Reflections on the specificity of synaptic connections

Circuits and Synapses: Hypothesis, Observation, Controversy and Serendipity - An Opinion Piece

More than a century of dedicated research has resulted in what we now know, and what we think we know, about synapses and neural circuits. This piece asks to what extent some of the major advances - both theoretical and practical - have resulted from carefully considered theory, or experimental design: endeavors that aim to address a question, or to refute an existing hypothesis. It also, however, addresses the important part that serendipity and chance have played. There are cases where hypothesis driven research has resulted in important progress. There are also examples where a hypothesis, a model, or even an experimental approach - particularly one that seems to provide welcome simplification - has become so popular that it becomes dogma and stifles advance in other directions. The nervous system rejoices in complexity, which should neither be ignored, nor run from. The emergence of testable "rules" that can simplify our understanding of neuronal circuits has required the collection of large amounts of data that were difficult to obtain. And although those collecting these data have been criticized for not advancing hypotheses while they were "collecting butterflies," the beauty of the butterflies always enticed us toward further exploration.

Synaptic organization of cortico-cortical communication in primates

In cortical circuitry, synaptic communication across areas is based on two types of axon terminals, small and large, with modulatory and driving roles, respectively. In contrast, it is not known whether similar synaptic specializations exist for intra-areal projections. Using anterograde tracing and three-dimensional reconstruction by electron microscopy (3D-EM), we asked whether large boutons form synapses in the circuit of somatosensory cortical areas 3b and 1. In contrast to observations in macaque visual cortex, light microscopy showed both small and large boutons not only in inter-areal pathways, but also in long-distance intrinsic connections. 3D-EM showed that correlation of surface and volume provides a powerful tool for classifying cortical endings. Principal component analysis supported this observation and highlighted the significance of the size of mitochondria as a distinguishing feature of bouton type. The larger mitochondrion and higher degree of perforated postsynaptic density associated with large rather than to small boutons support the driver-like function of large boutons. In contrast to bouton size and complexity, the size of the postsynaptic density appeared invariant across the bouton types. Comparative studies in human supported that size is a major distinguishing factor of bouton type in the cerebral cortex. In conclusion, the driver-like function of the large endings could facilitate fast dissemination of tactile information within the intrinsic and inter-areal circuitry of areas 3b and 1.

Glia Promote Synaptogenesis through an IQGAP PES-7 in C. elegans

Synapses are fundamental to the normal function of the nervous system. Glia play a pivotal role in regulating synaptic formation. However, how presynaptic neurons assemble synaptic structure in response to the glial signals remains largely unexplored. To address this question, we use cima-1 mutant C. elegans as an in vivo model, in which the astrocyte-like VCSC glial processes ectopically reach an asynaptic neurite region and promote presynaptic formation there. Through an RNAi screen, we find that the Rho GTPase CDC-42 and IQGAP PES-7 are required in presynaptic neurons for VCSC glia-induced presynaptic formation. In addition, we find that cdc-42 and pes-7 are also required for normal synaptogenesis during postembryonic developmental stages. PES-7 activated by CDC-42 promotes presynaptic formation, most likely through regulating F-actin assembly. Given the evolutionary conservation of CDC-42 and IQGAPs, we speculate that our findings in C. elegans apply to vertebrates.

Allometric Scaling of physiologically-relevant organoids

The functional and structural resemblance of organoids to mammalian organs suggests that they might follow the same allometric scaling rules. However, despite their remarkable likeness to downscaled organs, non-luminal organoids are often reported to possess necrotic cores due to oxygen diffusion limits. To assess their potential as physiologically relevant in vitro models, we determined the range of organoid masses in which quarter power scaling as well as a minimum threshold oxygen concentration is maintained. Using data on brain organoids as a reference, computational models were developed to estimate oxygen consumption and diffusion at different stages of growth. The results show that mature brain (or other non-luminal) organoids generated using current protocols must lie within a narrow range of masses to maintain both quarter power scaling and viable cores. However, micro-fluidic oxygen delivery methods could be designed to widen this range, ensuring a minimum viable oxygen threshold throughout the constructs and mass dependent metabolic scaling. The results provide new insights into the significance of the allometric exponent in systems without a resource-supplying network and may be used to guide the design of more predictive and physiologically relevant in vitro models, providing an effective alternative to animals in research.

