Synaptic connections between layer 5B pyramidal neurons in mouse somatosensory cortex are independent of apical dendrite bundling

A dendritic mechanism for balancing synaptic flexibility and stability

Biological and artificial neural networks learn by modifying synaptic weights, but it is unclear how these systems retain previous knowledge and also acquire new information. Here, we show that cortical pyramidal neurons can solve this plasticity-versus-stability dilemma by differentially regulating synaptic plasticity at distinct dendritic compartments. Oblique dendrites of adult mouse layer 5 cortical pyramidal neurons selectively receive monosynaptic thalamic input, integrate linearly, and lack burst-timing synaptic potentiation. In contrast, basal dendrites, which do not receive thalamic input, exhibit conventional NMDA receptor (NMDAR)-mediated supralinear integration and synaptic potentiation. Congruently, spiny synapses on oblique branches show decreased structural plasticity in vivo. The selective decline in NMDAR activity and expression at synapses on oblique dendrites is controlled by a critical period of visual experience. Our results demonstrate a biological mechanism for how single neurons can safeguard a set of inputs from ongoing plasticity by altering synaptic properties at distinct dendritic domains.

SRT-Server: powering the analysis of spatial transcriptomic data

BACKGROUND

Spatial resolved transcriptomics (SRT) encompasses a rapidly developing set of technologies that enable the measurement of gene expression in tissue while retaining spatial localization information. SRT technologies and the enabled SRT studies have provided unprecedent insights into the structural and functional underpinnings of complex tissues. As SRT technologies have advanced and an increasing number of SRT studies have emerged, numerous sophisticated statistical and computational methods have been developed to facilitate the analysis and interpretation of SRT data. However, despite the growing popularity of SRT studies and the widespread availability of SRT analysis methods, analysis of large-scale and complex SRT datasets remains challenging and not easily accessible to researchers with limited statistical and computational backgrounds.

RESULTS

Here, we present SRT-Server, the first webserver designed to carry out comprehensive SRT analyses for a wide variety of SRT technologies while requiring minimal prior computational knowledge. Implemented with cutting-edge web development technologies, SRT-Server is user-friendly and features multiple analytic modules that can perform a range of SRT analyses. With a flowchart-style interface, these different analytic modules on the SRT-Server can be dragged into the main panel and connected to each other to create custom analytic pipelines. SRT-Server then automatically executes the desired analyses, generates corresponding figures, and outputs results-all without requiring prior programming knowledge. We demonstrate the advantages of SRT-Server through three case studies utilizing SRT data collected from two common platforms, highlighting its versatility and values to researchers with varying analytic expertise.

CONCLUSIONS

Overall, SRT-Server presents a user-friendly, efficient, effective, secure, and expandable solution for SRT data analysis, opening new doors for researchers in the field. SRT-Server is freely available at https://spatialtranscriptomicsanalysis.com/ .

Visual evoked feedforward-feedback traveling waves organize neural activity across the cortical hierarchy in mice

Sensory processing is distributed among many brain regions that interact via feedforward and feedback signaling. Neuronal oscillations have been shown to mediate intercortical feedforward and feedback interactions. Yet, the macroscopic structure of the multitude of such oscillations remains unclear. Here, we show that simple visual stimuli reliably evoke two traveling waves with spatial wavelengths that cover much of the cerebral hemisphere in awake mice. 30-50 Hz feedforward waves arise in primary visual cortex (V1) and propagate rostrally, while 3-6 Hz feedback waves originate in the association cortex and flow caudally. The phase of the feedback wave modulates the amplitude of the feedforward wave and synchronizes firing between V1 and parietal cortex. Altogether, these results provide direct experimental evidence that visual evoked traveling waves percolate through the cerebral cortex and coordinate neuronal activity across broadly distributed networks mediating visual processing.

The impact of neuron morphology on cortical network architecture

The neurons in the cerebral cortex are not randomly interconnected. This specificity in wiring can result from synapse formation mechanisms that connect neurons, depending on their electrical activity and genetically defined identity. Here, we report that the morphological properties of the neurons provide an additional prominent source by which wiring specificity emerges in cortical networks. This morphologically determined wiring specificity reflects similarities between the neurons’ axo-dendritic projections patterns, the packing density, and the cellular diversity of the neuropil. The higher these three factors are, the more recurrent is the topology of the network. Conversely, the lower these factors are, the more feedforward is the network’s topology. These principles predict the empirically observed occurrences of clusters of synapses, cell type-specific connectivity patterns, and nonrandom network motifs. Thus, we demonstrate that wiring specificity emerges in the cerebral cortex at subcellular, cellular, and network scales from the specific morphological properties of its neuronal constituents.

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Neuronal network architectures reflect the morphologies of their constituents

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Morphology predicts nonrandom connectivity from subcellular to network scales

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Morphology predicts connectivity patterns consistent with those observed empirically

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Neuron morphology is a major source for wiring specificity in the cerebral cortex

Activation of Corticothalamic Layer 6 Cells Decreases Angular Tuning in Mouse Barrel Cortex

In the mouse whisker system, the contribution of L6 corticothalamic cells (L6 CT) to cortical and thalamic processing of the whisker deflection direction was investigated. A genetically defined population of L6 CT cells project to infragranular GABAergic interneurons that hyperpolarize neurons in somatosensory barrel cortex (BC). Optogenetic activation of these neurons switched BC to an adapted mode in which excitatory cells lost their angular tuning. In contrast, however, this was not the case with a general activation of inhibitory interneurons via optogenetic activation of Gad2-expressing cells. The decrease in angular tuning, when L6 CT cells were activated, was due to changes in cortical inhibition, and not inherited from changes in the thalamic output. Furthermore, L6 CT driven cortical inhibition, but not the general activation of GABAergic interneurons, abolished adaptation to whisker responses. In the present study, evidence is presented that a subpopulation of L6 CT activates a specific circuit of GABAergic interneurons that will predispose neocortex toward processing of tactile information requiring multiple whisker touches, such as in a texture discrimination task.

