategies to detect, monitor, and treat glaucoma in humans.

View details for DOI 10.1523/JNEUROSCI.1419-14.2015

View details for Web of Science ID 000349686500003

View details for PubMedID 25673829

The visual system is a powerful model for probing the development, connectivity, and function of neural circuits. Two genetically tractable species, mice and flies, are together providing a great deal of understanding of these processes. Current efforts focus on integrating knowledge gained from three cross-fostering fields of research: (1) understanding how the fates of different cell types are specified during development, (2) revealing the synaptic connections between identified cell types ("connectomics") by high-resolution three-dimensional circuit anatomy, and (3) causal testing of how identified circuit elements contribute to visual perception and behavior. Here we discuss representative examples from fly and mouse models to illustrate the ongoing success of this tripartite strategy, focusing on the ways it is enhancing our understanding of visual processing and other sensory systems.

View details for DOI 10.1101/gad.248245.114

View details for Web of Science ID 000345812000001

View details for PubMedID 25452270

View details for PubMedCentralID PMC4248288

How axons select their appropriate targets in the brain remains poorly understood. Here, we explore the cellular mechanisms of axon target matching in the developing visual system by comparing four transgenic mouse lines, each with a different population of genetically labeled retinal ganglion cells (RGCs) that connect to unique combinations of brain targets. We find that the time when an RGC axon arrives in the brain is correlated with its target selection strategy. Early-born, early-arriving RGC axons initially innervate multiple targets. Subsequently, most of those connections are removed. By contrast, later-born, later-arriving RGC axons are highly accurate in their initial target choices. These data reveal the diversity of cellular mechanisms that mammalian CNS axons use to pick their targets and highlight the key role of birthdate and outgrowth timing in influencing this precision. Timing-based mechanisms may underlie the assembly of the other sensory pathways and complex neural circuitry in the brain.

View details for DOI 10.1016/j.celrep.2014.06.063

View details for Web of Science ID 000341573500011

View details for PubMedID 25088424

View details for PubMedCentralID PMC4143387

How specific features in the environment are represented within the brain is an important unanswered question in neuroscience. A subset of retinal neurons, called direction-selective ganglion cells (DSGCs), are specialized for detecting motion along specific axes of the visual field. Despite extensive study of the retinal circuitry that endows DSGCs with their unique tuning properties, their downstream circuitry in the brain and thus their contribution to visual processing has remained unclear. In mice, several different types of DSGCs connect to the dorsal lateral geniculate nucleus (dLGN), the visual thalamic structure that harbours cortical relay neurons. Whether direction-selective information computed at the level of the retina is routed to cortical circuits and integrated with other visual channels, however, is unknown. Here we show that there is a di-synaptic circuit linking DSGCs with the superficial layers of the primary visual cortex (V1) by using viral trans-synaptic circuit mapping and functional imaging of visually driven calcium signals in thalamocortical axons. This circuit pools information from several types of DSGCs, converges in a specialized subdivision of the dLGN, and delivers direction-tuned and orientation-tuned signals to superficial V1. Notably, this circuit is anatomically segregated from the retino-geniculo-cortical pathway carrying non-direction-tuned visual information to deeper layers of V1, such as layer 4. Thus, the mouse harbours several functionally specialized, parallel retino-geniculo-cortical pathways, one of which originates with retinal DSGCs and delivers direction- and orientation-tuned information specifically to the superficial layers of the primary visual cortex. These data provide evidence that direction and orientation selectivity of some V1 neurons may be influenced by the activation of DSGCs.

View details for DOI 10.1038/nature12989

View details for Web of Science ID 000333029000034

View details for PubMedID 24572358

View details for PubMedCentralID PMC4143386

Unlike humans, monkeys, or carnivores, mice are thought to lack a retinal subregion devoted to high-resolution vision; systematic analysis has now shown that mice encode visual space non-uniformly, increasing their spatial sampling of the binocular visual field.

View details for DOI 10.1016/j.cub.2013.12.045

View details for Web of Science ID 000331718900010

View details for PubMedID 24556437

Everything the brain knows about the content of the visual world is built from the spiking activity of retinal ganglion cells (RGCs). As the output neurons of the eye, RGCs include ∼20 different subtypes, each responding best to a specific feature in the visual scene. Here we discuss recent advances in identifying where different RGC subtypes route visual information in the brain, including which targets they connect to and how their organization within those targets influences visual processing. We also highlight examples where causal links have been established between specific RGC subtypes, their maps of central connections and defined aspects of light-mediated behavior and we suggest the use of techniques that stand to extend these sorts of analyses to circuits underlying visual perception.

