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Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

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Plasticity-Driven Self-Organization under Topological Constraints Accounts for Non-Random Features of Cortical Synaptic Wiring.

Understanding the structure and dynamics of cortical connectivity is vital to understanding cortical function. Experimental data strongly suggest that local recurrent connectivity in the cortex is significantly non-random, exhibiting, for example, above-chance bidirectionality and an overrepresentation of certain triangular motifs. Additional evidence suggests a significant distance dependency to connectivity over a local scale of a few hundred microns, and particular patterns of synaptic turnover dynamics, including a heavy-tailed distribution of synaptic efficacies, a power law distribution of synaptic lifetimes, and a tendency for stronger synapses to be more stable over time. Understanding how many of these non-random features simultaneously arise would provide valuable insights into the development and function of the cortex. While previous work has modeled some of the individual features of local cortical wiring, there is no model that begins to comprehensively account for all of them. We present a spiking network model of a rodent Layer 5 cortical slice which, via the interactions of a few simple biologically motivated intrinsic, synaptic, and structural plasticity mechanisms, qualitatively reproduces these non-random effects when combined with simple topological constraints. Our model suggests that mechanisms of self-organization arising from a small number of plasticity rules provide a parsimonious explanation for numerous experimentally observed non-random features of recurrent cortical wiring. Interestingly, similar mechanisms have been shown to endow recurrent networks with powerful learning abilities, suggesting that these mechanism are central to understanding both structure and function of cortical synaptic wiring.\n\nAuthor SummaryThe problem of how the brain wires itself up has important implications for the understanding of both brain development and cognition. The microscopic structure of the circuits of the adult neocortex, often considered the seat of our highest cognitive abilities, is still poorly understood. Recent experiments have provided a first set of findings on the structural features of these circuits, but it is unknown how these features come about and how they are maintained. Here we present a neural network model that shows how these features might come about. It gives rise to numerous connectivity features, which have been observed in experiments, but never before simultaneously produced by a single model. Our model explains the development of these structural features as the result of a process of self-organization. The results imply that only a few simple mechanisms and constraints are required to produce, at least to the first approximation, various characteristic features of a typical fragment of brain microcircuitry. In the absence of any of these mechanisms, simultaneous production of all desired features fails, suggesting a minimal set of necessary mechanisms for their production.

Neuroscience

A Serial Multiplex Immunogold Labeling Method for Identifying Peptidergic Neurons in Connectomes

Electron microscopy-based connectomics aims to comprehensively map synaptic connections in neural tissue. However, current approaches are limited in their capacity to directly assign molecular identities to neurons. Here, we use serial multiplex immunogold labeling (siGOLD) and serial-section transmission electron microscopy (ssTEM) to identify multiple peptidergic neurons in a connectome. The high immunogenicity of neuropeptides and their broad distribution along axons, allowed us to identify distinct neurons by immunolabeling small subsets of sections within larger series. We demonstrate the scalability of siGOLD by using 11 neuropeptide antibodies on a full-body larval ssTEM dataset of the annelid Platynereis. We also reconstruct a peptidergic circuitry comprising the sensory nuchal organs, found by siGOLD to express pigment-dispersing factor, a circadian neuropeptide. Our approach enables the direct overlaying of chemical neuromodulatory maps onto synaptic connectomic maps in the study of nervous systems.

Neuroscience

Mixed Effects Models for Resampled Network Statistics Improves Statistical Power to Find Differences in Multi-Subject Functional Connectivity