Slow Dynamics in Microcolumnar Gap Junction Network of Developing Neocortical Pyramidal Neurons

Gap junctions mediate electrical coupling between neurons and modulate their firing activity. In mouse neocortical layer 5, the major types of pyramidal neurons organize into cell type-specific microcolumns that exhibit modular neuronal activity. During cortical development, microcolumn neurons are electrically coupled in a cell type-specific manner at the stage of synaptogenesis, forming a dense network of gap junctions. However, modulation of neuronal activity by the gap junction network has not been examined. Here, we show that the electrical coupling induces amplification and slow synchronization of action potentials. This slow synchronization is mediated by electrical transmission that is an order of magnitude slower than that of gap junction-coupled neurons of other types. Theoretical and structural analyses suggested that apical dendrites are a major site of electrical coupling, providing slow electrical transmission. These results suggest that the gap junction network organizes neuronal activity of developing cortical circuit modules with unique slow dynamics.

The development of local circuits in the neocortex: recent lessons from the mouse visual cortex

Precise synaptic connections among neurons in the neocortex generate the circuits that underlie a broad repertoire of cortical functions including perception, learning and memory, and complex problem solving. The specific patterns and properties of these synaptic connections are fundamental to the computations cortical neurons perform. How such specificity arises in cortical circuits has remained elusive. Here, we first consider the cell-type, subcellular and synaptic specificity required for generating mature patterns of cortical connectivity and responses. Next, we focus on recent progress in understanding how the synaptic connections among excitatory cortical projection neurons are established during development using the primary visual cortex of the mouse as a model.

Hyperexcitability of the network contributes to synchronization processes in the human epileptic neocortex

KEY POINTS

Hyperexcitability and hypersynchrony of neuronal networks are thought to be linked to the generation of epileptic activity in both humans and animal models. Here we show that human epileptic postoperative neocortical tissue is able to generate two different types of synchronies in vitro. Epileptiform bursts occurred only in slices derived from epileptic patients and were hypersynchronous events characterized by high levels of excitability. Spontaneous population activity emerged in both epileptic and non-epileptic tissue, with a significantly lower degree of excitability and synchrony, and could not be linked to epilepsy. These results help us to understand better the role of excitatory and inhibitory neuronal circuits in the generation of population events, and to define the subtle border between physiological and pathological synchronies.

ABSTRACT

Interictal activity is a hallmark of epilepsy diagnostics and is linked to neuronal hypersynchrony. Little is known about perturbations in human epileptic neocortical microcircuits, and their role in generating pathological synchronies. To explore hyperexcitability of the human epileptic network, and its contribution to convulsive activity, we investigated an in vitro model of synchronous burst activity spontaneously occurring in postoperative tissue slices derived from patients with or without preoperative clinical and electrographic manifestations of epileptic activity. Human neocortical slices generated two types of synchronies. Interictal-like discharges (classified as epileptiform events) emerged only in epileptic samples, and were hypersynchronous bursts characterized by considerably elevated levels of excitation. Synchronous population activity was initiated in both epileptic and non-epileptic tissue, with a significantly lower degree of excitability and synchrony, and could not be linked to epilepsy. However, in pharmacoresistant epileptic tissue, a higher percentage of slices exhibited population activity, with higher local field potential gradient amplitudes. More intracellularly recorded neurons received depolarizing synaptic potentials, discharging more reliably during the events. Light and electron microscopic examinations showed slightly lower neuron densities and higher densities of excitatory synapses in the human epileptic neocortex. Our data suggest that human neocortical microcircuits retain their functionality and plasticity in vitro, and can generate two significantly different synchronies. We propose that population bursts might not be pathological events while interictal-like discharges may reflect the epileptogenicity of the human cortex. Our results show that hyperexcitability characterizes the human epileptic neocortical network, and that it is closely related to the emergence of synchronies.

From single cells and single columns to cortical networks: dendritic excitability, coincidence detection and synaptic transmission in brain slices and brains