View details for DOI 10.1016/j.conb.2013.08.006

View details for Web of Science ID 000331509500020

View details for PubMedID 24492089

View details for PubMedCentralID PMC4086677

When the head rotates, the image of the visual world slips across the retina. A dedicated set of retinal ganglion cells (RGCs) and brainstem visual nuclei termed the "accessory optic system" (AOS) generate slip-compensating eye movements that stabilize visual images on the retina and improve visual performance. Which types of RGCs project to each of the various AOS nuclei remain unresolved. Here we report a new transgenic mouse line, Hoxd10-GFP, in which the RGCs projecting to all the AOS nuclei are fluorescently labeled. Electrophysiological recordings of Hoxd10-GFP RGCs revealed that they include all three subtypes of On direction-selective RGCs (On-DSGCs), responding to upward, downward, or forward motion. Hoxd10-GFP RGCs also include one subtype of On-Off DSGCs tuned for forward motion. Retrograde circuit mapping with modified rabies viruses revealed that the On-DSGCs project to the brainstem centers involved in both horizontal and vertical retinal slip compensation. In contrast, the On-Off DSGCs labeled in Hoxd10-GFP mice projected to AOS nuclei controlling horizontal but not vertical image stabilization. Moreover, the forward tuned On-Off DSGCs appear physiologically and molecularly distinct from all previously genetically identified On-Off DSGCs. These data begin to clarify the cell types and circuits underlying image stabilization during self-motion, and they support an unexpected diversity of DSGC subtypes.

View details for DOI 10.1523/JNEUROSCI.2778-13.2013

View details for Web of Science ID 000327019100027

View details for PubMedID 24198370

View details for PubMedCentralID PMC3818553

The thalamus is crucial in determining the sensory information conveyed to cortex. In the visual system, the thalamic lateral geniculate nucleus (LGN) is generally thought to encode simple center-surround receptive fields, which are combined into more sophisticated features in cortex, such as orientation and direction selectivity. However, recent evidence suggests that a more diverse set of retinal ganglion cells projects to the LGN. We therefore used multisite extracellular recordings to define the repertoire of visual features represented in the LGN of mouse, an emerging model for visual processing. In addition to center-surround cells, we discovered a substantial population with more selective coding properties, including direction and orientation selectivity, as well as neurons that signal absence of contrast in a visual scene. The direction and orientation selective neurons were enriched in regions that match the termination zones of direction selective ganglion cells from the retina, suggesting a source for their tuning. Together, these data demonstrate that the mouse LGN contains a far more elaborate representation of the visual scene than current models posit. These findings should therefore have a significant impact on our understanding of the computations performed in mouse visual cortex.

View details for DOI 10.1523/JNEUROSCI.5187-12.2013

View details for Web of Science ID 000316119200003

View details for PubMedID 23486939

The use of neurotropic viruses as transsynaptic tracers was first described in the 1960s, but only recently have such viruses gained popularity as a method for labeling neural circuits. The development of retrograde monosynaptic tracing vectors has enabled visualization of the presynaptic sources onto defined sets of postsynaptic neurons. Here, we describe the first application of a novel viral tracer, based on vesicular stomatitis virus (VSV), which directs retrograde transsynaptic viral spread between defined cell types. We use this virus in the mouse retina to show connectivity between starburst amacrine cells (SACs) and their known synaptic partners, direction-selective retinal ganglion cells, as well as to discover previously unknown connectivity between SACs and other retinal ganglion cell types. These novel connections were confirmed using physiological recordings. VSV transsynaptic tracing enables cell type-specific dissection of neural circuitry and can reveal synaptic relationships among neurons that are otherwise obscured due to the complexity and density of neuropil.

View details for DOI 10.1523/JNEUROSCI.0245-12.2013

View details for Web of Science ID 000313046500006

View details for PubMedID 23283320

View details for Web of Science ID 000299603500002

View details for PubMedID 22281710

Rats can discriminate simple shapes visually, even if they are moved around, made smaller, or partially covered up; the strategy they use may help shed light on human brain mechanisms for discriminating complex features, such as faces.

View details for DOI 10.1016/j.cub.2011.11.047

View details for Web of Science ID 000299144200009

View details for PubMedID 22240473

Understanding the neural basis of visual perception is a long-standing fundamental goal of neuroscience. Historically, most vision studies were carried out on humans, macaques and cats. Over the past 5 years, however, a growing number of researchers have begun using mice to parse the mechanisms underlying visual processing; the rationale is that, despite having relatively poor acuity, mice are unmatched in terms of the variety and sophistication of tools available to label, monitor and manipulate specific cell types and circuits. In this review, we discuss recent advances in understanding the mouse visual system at the anatomical, receptive field and perceptual level, focusing on the opportunities and constraints those features provide toward the goal of understanding how vision works.

View details for DOI 10.1016/j.tins.2011.07.002

View details for Web of Science ID 000294941300003

View details for PubMedID 21840069

Neural circuits consist of highly precise connections among specific types of neurons that serve a common functional goal. How neurons distinguish among different synaptic targets to form functionally precise circuits remains largely unknown. Here, we show that during development, the adhesion molecule cadherin-6 (Cdh6) is expressed by a subset of retinal ganglion cells (RGCs) and also by their targets in the brain. All of the Cdh6-expressing retinorecipient nuclei mediate non-image-forming visual functions. A screen of mice expressing GFP in specific subsets of RGCs revealed that Cdh3-RGCs which also express Cdh6 selectively innervate Cdh6-expressing retinorecipient targets. Moreover, in Cdh6-deficient mice, the axons of Cdh3-RGCs fail to properly innervate their targets and instead project to other visual nuclei. These findings provide functional evidence that classical cadherins promote mammalian CNS circuit development by ensuring that axons of specific cell types connect to their appropriate synaptic targets.