Many complex brain disorders, such as autism spectrum disorders, exhibit a wide range of symptoms and disability. To understand how brain communication is impaired in such conditions, functional connectivity studies seek to understand individual differences in brain network structure in terms of covariates that measure symptom severity. In practice, however, functional connectivity is not observed but estimated from complex and noisy neural activity measurements. Imperfect subject network estimates can compromise subsequent efforts to detect covariate effects on network structure. We address this problem in the case of Gaussian graphical models of functional connectivity, by proposing novel two-level models that treat both subject level networks and population level covariate effects as unknown parameters. To account for imperfectly estimated subject level networks when fitting these models, we propose two related approaches -- R2 based on resampling and random effects test statistics, and R3 that additionally employs random adaptive penalization. Simulation studies using realistic graph structures reveal that R2 and R3 have superior statistical power to detect covariate effects compared to existing approaches, particularly when the number of within subject observations is comparable to the size of subject networks. Using our novel models and methods to study parts of the ABIDE dataset, we find evidence of hypoconnectivity associated with symptom severity in autism spectrum disorders, in frontoparietal and limbic systems as well as in anterior and posterior cingulate cortices.

Neuroscience

Neural and non-neural contributions to sexual dimorphism of mid-day sleep in Drosophila: A pilot study

Many of the characteristics associated with mammalian sleep are also observed in Drosophila, making the fruit-fly a powerful model organism for studying the genetics of this important process. Among these similarities is the presence of sexual dimorphic sleep patterns, which in flies, is manifested as increased mid-day sleep ( siesta) in males, compared to females. Here, we have used targeted miss-expression of the gene transformer (tra) and tra2 to either feminise or masculinise specific neural and non-neural tissues in the fly. Feminization of males using three different GAL4 drivers which are expressed in the mushroom bodies induced a female-like reduced siesta, while the masculinisation of females using these drivers triggered the male-like increased siesta. We also observed a similar reversal of sex-specific sleep by miss-expressing tra in the fat body, a key tissue in energy metabolism and hormone secretion. In addition, the daily expression levels of takeout, an important circadian clock output gene, were sexually dimorphic. Taken together, our experiments suggest that sleep-sexual dimorphism in Drosophila is driven by multiple neural and non-neural circuits, within and outside the brain.

Neuroscience

TRPA1 tunes mosquito thermotaxis to host temperatures

While most ectotherms thermotax only to regulate their temperature, female mosquitoes are attracted to human body heat during pursuit of a blood meal. Here we elucidate the basic rules of Aedes aegypti thermotaxis and test the function of candidate thermoreceptors in this important behavior. We show that host-seeking mosquitoes are maximally attracted to thermal stimuli approximating host body temperatures, seeking relative warmth while avoiding both relative cooling and stimuli exceeding host body temperature. We found that the cation channel TRPA1, in addition to playing a conserved role in thermoregulation and chemosensation, is required for this specialized host-selective thermotaxis in mosquitoes. During host-seeking, AaegTRPA1-/- mutants failed to avoid stimuli exceeding host temperature, and were unable to discriminate between host-temperature and high-temperature stimuli. TRPA1-dependent tuning of thermotaxis is likely critical for mosquitoes host-seeking in a complex thermal environment in which humans are warmer than ambient air, but cooler than surrounding sun-warmed surfaces.

Neuroscience

DoOR 2.0 - Comprehensive Mapping of Drosophila melanogaster Odorant Responses

Odors elicit complex patterns of activated olfactory sensory neurons. Knowing the complete olfactome, i.e. responses in all sensory neurons for all odorants, is desirable to understand olfactory coding. The DoOR project combines all available Drosophila odorant response data into a single consensus response matrix. Since its first release many studies were published: receptors were deorphanized and several response profiles were expanded. In this study, we add to the odor-response profiles for four odorant receptors (Or10a, Or42b, Or47b, Or56a). We deorphanize Or69a, showing a broad response spectrum with the best ligands including 3-hydroxyhexanoate, alpha-terpineol, 3-octanol and linalool. We include these datasets into DoOR, and provide a comprehensive update of both code and data. The DoOR project has a web interface for quick queries (http://neuro.uni.kn/DoOR), and a downloadable, open source toolbox written in R, including all processed and original datasets. DoOR now gives reliable odorant-responses for nearly all Drosophila olfactory responding units, listing 693 odorants, for a total of 7381 data points.\n\nAt the time of uploading this preprint, a preview of the DoOR 2.0 webpage is available at: http://neuro.uni.kn/DoOR/2.0

