Weak evidence for neural correlates of task-switching in macaque V1.

A central goal of systems neuroscience is to understand how populations of sensory neurons encode and relay information to the rest of the brain. Three key quantities of interest are 1) how mean neural activity depends on the stimulus (sensitivity), 2) how neural activity (co)varies around the mean (noise correlations), and 3) how predictive these variations are of the subject's behavior (choice probability). Previous empirical work suggests that both choice probability and noise correlations are affected by task training, with decision-related information fed back to sensory areas and aligned to neural sensitivity on a task-by-task basis. We used Utah arrays to record activity from populations of primary visual cortex (V1) neurons from two macaque monkeys that were trained to switch between two coarse orientation-discrimination tasks. Surprisingly, we find no evidence for significant trial-by-trial changes in noise covariance between tasks, nor do we find a consistent relationship between neural sensitivity and choice probability, despite recording from well-tuned task-sensitive neurons, many of which were histologically confirmed to be in supragranular V1, and despite behavioral evidence that the monkeys switched their strategy between tasks. Thus our data at best provide weak support for the hypothesis that trial-by-trial task-switching induces changes to noise correlations and choice probabilities in V1. However, our data agree with a recent finding of a single "choice axis" across tasks. They also raise the intriguing possibility that choice-related signals in early sensory areas are less indicative of task learning per se and instead reflect perceptual learning that occurs in highly overtrained subjects.NEW & NOTEWORTHY Converging evidence suggests that decision processes affect sensory neural activity, and this has informed numerous theories of neural processing. We set out to replicate and extend previous results on decision-related information and noise correlations in V1 of macaque monkeys. However, in our data, we find little evidence for a number of expected effects. Our null results therefore call attention to differences in task training, stimulus design, recording, and analysis techniques between our and prior studies.

Munc13 supports fusogenicity of non-docked vesicles at synapses with disrupted active zones.

Active zones consist of protein scaffolds that are tightly attached to the presynaptic plasma membrane. They dock and prime synaptic vesicles, couple them to voltage-gated Ca2+ channels, and direct neurotransmitter release toward postsynaptic receptor domains. Simultaneous RIM + ELKS ablation disrupts these scaffolds, abolishes vesicle docking, and removes active zone-targeted Munc13, but some vesicles remain releasable. To assess whether this enduring vesicular fusogenicity is mediated by non-active zone-anchored Munc13 or is Munc13-independent, we ablated Munc13-1 and Munc13-2 in addition to RIM + ELKS in mouse hippocampal neurons. The hextuple knockout synapses lacked docked vesicles, but other ultrastructural features were near-normal despite the strong genetic manipulation. Removing Munc13 in addition to RIM + ELKS impaired action potential-evoked vesicle fusion more strongly than RIM + ELKS knockout by further decreasing the releasable vesicle pool. Hence, Munc13 can support some fusogenicity without RIM and ELKS, and presynaptic recruitment of Munc13, even without active zone anchoring, suffices to generate some fusion-competent vesicles.

Illusions, Delusions, and Your Backwards Bayesian Brain: A Biased Visual Perspective.

The retinal image is insufficient for determining what is "out there," because many different real-world geometries could produce any given retinal image. Thus, the visual system must infer which external cause is most likely, given both the sensory data and prior knowledge that is either innate or learned via interactions with the environment. We will describe a general framework of "hierarchical Bayesian inference" that we and others have used to explore the role of cortico-cortical feedback in the visual system, and we will further argue that this approach to "seeing" makes our visual systems prone to perceptual errors in a variety of different ways. In this deliberately provocative and biased perspective, we argue that the neuromodulator, dopamine, may be a crucial link between neural circuits performing Bayesian inference and the perceptual idiosyncrasies of people with schizophrenia.

Banishing "Black/White Thinking": A Trio of Teaching Tricks.

Literally hundreds of statisticians have rightly called for an end to statistical significance testing (Amrhein et al., 2019; Wasserstein et al., 2019). But the practice of arbitrarily thresholding p values is not only deeply embedded in statistical practice, it is also congenial to the human mind. It is thus not sufficient to tell our students, "Don't do this." We must vividly show them why the practice is wrong and its effects detrimental to scientific progress. I offer three teaching examples I have found to be useful in prompting students to think more deeply about the problem and to begin to interpret the results of statistical procedures as measures of how evidence should change our beliefs, and not as bright lines separating truth from falsehood.

