Neocortical areas, layers, connections, and gene expression

Repairing the in situ hybridization missing data in the hippocampus region by using a 3D residual U-Net model

The hippocampus is a critical brain region. Transcriptome data provides valuable insights into the structure and function of the hippocampus at the gene level. However, transcriptome data is often incomplete. To address this issue, we use the convolutional neural network model to repair the missing voxels in the hippocampus region, based on Allen institute coronal slices in situ hybridization (ISH) dataset. Moreover, we analyze the gene expression correlation between coronal and sagittal dataset in the hippocampus region. The results demonstrated that the trend of gene expression correlation between the coronal and sagittal datasets remained consistent following the repair of missing data in the coronal ISH dataset. In the last, we use repaired ISH dataset to identify novel genes specific to hippocampal subregions. Our findings demonstrate the accuracy and effectiveness of using deep learning method to repair ISH missing data. After being repaired, ISH has the potential to improve our comprehension of the hippocampus's structure and function.

Microenvironments Matter: Advances in Brain-on-Chip

To highlight the particular needs with respect to modeling the unique and complex organization of the human brain structure, we reviewed the state-of-the-art in devising brain models with engineered instructive microenvironments. To acquire a better perspective on the brain's working mechanisms, we first summarize the importance of regional stiffness gradients in brain tissue, varying per layer and the cellular diversities of the layers. Through this, one can acquire an understanding of the essential parameters in emulating the brain in vitro. In addition to the brain's organizational architecture, we addressed also how the mechanical properties have an impact on neuronal cell responses. In this respect, advanced in vitro platforms emerged and profoundly changed the methods of brain modeling efforts from the past, mainly focusing on animal or cell line research. The main challenges in imitating features of the brain in a dish are with regard to composition and functionality. In neurobiological research, there are now methods that aim to cope with such challenges by the self-assembly of human-derived pluripotent stem cells (hPSCs), i.e., brainoids. Alternatively, these brainoids can be used stand-alone or in conjunction with Brain-on-Chip (BoC) platform technology, 3D-printed gels, and other types of engineered guidance features. Currently, advanced in vitro methods have made a giant leap forward regarding cost-effectiveness, ease-of-use, and availability. We bring these recent developments together into one review. We believe our conclusions will give a novel perspective towards advancing instructive microenvironments for BoCs and the understanding of the brain's cellular functions either in modeling healthy or diseased states of the brain.

Layer-specific, retinotopically-diffuse modulation in human visual cortex in response to viewing emotionally expressive faces

Viewing faces that are perceived as emotionally expressive evokes enhanced neural responses in multiple brain regions, a phenomenon thought to depend critically on the amygdala. This emotion-related modulation is evident even in primary visual cortex (V1), providing a potential neural substrate by which emotionally salient stimuli can affect perception. How does emotional valence information, computed in the amygdala, reach V1? Here we use high-resolution functional MRI to investigate the layer profile and retinotopic distribution of neural activity specific to emotional facial expressions. Across three experiments, human participants viewed centrally presented face stimuli varying in emotional expression and performed a gender judgment task. We found that facial valence sensitivity was evident only in superficial cortical layers and was not restricted to the retinotopic location of the stimuli, consistent with diffuse feedback-like projections from the amygdala. Together, our results provide a feedback mechanism by which the amygdala directly modulates activity at the earliest stage of visual processing.

Distribution and Morphological Characteristics of Oligodendrocytes in Selected Areas of the Brain of Male and Female Red Kangaroos (Macropus rufus)

This study was carried out on six adult red kangaroos of both sexes. To determine the location of the oligodendrocytes (OLGs) of the hippocampus (Hip) and corpus callosum (CC), the method of impregnation of the neuroglia with silver salts was applied. The iron distribution in the OLGs was determined by the histochemical method. The Nissl method was used to determine the location of the brain structure and to analyze the number of OLGs. In the Hip, these cells are located one beside another, mainly in blood vessels and neurons; in the neocortex (NC), they are located in layers I–VI; and in the CC, they are arranged in characteristic rows and accompany both nerve fibers and blood vessels. The analysis of the results obtained by the chosen methods in the Hip, NC, and CC in males and females did not show statistically significant differences in the distribution and location of the red kangaroo OLGs. The involvement of these cells is a physiological process that proceeds in a similar manner throughout the life of individuals and actively influences the metabolism of neurons and myelin.