Although patch pipettes were initially designed to record extracellularly the elementary current events from muscle and neuron membranes, the whole-cell and loose cell-attached recording configurations proved to be useful tools for examination of signalling within and between nerve cells. In this Paton Prize Lecture, I will initially summarize work on electrical signalling within single neurons, describing communication between the dendritic compartments, soma and nerve terminals via forward- and backward-propagating action potentials. The newly discovered dendritic excitability endows neurons with the capacity for coincidence detection of spatially separated subthreshold inputs. When these are occurring during a time window of tens of milliseconds, this information is broadcast to other cells by the initiation of bursts of action potentials (AP bursts). The occurrence of AP bursts critically impacts signalling between neurons that are controlled by target-cell-specific transmitter release mechanisms at downstream synapses even in different terminals of the same neuron. This can, in turn, induce mechanisms that underly synaptic plasticity when AP bursts occur within a short time window, both presynaptically in terminals and postsynaptically in dendrites. A fundamental question that arises from these findings is: 'what are the possible functions of active dendritic excitability with respect to network dynamics in the intact cortex of behaving animals?' To answer this question, I highlight in this review the functional and anatomical architectures of an average cortical column in the vibrissal (whisker) field of the somatosensory cortex (vS1), with an emphasis on the functions of layer 5 thick-tufted cells (L5tt) embedded in this structure. Sensory-evoked synaptic and action potential responses of these major cortical output neurons are compared with responses in the afferent pathway, viz. the neurons in primary somatosensory thalamus and in one of their efferent targets, the secondary somatosensory thalamus. Coincidence-detection mechanisms appear to be implemented in vivo as judged from the occurrence of AP bursts. Three-dimensional reconstructions of anatomical projections suggest that inputs of several combinations of thalamocortical projections and intra- and transcolumnar connections, specifically those from infragranular layers, could trigger active dendritic mechanisms that generate AP bursts. Finally, recordings from target cells of a column reveal the importance of AP bursts for signal transfer to these cells. The observations lead to the hypothesis that in vS1 cortex, the sensory afferent sensory code is transformed, at least in part, from a rate to an interval (burst) code that broadcasts the occurrence of whisker touch to different targets of L5tt cells. In addition, the occurrence of pre- and postsynaptic AP bursts may, in the long run, alter touch representation in cortex.

Inhibitory Circuits in Cortical Layer 5

Inhibitory neurons play a fundamental role in cortical computation and behavior. Recent technological advances, such as two photon imaging, targeted in vivo recording, and molecular profiling, have improved our understanding of the function and diversity of cortical interneurons, but for technical reasons most work has been directed towards inhibitory neurons in the superficial cortical layers. Here we review current knowledge specifically on layer 5 (L5) inhibitory microcircuits, which play a critical role in controlling cortical output. We focus on recent work from the well-studied rodent barrel cortex, but also draw on evidence from studies in primary visual cortex and other cortical areas. The diversity of both deep inhibitory neurons and their pyramidal cell targets make this a challenging but essential area of study in cortical computation and sensory processing.

Detection and spatial characterization of minicolumnarity in the human cerebral cortex

BACKGROUND

Spatial characterization of vertical organization of neurons in human cerebral cortex, cortical columnarity or minicolumns, and its possible association with various psychiatric and neurological diseases has been investigated for many years.

NEW METHOD

In this study, we obtained 3D coordinates of disector sampled cells from layer III of Brodmann area 4 of the human cerebral cortex using light microscopy and 140-μm-thick glycolmethacrylate sections. A new analytical tool called cylindrical K-function was applied for spatial point pattern analysis of 3D datasets to see whether there is a spatially organized columnar structure. In order to demonstrate the behaviour of the cylindrical K-function, the result from brain tissues was compared with two models: A homogeneous Poisson process exhibiting complete spatial randomness, and a Poisson line cluster point process. The latter is a point process model in 3D space, which exhibits spatial structure of points similar to minicolumns.

RESULTS

The data show in three out of four samples nonrandom patterns in the 3D neuronal positions with the direction of minicolumns perpendicular to the pial surface of the brain - without a priori assuming the existence of minicolumns.

COMPARISON WITH EXISTING METHODS

Studies on columnarity are difficult and have mainly been based on two-dimensional images analysis of thin sections of the cerebral cortex with the a priori assumption that minicolumns existed.

CONCLUSIONS

A clear difference from complete spatial randomness in the data could be detected with the new tool, the cylindrical K-function, although classical functional summary statistics are less useful in this connection.

Saturated Reconstruction of a Volume of Neocortex

We describe automated technologies to probe the structure of neural tissue at nanometer resolution and use them to generate a saturated reconstruction of a sub-volume of mouse neocortex in which all cellular objects (axons, dendrites, and glia) and many sub-cellular components (synapses, synaptic vesicles, spines, spine apparati, postsynaptic densities, and mitochondria) are rendered and itemized in a database. We explore these data to study physical properties of brain tissue. For example, by tracing the trajectories of all excitatory axons and noting their juxtapositions, both synaptic and non-synaptic, with every dendritic spine we refute the idea that physical proximity is sufficient to predict synaptic connectivity (the so-called Peters' rule). This online minable database provides general access to the intrinsic complexity of the neocortex and enables further data-driven inquiries.

Hebbian and Homeostatic Plasticity Mechanisms in Regular Spiking and Intrinsic Bursting Cells of Cortical Layer 5

Layer 5 contains the major projection neurons of the neocortex and is composed of two major cell types: regular spiking (RS) cells, which have cortico-cortical projections, and intrinsic bursting cells (IB), which have subcortical projections. Little is known about the plasticity processes and specifically the molecular mechanisms by which these two cell classes develop and maintain their unique integrative properties. In this study, we find that RS and IB cells show fundementally different experience-dependent plasticity processes and integrate Hebbian and homeostatic components of plasticity differently. Both RS and IB cells showed TNFα-dependent homeostatic plasticity in response to sensory deprivation, but IB cells were capable of a much faster synaptic depression and homeostatic rebound than RS cells. Only IB cells showed input-specific potentiation that depended on CaMKII autophosphorylation. Our findings demonstrate that plasticity mechanisms are not uniform within the neocortex, even within a cortical layer, but are specialized within subcircuits.