Social Isolation During the Critical Period Reduces Synaptic and Intrinsic Excitability of a Subtype of Pyramidal Cell in Mouse Prefrontal Cortex

Juvenile social experience is crucial for the functional development of forebrain regions, especially the prefrontal cortex (PFC). We previously reported that social isolation for 2 weeks after weaning induces prefrontal cortex dysfunction and hypomyelination. However, the effect of social isolation on physiological properties of PFC neuronal circuit remained unknown. Since hypomyelination due to isolation is prominent in deep-layer of medial PFC (mPFC), we focused on 2 types of Layer-5 pyramidal cells in the mPFC: prominent h-current (PH) cells and nonprominent h-current (non-PH) cells. We found that a 2-week social isolation after weaning leads to a specific deterioration in action potential properties and reduction in excitatory synaptic inputs in PH cells. The effects of social isolation on PH cells, which involve reduction in functional glutamatergic synapses and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid/N-methyl-d-aspartate charge ratio, are specific to the 2 weeks after weaning and to the mPFC. We conclude that juvenile social experience plays crucial roles in the functional development in a subtype of Layer-5 pyramidal cells in the mPFC. Since these neurons project to subcortical structures, a deficit in social experience during the critical period may result in immature neural circuitry between mPFC and subcortical targets.

Study of the Size and Shape of Synapses in the Juvenile Rat Somatosensory Cortex with 3D Electron Microscopy

Changes in the size of the synaptic junction are thought to have significant functional consequences. We used focused ion beam milling and scanning electron microscopy (FIB/SEM) to obtain stacks of serial sections from the six layers of the rat somatosensory cortex. We have segmented in 3D a large number of synapses (n = 6891) to analyze the size and shape of excitatory (asymmetric) and inhibitory (symmetric) synapses, using dedicated software. This study provided three main findings. Firstly, the mean synaptic sizes were smaller for asymmetric than for symmetric synapses in all cortical layers. In all cases, synaptic junction sizes followed a log-normal distribution. Secondly, most cortical synapses had disc-shaped postsynaptic densities (PSDs; 93%). A few were perforated (4.5%), while a smaller proportion (2.5%) showed a tortuous horseshoe-shaped perimeter. Thirdly, the curvature was larger for symmetric than for asymmetric synapses in all layers. However, there was no correlation between synaptic area and curvature.

The Sensory Neocortex and Associative Memory

Most behaviors in mammals are directly or indirectly guided by prior experience and therefore depend on the ability of our brains to form memories. The ability to form an association between an initially possibly neutral sensory stimulus and its behavioral relevance is essential for our ability to navigate in a changing environment. The formation of a memory is a complex process involving many areas of the brain. In this chapter we review classic and recent work that has shed light on the specific contribution of sensory cortical areas to the formation of associative memories. We discuss synaptic and circuit mechanisms that mediate plastic adaptations of functional properties in individual neurons as well as larger neuronal populations forming topographically organized representations. Furthermore, we describe commonly used behavioral paradigms that are used to study the mechanisms of memory formation. We focus on the auditory modality that is receiving increasing attention for the study of associative memory in rodent model systems. We argue that sensory cortical areas may play an important role for the memory-dependent categorical recognition of previously encountered sensory stimuli.

Volume electron microscopy of the distribution of synapses in the neuropil of the juvenile rat somatosensory cortex

Knowing the proportions of asymmetric (excitatory) and symmetric (inhibitory) synapses in the neuropil is critical for understanding the design of cortical circuits. We used focused ion beam milling and scanning electron microscopy (FIB/SEM) to obtain stacks of serial sections from the six layers of the juvenile rat (postnatal day 14) somatosensory cortex (hindlimb representation). We segmented in three-dimensions 6184 synaptic junctions and determined whether they were established on dendritic spines or dendritic shafts. Of all these synapses, 87–94% were asymmetric and 6–13% were symmetric. Asymmetric synapses were preferentially located on dendritic spines in all layers (80–91%) while symmetric synapses were mainly located on dendritic shafts (62–86%). Furthermore, we found that less than 6% of the dendritic spines establish more than one synapse. The vast majority of axospinous synapses were established on the spine head. Synapses on the spine neck were scarce, although they were more common when the dendritic spine established multiple synapses. This study provides a new large quantitative dataset that may contribute not only to the knowledge of the ultrastructure of the cortex, but also towards defining the connectivity patterns through all cortical layers.