View details for DOI 10.1016/j.neuron.2011.07.006

View details for Web of Science ID 000294521600009

View details for PubMedID 21867880

View details for PubMedCentralID PMC3513360

A hallmark of mammalian neural circuit development is the refinement of initially imprecise connections by competitive activity-dependent processes. In the developing visual system retinal ganglion cell (RGC) axons from the two eyes undergo activity-dependent competition for territory in the dorsal lateral geniculate nucleus (dLGN). The direct contributions of synaptic transmission to this process, however, remain unclear. We used a genetic approach to reduce glutamate release selectively from ipsilateral-projecting RGCs and found that their release-deficient axons failed to exclude competing axons from the ipsilateral eye territory in the dLGN. Nevertheless, the release-deficient axons consolidated and maintained their normal amount of dLGN territory, even in the face of fully active competing axons. These results show that during visual circuit refinement glutamatergic transmission plays a direct role in excluding competing axons from inappropriate target regions, but they argue that consolidation and maintenance of axonal territory are largely insensitive to alterations in synaptic activity levels.

View details for DOI 10.1016/j.neuron.2011.05.045

View details for Web of Science ID 000293433900008

View details for PubMedID 21791283

On-Off direction-selective retinal ganglion cells (DSGCs) encode the axis of visual motion. They respond strongly to an object moving in a preferred direction and weakly to an object moving in the opposite, "null," direction. Historically, On-Off DSGCs were classified into four subtypes according to their directional preference (anterior, posterior, superior, or inferior). Here, we compare two genetically identified populations of On-Off DSGCs: dopamine receptor 4 (DRD4)-DSGCs and thyrotropin-releasing hormone receptor (TRHR)-DSGCs. We find that although both populations are tuned for posterior motion, they can be distinguished by a variety of physiological and anatomical criteria. First, the directional tuning of TRHR-DSGCs is broader than that of DRD4-DSGCs. Second, whereas both populations project similarly to the dorsal lateral geniculate nucleus, they project differently to the ventral lateral geniculate nucleus and the superior colliculus. Moreover, TRHR-DSGCs, but not DRD4-DSGCs, also project to the zona incerta, a thalamic area not previously known to receive direction-tuned visual information. Our findings reveal unexpected diversity among mouse On-Off DSGC subtypes that uniquely process and convey image motion to the brain.

View details for DOI 10.1523/JNEUROSCI.0564-11.2011

View details for Web of Science ID 000291642800009

View details for PubMedID 21677160

View details for PubMedCentralID PMC3139540

Down syndrome (DS) is a developmental disorder caused by a third chromosome 21 in humans (Trisomy 21), leading to neurological deficits and cognitive impairment. Studies in mouse models of DS suggest that cognitive deficits in the adult are associated with deficits in synaptic learning and memory mechanisms, but it is unclear whether alterations in the early wiring and refinement of neuronal circuits contribute to these deficits. Here, we show that early developmental refinement of visual circuits is perturbed in mouse models of Down syndrome. Specifically, we find excessive eye-specific segregation of retinal axons in the dorsal lateral geniculate nucleus. Indeed, the degree of refinement scales with defects in the "Down syndrome critical region" (DSCR) in a dose-dependent manner. We further identify Dscam (Down syndrome cell adhesion molecule), a gene within the DSCR, as a regulator of eye-specific segregation of retinogeniculate projections. Although Dscam is not the sole gene in the DSCR contributing to enhanced refinement in trisomy, Dscam dosage clearly regulates cell spacing and dendritic fasciculation in a specific class of retinal ganglion cells. Thus, altered developmental refinement of visual circuits that occurs before sensory experience is likely to contribute to visual impairment in individuals with Down syndrome.

View details for DOI 10.1523/JNEUROSCI.6015-10.2011

View details for Web of Science ID 000289472400026

View details for PubMedID 21490218

View details for PubMedCentralID PMC3230532

Throughout the nervous system, neurons restrict their connections to specific depths or "layers" of their targets to constrain the type and number of synapses they make. Despite the importance of lamina-specific synaptic connectivity, the mechanisms that give rise to this feature in mammals remain poorly understood. Here we examined the cellular events underlying the formation of lamina-specific retinal ganglion cell (RGC) axonal projections to the superior colliculus (SC) of the mouse. By combining a genetically encoded marker of a defined RGC subtype (OFF-αRGCs) with serial immunoelectron microscopy, we resolved the ultrastructure of axon terminals fated for laminar stabilization versus those fated for removal. We found that OFF-αRGCs form synapses across the full depth of the retinorecipient SC before undergoing lamina-specific arbor retraction and synapse elimination to arrive at their mature, restricted pattern of connectivity. Interestingly, we did not observe evidence of axon degeneration or glia-induced synapse engulfment during this process. These findings indicate that lamina-specific visual connections are generated through the selective stabilization of correctly targeted axon arbors and suggest that the decision to maintain or eliminate an axonal projection reflects the molecular compatibility of presynaptic and postsynaptic neurons at a given laminar depth.