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RS and IB cells exhibit TNFα-dependent homeostatic recovery from depression

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IB cells exhibit CaMKII-dependent, input-specific potentiation, but RS cells do not

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TNFα-dependent homeostatic plasticity persists into adulthood in cortical layer 5

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mEPSCs of RS and IB cells mirror changes in their sensory evoked spike firing rates

A computational model for the loss of neuronal organization in microcolumns

A population of neurons in the cerebral cortex of humans and other mammals organize themselves into vertical microcolumns perpendicular to the pial surface. Anatomical changes to these microcolumns have been correlated with neurological diseases and normal aging; in particular, in area 46 of the rhesus monkey brain, the strength of microcolumns was shown to decrease with age. These changes can be caused by alterations in the spatial distribution of the neurons in microcolumns and/or neuronal loss. Using a three-dimensional computational model of neuronal arrangements derived from thin tissue sections and validated in brain tissue from rhesus monkeys, we show that neuronal loss is inconsistent with the findings in aged individuals. In contrast, a model of simple random neuronal displacements, constrained in magnitude by restorative harmonic forces, is consistent with observed changes and provides mechanistic insights into the age-induced loss of microcolumnar structure. Connection of the model to normal aging and disease are discussed.

Structure-function analysis of genetically defined neuronal populations

Morphological and functional classification of individual neurons is a crucial aspect of the characterization of neuronal networks. Systematic structural and functional analysis of individual neurons is now possible using transgenic mice with genetically defined neurons that can be visualized in vivo or in brain slice preparations. Genetically defined neurons are useful for studying a particular class of neurons and also for more comprehensive studies of the neuronal content of a network. Specific subsets of neurons can be identified by fluorescence imaging of enhanced green fluorescent protein (eGFP) or another fluorophore expressed under the control of a cell-type-specific promoter. The advantages of such genetically defined neurons are not only their homogeneity and suitability for systematic descriptions of networks, but also their tremendous potential for cell-type-specific manipulation of neuronal networks in vivo. This article describes a selection of procedures for visualizing and studying the anatomy and physiology of genetically defined neurons in transgenic mice. We provide information about basic equipment, reagents, procedures, and analytical approaches for obtaining three-dimensional (3D) cell morphologies and determining the axonal input and output of genetically defined neurons. We exemplify with genetically labeled cortical neurons, but the procedures are applicable to other brain regions with little or no alterations.

Axon initial segment structural plasticity in animal models of genetic and acquired epilepsy

A novel form of neuronal plasticity, occurring at the axon initial segment (AIS), has recently been described. Lengthening of the AIS and movement away from the soma are consequences of changes in neuronal input and result in alterations in neuronal excitability. We hypothesised that AIS plasticity may play a role in epilepsy, due to chronic changes in neuronal activity. Immunohistochemistry and confocal microscopy were used to analyse AIS length and position in pyramidal neurons in deep layer 5 of the somatosensory cortex from 5 mice with genetic epilepsy and 4 controls, and from 3 rats subjected to amygdala kindling and 3 controls. The effect of a subtle alteration of AIS position was modelled computationally. We identified a difference in the position of the AIS in animals with seizures: in mice the AIS was positioned 0.2 μm further away from the soma, and in rats the AIS was positioned 0.6 μm closer to the soma compared with controls. Computational modelling indicated that a subtle alteration in AIS position could result in a change in action potential firing threshold. The identification of AIS plasticity in animal models of epilepsy is significant in furthering our understanding of the pathophysiological mechanisms involved in this disorder.

RipleyGUI: software for analyzing spatial patterns in 3D cell distributions

The true revolution in the age of digital neuroanatomy is the ability to extensively quantify anatomical structures and thus investigate structure-function relationships in great detail. To facilitate the quantification of neuronal cell patterns we have developed RipleyGUI, a MATLAB-based software that can be used to detect patterns in the 3D distribution of cells. RipleyGUI uses Ripley's K-function to analyze spatial distributions. In addition the software contains statistical tools to determine quantitative statistical differences, and tools for spatial transformations that are useful for analyzing non-stationary point patterns. The software has a graphical user interface making it easy to use without programming experience, and an extensive user manual explaining the basic concepts underlying the different statistical tools used to analyze spatial point patterns. The described analysis tool can be used for determining the spatial organization of neurons that is important for a detailed study of structure-function relationships. For example, neocortex that can be subdivided into six layers based on cell density and cell types can also be analyzed in terms of organizational principles distinguishing the layers.

Distinct developmental principles underlie the formation of ipsilateral and contralateral whisker-related axonal patterns of layer 2/3 neurons in the barrel cortex

Axonal organizations with specific patterns underlie the functioning of local intracortical circuitry, but their precise anatomy and development still remain elusive. Here, we selectively visualized layer 2/3 neurons using in utero electroporation and examined their axonal organization in the barrel cortex contralateral to the electroporated side. We found that callosal axons run preferentially in septal regions of layer 4 and showed a whisker-related pattern in the contralateral barrel cortex in rats and mice. In addition, presynaptic marker proteins were found in this whisker-related axonal organization. Although the whisker-related patterns were observed in both the ipsilateral and contralateral barrel cortex, we found a difference in their developmental processes. While the formation of the whisker-related pattern in the ipsilateral cortex consisted of two distinct steps, that in the contralateral cortex did not have the 1st step, in which the axons were diffusely distributed without preference to septal or barrel regions. We also found that these more diffuse axons ran close to radial glial fibers. Together, our results uncovered a whisker-related axonal pattern of callosal axons and two independent developmental processes involved in the formation of the axonal trajectories of layer 2/3 neurons.