The relationship between transcription and eccentricity in human V1

Gene expression gradients radiating from regions of primary sensory cortices have recently been described and are thought to underlie the large-scale organization of the human cerebral cortex. However, the role of transcription in the functional layout of a single region within the adult brain has yet to be clarified, likely owing to the difficulty of identifying a brain region anatomically consistent enough across individuals with dense enough tissue sampling. Overcoming these hurdles in human primary visual cortex (V1), we show a relationship between differential gene expression and the cortical layout of eccentricity in human V1. Interestingly, these genes are unique from those previously identified that contribute to the positioning of cortical areas in the visual processing hierarchy. Enrichment analyses show that a subset of the identified genes encode for structures related to inhibitory interneurons, ion channels, as well as cellular projections, and are expressed more in foveal compared to peripheral portions of human V1. These findings predict that tissue density should be higher in foveal compared to peripheral V1. Using a histological pipeline, we validate this prediction using Nissl-stained sections of postmortem occipital cortex. We discuss these findings relative to previous studies in non-human primates, as well as in the context of an organizational pattern in which the adult human brain employs transcription gradients at multiple spatial scales: across the cerebral cortex, across areas within processing hierarchies, and within single cortical areas.

The nonhuman primate neuroimaging and neuroanatomy project

Multi-modal neuroimaging projects such as the Human Connectome Project (HCP) and UK Biobank are advancing our understanding of human brain architecture, function, connectivity, and their variability across individuals using high-quality non-invasive data from many subjects. Such efforts depend upon the accuracy of non-invasive brain imaging measures. However, 'ground truth' validation of connectivity using invasive tracers is not feasible in humans. Studies using nonhuman primates (NHPs) enable comparisons between invasive and non-invasive measures, including exploration of how "functional connectivity" from fMRI and "tractographic connectivity" from diffusion MRI compare with long-distance connections measured using tract tracing. Our NonHuman Primate Neuroimaging & Neuroanatomy Project (NHP_NNP) is an international effort (6 laboratories in 5 countries) to: (i) acquire and analyze high-quality multi-modal brain imaging data of macaque and marmoset monkeys using protocols and methods adapted from the HCP; (ii) acquire quantitative invasive tract-tracing data for cortical and subcortical projections to cortical areas; and (iii) map the distributions of different brain cell types with immunocytochemical stains to better define brain areal boundaries. We are acquiring high-resolution structural, functional, and diffusion MRI data together with behavioral measures from over 100 individual macaques and marmosets in order to generate non-invasive measures of brain architecture such as myelin and cortical thickness maps, as well as functional and diffusion tractography-based connectomes. We are using classical and next-generation anatomical tracers to generate quantitative connectivity maps based on brain-wide counting of labeled cortical and subcortical neurons, providing ground truth measures of connectivity. Advanced statistical modeling techniques address the consistency of both kinds of data across individuals, allowing comparison of tracer-based and non-invasive MRI-based connectivity measures. We aim to develop improved cortical and subcortical areal atlases by combining histological and imaging methods. Finally, we are collecting genetic and sociality-associated behavioral data in all animals in an effort to understand how genetic variation shapes the connectome and behavior.