Gene Transfer with AAV9-PHP.B Rescues Hearing in a Mouse Model of Usher Syndrome 3A and Transduces Hair Cells in a Non-human Primate.

Hereditary hearing loss often results from mutation of genes expressed by cochlear hair cells. Gene addition using AAV vectors has shown some efficacy in mouse models, but clinical application requires two additional advances. First, new AAV capsids must mediate efficient transgene expression in both inner and outer hair cells of the cochlea. Second, to have the best chance of clinical translation, these new vectors must also transduce hair cells in non-human primates. Here, we show that an AAV9 capsid variant, PHP.B, produces efficient transgene expression of a GFP reporter in both inner and outer hair cells of neonatal mice. We show also that AAV9-PHP.B mediates almost complete transduction of inner and outer HCs in a non-human primate. In a mouse model of Usher syndrome type 3A deafness (gene CLRN1), we use AAV9-PHP.B encoding Clrn1 to partially rescue hearing. Thus, we have identified a vector with promise for clinical treatment of hereditary hearing disorders, and we demonstrate, for the first time, viral transduction of the inner ear of a primate with an AAV vector.

Bottom-Up and Top-Down Input Augment the Variability of Cortical Neurons.

Neurons in the cerebral cortex respond inconsistently to a repeated sensory stimulus, yet they underlie our stable sensory experiences. Although the nature of this variability is unknown, its ubiquity has encouraged the general view that each cell produces random spike patterns that noisily represent its response rate. In contrast, here we show that reversibly inactivating distant sources of either bottom-up or top-down input to cortical visual areas in the alert primate reduces both the spike train irregularity and the trial-to-trial variability of single neurons. A simple model in which a fraction of the pre-synaptic input is silenced can reproduce this reduction in variability, provided that there exist temporal correlations primarily within, but not between, excitatory and inhibitory input pools. A large component of the variability of cortical neurons may therefore arise from synchronous input produced by signals arriving from multiple sources.

Neuroanatomy goes viral!

The nervous system is complex not simply because of the enormous number of neurons it contains but by virtue of the specificity with which they are connected. Unraveling this specificity is the task of neuroanatomy. In this endeavor, neuroanatomists have traditionally exploited an impressive array of tools ranging from the Golgi method to electron microscopy. An ideal method for studying anatomy would label neurons that are interconnected, and, in addition, allow expression of foreign genes in these neurons. Fortuitously, nature has already partially developed such a method in the form of neurotropic viruses, which have evolved to deliver their genetic material between synaptically connected neurons while largely eluding glia and the immune system. While these characteristics make some of these viruses a threat to human health, simple modifications allow them to be used in controlled experimental settings, thus enabling neuroanatomists to trace multi-synaptic connections within and across brain regions. Wild-type neurotropic viruses, such as rabies and alpha-herpes virus, have already contributed greatly to our understanding of brain connectivity, and modern molecular techniques have enabled the construction of recombinant forms of these and other viruses. These newly engineered reagents are particularly useful, as they can target genetically defined populations of neurons, spread only one synapse to either inputs or outputs, and carry instructions by which the targeted neurons can be made to express exogenous proteins, such as calcium sensors or light-sensitive ion channels, that can be used to study neuronal function. In this review, we address these uniquely powerful features of the viruses already in the neuroanatomist's toolbox, as well as the aspects of their biology that currently limit their utility. Based on the latter, we consider strategies for improving viral tracing methods by reducing toxicity, improving control of transsynaptic spread, and extending the range of species that can be studied.

A Modality-Specific Feedforward Component of Choice-Related Activity in MT.

The activity of individual sensory neurons can be predictive of an animal's choices. These decision signals arise from network properties dependent on feedforward and feedback inputs; however, the relative contributions of these inputs are poorly understood. We determined the role of feedforward pathways to decision signals in MT by recording neuronal activity while monkeys performed motion and depth tasks. During each session, we reversibly inactivated V2 and V3, which provide feedforward input to MT that conveys more information about depth than motion. We thus monitored the choice-related activity of the same neuron both before and during V2/V3 inactivation. During inactivation, MT neurons became less predictive of decisions for the depth task but not the motion task, indicating that a feedforward pathway that gives rise to tuning preferences also contributes to decision signals. We show that our data are consistent with V2/V3 input conferring structured noise correlations onto the MT population.

The quantitative methods boot camp: teaching quantitative thinking and computing skills to graduate students in the life sciences.