A synaptic organizing principle for cortical neuronal groups

Neuronal circuitry is often considered a clean slate that can be dynamically and arbitrarily molded by experience. However, when we investigated synaptic connectivity in groups of pyramidal neurons in the neocortex, we found that both connectivity and synaptic weights were surprisingly predictable. Synaptic weights follow very closely the number of connections in a group of neurons, saturating after only 20% of possible connections are formed between neurons in a group. When we examined the network topology of connectivity between neurons, we found that the neurons cluster into small world networks that are not scale-free, with less than 2 degrees of separation. We found a simple clustering rule where connectivity is directly proportional to the number of common neighbors, which accounts for these small world networks and accurately predicts the connection probability between any two neurons. This pyramidal neuron network clusters into multiple groups of a few dozen neurons each. The neurons composing each group are surprisingly distributed, typically more than 100 μm apart, allowing for multiple groups to be interlaced in the same space. In summary, we discovered a synaptic organizing principle that groups neurons in a manner that is common across animals and hence, independent of individual experiences. We speculate that these elementary neuronal groups are prescribed Lego-like building blocks of perception and that acquired memory relies more on combining these elementary assemblies into higher-order constructs.

Neuronal circuits with whisker-related patterns

Neuronal circuits with whisker-related patterns, such as those observed in the rodent somatosensory barrel cortex, have been widely used as a model system for investigating the anatomical organization, development and physiological roles of functional neuronal circuits. Whisker-related patterns exist not only in the barrel cortex but also in subcortical structures along the trigeminal neuraxis from the brainstem to the cortex. Here, we briefly summarize the organization, formation, and function of each neuronal circuit with whisker-related patterns, including the novel axonal trajectories that we recently found with the aid of in utero electroporation. We also discuss their biological implications as model systems for the studies of functional neuronal circuits.

Polarized targeting of L1-CAM regulates axonal and dendritic bundling in vitro

Proper axonal and dendritic bundling is essential for the establishment of neuronal connections and the synchronization of synaptic inputs, respectively. Cell adhesion molecules of the L1-CAM (L1-cell adhesion molecule) family regulate axon guidance and fasciculation, neuron migration, dendrite morphology, and synaptic plasticity. It remains unclear how these molecules play so many different roles. Here we show that polarized axon-dendrite targeting of an avian L1-CAM protein, NgCAM (neuron-glia cell adhesion molecule), can regulate the switch of bundling of the two major compartments of rat hippocampal neurons. Using a new in-vitro model for studying neurite-neurite interactions, we found that expressed axonal NgCAM induced robust axonal bundling via the trans-homophilic interaction of immunoglobulin domains. Interestingly, dendritic bundling was induced by the dendritic targeting of NgCAM, caused by either deleting its fibronectin repeats or blocking activities of protein kinases. Consistent with the NgCAM results, expression of mouse L1-CAM also induced axonal bundling and blocking kinase activities disrupted its axonal targeting. Furthermore, the trans-homophilic interaction stabilized the bundle formation, probably through recruiting NgCAM proteins to contact sites and promoting guided axon outgrowth. Taken together, our results suggest that precise localization of L1-CAM is important for establishing proper cell-cell contacts in neural circuits.

Neurotrophin-3 is involved in the formation of apical dendritic bundles in cortical layer 2 of the rat

Apical dendritic bundles from pyramidal neurons are a prominent feature of cortical neuropil but with significant area specializations. Here, we investigate mechanisms of bundle formation, focusing on layer (L) 2 bundles in rat granular retrosplenial cortex (GRS), a limbic area implicated in spatial memory. By using microarrays, we first searched for genes highly and specifically expressed in GRS L2 at postnatal day (P) 3 versus GRS L2 at P12 (respectively, before and after bundle formation), versus GRS L5 (at P3), and versus L2 in barrel field cortex (BF) (at P3). Several genes, including neurotrophin-3 (NT-3), were identified as transiently and specifically expressed in GRS L2. Three of these were cloned and confirmed by in situ hybridization. To test that NT-3-mediated events are causally involved in bundle formation, we used in utero electroporation to overexpress NT-3 in other cortical areas. This produced prominent bundles of dendrites originating from L2 neurons in BF, where L2 bundles are normally absent. Intracellular biocytin fills, after physiological recording in vitro, revealed increased dendritic branching in L1 of BF. The controlled ectopic induction of dendritic bundles identifies a new role for NT-3 and a new in vivo model for investigating dendritic bundles and their formation.