Transcriptional profiles of supragranular-enriched genes associate with corticocortical network architecture in the human brain

The human brain is patterned with disproportionately large, distributed cerebral networks that connect multiple association zones in the frontal, temporal, and parietal lobes. The expansion of the cortical surface, along with the emergence of long-range connectivity networks, may be reflected in changes to the underlying molecular architecture. Using the Allen Institute's human brain transcriptional atlas, we demonstrate that genes particularly enriched in supragranular layers of the human cerebral cortex relative to mouse distinguish major cortical classes. The topography of transcriptional expression reflects large-scale brain network organization consistent with estimates from functional connectivity MRI and anatomical tracing in nonhuman primates. Microarray expression data for genes preferentially expressed in human upper layers (II/III), but enriched only in lower layers (V/VI) of mouse, were cross-correlated to identify molecular profiles across the cerebral cortex of postmortem human brains (n = 6). Unimodal sensory and motor zones have similar molecular profiles, despite being distributed across the cortical mantle. Sensory/motor profiles were anticorrelated with paralimbic and certain distributed association network profiles. Tests of alternative gene sets did not consistently distinguish sensory and motor regions from paralimbic and association regions: (i) genes enriched in supragranular layers in both humans and mice, (ii) genes cortically enriched in humans relative to nonhuman primates, (iii) genes related to connectivity in rodents, (iv) genes associated with human and mouse connectivity, and (v) 1,454 gene sets curated from known gene ontologies. Molecular innovations of upper cortical layers may be an important component in the evolution of long-range corticocortical projections.

In Vivo Two-Photon Imaging of Dendritic Spines in Marmoset Neocortex

Two-photon microscopy in combination with a technique involving the artificial expression of fluorescent protein has enabled the direct observation of dendritic spines in living brains. However, the application of this method to primate brains has been hindered by the lack of appropriate labeling techniques for visualizing dendritic spines. Here, we developed an adeno-associated virus vector-based fluorescent protein expression system for visualizing dendritic spines in vivo in the marmoset neocortex. For the clear visualization of each spine, the expression of reporter fluorescent protein should be both sparse and strong. To fulfill these requirements, we amplified fluorescent signals using the tetracycline transactivator (tTA)–tetracycline-responsive element system and by titrating down the amount of Thy1S promoter-driven tTA for sparse expression. By this method, we were able to visualize dendritic spines in the marmoset cortex by two-photon microscopy in vivo and analyze the turnover of spines in the prefrontal cortex. Our results demonstrated that short spines in the marmoset cortex tend to change more frequently than long spines. The comparison of in vivo samples with fixed samples showed that we did not detect all existing spines by our method. Although we found glial cell proliferation, the damage of tissues caused by window construction was relatively small, judging from the comparison of spine length between samples with or without window construction. Our new labeling technique for two-photon imaging to visualize in vivo dendritic spines of the marmoset neocortex can be applicable to examining circuit reorganization and synaptic plasticity in primates.

Long-range intralaminar noise correlations in the barrel cortex

Identifying the properties of correlations in the firing of neocortical neurons is central to our understanding of cortical information processing. It has been generally assumed, by virtue of the columnar organization of the neocortex, that the firing of neurons residing in a certain vertical domain is highly correlated. On the other hand, firing correlations between neurons steeply decline with horizontal distance. Technical difficulties in sampling neurons with sufficient spatial information have precluded the critical evaluation of these notions. We used 128-channel "silicon probes" to examine the spike-count noise correlations during spontaneous activity between multiple neurons with identified laminar position and over large horizontal distances in the anesthetized rat barrel cortex. Eigen decomposition of correlation coefficient matrices revealed that the laminar position of a neuron is a significant determinant of these correlations, such that the fluctuations of layer 5B/6 neurons are in opposite direction to those of layers 5A and 4. Moreover, we found that within each experiment, the distribution of horizontal, intralaminar spike-count correlation coefficients, up to a distance of ∼1.5 mm, is practically identical to the distribution of vertical correlations. Taken together, these data reveal that the neuron's laminar position crucially affects its role in cortical processing. Moreover, our analyses reveal that this laminar effect extends over several functional columns. We propose that within the cortex the influence of the horizontal elements exists in a dynamic balance with the influence of the vertical domain and this balance is modulated with brain states to shape the network's behavior.