The past decade has seen a rapid increase in the ability of biologists to collect large amounts of data. It is therefore vital that research biologists acquire the necessary skills during their training to visualize, analyze, and interpret such data. To begin to meet this need, we have developed a "boot camp" in quantitative methods for biology graduate students at Harvard Medical School. The goal of this short, intensive course is to enable students to use computational tools to visualize and analyze data, to strengthen their computational thinking skills, and to simulate and thus extend their intuition about the behavior of complex biological systems. The boot camp teaches basic programming using biological examples from statistics, image processing, and data analysis. This integrative approach to teaching programming and quantitative reasoning motivates students' engagement by demonstrating the relevance of these skills to their work in life science laboratories. Students also have the opportunity to analyze their own data or explore a topic of interest in more detail. The class is taught with a mixture of short lectures, Socratic discussion, and in-class exercises. Students spend approximately 40% of their class time working through both short and long problems. A high instructor-to-student ratio allows students to get assistance or additional challenges when needed, thus enhancing the experience for students at all levels of mastery. Data collected from end-of-course surveys from the last five offerings of the course (between 2012 and 2014) show that students report high learning gains and feel that the course prepares them for solving quantitative and computational problems they will encounter in their research. We outline our course here which, together with the course materials freely available online under a Creative Commons License, should help to facilitate similar efforts by others.

Input-gain control produces feature-specific surround suppression.

In primary visual cortex (V1), neuronal responses are sensitive to context. For example, responses to stimuli presented within the receptive field (RF) center are often suppressed by stimuli within the RF surround, and this suppression tends to be strongest when the center and surround stimuli match. We sought to identify the mechanism that gives rise to these properties of surround modulation. To do so, we exploited the stability of implanted multielectrode arrays to record from neurons in V1 of alert monkeys with multiple stimulus sets that more exhaustively probed center-surround interactions. We first replicated previous results concerning center-surround similarity using gratings representing all combinations of center and surround orientation. With this stimulus set, the surround simply scaled population responses to the center, such that the overall population tuning curve had the same shape and peak response. However, when the center contained two superimposed gratings (i.e., a visual "plaid"), one component of which always matched the surround orientation, suppression selectively affected the portion of the response driven by the matching center component, thereby producing shifts in the peak of the population orientation tuning curve. In effect, the surround caused neurons to respond predominantly to the component grating of the center plaid that was unmatched to the surround grating, as if by reducing the effective strength of whichever stimulus attributes were matched to the surround. These results provide key physiological support for theoretical models that propose feature-specific, input-gain control as the mechanism underlying surround suppression.

Vesicular stomatitis virus enables gene transfer and transsynaptic tracing in a wide range of organisms.

Current limitations in technology have prevented an extensive analysis of the connections among neurons, particularly within nonmammalian organisms. We developed a transsynaptic viral tracer originally for use in mice, and then tested its utility in a broader range of organisms. By engineering the vesicular stomatitis virus (VSV) to encode a fluorophore and either the rabies virus glycoprotein (RABV-G) or its own glycoprotein (VSV-G), we created viruses that can transsynaptically label neuronal circuits in either the retrograde or anterograde direction, respectively. The vectors were investigated for their utility as polysynaptic tracers of chicken and zebrafish visual pathways. They showed patterns of connectivity consistent with previously characterized visual system connections, and revealed several potentially novel connections. Further, these vectors were shown to infect neurons in several other vertebrates, including Old and New World monkeys, seahorses, axolotls, and Xenopus. They were also shown to infect two invertebrates, Drosophila melanogaster, and the box jellyfish, Tripedalia cystophora, a species previously intractable for gene transfer, although no clear evidence of transsynaptic spread was observed in these species. These vectors provide a starting point for transsynaptic tracing in most vertebrates, and are also excellent candidates for gene transfer in organisms that have been refractory to other methods.

Cortical magnification plus cortical plasticity equals vision?