Cell type-specific thalamic innervation in a column of rat vibrissal cortex

This is the concluding article in a series of 3 studies that investigate the anatomical determinants of thalamocortical (TC) input to excitatory neurons in a cortical column of rat primary somatosensory cortex (S1). We used viral synaptophysin-enhanced green fluorescent protein expression in thalamic neurons and reconstructions of biocytin-labeled cortical neurons in TC slices to quantify the number and distribution of boutons from the ventral posterior medial (VPM) and posteromedial (POm) nuclei potentially innervating dendritic arbors of excitatory neurons located in layers (L)2–6 of a cortical column in rat somatosensory cortex. We found that 1) all types of excitatory neurons potentially receive substantial TC input (90–580 boutons per neuron); 2) pyramidal neurons in L3–L6 receive dual TC input from both VPM and POm that is potentially of equal magnitude for thick-tufted L5 pyramidal neurons (ca. 300 boutons each from VPM and POm); 3) L3, L4, and L5 pyramidal neurons have multiple (2–4) subcellular TC innervation domains that match the dendritic compartments of pyramidal cells; and 4) a subtype of thick-tufted L5 pyramidal neurons has an additional VPM innervation domain in L4. The multiple subcellular TC innervation domains of L5 pyramidal neurons may partly explain their specific action potential patterns observed in vivo. We conclude that the substantial potential TC innervation of all excitatory neuron types in a cortical column constitutes an anatomical basis for the initial near-simultaneous representation of a sensory stimulus in different neuron types.

Number and laminar distribution of neurons in a thalamocortical projection column of rat vibrissal cortex

This is the second article in a series of three studies that investigate the anatomical determinants of thalamocortical (TC) input to excitatory neurons in a cortical column of rat primary somatosensory cortex (S1). Here, we report the number and distribution of NeuN-positive neurons within the C2, D2, and D3 TC projection columns in P27 rat somatosensory barrel cortex based on an exhaustive identification of 89,834 somata in a 1.15 mm(3) volume of cortex. A single column contained 19,109 ± 444 neurons (17,560 ± 399 when normalized to a standard-size projection column). Neuron density differences along the vertical column axis delineated "cytoarchitectonic" layers. The resulting neuron numbers per layer in the average column were 63 ± 10 (L1), 2039 ± 524 (L2), 3735 ± 905 (L3), 4447 ± 439 (L4), 1737 ± 251 (L5A), 2235 ± 99 (L5B), 3786 ± 168 (L6A), and 1066 ± 170 (L6B). These data were then used to derive the layer-specific action potential (AP) output of a projection column. The estimates confirmed previous reports suggesting that the ensembles of spiny L4 and thick-tufted pyramidal neurons emit the major fraction of APs of a column. The number of APs evoked in a column by a sensory stimulus (principal whisker deflection) was estimated as 4441 within 100 ms post-stimulus.

Five points on columns

“Column,” like “gene,” has both conceptual and linguistic shortcomings. The simple question “what is a column” is not easy to answer and the word itself is not easy to replace. In the present article, I have selected five points, in no way comprehensive or canonical, but which may nevertheless serve as a prompt and aid for further discussions and re-evaluation. These are: that anatomical columns are not solid structures, that they are part of locally interdigitating systems, that any delimited column also participates in a widely distributed network, that columns are not an obligatory cortical feature, and that columns (as “modules”) occur widely in the brain in non-cortical structures. I focus on the larger scale macrocolumns, mainly from an anatomical perspective. My position is that cortical organization is inherently dynamic and likely to incorporate multiple processing styles. One can speculate that the distributed mappings within areas like piriform cortex may resemble at least one mode of neocortical processing strategy.

A cortical sparse distributed coding model linking mini- and macrocolumn-scale functionality

No generic function for the minicolumn – i.e., one that would apply equally well to all cortical areas and species – has yet been proposed. I propose that the minicolumn does have a generic functionality, which only becomes clear when seen in the context of the function of the higher-level, subsuming unit, the macrocolumn. I propose that: (a) a macrocolumn's function is to store sparse distributed representations of its inputs and to be a recognizer of those inputs; and (b) the generic function of the minicolumn is to enforce macrocolumnar code sparseness. The minicolumn, defined here as a physically localized pool of ∼20 L2/3 pyramidals, does this by acting as a winner-take-all (WTA) competitive module, implying that macrocolumnar codes consist of ∼70 active L2/3 cells, assuming ∼70 minicolumns per macrocolumn. I describe an algorithm for activating these codes during both learning and retrievals, which causes more similar inputs to map to more highly intersecting codes, a property which yields ultra-fast (immediate, first-shot) storage and retrieval. The algorithm achieves this by adding an amount of randomness (noise) into the code selection process, which is inversely proportional to an input's familiarity. I propose a possible mapping of the algorithm onto cortical circuitry, and adduce evidence for a neuromodulatory implementation of this familiarity-contingent noise mechanism. The model is distinguished from other recent columnar cortical circuit models in proposing a generic minicolumnar function in which a group of cells within the minicolumn, the L2/3 pyramidals, compete (WTA) to be part of the sparse distributed macrocolumnar code.

Whose Cortical Column Would that Be?

The cortical column has been an invaluable concept to explain the functional organization of the neocortex. While this idea was born out of experiments that cleverly combined electrophysiological recordings with anatomy, no one has ‘seen’ the anatomy of a column. All we know is that when we record through the cortex of primates, ungulates, and carnivores in a trajectory perpendicular to its surface there is a remarkable constancy in the receptive field properties of the neurons regarding one set of stimulus features. There is no obvious morphological analog for this functional architecture, in fact much of the anatomical data seems to challenge it. Here we describe historically the origins of the concept of the cortical column and the struggles of the pioneers to define the columnar architecture. We suggest that in the concept of a ‘canonical circuit’ we may find the means to reconcile the structure of neocortex with its functional architecture. The canonical microcircuit respects the known connectivity of the neocortex, and it is flexible enough to change transiently the architecture of its network in order to perform the required computations.