Anisotropy of ongoing neural activity in the primate visual cortex

The mammalian neocortex features distinct anatomical variation in its tangential and radial extents. This review consolidates previously published findings from our group in order to compare and contrast the spatial profile of neural activity coherence across these distinct cortical dimensions. We focus on studies of ongoing local field potential (LFP) data obtained simultaneously from multiple sites in the primary visual cortex in two types of experiments in which electrode contacts were spaced either along the cortical surface or at different laminar positions. These studies demonstrate that across both dimensions the coherence of ongoing LFP fluctuations diminishes as a function of interelectrode distance, although the nature and spatial scale of this falloff is very different. Along the cortical surface, the overall LFP coherence declines gradually and continuously away from a given position. In contrast, across the cortical layers, LFP coherence is discontinuous and compartmentalized as a function of depth. Specifically, regions of high LFP coherence fall into discrete superficial and deep laminar zones, with an abrupt discontinuity between the granular and infragranular layers. This spatial pattern of ongoing LFP coherence is similar when animals are at rest and when they are engaged in a behavioral task. These results point to the existence of partially segregated laminar zones of cortical processing that extend tangentially within the laminar compartments and are thus oriented orthogonal to the cortical columns. We interpret these electrophysiological observations in light of the known anatomical organization of the cortical microcircuit.

Comparative analyses of adeno-associated viral vector serotypes 1, 2, 5, 8 and 9 in marmoset, mouse and macaque cerebral cortex

Here we investigated the transduction characteristics of adeno-associated viral vector (AAV) serotypes 1, 2, 5, 8 and 9 in the marmoset cerebral cortex. Using three constructs that each has hrGFP under ubiquitous (CMV), or neuron-specific (CaMKII and Synapsin I (SynI)) promoters, we investigated (1) the extent of viral spread, (2) cell type tropism, and (3) neuronal transduction efficiency of each serotype. AAV2 was clearly distinct from other serotypes in small spreading and neuronal tropism. We did not observe significant differences in viral spread among other serotypes. Regarding the cell tropism, AAV1, 5, 8 and 9 exhibited mostly glial expression for CMV construct. However, when the CaMKII construct was tested, cortical neurons were efficiently transduced (>∼70% in layer 3) by all serotypes, suggesting that glial expression obscured neuronal expression for CMV construct. For both SynI and CaMKII constructs, we observed generally high-level expression in large pyramidal cells especially in layer 5, as well as in parvalbumin-positive interneurons. The expression from the CaMKII construct was more uniformly observed in excitatory cells compared with SynI construct. Injection of the same viral preparations in mouse and macaque cortex resulted in essentially the same result with some species-specific differences.

Towards a unified scheme of cortical lamination for primary visual cortex across primates: insights from NeuN and VGLUT2 immunoreactivity

Primary visual cortex (V1) is clearly distinguishable from other cortical areas by its distinctive pattern of neocortical lamination across mammalian species. In some mammals, primates in particular, the layers of V1 are further divided into a number of sublayers based on their anatomical and functional characteristics. While these sublayers are easily recognizable across a range of primates, the exact number of divisions in each layer and their relative position within the depth of V1 has been inconsistently reported, largely due to conflicting schemes of nomenclature for the V1 layers. This conflict centers on the definition of layer 4 in primate V1, and the subdivisions of layer 4 that can be consistently identified across primate species. Brodmann’s (1909) laminar scheme for V1 delineates three subdivisions of layer 4 in primates, based on cellular morphology and geniculate inputs in anthropoid monkeys. In contrast, Hässler’s (1967) laminar scheme delineates a single layer 4 and multiple subdivisions of layer 3, based on comparisons of V1 lamination across the primate lineage. In order to clarify laminar divisions in primate visual cortex, we performed NeuN and VGLUT2 immunohistochemistry in V1 of chimpanzees, Old World macaque monkeys, New World squirrel, owl, and marmoset monkeys, prosimian galagos and mouse lemurs, and non-primate, but highly visual, tree shrews. By comparing the laminar divisions identified by each method across species, we find that Hässler’s (1967) laminar scheme for V1 provides a more consistent representation of neocortical layers across all primates, including humans, and facilitates comparisons of V1 lamination with non-primate species. These findings, along with many others, support the consistent use of Hässler’s laminar scheme in V1 research.