View details for DOI 10.1523/JNEUROSCI.3455-10.2010

View details for Web of Science ID 000284999900031

View details for PubMedID 21123583

View details for PubMedCentralID PMC3073606

The specificity of synaptic connections is directly related to the functional integrity of neural circuits. Long-range axon guidance and topographic mapping mechanisms bring axons into spatial proximity of target cells and thus limit the number of potential synaptic partners. Synaptic specificity is then achieved by extracellular short-range guidance cues and cell-surface recognition cues. Neural activity may enhance the precision and strength of specific circuit connections. Here, we focus on one of the final steps of synaptic matchmaking: the targeting of synaptic layers and the mutual recognition of axons and dendrites within these layers.

View details for DOI 10.1101/cshperspect.a001743

View details for Web of Science ID 000279881700009

View details for PubMedID 20300211

View details for PubMedCentralID PMC2829955

All information about the visual world is conveyed to the brain by a single type of neurons at the back of the eye called retinal ganglion cells (RGCs). Understanding how RGC axons locate and wire up with their targets is therefore critical to understanding visual development. In recent years, several important technological and conceptual advances have been made in this area, and yet, many fundamental questions remain unanswered. Indeed, while much is now known about how RGC axons pathfind at the optic chiasm and form retinotopic maps within their targets, how RGCs select their overall targets in the first place is poorly understood. Moreover, the signals that direct mammalian RGC axons to their appropriate layer within those targets remain unknown. The recent advent of genetic tools to selectively label and manipulate defined groups of RGCs is starting to provide a way to resolve these and other important questions about RGC wiring specificity. This field is therefore positioned to reveal new principles of visual circuit development that no doubt will extend to other regions of the CNS.

View details for DOI 10.1016/S0070-2153(10)93008-1

View details for Web of Science ID 000283820000008

View details for PubMedID 20959168

Motion detection is an essential component of visual processing. On-Off direction-selective retinal ganglion cells (On-Off DSGCs) detect objects moving along specific axes of the visual field due to their precise retinal circuitry. The brain circuitry of On-Off DSGCs, however, is largely unknown. We report a mouse with GFP expressed selectively by the On-Off DSGCs that detect posterior motion (On-Off pDSGCs), allowing two-photon targeted recordings of their light responses and delineation of their complete map of central connections. On-Off pDSGCs project exclusively to the dorsal lateral geniculate nucleus and superior colliculus and in both targets form synaptic lamina that are separate from a lamina corresponding to non-DSGCs. Thus, individual On-Off DSGC subtypes are molecularly distinct and establish circuits that map specific qualities of directional motion to dedicated subcortical areas. This suggests that each RGC subtype represents a unique parallel pathway whose synaptic specificity in the retina is recapitulated in central targets.

View details for DOI 10.1016/j.neuron.2009.04.014

View details for Web of Science ID 000266146100005

View details for PubMedID 19447089

View details for PubMedCentralID PMC3140054

Our understanding of how mammalian sensory circuits are organized and develop has long been hindered by the lack of genetic markers of neurons with discrete functions. Here, we report a transgenic mouse selectively expressing GFP in a complete mosaic of transient OFF-alpha retinal ganglion cells (tOFF-alphaRGCs). This enabled us to relate the mosaic spacing, dendritic anatomy, and electrophysiology of these RGCs to their complete map of projections in the brain. We find that tOFF-alphaRGCs project exclusively to the superior colliculus (SC) and dorsal lateral geniculate nucleus and are restricted to a specific laminar depth within each of these targets. The axons of tOFF-alphaRGC are also organized into columns in the SC. Both laminar and columnar specificity develop through axon refinement. Disruption of cholinergic retinal waves prevents the emergence of columnar- but not laminar-specific tOFF-alphaRGC connections. Our findings reveal that in a genetically identified sensory map, spontaneous activity promotes synaptic specificity by segregating axons arising from RGCs of the same subtype.

View details for DOI 10.1016/j.neuron.2008.07.018

View details for Web of Science ID 000258565500011

View details for PubMedID 18701068

Patterns of synaptic connections in the visual system are remarkably precise. These connections dictate the receptive field properties of individual visual neurons and ultimately determine the quality of visual perception. Spontaneous neural activity is necessary for the development of various receptive field properties and visual feature maps. In recent years, attention has shifted to understanding the mechanisms by which spontaneous activity in the developing retina, lateral geniculate nucleus, and visual cortex instruct the axonal and dendritic refinements that give rise to orderly connections in the visual system. Axon guidance cues and a growing list of other molecules, including immune system factors, have also recently been implicated in visual circuit wiring. A major goal now is to determine how these molecules cooperate with spontaneous and visually evoked activity to give rise to the circuits underlying precise receptive field tuning and orderly visual maps.

View details for DOI 10.1146/annurev.neuro.31.060407.125533

View details for Web of Science ID 000257992200020

View details for PubMedID 18558864

View details for PubMedCentralID PMC2655105

During development, the formation of mature neural circuits requires the selective elimination of inappropriate synaptic connections. Here we show that C1q, the initiating protein in the classical complement cascade, is expressed by postnatal neurons in response to immature astrocytes and is localized to synapses throughout the postnatal CNS and retina. Mice deficient in complement protein C1q or the downstream complement protein C3 exhibit large sustained defects in CNS synapse elimination, as shown by the failure of anatomical refinement of retinogeniculate connections and the retention of excess retinal innervation by lateral geniculate neurons. Neuronal C1q is normally downregulated in the adult CNS; however, in a mouse model of glaucoma, C1q becomes upregulated and synaptically relocalized in the adult retina early in the disease. These findings support a model in which unwanted synapses are tagged by complement for elimination and suggest that complement-mediated synapse elimination may become aberrantly reactivated in neurodegenerative disease.