Spatial Point Pattern Analysis of Neurons Using Ripley's K-Function in 3D

The aim of this paper is to apply a non-parametric statistical tool, Ripley's K-function, to analyze the 3-dimensional distribution of pyramidal neurons. Ripley's K-function is a widely used tool in spatial point pattern analysis. There are several approaches in 2D domains in which this function is executed and analyzed. Drawing consistent inferences on the underlying 3D point pattern distributions in various applications is of great importance as the acquisition of 3D biological data now poses lesser of a challenge due to technological progress. As of now, most of the applications of Ripley's K-function in 3D domains do not focus on the phenomenon of edge correction, which is discussed thoroughly in this paper. The main goal is to extend the theoretical and practical utilization of Ripley's K-function and corresponding tests based on bootstrap resampling from 2D to 3D domains.

Dendritic bundles, minicolumns, columns, and cortical output units

THE SEARCH FOR THE FUNDAMENTAL BUILDING BLOCK OF THE CEREBRAL CORTEX HAS HIGHLIGHTED THREE STRUCTURES, PERPENDICULAR TO THE CORTICAL SURFACE: (i) columns of neurons with radially invariant response properties, e.g., receptive field position, sensory modality, stimulus orientation or direction, frequency tuning etc., (ii) minicolumns of radially aligned cell bodies and (iii) bundles, constituted by the apical dendrites of pyramidal neurons with cell bodies in different layers. The latter were described in detail, and sometimes quantitatively, in several species and areas. It was recently suggested that the dendritic bundles consist of apical dendrites belonging to neurons projecting their axons to specific targets. We review the concept above and suggest that another structural and computational unit of cerebral cortex is the cortical output unit, i.e., an assembly of bundles of apical dendrites and their parent cell bodies including each of the outputs to distant cortical or subcortical structures, of a given cortical locus (area or part of an area). This somato-dendritic assembly receives inputs some of which are common to the whole assembly and determine its radially invariant response properties, others are specific to one or more dendritic bundles, and determine the specific response signature of neurons in the different cortical layers and projecting to different targets.

Whisker-related axonal patterns and plasticity of layer 2/3 neurons in the mouse barrel cortex

Elucidating neuronal circuits and their plasticity in the cerebral cortex is one of the important questions in neuroscience research. Here we report novel axonal trajectories and their plasticity in the mouse somatosensory barrel cortex. We selectively visualized layer 2/3 neurons using in utero electroporation and examined the axonal trajectories of layer 2/3 neurons. We found that the axons of layer 2/3 neurons preferentially run in the septal regions of layer 4 and named this axonal pattern "barrel nets." The intensity of green fluorescent protein in the septal regions was markedly higher compared with that in barrel hollows. Focal in utero electroporation revealed that the axons in barrel nets were indeed derived from layer 2/3 neurons in the barrel cortex. During development, barrel nets became visible at postnatal day 10, which was well after the initial appearance of barrels. When whisker follicles were cauterized within 3 d after birth, the whisker-related pattern of barrel nets was altered, suggesting that cauterization of whisker follicles results in developmental plasticity of barrel nets. Our results uncover the novel axonal trajectories of layer 2/3 neurons with whisker-related patterns and their developmental plasticity in the mouse somatosensory cortex. Barrel nets should be useful for investigating the pattern formation and axonal reorganization of intracortical neuronal circuits.

Intact long-term potentiation but reduced connectivity between neocortical layer 5 pyramidal neurons in a mouse model of Rett syndrome

Mutations in MECP2 cause Rett syndrome and some related forms of mental retardation and autism. Mecp2-null mice exhibit symptoms reminiscent of Rett syndrome including deficits in learning. Previous reports demonstrated impaired long-term potentiation (LTP) in slices of symptomatic Mecp2-null mice, and decreased excitatory neurotransmission, but the causal relationship between these phenomena is unclear. Reduced plasticity could lead to altered transmission, or reduced excitatory transmission could alter the ability to induce LTP. To help distinguish these possibilities, we compared LTP induction and baseline synaptic transmission at synapses between layer 5 cortical pyramidal neurons in slices of wild-type and Mecp2-null mice. Paired recordings reveal that LTP induction mechanisms are intact in Mecp2-null connections, even after the onset of symptoms. However, fewer connections were found in Mecp2-null mice and individual connections were weaker. These data suggest that loss of MeCP2 function reduces excitatory synaptic connectivity and that this precedes deficits in plasticity.

Cell-type specific properties of pyramidal neurons in neocortex underlying a layout that is modifiable depending on the cortical area

To understand sensory representation in cortex, it is crucial to identify its constituent cellular components based on cell-type-specific criteria. With the identification of cell types, an important question can be addressed: to what degree does the cellular properties of neurons depend on cortical location? We tested this question using pyramidal neurons in layer 5 (L5) because of their role in providing major cortical output to subcortical targets. Recently developed transgenic mice with cell-type-specific enhanced green fluorescent protein labeling of neuronal subtypes allow reliable identification of 2 cortical cell types in L5 throughout the entire neocortex. A comprehensive investigation of anatomical and functional properties of these 2 cell types in visual and somatosensory cortex demonstrates that, with important exceptions, most properties appear to be cell-type-specific rather than dependent on cortical area. This result suggests that although cortical output neurons share a basic layout throughout the sensory cortex, fine differences in properties are tuned to the cortical area in which neurons reside.