Physiology and morphology of inverted pyramidal neurons in the rodent neocortex

An increasing number of studies indicate that there exists greater diversity of cortical neurons than previously appreciated. In the present report, we use a combination of physiological and morphological methods to characterize cortical neurons in infragranular layers with apical dendrites pointing toward the white-matter compared to those neurons with apical dendrites pointing toward the pia in both mouse and rat neocortex. Several features of the dendritic morphology and intrinsic and synaptic physiology of these "inverted" neurons revealed numerous differences among this cell type between species. We also found differences between the different cell types within the same species. These data reveal that similar cell types in the rat and mouse may not always share similar physiological and morphological properties. These data are relevant to models of information processing through micro- and larger neocortical circuits and indicate that different cell types found within similar lamina can have different functional properties.

The diameter of cortical axons depends both on the area of origin and target

In primates, different cortical areas send axons of different diameters into comparable tracts, notably the corpus callosum (Tomasi S, Caminiti R, Innocenti GM. 2012. Areal differences in diameter and length of corticofugal projections. Cereb Cortex. 22:1463-1472). We now explored if an area also sends axons of different diameters to different targets. We find that the parietal area PEc sends thicker axons to area 4 and 6, and thinner ones to the cingulate region (area 24). Areas 4 and 9, each sends axons of different diameters to the nucleus caudatus, to different levels of the internal capsule, and to the thalamus. The internal capsule receives the thickest axon, followed by thalamus and nucleus caudatus. The 2 areas (4 and 9) differ in the diameter and length of axons to corresponding targets. We calculated how diameter determines conduction velocity of the axons and together with pathway length determines transmission delays between different brain sites. We propose that projections from and within the cerebral cortex consist of a complex system of lines of communication with different geometrical and time computing properties.

Transcriptional architecture of the primate neocortex

Genome-wide transcriptional profiling was used to characterize the molecular underpinnings of neocortical organization in rhesus macaque, including cortical areal specialization and laminar cell-type diversity. Microarray analysis of individual cortical layers across sensorimotor and association cortices identified robust and specific molecular signatures for individual cortical layers and areas, prominently involving genes associated with specialized neuronal function. Overall, transcriptome-based relationships were related to spatial proximity, being strongest between neighboring cortical areas and between proximal layers. Primary visual cortex (V1) displayed the most distinctive gene expression compared to other cortical regions in rhesus and human, both in the specialized layer 4 as well as other layers. Laminar patterns were more similar between macaque and human compared to mouse, as was the unique V1 profile that was not observed in mouse. These data provide a unique resource detailing neocortical transcription patterns in a nonhuman primate with great similarity in gene expression to human.

Differential expression patterns of striate cortex-enriched genes among Old World, New World, and prosimian primates

A group of 5 genes, OCC1, testican-1, testican-2, 5-HT1B, and 5-HT2A, are selectively expressed in layer 4 (4C of Brodmann) of striate cortex (visual area V1) of both Old World macaques and New World marmoset monkeys. The expression of these genes is activity dependent, as expression is reduced after blocking retinal activity. Surprisingly, the pronounced expression pattern has not been found in rodents or carnivores. Thus, these genes may be highly expressed in V1 of some but perhaps not all primates. Here, we compared the gene expression in members of 3 major branches of primate evolution: prosimians, New World monkeys, and Old World monkeys. Although the expression pattern of 5-HT1B was well conserved, those of the other genes varied from the least distinct in prosimian galagos to successively more in New World owl monkeys, marmosets, squirrel monkeys, and Old World macaque monkeys. In owl monkeys, the expression of 5-HT2A was significantly reduced by monocular tetrodotoxin injection, while those of OCC1 and 5-HT1B were not. Thus, we propose that early primates had low levels of expression and higher levels emerged with anthropoid primates and became further enhanced in the Old World catarrhine monkeys that are more closely related to humans.