View details for DOI 10.1016/j.cell.2007.10.036

View details for PubMedID 18083105

Eye-specific visual connections are a prominent model system for exploring how precise circuits develop in the CNS and, in particular, for addressing the role of neural activity in synapse elimination and axon refinement. Recent experiments have identified the features of spontaneous retinal activity that mediate eye-specific retinogeniculate segregation, the synaptic events associated with this process, and the importance of axon guidance cues for organizing the overall layout of eye-specific maps. The classic model of ocular dominance column development, in which spontaneous retinal activity plays a crucial role, has also gained new support. Although many outstanding questions remain, the mechanisms that instruct eye-specific circuit development are becoming clear.

View details for DOI 10.1016/j.conb.2007.01.005

View details for Web of Science ID 000244771100011

View details for PubMedID 17254766

The mechanisms that give rise to ocular dominance columns (ODCs) during development are controversial. Early experiments indicated a key role for retinal activity in ODC formation. However, later studies showed that in those early experiments, the retinal activity perturbation was initiated after ODCs had already formed. Moreover, recent studies concluded that early eye removals do not impact ODC segregation. Here we blocked spontaneous retinal activity during the very early stages of ODC development. This permanently disrupted the anatomical organization of ODCs and led to a dramatic increase in receptive field size for binocular cells in primary visual cortex. Our data suggest that early spontaneous retinal activity conveys crucial information about whether thalamocortical axons represent one or the other eye and that this activity mediates binocular competition important for shaping receptive fields in primary visual cortex.

View details for DOI 10.1016/j.neuron.2006.07.028

View details for Web of Science ID 000241799900006

View details for PubMedID 17046688

View details for PubMedCentralID PMC2647846

Neuronal pentraxins (NPs) define a family of proteins that are homologous to C-reactive and acute-phase proteins in the immune system and have been hypothesized to be involved in activity-dependent synaptic plasticity. To investigate the role of NPs in vivo, we generated mice that lack one, two, or all three NPs. NP1/2 knock-out mice exhibited defects in the segregation of eye-specific retinal ganglion cell (RGC) projections to the dorsal lateral geniculate nucleus, a process that involves activity-dependent synapse formation and elimination. Retinas from mice lacking NP1 and NP2 had cholinergically driven waves of activity that occurred at a frequency similar to that of wild-type mice, but several other parameters of retinal activity were altered. RGCs cultured from these mice exhibited a significant delay in functional maturation of glutamatergic synapses. Other developmental processes, such as pathfinding of RGCs at the optic chiasm and hippocampal long-term potentiation and long-term depression, appeared normal in NP-deficient mice. These data indicate that NPs are necessary for early synaptic refinements in the mammalian retina and dorsal lateral geniculate nucleus. We speculate that NPs exert their effects through mechanisms that parallel the known role of short pentraxins outside the CNS.

View details for DOI 10.1523/jneurosci.4212-05.2006

View details for Web of Science ID 000238174600017

View details for PubMedID 16763034

View details for PubMedCentralID PMC2579897

Correlated spontaneous activity in the form of retinal "waves" has been observed in a wide variety of developing animals, but whether retinal waves occur in the primate has not been determined previously. To address this issue, we recorded from isolated retinas using multielectrode arrays at six fetal ages: embryonic day 51 (E51), E55, E60, E67, E71, and E76. These recordings revealed that the fetal monkey retina is essentially silent at E51 and E55, with only few cells firing on rare occasions and without any obvious spatial or temporal order. Because previous work has shown that the magnocellular and parvocellular subdivisions of the dorsal lateral geniculate are selectively innervated during this early period, our results suggest that this process is unlikely to be regulated by retinal activity. Highly structured retinal waves were first observed at E60, >1 week before the segregation of eye-specific retinal dorsal lateral geniculate nucleus projections commences. The incidence of such waves decreased rapidly and progressively during the developmental period (E67-E76) when segregated eye-specific projections become established. Our findings indicate that retinal waves first occur in the fetal monkey at a remarkably early stage of development, >100 d before birth, and that this activity undergoes rapid changes in salient properties when eye-specific retinogeniculate projections are being formed.

View details for DOI 10.1523/JNEUROSCI.0328-06.2006

View details for Web of Science ID 000237450300021

View details for PubMedID 16687510

Spontaneous retinal activity is necessary to establish and maintain eye-specific projections to the LGN, but whether the spatial and temporal structure of this activity is important remains unclear. A new study by Demas et al. in the current issue of Neuron shows that when the frequency of spontaneous retinal waves is increased and waves abnormally persist past eye opening, eye-specific projections to the LGN desegregate. These results provide important new insight into the mechanisms that drive eye-specific refinement and stabilization.