Age-related reduction in microcolumnar structure correlates with cognitive decline in ventral but not dorsal area 46 of the rhesus monkey

The age-related decline in cognitive function that is observed in normal aging monkeys and humans occurs without significant loss of cortical neurons. This suggests that cognitive impairment results from subtle, sub-lethal changes in the cortex. Recently, changes in the structural coherence in mini- or microcolumns without loss of neurons have been linked to loss of function. Here we use a density map method to quantify microcolumnar structure in both banks of the sulcus principalis (prefrontal cortical area 46) of 16 (ventral) and 19 (dorsal) behaviorally tested female rhesus monkeys from 6 to 33 years of age. While total neuronal density does not change with age in either of these banks, there is a significant age-related reduction in the strength of microcolumns in both regions on the order of 40%. This likely reflects a subtle but definite loss of organization in the structure of the cortical microcolumn. The reduction in strength in ventral area 46 correlates with cognitive impairments in learning and memory while the reduction in dorsal area 46 does not. This result is congruent with published data attributing cognitive functions to ventral area 46 that are similar to our particular cognitive battery which does not optimally tap cognitive functions attributed to dorsal area 46. While the exact mechanisms underlying this loss of microcolumnar organization remain to be determined, it is plausible that they reflect age-related alterations in dendritic and/or axonal organization which alter connectivity and may contribute to age-related declines in cognitive performance.

Comparative molecular neuroanatomy of mammalian neocortex: what can gene expression tell us about areas and layers?

It is over 100 years since Brodmann proposed the homology of layer and area structure of the cerebral cortex across species. His proposal was based on the extensive comparative analyses of various mammalian brains. Although such homology is now well accepted, the recent data in our laboratory showed striking variations of gene expression patterns across areas and species. Are cortical layers and areas really homologous? If they are, to what extent and how are they similar or different? We are trying to answer these questions by identifying the homologous neuronal types common to various areas and species. Toward this goal, we started to classify the cortical pyramidal neurons by expression of particular sets of genes. By using fluorescent double in situ hybridization combined with retrograde tracers, we are characterizing the gene expression phenotypes and projection specificity of cortical excitatory neuron types. In this review, I discuss the recent findings in our laboratory in light of the past and present knowledge about cortical cell types, which provides insight to the homology (and lack thereof) of the mammalian neocortical organization.

Changes in apical dendritic structure correlate with sustained ERK1/2 phosphorylation in medial prefrontal cortex of a rat model of dopamine D1 receptor agonist sensitization

Rats lesioned with 6-hydroxydopamine (6-OHDA) as neonates exhibit behavioral and neurochemical abnormalities in adulthood that mimic Lesch-Nyhan disease, schizophrenia, and other developmental disorders of frontostriatal circuit dysfunction. In these animals a latent sensitivity to D1 agonists is maximally exposed by repeated administration of dopamine agonists in the postpubertal period (D1 priming). In neonate-lesioned, adult rats primed with SKF-38393, we found selective, persistent alterations in the morphology of pyramidal neuron apical dendrites in the prelimbic area of the medial prefrontal cortex (mPFC). In these animals, dendrite bundling patterns and the typically straight trajectories of primary dendritic shafts were disrupted, whereas the diameter of higher-order oblique branches was increased. Although not present in neonate-lesioned rats treated with saline, these morphological changes persisted at least 21 days after repeated dosing with SKF-38393, and were not accompanied by markers of neurodegenerative change. A sustained increase in phospho-ERK immunoreactivity in wavy dendritic shafts over the same period suggested a relationship between prolonged ERK phosphorylation and dendritic remodeling in D1-primed rats. In support of this hypothesis, pretreatment with the MEK1/2-ERK1/2 pathway inhibitors PD98059 or SL327, prior to each priming dose of SKF-38393, prevented the morphological changes associated with D1 priming. Together, these findings demonstrate that repeated stimulation of D1 receptors in adulthood interacts with the developmental loss of dopamine to profoundly and persistently modify neuronal signaling and dendrite morphology in the mature prefrontal cortex. Furthermore, sustained elevation of ERK activity in mPFC pyramidal neurons may play a role in guiding these morphological changes in vivo.

Generating a model of the three-dimensional spatial distribution of neurons using density maps

Microcolumns are a vertical arrangement of neocortical neurons that may constitute a fundamental computational ensemble but have been difficult to study morphologically because of the challenges of determining the three-dimensional (3D) spatial arrangements of individual neurons in the ensemble. Previously, a statistical density map method was developed to characterize microcolumns using two-dimensional (2D) coordinates of neurons from thin tissue sections. Here we extend this approach to derive the relationship between these 2D density maps and the actual 3D properties of microcolumns by creating a theoretical 3D model of cortical neurons. In seven steps, we transform a 3D initial arrangement of neurons from a crystalline lattice, with distances and neuron numbers approximating the idealized cortical microcolumn as assayed by our 2D density map analysis, into a model whose neuronal locations represent a plausible 3D arrangement of neurons in the brain. Because we constrain the transformations on the 3D model by the 2D density map properties, the transformed 3D model will exhibit properties that are consistent with experimental findings regarding microcolumnar anatomy in the brain. Moreover, because our methodology only requires the x,y locations of neurons from thin sections, it is readily accessible to any set of input data regardless of preparation or staining, from human or animals. By generating 3D model neuronal arrangements and comparing between control, aged, and diseased brain, our method can be used to test hypotheses about the effects of neurological diseases as well as normal aging on the 3D structure of microcolumns in the brain.