Most approaches to visual prostheses have focused on the retina, and for good reasons. The earlier that one introduces signals into the visual system, the more one can take advantage of its prodigious computational abilities. For methods that make use of microelectrodes to introduce electrical signals, however, the limited density and volume occupying nature of the electrodes place severe limits on the image resolution that can be provided to the brain. In this regard, non-retinal areas in general, and the primary visual cortex in particular, possess one large advantage: "magnification factor" (MF)-a value that represents the distance across a sheet of neurons that represents a given angle of the visual field. In the foveal representation of primate primary visual cortex, the MF is enormous-on the order of 15-20 mm/deg in monkeys and humans, whereas on the retina, the MF is limited by the optical design of the eye to around 0.3m m/deg. This means that, for an electrode array of a given density, a much higher-resolution image can be introduced into V1 than onto the retina (or any other visual structure). In addition to this tremendous advantage in resolution, visual cortex is plastic at many different levels ranging from a very local ability to learn to better detect electrical stimulation to higher levels of learning that permit human observers to adapt to radical changes to their visual inputs. We argue that the combination of the large magnification factor and the impressive ability of the cerebral cortex to learn to recognize arbitrary patterns, might outweigh the disadvantages of bypassing earlier processing stages and makes V1 a viable option for the restoration of vision.

Feature attention for binocular disparity in primate area MT depends on tuning strength.

Attending to a stimulus modulates the responses of sensory neurons that represent features of that stimulus, a phenomenon named "feature attention." For example, attending to a stimulus containing upward motion enhances the responses of upward-preferring direction-selective neurons in the middle temporal area (MT) and suppresses the responses of downward-preferring neurons, even when the attended stimulus is outside of the spatial receptive fields of the recorded neurons (Treue S, Martinez-Trujillo JC. Nature 399: 575-579, 1999). This modulation renders the representation of sensory information across a neuronal population more selective for the features present in the attended stimulus (Martinez-Trujillo JC, Treue S. Curr Biol 14: 744-751, 2004). We hypothesized that if feature attention modulates neurons according to their tuning preferences, it should also be sensitive to their tuning strength, which is the magnitude of the difference in responses to preferred and null stimuli. We measured how the effects of feature attention on MT neurons in rhesus monkeys (Macaca mulatta) depended on the relationship between features-in our case, direction of motion and binocular disparity-of the attended stimulus and a neuron's tuning for those features. We found that, as for direction, attention to stimuli containing binocular disparity cues modulated the responses of MT neurons and that the magnitude of the modulation depended on both a neuron's tuning preferences and its tuning strength. Our results suggest that modulation by feature attention may depend not just on which features a neuron represents but also on how well the neuron represents those features.

Corticocortical feedback increases the spatial extent of normalization.

Normalization has been proposed as a canonical computation operating across different brain regions, sensory modalities, and species. It provides a good phenomenological description of non-linear response properties in primary visual cortex (V1), including the contrast response function and surround suppression. Despite its widespread application throughout the visual system, the underlying neural mechanisms remain largely unknown. We recently observed that corticocortical feedback contributes to surround suppression in V1, raising the possibility that feedback acts through normalization. To test this idea, we characterized area summation and contrast response properties in V1 with and without feedback from V2 and V3 in alert macaques and applied a standard normalization model to the data. Area summation properties were well explained by a form of divisive normalization, which computes the ratio between a neuron's driving input and the spatially integrated activity of a "normalization pool." Feedback inactivation reduced surround suppression by shrinking the spatial extent of the normalization pool. This effect was independent of the gain modulation thought to mediate the influence of contrast on area summation, which remained intact during feedback inactivation. Contrast sensitivity within the receptive field center was also unaffected by feedback inactivation, providing further evidence that feedback participates in normalization independent of the circuit mechanisms involved in modulating contrast gain and saturation. These results suggest that corticocortical feedback contributes to surround suppression by increasing the visuotopic extent of normalization and, via this mechanism, feedback can play a critical role in contextual information processing.

Joint tuning for direction of motion and binocular disparity in macaque MT is largely separable.

Neurons in sensory cortical areas are tuned to multiple dimensions, or features, of their sensory space. Understanding how single neurons represent multiple features is of great interest for determining the informative dimensions of the neurons' response, the decoding algorithms appropriate for extracting this information from the neuronal population, and for determining where specific transformations occur along the visual hierarchy. Despite the established role of cortical area MT in judgments of motion and depth, it is not known how individual neurons jointly encode the two dimensions. We investigated the joint tuning of individual MT neurons for two visual features: direction of motion and binocular disparity, an important depth cue. We found that a separable, multiplicative combination of tuning for the two features can account for more than 90% of the variance in the joint tuning function for over 91% of MT neurons. These results suggest 1) that each feature can be read out independently from MT by simply averaging across the population without regard to the other feature and 2) that the inseparable representations seen in subsequent areas, such as MST, must be computed beyond MT. Intriguingly, we found that the remaining nonseparable component of the joint tuning function often manifested as small but systematic changes in the neurons' preferences for one feature as the other one was varied. We believe this reflects the local columnar organization of tuning for direction and binocular disparity in MT, indicating that joint tuning may provide a new tool with which to probe functional architecture.