View details for DOI 10.1016/j.neuron.2006.04.006

View details for Web of Science ID 000237176700002

View details for PubMedID 16630826

View details for DOI 10.1523/JNEUROSCI.4456-05.2006

View details for Web of Science ID 000234896200002

View details for PubMedID 16436591

Axon guidance cues contributing to the development of eye-specific visual projections to the lateral geniculate nucleus (LGN) have not previously been identified. Here we show that gradients of ephrin-As and their receptors (EphAs) direct retinal ganglion cell (RGC) axons from the two eyes into their stereotyped pattern of layers in the LGN. Overexpression of EphAs in ferret RGCs using in vivo electroporation induced axons from both eyes to misproject within the LGN. The effects of EphA overexpression were competition-dependent and restricted to the early postnatal period. These findings represent the first demonstration of eye-specific pathfinding mediated by axon guidance cues and, taken with other reports, indicate that ephrin-As can mediate several mapping functions within individual target structures.

View details for DOI 10.1038/nn1505

View details for Web of Science ID 000230760200012

View details for PubMedID 16025110

View details for PubMedCentralID PMC2652399

The emergence of eye-specific axonal projections to the dorsal lateral geniculate nucleus (dLGN) is a well established model system for exploring the mechanisms underlying afferent targeting during development. Using modern tract tracing methods, we examined the development of this feature in the macaque, an Old World Primate with a visual system similar to that of humans. Cholera toxin beta fragment conjugated to Alexa 488 was injected into the vitreous of one eye, and CTbeta conjugated to Alexa 594 into the other eye of embryos at known gestational ages. On embryonic day 69 (E69), which is approximately 100 d before birth, inputs from the two eyes were extensively intermingled in the dLGN. However, even at this early age, portions of the dLGN were preferentially innervated by the right or left eye, and segregation is complete within the dorsalmost layers 5 and 6. By E78, eye-specific segregation is clearly established throughout the parvocellular division of the dLGN, and substantial ocular segregation is present in the magnocellular division. By E84, segregation of left and right eye axons is essentially complete, and the six eye-specific domains that characterize the mature macaque dLGN are clearly discernable. These findings reveal that targeting of eye-specific axonal projections in the macaque occurs much earlier and more rapidly than previously reported. This segregation process is completed before the reported onset of ganglion cell axon loss and retino-dLGN synapse elimination, suggesting that, in the primate, eye-specific targeting occurs independent of traditional forms of synaptic plasticity.

View details for DOI 10.1523/JNEUROSCI.4292-04.2005

View details for Web of Science ID 000228542600003

View details for PubMedID 15843603

View details for PubMedCentralID PMC2709237

To determine whether there is a critical period for development of eye-specific layers in the lateral geniculate nucleus (LGN), we prevented the normal segregation of retinogeniculate afferents and then allowed an extended period of time for recovery. After recovery, both anatomy and physiology revealed strictly nonoverlapping territories of input from the two eyes. However, the normal stereotyped pattern of eye-specific afferent and cellular layers never developed. Instead, the eye-specific territories of afferent input emerged as variable and disorganized patches with no corresponding interlaminar spaces in the LGN. These findings reveal a critical period for coordinating the development of three processes in the LGN: the segregation of afferents from the two eyes, the spatial organization of those afferents into layers, and the alignment of postsynaptic cytoarchitecture with the afferent inputs. We also assessed the physiological consequences of preventing normal lamination and found normal single-cell responses and topographic representation of visual space in the LGN. Clusters of ON-center and OFF-center LGN cells were segregated from one another as in normal animals. However, the organization of ON and OFF sublaminas in the treated animals was disrupted.

View details for Web of Science ID 000179031600032

View details for PubMedID 12417667

View details for PubMedCentralID PMC2662346

Neuroscience

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Program Overview

When you join Stanford Biosciences, you join a collaborative network tackling some of the world’s toughest questions.  The Stanford Biosciences  Home Programs  comprise nine departments and five interdisciplinary programs, which span the School of Medicine and the School of Humanities and Sciences.  These Home Programs are the foundation of our collaborative culture, offering students the opportunity to tailor their graduate education  by working within an entire network of faculty, labs, and approaches to pursue their research.

Each student is admitted to a particular Home Program and initiates training with a core group of faculty, students, and postdoctoral fellows who share scientific interests. Many Home Programs host annual retreats—facilitating the exchange of ideas between Stanford colleagues and fostering team-building—as well as seminar series that invite outside speakers.

In addition to that intimate setting, all Biosciences students have access to faculty in every Home Program for laboratory rotations and potential thesis work.  One of Stanford Biosciences’ biggest strengths is the physical proximity of programs and labs , encouraging face-to-face collaboration and feeding an environment of interdisciplinary innovation. Indeed, the Biosciences PhD Programs combine the supportive atmosphere of a small program with the many opportunities afforded by a large umbrella program—the best of both worlds.

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The 14 Home Programs in Stanford Biosciences’ collaborative network:

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Providing a select group of medical students with an opportunity to pursue a training program designed to equip them for careers in academic investigative medicine.

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About Stanford Neurosciences

The Stanford Neurosciences Interdepartmental Program uses rigorous training in fundamental principles of neuroscience research to develop leaders at every level of our society. The signature feature of the Stanford Neurosciences Program is the combination of outstanding faculty researchers and exceedingly bright, energetic students in a community that shares a firm and longstanding commitment to understanding the nervous system at all its levels of function.

Since 1962, the philosophy of the the interdepartmental PhD Program is to offer a single program to train future leaders in neuroscience, with directors and faculty from all relevant departments, rather than several small competing departments. 