A Manual Segmentation Tool for Three-Dimensional Neuron Datasets

To date, automated or semi-automated software and algorithms for segmentation of neurons from three-dimensional imaging datasets have had limited success. The gold standard for neural segmentation is considered to be the manual isolation performed by an expert. To facilitate the manual isolation of complex objects from image stacks, such as neurons in their native arrangement within the brain, a new Manual Segmentation Tool (ManSegTool) has been developed. ManSegTool allows user to load an image stack, scroll down the images and to manually draw the structures of interest stack-by-stack. Users can eliminate unwanted regions or split structures (i.e., branches from different neurons that are too close each other, but, to the experienced eye, clearly belong to a unique cell), to view the object in 3D and save the results obtained. The tool can be used for testing the performance of a single-neuron segmentation algorithm or to extract complex objects, where the available automated methods still fail. Here we describe the software's main features and then show an example of how ManSegTool can be used to segment neuron images acquired using a confocal microscope. In particular, expert neuroscientists were asked to segment different neurons from which morphometric variables were subsequently extracted as a benchmark for precision. In addition, a literature-defined index for evaluating the goodness of segmentation was used as a benchmark for accuracy. Neocortical layer axons from a DIADEM challenge dataset were also segmented with ManSegTool and compared with the manual “gold-standard” generated for the competition.

Understanding Synaptogenesis and Functional Connectome in C. elegans by Imaging Technology

Formation of functional synapses is a fundamental process for establishing neural circuits and ultimately for expressing complex behavior. Extensive research has interrogated how such functional synapses are formed and how synapse formation contributes to the generation of neural circuitry and behavior. The nervous system of Caenorhabditis elegans, due to its relatively simple structure, the transparent body, and tractable genetic system, has been adapted as an excellent model to investigate synapses and the functional connectome. Advances in imaging technology together with the improvement of genetically encoded molecular tools enabled us to visualize synapses and neural circuits of the animal model, which provide insights into our understanding of molecules and their signaling pathways that mediate synapse formation and neuronal network modulation. Here, we review synaptogenesis in active zones and the mapping of local connectome in C. elegans nervous system whose understandings have been extended by the advances in imaging technology along with the genetic molecular tools.

The anatomical problem posed by brain complexity and size: a potential solution

Over the years the field of neuroanatomy has evolved considerably but unraveling the extraordinary structural and functional complexity of the brain seems to be an unattainable goal, partly due to the fact that it is only possible to obtain an imprecise connection matrix of the brain. The reasons why reaching such a goal appears almost impossible to date is discussed here, together with suggestions of how we could overcome this anatomical problem by establishing new methodologies to study the brain and by promoting interdisciplinary collaboration. Generating a realistic computational model seems to be the solution rather than attempting to fully reconstruct the whole brain or a particular brain region.

Input clustering and the microscale structure of local circuits

The recent development of powerful tools for high-throughput mapping of synaptic networks promises major advances in understanding brain function. One open question is how circuits integrate and store information. Competing models based on random vs. structured connectivity make distinct predictions regarding the dendritic addressing of synaptic inputs. In this article we review recent experimental tests of one of these models, the input clustering hypothesis. Across circuits, brain regions and species, there is growing evidence of a link between synaptic co-activation and dendritic location, although this finding is not universal. The functional implications of input clustering and future challenges are discussed.

NEuronMOrphological analysis tool: open-source software for quantitative morphometrics

Morphometric analysis of neurons and brain tissue is relevant to the study of neuron circuitry development during the first phases of brain growth or for probing the link between microstructural morphology and degenerative diseases. As neural imaging techniques become ever more sophisticated, so does the amount and complexity of data generated. The NEuronMOrphological analysis tool NEMO was purposely developed to handle and process large numbers of optical microscopy image files of neurons in culture or slices in order to automatically run batch routines, store data and apply multivariate classification and feature extraction using 3-way principal component analysis (PCA). Here we describe the software's main features, underlining the differences between NEMO and other commercial and non-commercial image processing tools, and show an example of how NEMO can be used to classify neurons from wild-type mice and from animal models of autism.

Maturation of a recurrent excitatory neocortical circuit by experience-dependent unsilencing of newly formed dendritic spines

Local recurrent excitatory circuits are ubiquitous in neocortex, yet little is known about their development or architecture. Here we introduce a quantitative technique for efficient single-cell resolution circuit mapping using 2-photon (2P) glutamate uncaging and analyze experience-dependent neonatal development of the layer 4 barrel cortex local excitatory circuit. We show that sensory experience specifically drives a 3-fold increase in connectivity at postnatal day (P) 9, producing a highly recurrent network. A profound dendritic spinogenesis occurs concurrent with the connectivity increase, but this is not experience dependent. However, in experience-deprived cortex, a much greater proportion of spines lack postsynaptic AMPA receptors (AMPARs) and synaptic connectivity via NMDA receptors (NMDARs) is the same as in normally developing cortex. Thus we describe a approach for quantitative circuit mapping and show that sensory experience sculpts an intrinsically developing template network, which is based on NMDAR-only synapses, by driving AMPARs into newly formed silent spines.