Corticocortical feedback contributes to surround suppression in V1 of the alert primate.

Feedback connections are prevalent throughout the cerebral cortex, yet their function remains poorly understood. Previous studies in anesthetized monkeys found that inactivating feedback from extrastriate visual cortex produced effects in striate cortex that were relatively weak, generally suppressive, largest for visual stimuli confined to the receptive field center, and detectable only at low stimulus contrast. We studied the influence of corticocortical feedback in alert monkeys using cortical cooling to reversibly inactivate visual areas 2 (V2) and 3 (V3) while characterizing receptive field properties in primary visual cortex (V1). We show that inactivation of feedback from areas V2 and V3 results in both response suppression and facilitation for stimuli restricted to the receptive field center, in most cases leading to a small reduction in the degree of orientation selectivity but no change in orientation preference. For larger-diameter stimuli that engage regions beyond the center of the receptive field, eliminating feedback from V2 and V3 results in strong and consistent response facilitation, effectively reducing the strength of surround suppression in V1 for stimuli of both low and high contrast. For extended contours, eliminating feedback had the effect of reducing end stopping. Inactivation effects were largest for neurons that exhibited strong surround suppression before inactivation, and their timing matched the dynamics of surround suppression under control conditions. Our results provide direct evidence that feedback contributes to surround suppression, which is an important source of contextual influences essential to vision.

Adaptation to speed in macaque middle temporal and medial superior temporal areas.

The response of a sensory neuron to an unchanging stimulus typically adapts, showing decreases in response gain that are accompanied by changes in the shape of tuning curves. It remains unclear whether these changes arise purely due to spike rate adaptation within single neurons or whether they are dependent on network interactions between neurons. Further, it is unclear how the timescales of neural and perceptual adaptation are related. To examine this issue, we compared speed tuning of middle temporal (MT) and medial superior temporal neurons in macaque visual cortex after adaptation to two different reference speeds. For 75% of speed-tuned units, adaptation caused significant changes in tuning that could be explained equally well as lateral shifts, vertical gain changes, or both. These tuning changes occurred rapidly, as both neuronal firing rate and Fano factor showed no evidence of changing beyond the first 500 ms after motion onset, and the magnitude of tuning curve changes showed no difference between trials with adaptation durations shorter or longer than 1 s. Importantly, the magnitude of tuning shifts was correlated with the transient-sustained index, which measures a well characterized form of rapid response adaptation in MT, and is likely associated with changes at the level of neuronal networks. Tuning curves changed in a manner that increased neuronal sensitivity around the adapting speed, consistent with improvements in human and macaque psychophysical performance that we observed over the first several hundred ms of adaptation.

Segregation of feedforward and feedback projections in mouse visual cortex.

Hierarchical organization is a common feature of mammalian neocortex. Neurons that send their axons from lower to higher areas of the hierarchy are referred to as "feedforward" (FF) neurons, whereas those projecting in the opposite direction are called "feedback" (FB) neurons. Anatomical, functional, and theoretical studies suggest that these different classes of projections play fundamentally different roles in perception. In primates, laminar differences in projection patterns often distinguish the two projection streams. In rodents, however, these differences are less clear, despite an established hierarchy of visual areas. Thus the rodent provides a strong test of the hypothesis that FF and FB neurons form distinct populations. We tested this hypothesis by injecting retrograde tracers into two different hierarchical levels of mouse visual cortex (area 17 and anterolateral area [AL]) and then determining the relative proportions of double-labeled FF and FB neurons in an area intermediate to them (lateromedial area [LM]). Despite finding singly labeled neurons densely intermingled with no laminar segregation, we found few double-labeled neurons (≈5% of each singly labeled population). We also examined the development of FF and FB connections. FF connections were present at the earliest timepoint we examined (postnatal day 2, P2), while FB connections were not detectable until P11. Our findings indicate that, even in cortices without laminar segregation of FF and FB neurons, the two projection systems are largely distinct at the neuronal level and also differ with respect to the timing of their axonal outgrowth.