Neuroscience

Neuronal actin dynamics, spine density and neuronal dendritic complexity are regulated by CAP2

Actin remodeling is indispensable for dendritic spine development, morphology and density which signify learning, memory and motor skills. CAP2 is a regulator of actin dynamics through sequestering G-actin and severing F-actin. In a mouse model, ablation of CAP2 leads to cardiovascular defects and delayed wound healing. This report investigates the role of CAP2 in the brain using Cap2gt/gt mice. Dendritic spine density and neuronal dendritic length were altered in Cap2gt/gt. This was accompanied by increased F-actin content and F-actin accumulation in cultured Cap2gt/gt neurons. In membrane depolarization assays, Cap2gt/gt synaptosomes exhibit an impaired F/G actin ratio, indicating altered actin dynamics. We show an interaction between CAP2 and n-cofilin, presumably mediated through the C-terminal domain of CAP2 and is cofilin ser3 phosphorylation dependent. In vivo, the consequences of this interaction were altered phosphorylated cofilin levels and formation of cofilin aggregates in the neurons. Thus, our studies identify a novel role of CAP2 in neuronal development and neuronal actin dynamics.

Neuroscience

Untangling cortico-striatal connectivity and cross-frequency coupling in L-DOPA-induced dyskinesia

We simultaneously recorded local field potentials in the primary motor cortex and sensorimotor striatum in awake, freely behaving, 6-OHDA lesioned hemi-parkinsonian rats in order to study the features directly related to pathological states such as parkinsonian state and levodopa-induced dyskinesia. We analysed the spectral characteristics of the obtained signals and observed that during dyskinesia the most prominent feature was a relative power increase in the high gamma frequency range at around 80 Hz, while for the parkinsonian state it was in the beta frequency range. Here we show that during both pathological states effective connectivity in terms of Granger causality is bidirectional with an accent on the striatal influence on the cortex. In the case of dyskinesia, we also found a high increase in effective connectivity at 80 Hz. In order to further understand the 80- Hz phenomenon, we performed cross-frequency analysis and observed characteristic patterns in the case of dyskinesia but not in the case of the parkinsonian state or the control state. We noted a large decrease in the modulation of the amplitude at 80 Hz by the phase of low frequency oscillations (up to ~10 Hz) across both structures in the case of dyskinesia. This may suggest a lack of coupling between the low frequency activity of the recorded network and the group of neurons active at ~80 Hz.

Neuroscience

Complete firing-rate response of neurons with complex intrinsic dynamics

The response of a neuronal population over a space of inputs depends on the intrinsic properties of its constituent neurons. Two main modes of single neuron dynamics-integration and resonance-have been distinguished. While resonator cell types exist in a variety of brain areas, few models incorporate this feature and fewer have investigated its effects. To understand better how a resonators frequency preference emerges from its intrinsic dynamics and contributes to its local areas population firing rate dynamics, we analyze the dynamic gain of an analytically solvable two-degree of freedom neuron model. In the Fokker-Planck approach, the dynamic gain is intractable. The alternative Gauss-Rice approach lifts the resetting of the voltage after a spike. This allows us to derive a complete expression for the dynamic gain of a resonator neuron model in terms of a cascade of filters on the input. We find six distinct response types and use them to fully characterize the routes to resonance across all values of the relevant timescales. We find that resonance arises primarily due to slow adaptation with an intrinsic frequency acting to sharpen and adjust the location of the resonant peak. We determine the parameter regions for the existence of an intrinsic frequency and for subthreshold and spiking resonance, finding all possible intersections of the three. The expressions and analysis presented here provide an account of how intrinsic neuron dynamics shape dynamic population response properties and can facilitate the construction of an exact theory of correlations and stability of population activity in networks containing populations of resonator neurons.\n\nAuthor SummaryDynamic gain, the amount by which features at specific frequencies in the input to a neuron are amplified or attenuated in its output spiking, is fundamental for the encoding of information by neural populations. Most studies of dynamic gain have focused on neurons without intrinsic degrees of freedom exhibiting integrator-type subthreshold dynamics. Many neuron types in the brain, however, exhibit complex subthreshold dynamics such as resonance, found for instance in cortical interneurons, stellate cells, and mitral cells. A resonator neuron has at least two degrees of freedom for which the classical Fokker-Planck approach to calculating the dynamic gain is largely intractable. Here, we lift the voltage-reset rule after a spike, allowing us to derive for the first time a complete expression of the dynamic gain of a resonator neuron model. We find the gain can exhibit only six shapes. The resonant ones have peaks that become large due to intrinsic adaptation and become sharp due to an intrinsic frequency. A resonance can nevertheless result from either property. The analysis presented here helps explain how intrinsic neuron dynamics shape population-level response properties and provides a powerful tool for developing theories of inter-neuron correlations and dynamic responses of neural populations.