The Neurosciences Ph.D. program is one of 14 Biosciences Home Programs in the Stanford School of Medicine.

Affiliated Departments and Programs

Applied Physics

Biochemistry

Bioengineering

Chemical and Systems Biology

Comparative Medicine

Computer Science

Developmental Biology

Electrical Engineering

Microbiology and Immunology

Molecular and Cellular Physiology

Neurobiology

Neurology and Neurological Sciences

Neurosurgery

Ophthalmology

Otolaryngology

Psychiatry and Behavioral Sciences

The Educational Neuroscience Initiative at the  Stanford Graduate School of Education  is aimed at creating a new form of actionable research that links school-based educational innovation with advances in the neuroscience of emerging math and reading.

We partner with  local schools  to bring unique neuroscience learning opportunities to students, and explore how changes in the brain's neural circuitry support emerging skills that are foundational to education, and how school experiences help to change, shape and tune brain circuitry that are critical to the emergence of the educated mind.  Embedding EEG research within schools and infusing developmental cognitive neuroscience insights into educational approaches provide the basis for the new form of research we call Educational Neuroscience. 

This initiative also supports cutting-edge developments in the use of  Steady-State Visual Evoked Potentials (SSVEP)  and  Reliable Components Analysis  to track changes in neural circuits over the course of schooling experiences, as well as novel ways of connecting large scale developmental cognitive neuroscience datasets with corresponding evidence of educational opportunity, inequity, and change.

Brainwave Learning Center

Middle School Research Assistant Program

Recent news, putting neuroscience in the classroom: how the brain changes as we learn.

Bruce and Liz's article on neuroscience in the classroom is out on PEW Trend Magazine.

April 13, 2020

Educational Neuroscience on "Science of Reading: The Podcast"

Bruce talks about combining neuroscience with education on Amplify's "Science of Reading" podcast.

March 18, 2020

Stanford GSE features the Brainwave Learning Center

The Brainwave Learning Center at Synapse School is featured in an article published by the Stanford Graduate School of Education.

August 07, 2019

NEURS-MS - Neurosciences (MS)

Program overview.

The Neurosciences IDP does not offer a terminal or coterminal MS degree. An MS degree may only be pursued in combination with a doctoral degree from another department within the university or one of the university’s professional schools. Please see the degree requirements for the program under the Requirements section.

Admissions Information

Students interested in pursuing the MS must submit an unofficial Stanford transcript and a written scientific justification for adding the MS degree to the Neurosciences Student Services Officer no later than February 1, 2024.

Law Neurosciences IDP, School of Medicine, NEURS

Jd/neurs-phd.

As evidenced by the Stanford Program in Neuroscience and Society based in the Law School, neuroscience and law are intimately tied together at the academic and public policy level. The joint degree program provides an opportunity for students to develop expertise in both fields, and in some cases, to prepare themselves intensively for careers in areas relating to both neuroscience and law.

Course Requirements

The Law School shall approve courses from the Neurosciences program that may count toward the JD degree, and the Neurosciences program shall approve courses from the Law School that may count toward the Ph.D. degree in the Neurosciences. In either case, approval may consist of a list applicable to all joint degree students or may be tailored to each individual student’s program.

Note to applicants:  The Knight-Hennessy Scholars program awards full funding to Stanford graduate students from all disciplines, with additional opportunities for leadership training and collaboration across fields. Joint Degree applicants are encouraged to apply to the  Knight – Hennessy Scholars Program.  Please be aware that the Knight-Hennessy Scholars applications are due in early Autumn one year prior to enrollment. View dates and deadlines: knight-hennessy.stanford.edu/dates-and-deadlines .

Henry T. Greely

• Deane F. and Kate Edelman Johnson Professor of Law
• Director, Center for Law and the Biosciences
• Professor, by courtesy, Genetics
• Chair, Steering Committee of the Center for Biomedical Ethics
• Director, Stanford Program in Neuroscience and Society

NeuroTech Graduate Training Program 2024

The NeuroTech Training Program application is now open.

Application Deadline: Monday. May 6, 2024!

The NeuroTech training program draws Stanford graduate students from the technical disciplines of Applied Physics, BioEngineering, Chemical Engineering, Computer Science, Electrical Engineering, Material Sciences and Engineering, Mechanical Engineering, Physics or Statistics into the emerging world of neurotechnology. As a NeuroTech trainee, you will spend three years immersed in coursework, research, seminars and travel opportunities designed to introduce you to the unique questions and challenges facing the field of neuroscience, so you can apply your technical skills to advancing neuroscience discovery and human health. Working together with faculty mentors and fellow trainees, NeuroTech students prepare to tackle these challenges and to become leaders in the emerging field of neurotechnology. Learn more at  bit.ly/neurotechgrad .

Eligibility and Requirements: 

Visit our  Application and Eligibility webpage  to learn more.

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Pathways to Neurosciences

The Pathways to Neurosciences program aims to foster belonging, excellence, and leadership in the next generation of Stanford neuroscience trainees.

This program is part of an NIH-funded research study that seeks to collect actionable data about how to effectively increase social connection and feelings of belonging for historically underrepresented trainees in the neurosciences.