Selective gene expression in regions of primate neocortex: implications for cortical specialization

The neocortex, which is characteristic of mammals, has evolved to play important roles in cognitive and perceptual functions. The localization of different functions in different regions of the neocortex was well established within the last century. Studies on the formation of the neocortex have advanced at the molecular level, thus clarifying the mechanisms that control neural or glial cell differentiation and sensory projections. However, mechanisms that underlie cortical area specialization remain unsolved. To address this problem, our approach has been to isolate and characterize the genes that are selectively expressed in particular subsets of neocortical areas in primates; these areas are most distinctive among mammals. By differential display and restriction landmark cDNA scanning (RLCS) methods, we have identified two major classes of genes that are specifically expressed in the adult macaque monkey neocortical areas: one is expressed in the primary sensory areas, particularly, in the primary visual cortex (V1) and the other is expressed in the association areas. The genes that show these specific expression patterns are limited to only several gene families among our large-scale screening. In this review, I first describe the isolation and characterization of these genes, along with another class of genes specifically expressed in motor areas. Then, I discuss their functional significance in the primate neocortex. Finally, I discuss the implication of these gene expression patterns in neocortical specialization in primates and possible future research directions.

Relationships among the hippocampus, dentate gyrus, mammillary body, fornix, and anterior commissure from a viewpoint of elements

To elucidate the relationships among the brain regions belonging to the limbic system, the authors investigated the relationships among the hippocampus, dentate gyrus, mammillary body, and fornix, using the anterior commissure as a control, from a viewpoint of elements. After ordinary dissections at Nara Medical University were finished, the hippocampi, dentate gyri, mammillary bodies, fornices, and anterior commissures were resected from identical cerebra of the subjects. The subjects consisted of 23 men and 23 women, ranging in age from 70 to 101 years (average age = 83.5 ± 7.5 years). After ashing with nitric acid and perchloric acid, element contents were determined by inductively coupled plasma-atomic emission spectrometry. With regard to seven elements of Ca, P, S, Mg, Zn, Fe, and Na, it was examined whether there were significant correlations among the hippocampus, dentate gyrus, mammillary body, fornix, and anterior commissure. It was found that there were extremely or very significant direct correlations among all of the five brain regions of the hippocampus, dentate gyrus, mammillary body, fornix, and anterior commissure in the P content. Likewise, with regard to the Fe content, there were significant direct correlations among the four brain regions belonging to the limbic system, except for the anterior commissure. In both the Ca and Zn contents, there were extremely or very significant direct correlations among the hippocampus, dentate gyrus, and mammillary body of the gray matter.

Gene expression in the rat brain: high similarity but unique differences between frontomedial-, temporal- and occipital cortex

BACKGROUND

The six-layered neocortex of the mammalian brain may appear largely homologous, but is in reality a modular structure of anatomically and functionally distinct areas. However, global gene expression seems to be almost identical across the cerebral cortex and only a few genes have so far been reported to show regional enrichment in specific cortical areas.

RESULTS

In the present study on adult rat brain, we have corroborated the strikingly similar gene expression among cortical areas. However, differential expression analysis has allowed for the identification of 30, 24 and 11 genes enriched in frontomedial -, temporal- or occipital cortex, respectively. A large proportion of these 65 genes appear to be involved in signal transduction, including the ion channel Fxyd6, the neuropeptide Grp and the nuclear receptor Rorb. We also find that the majority of these genes display increased expression levels around birth and show distinct preferences for certain cortical layers and cell types in rodents.

CONCLUSIONS

Since specific patterns of expression often are linked to equally specialised biological functions, we propose that these cortex sub-region enriched genes are important for proper functioning of the cortical regions in question.