Neuroscience

Inferred Model of the Prefrontal Cortex Activity Unveils Cell Assemblies and Memory Replay

Cell assemblies are thought to be the units of information representation in the brain, yet their detection from experimental data is arduous. Here, we propose to infer effective coupling networks and model distributions for the activity of simultaneously recorded neurons in prefrontal cortex, during the performance of a decision-making task, and during preceding and following sleep epochs. Our approach, inspired from statistical physics, allows us to define putative cell assemblies as the groups of co-activated neurons in the models of the three recorded epochs. It reveals the existence of task-related changes of the effective couplings between the sleep epochs. The assemblies which strongly coactivate during the task epoch are found to replay during subsequent sleep, in correspondence to the changes of the inferred network. Across sessions, a variety of different network scenarios is observed, providing insight in cell assembly formation and replay.\n\nAuthor SummaryMemories are thought to be represented in the brain through groups of coactivating neurons, the so-called cell assemblies. We propose an approach to identify cell assemblies from multi-electrode recordings of neural activity in vivo, and apply it to the prefrontal cortex activity of a behaving rat. Our statistical physics inspired approach consists in inferring effective interactions between the recorded cells, which reproduce the correlations in their spiking activities. The analysis of the effective interaction networks and of the model distributions allows us to identify cell assemblies, which strongly co-activate when the rat is learning, and also during subsequent sleep. Our approach is thus capable of providing detailed insights in cell-assembly formation and replay, crucial for memory consolidation.

Neuroscience

Hemodynamic response function in resting brain: disambiguating neural events and autonomic effects

It has been shown that resting state brain dynamics can be characterized by looking at sparse blood-oxygen-level dependent (BOLD) events, which can be retrieved by point process analysis. Cardiac activity can also induce changes in the BOLD signal, thus affect both the number of these events and the mapping between neural events and BOLD signal, namely the hemodynamic response. To isolate neural activity and autonomic effects, we compare the resting state hemodynamic response retrieved by means of a point process analysis with and without deconvolving the cardiac fluctuations. Brainstem and the surrounding cortical area (such as precuneus, insula etc.) are found to be significantly affected by cardiac pulses. Methodological and physiological implications are then discussed.

Neuroscience

Projection-specific visual feature encoding by layer 5 cortical subnetworks.

Primary neocortical sensory areas act as central hubs, distributing afferent information to numerous cortical and subcortical structures. However, it remains unclear whether each downstream target receives distinct versions of sensory information. We used in vivo calcium imaging combined with retrograde tracing to monitor visual response properties of three distinct subpopulations of projection neurons in primary visual cortex. While there is overlap across the groups, on average corticotectal (CT) cells exhibit lower contrast thresholds and broader tuning for orientation and spatial frequency in comparison to corticostriatal (CS) cells, while corticocortical (CC) cells have intermediate properties. Noise correlational analyses support the hypothesis that CT cells integrate information across diverse layer 5 populations, whereas CS and CC cells form more selectively interconnected groups. Overall, our findings demonstrate the existence of functional subnetworks within layer 5 that may differentially route visual information to behaviorally relevant downstream targets.