Biocytin-labelling and its impact on late 20th century studies of cortical circuitry

In recognition of the impact that a powerful new anatomical tool, such as the Golgi method, can have, this essay highlights the enormous influence that biocytin-filling has had on modern neuroscience. This method has allowed neurones that have been recorded intracellularly, 'whole-cell' or juxta-cellularly, to be identified anatomically, forming a vital link between functional and structural studies. It has been applied throughout the nervous system and has become a fundamental component of our technical armoury. A comprehensive survey of the applications to which the biocytin-filling approach has been put, would fill a large volume. This essay therefore focuses on one area, neocortical microcircuitry and the ways in which combining physiology and anatomy have revealed rules that help us explain its previously indecipherable variability and complexity.

Expression of the NR2B-NMDA receptor trafficking complex in prefrontal cortex from a group of elderly patients with schizophrenia

Dysregulated glutamate neurotransmission has been implicated in the pathophysiology of schizophrenia. In particular, hypofunction of the NMDA glutamate receptor has been proposed to play an important role in mediating cognitive deficits in patients. The two NMDA receptor subunits, NR2A and NR2B, are distinctly regulated during development and are associated with different intracellular pathways and functions, which suggest that these receptors play separate roles in the control of higher cognitive functions such as learning and memory. Trafficking of the NR2B subunit-containing receptor is regulated by a microtubule-associated trafficking complex consisting of the KIF17, APBA1, CASK, and mLin7 proteins. Several studies have demonstrated an integrated functional regulation of this trafficking complex with NR2B receptor subunit expression, which in turn has been linked to higher cognitive functions. In the present work, we investigated whether expression of this NR2B-associated trafficking complex might be abnormal in schizophrenia. We analyzed the expression of KIF17, APBA1, CASK, mLin7A and mLin7C in postmortem brain from patients with schizophrenia a comparison group. Analysis of transcripts for all of these proteins revealed particularly prominent expression in cortical layer III and layer IV, which overlapped with NR2B but not NR2A transcripts. We found altered expression of transcripts for the CASK, ABPA1, and mLin7 molecules and the CASK, mLin7 proteins, suggesting that NR2B-containing NMDA receptor transport could be selectively compromised in schizophrenia, and that these changes likely involve altered NR2B function in a subset of cortical neurons.

Missed connections: photoreceptor axon seeks target neuron for synaptogenesis

Extending axons must choose the appropriate synaptic target cells in order to assemble functional neural circuitry. The axons of the Drosophila color-sensitive photoreceptors R7 and R8 project as a single fascicle from each ommatidium, but their terminals are segregated into distinct layers within their target region. Recent studies have begun to reveal the molecular mechanisms that establish this projection pattern. Both homophilic adhesion molecules and specific ligand-receptor interactions make important contributions to stabilizing R7 and R8 terminals in the appropriate target layers. These cell recognition molecules are regulated by the same transcription factors that control R7 and R8 cell fates. Autocrine and repulsive signaling mechanisms prevent photoreceptor terminals from encroaching on their neighbors, preserving the spatial resolution of visual information.

Molecular mechanisms of synaptic specificity

Synapses are specialized junctions that mediate information flow between neurons and their targets. A striking feature of the nervous system is the specificity of its synaptic connections: an individual neuron will form synapses only with a small subset of available presynaptic and postsynaptic partners. Synaptic specificity has been classically thought to arise from homophilic or heterophilic interactions between adhesive molecules acting across the synaptic cleft. Over the past decade, many new mechanisms giving rise to synaptic specificity have been identified. Synapses can be specified by secreted molecules that promote or inhibit synaptogenesis, and their source can be a neighboring guidepost cell, not just presynaptic and postsynaptic neurons. Furthermore, lineage, fate, and timing of development can also play critical roles in shaping neural circuits. Future work utilizing large-scale screens will aim to elucidate the full scope of cellular mechanisms and molecular players that can give rise to synaptic specificity.