Fluorescent in situ hybridization technique for cell type identification and characterization in the central nervous system

Central nervous system consists of a myriad of cell types. In particular, many subtypes of neuronal cells, which are interconnected with each other, form the basis of functional circuits. With the advent of genomic era, there have been systematic efforts to map gene expression profiles by in situ hybridization (ISH) and enhancer-trapping strategy. To make full use of such information, it is important to correlate "cell types" to gene expression. Toward this end, we have developed highly sensitive method of fluorescent dual-probe ISH, which is essential to distinguish two cell types expressing distinct marker genes. Importantly, we were able to combine ISH with retrograde tracing and antibody staining including BrdU staining that enables birthdating. These techniques should prove useful in identifying and characterizing the cell types of the neural tissues. In this article, we describe the methodology of these techniques, taking examples from our analyses of the mammalian cerebral cortex.

Recurrent spatiotemporal firing patterns in large spiking neural networks with ontogenetic and epigenetic processes

Neural development and differentiation are characterized by an overproduction of cells and a transient exuberant number of connections followed by cell death and selective synaptic pruning. We simulated large spiking neural networks (10,000 units at its maximum size) with and without an ontogenetic process corresponding to a brief initial phase of apoptosis driven by an excessive firing rate mimicking cell death due to glutamatergic neurotoxicity and glutamate-triggered apoptosis. This phase was followed by the onset of spike timing dependent synaptic plasticity (STDP), driven by spatiotemporal patterns of stimulation. Despite the reduction in cell counts the apoptosis tended to increase the excitatory/inhibitory ratio because the inhibitory cells were affected at first. Recurrent spatiotemporal firing patterns emerged in both developmental condition but they differed in dynamics. They were less numerous but repeated more often after apoptosis. The results suggest that initial cell death may be necessary for the emergence of stable cell assemblies, able to sustain and process temporal information, from the initially randomly connected networks.

Enriched expression of serotonin 1B and 2A receptor genes in macaque visual cortex and their bidirectional modulatory effects on neuronal responses

To study the molecular mechanism how cortical areas are specialized in adult primates, we searched for area-specific genes in macaque monkeys and found striking enrichment of serotonin (5-hydroxytryptamine, 5-HT) 1B receptor mRNA, and to a lesser extent, of 5-HT2A receptor mRNA, in the primary visual area (V1). In situ hybridization analyses revealed that both mRNA species were highly concentrated in the geniculorecipient layers IVA and IVC, where they were coexpressed in the same neurons. Monocular inactivation by tetrodotoxin injection resulted in a strong and rapid (<3 h) downregulation of these mRNAs, suggesting the retinal activity dependency of their expression. Consistent with the high expression level in V1, clear modulatory effects of 5-HT1B and 5-HT2A receptor agonists on the responses of V1 neurons were observed in in vivo electrophysiological experiments. The modulatory effect of the 5-HT1B agonist was dependent on the firing rate of the recorded neurons: The effect tended to be facilitative for neurons with a high firing rate, and suppressive for those with a low firing rate. The 5-HT2A agonist showed opposite effects. These results suggest that this serotonergic system controls the visual response in V1 for optimization of information processing toward the incoming visual inputs.

MRI of cellular layers in mouse brain in vivo

Noninvasive imaging of the brain of animal models demands the detection of increasingly smaller structures by in vivo MRI. The purpose of this work was to elucidate the spatial resolution and structural contrast that can be obtained for studying the brain of C57BL/6J mice by optimized T2-weighted fast spin-echo MRI at 9.4 T. As a prerequisite for high-resolution imaging in vivo, motion artifacts were abolished by combining volatile anesthetics and positive pressure ventilation with a specially designed animal bed for fixation. Multiple substructures in the cortex, olfactory bulb, hippocampus, and cerebellum were resolved at 30 to 40 microm in-plane resolution and 200 to 300 microm section thickness as well as for relatively long echo times of 65 to 82 ms. In particular, the approach resulted in the differentiation of up to five cortical layers. In the olfactory bulb the images unraveled the mitral cell layer which has a thickness of mostly single cells. In the hippocampus at least five substructures could be separated. The molecular layer, Purkinje layer, and granular layer of the cerebellum could be clearly differentiated from the white matter. In conclusion, even without the use of a contrast agent, suitable adjustments of a widely available T2-weighted MRI sequence at high field allow for structural MRI of living mice at near single-cell layer resolution.