Neuroscience

Frequency-dependent representation of reinforcement-related information in the human medial and lateral prefrontal cortex

The feedback-related negativity (FRN) is a commonly observed potential in scalp electroencephalography (EEG) studies related to the valence of feedback about a subjects performance. This potential classically manifests as a negative deflection in medial frontocentral EEG contacts following negative feedback. Recent work has shown prominence of theta power in the spectral composition of the FRN, placing it within the larger class of \"frontal midline theta\" cognitive control signals. Although the dorsal anterior cingulate cortex (dACC) is thought to be the cortical generator of the FRN, conclusive data regarding its origin and propagation are lacking. Here we examine intracranial electrophysiology from the human medial and lateral prefrontal cortex (PFC) in order to better understand the anatomical localization and communication patterns of the FRN. We show that the FRN is evident in both low- and high-frequency local field potentials (LFPs) recorded on electrocorticography. The FRN is larger in medial compared to lateral PFC, and coupling between theta band phase and high frequency LFP power is also greater in medial PFC. Using Granger causality and conditional mutual information analyses, we provide evidence that feedback-related information propagates from medial to lateral PFC, and that this information transfer oscillates with theta-range periodicity. These results provide evidence for the dACC as the cortical source of the FRN, provide insight into the local computation of frontal midline theta, and have implications for reinforcement learning models of cognitive control.\n\nSignificance Statement: Using intracranial electrophysiology in humans, this work addresses questions about a frequently studied feedback-related electroencephalographic signal, illuminating anatomical and functional properties of the representation of feedback-related reinforcement during decision-making across the medial to lateral extent of the human prefrontal cortex.

Neuroscience

Rapid three dimensional two photon neural population scanning

Recording the activity of neural populations at high sampling rates is a fundamental requirement for understanding computation in neural circuits. Two photon microscopy provides one promising approach towards this. However, neural circuits are three dimensional, and functional imaging in two dimensions fails to capture the 3D nature of neural dynamics. Electrically tunable lenses (ETLs) provide a simple and cheap method to extend laser scanning microscopy into the relatively unexploited third dimension. We have therefore incorporated them into our Adaptive Spiral Scanning (SSA) algorithm, which calculates kinematically efficient scanning strategies using radially modulated spiral paths. We characterised the response of the ETL, incorporated its dynamics using MATLAB models of the SSA algorithm and tested the models on populations of Izhikevich neurons of varying size and density. From this, we show that our algorithms can theoretically at least achieve sampling rates of 36.2Hz compared to 21.6Hz previously reported for 3D scanning techniques.

Neuroscience

Multi-Unit Activity contains information about spatial stimulus structure in mouse primary visual cortex

This study investigates the spatial and directional tuning of Multi-Unit Activity (MUA) in mouse primary visual cortex and how MUA can reflect spatiotemporal structures contained in moving gratings. Analysis of multi-shank laminar electrophysiological recordings from mouse primary visual cortex indicates a directional preference for moving gratings around 180{degrees}, while preferred spatial frequency peaks around 0.02 cycles per degree, which is similar as reported in single-unit studies. Using only features from MUA, we further achieved a significant performance in decoding spatial frequency or direction of moving gratings, with average decoding performances of up to 58.54% for 8 directions, and 44% correctly identified spatial frequencies against chance level of 16.7%.