Participants will take part in a mentorship and leadership training program that includes the following opportunities:

• NeuroCircles: Facilitated peer-to-peer mentoring groups. NeuroCircles meet every other week starting in the Fall. Each NeuroCircle cohort will last two years and will consist of 7-10 trainees who are approaching or have recently completed the transition from predoctoral to postdoctoral status.
• Pathways Mentors: Faculty available for one-on-one meetings centered around specific topics related to mentorship, scientific advancement, and networking. Pathways mentors will also attend select, topic-specific NeuroCircle meetings to meet with trainees as a group.
• Enrichment Funds: Grants for career development or scientific training experiences, such as travel to another lab to learn a technique or to a career development meeting.
• Grant-writing Academy Accelerator & Women’s Empowerment Workshop: Designed specifically for Pathways by Dr. Crystal Botham, the founder of the award-winning Grant Writing Academy program, these events will boost your ability to choose the right fellowship program and to develop a writing practice.
• BIOS 225 Diversity & Inclusion in STEMM (Science, Technology, Engineering, Mathematics, and Medicine): Participate in "DAIS", an established minicourse offered in the spring that combines didactics and team projects to enhance knowledge of diversity and inclusion concepts and practices.

Application will reopen in August 2024.

Pathways mentors.

Pathways trainees have access to one-on-one meetings with mentors where they can discuss their questions and request advice regarding mentorship, scientific advancement, and networking.

View Pathways Mentors

For questions about the program, please contact  Valerie Vargas-Zapata at [email protected] .

For questions about the rights of participants in our study or the efficacy of the program, call 1-866-680-2906.

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Photo by Supraja Varadarajan

Photo by Ioana Marin

Welcome to the department of neurobiology.

Message from the Chair

"Welcome to the Stanford Department of Neurobiology!  This is a uniquely exciting time to be or become a neuroscientist. We invite you to explore our website and contact any labs that pique your interests!"

Diversity, Equity & Inclusion

The Neurobiology Department is committed to providing a welcoming, supportive and respectful environment for all its members. Whether you are a student, postdoc, faculty, admin or research staff, you belong here: you and your contributions are valued. We recognize that racism and sexism still exist in the department, along with other entrenched systems of oppression that we are actively working to dismantle. In our academic community, and through our research, we strive towards social justice and equity for all individuals, regardless of race, ethnicity, gender, religion, socio-economic status, or ability. See our charter for our ongoing efforts and here for more information about our DEI Committee.

Please follow our monthly newsletter for the latest updates in our committee.

Support Our Research

With your gift, you make an investment in leading-edge research that advances understanding and enhances life for generations to come. Please contact Medical Center Development to discuss ways you can support the Department of Neurobiology.

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Neuroscience Seminar Series: Anna Schapiro, PhD

900 E. 57th St. Chicago , IL 60637 United States

Neuroscience Seminar Series - CNS Tuesday, April 16th, 11:00 am Anna Schapiro, PhD University of Pennsylvania KCBD 1103 “Learning representations of specifics and generalities over time”

Host: Wilma Bainbridge, PhD

Neuroscience Seminar Series Schedule

Autumn quarter 2023, winter quarter 2024, spring quarter 2024.

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SESP Ranked No. 5 by U.S. News

For the second year in a row, Northwestern University’s School of Education and Social Policy (SESP) has been ranked among the top five graduate schools of education according to the 2024-25 U.S. News and World Report Best Education Graduate Schools rankings.

The School of Education and Social Policy and Vanderbilt University tied for fifth place. Among specialities, SESP's education policy program tied for the No. 11 spot with the University of Virginia, rising from No. 12 the previous year.

“SESP is a place of possibility,” said School of Education and Social Policy Dean Bryan McKinley Jones Brayboy, the Carlos Montezuma Professor. “It is also a place of the now. We will continue to raise new sets of ideas, rooted in empirical research theories of human development, and learning theories, that create the conditions for thriving futures for the peoples, places, and communities that we serve.”

Overall, Columbia University and the University of Wisconsin Madison tied for the top spot. The University of California Los Angeles and the University of Michigan were ranked third and fourth. The rest of the top 10 included: University of Pennsylvania (No. 7), and Harvard University, Johns Hopkins University, New York University, Stanford University, University of Texas Austin and the University of Virginia (tied for No. 8).

The School of Education and Social Policy broke into the top ten US News rankings in 2001-02 and has remained in the top 15 every year since then. Its consistent designation as one of the top schools in the nation reflects an ambitious commitment to interdisciplinary work, research, and innovation.

The School’s three pioneering doctoral programs–learning sciences, human development and social policy, and the joint learning sciences + computer science program–were the first of their kind in the nation and have many imitators.

Our versatile faculty includes experts across an array of disciplines, including social science, natural science, education, psychology, sociology, economics, political science, anthropology, geography, neuroscience, history, and philosophy.

Other faculty highlights include:

• Seventeen National Academy of Education members.
• Thirteen American Educational Research Association Fellows
• Early career superstars. Two-thirds of full professors ages 40-55 are National Academy of Education Members – an award that generally recognizes lifetime achievement.

U.S. News evaluated education schools on research activity, academic excellence of entering students, faculty resources, and opinions on program quality from education school deans and school hiring professionals. Read more about the methodology.