Neuroscience

Spike Detection Using FRI Methods and Protein Calcium Sensors: Performance Analysis and Comparisons

Fast and accurate detection of action potentials from neurophysiological data is key to the study of information processing in the nervous system. Previous work has shown that finite rate of innovation (FRI) theory can be used to successfully reconstruct spike trains from noisy calcium imaging data. This is due to the fact that calcium imaging data can be modeled as streams of decaying exponentials which are a subclass of FRI signals. Recent progress in the development of genetically encoded calcium indicators (GECIs) has produced protein calcium sensors that exceed the sensitivity of the synthetic dyes traditionally used in calcium imaging experiments. In this paper, we compare the suitability for spike detection of the kinetics of a new family of GECIs (the GCaMP6 family) with the synthetic dye Oregon Green BAPTA-1. We demonstrate the high performance of the FRI algorithm on surrogate data for each calcium indicator and we calculate the Cramer-Rao lower bound on the uncertainty of the position of a detected spike in calcium imaging data for each calcium indicator.

Neuroscience

An integrated homeostatic reinforcement learning theory of motivation explains the transition to cocaine addiction

Drugs of abuse implicate both reward learning and homeostatic regulation mechanisms of the brain. Theories of addiction, thus, have mostly depicted this phenomenon as pathology in either habit-based learning system or homeostatic mechanisms. Showing the limits of those accounts, we hypothesize that compulsive drug seeking arises from drugs hijacking a system that integrates homeostatic regulation mechanism with goal-directed action/behavior. Building upon a recently developed homeostatic reinforcement learning theory, we present a computational theory proposing that cocaine reinforces goal-directed drug-seeking due to its rapid homeostatic corrective effect, whereas its chronic use induces slow and long-lasting changes in homeostatic setpoint. Our theory accounts for key behavioral and neurobiological features of addiction, most notably, escalation of cocaine use, drug-primed craving and relapse, and individual differences underlying susceptibility to addiction. The theory also generates unique predictions about the mechanisms of cocaine-intake regulation and about cocaine-primed craving and relapse that are confirmed by new experiments.\n\nSignificanceChronic use of addictive drugs renders increased motivation in planning to obtain and consume the drugs, despite their adverse social, occupational, and health consequences. It is as if addicts gradually develop a strong need for the drug and use their cognitive abilities and the knowledge of their environment in order to fulfil that need. In this paper, we build a mathematical model of this conception of addiction and show through quantitative simulations that such a model actually behaves in the same way that human addicts or laboratory animals that are exposed to cocaine behave. For example, the model shows gradually increasing motivation for drugs, relapse after long periods of abstinence, and individual differences in susceptibility to addiction.

Neuroscience

Visual features as stepping stones toward semantics: Explaining object similarity in IT and perception with non-negative least squares.

Object similarity, in brain representations and conscious perception, must reflect a combination of the visual appearance of the objects on the one hand and the categories the objects belong to on the other. Indeed, visual object features and category membership have each been shown to contribute to the object representation in human inferior temporal (IT) cortex, as well as to object-similarity judgments. However, the explanatory power of features and categories has not been directly compared. Here, we investigate whether the IT object representation and similarity judgments are best explained by a categorical or a feature-based model. We use rich models (> 100 dimensions) generated by human observers for a set of 96 real-world object images. The categorical model consists of a hierarchically nested set of category labels (such as \"human\", \"mammal\", \"animal\"). The feature model includes both object parts (such as \"eye\", \"tail\", \"handle\") and other descriptive features (such as \"circular\", \"green\", \"stubbly\"). We used nonnegative least squares to fit the models to the brain representations (estimated from functional magnetic resonance imaging data) and to similarity judgments. Model performance was estimated on held-out images not used in fitting. Both models explained significant variance in IT and the amounts explained were not significantly different. The combined model did not explain significant additional IT variance, suggesting that it is the shared model variance (features correlated with categories, categories correlated with features) that best explains IT. The similarity judgments were almost fully explained by the categorical model, which explained significantly more variance than the feature-based model. The combined model did not explain significant additional variance in the similarity judgments. Our findings suggest that IT uses features that help to distinguish categories as stepping stones toward a semantic representation. Similarity judgments contain additional categorical variance that is not explained by visual features, reflecting a higher-level more purely semantic representation.

Neuroscience