Localization of latexin-immunoreactive neurons in the adult cat cerebral cortex and claustrum/endopiriform formation

The distribution of neurons that are immunoreactive to latexin, which is an endogenous inhibitor of the A/B subfamily of metallocarboxypeptidases, was investigated in the adult cat telencephalon. Latexin-immunoreactive neurons were distributed in the lower layers of the neocortex and adjacent ventral mesocortex, as well as in the claustrum/endopiriform formation. There were marked regional and laminar differences in density and distribution of latexin-immunoreactive neurons in the cerebral cortex. The density followed a roughly lateral-to-medial decreasing gradient: it was high in lateral cortical regions, which included the insular, second somatosensory, and anterior sylvian areas, and in the temporal auditory field; moderate in laterodorsal cortical regions, which included the primary and second auditory fields; and low in dorsal cortical regions, which included visual areas 18 and 19. Latexin-immunoreactive neurons were absent in medial cortical regions, which included the motor, premotor, prefrontal, prelimbic, cingulate, and retrosplenial areas. The lateral-to-medial gradient was apparent even within a single cytoarchitectonic area in certain cortical regions. The allocortex was devoid of latexin-immunoreactive neurons, with the exception of the anteroventral part of the dentate gyrus. The majority of cortical latexin-immunoreactive neurons were localized in layers V and VI and appeared to correspond to the "modified pyramidal cells in the infragranular layers." The remaining latexin-immunoreactive neurons were localized in layer IV, as well as in lower layer III and in the white matter. There were no latexin-immunoreactive neurons from layer I through upper layer III. Latexin-immunoreactive neurons were present in telencephalic structures outside the cerebral cortex, with particularly high density in the claustrum/endopiriform formation. All these features, with the exception of that detected in the archicortex, are compatible with the features observed previously in the rat telencephalon. The similar pattern of distribution of latexin-immunoreactive neurons in several mammalian species from different orders suggests that latexin plays an important role in a specific cortical network.

Paraneoplastic antigen-like 5 gene (PNMA5) is preferentially expressed in the association areas in a primate specific manner

To understand the relationship between the structure and function of primate neocortical areas at a molecular level, we have been screening for genes differentially expressed across macaque neocortical areas by restriction landmark cDNA scanning (RLCS). Here, we report enriched expression of the paraneoplastic antigen-like 5 gene (PNMA5) in association areas but not in primary sensory areas, with the lowest expression level in primary visual cortex. In situ hybridization in the primary sensory areas revealed PNMA5 mRNA expression restricted to layer II. Along the ventral visual pathway, the expression gradually increased in the excitatory neurons from the primary to higher visual areas. This differential expression pattern was very similar to that of retinol-binding protein (RBP) mRNA, another association-area-enriched gene that we reported previously. Additional expression analysis for comparison of other genes in the PNMA gene family, PNMA1, PNMA2, PNMA3, and MOAP1 (PNMA4), showed that they were widely expressed across areas and layers but without the differentiated pattern of PNMA5. In mouse brains, PNMA1 was only faintly expressed and PNMA5 was not detected. Sequence analysis showed divergence of PNMA5 sequences among mammals. These findings suggest that PNMA5 acquired a certain specialized role in the association areas of the neocortex during primate evolution.

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.

Differential expression patterns of occ1-related genes in adult monkey visual cortex

We have previously revealed that occ1 is preferentially expressed in the primary visual area (V1) of the monkey neocortex. In our attempt to identify more area-selective genes in the macaque neocortex, we found that testican-1, an occ1-related gene, and its family members also exhibit characteristic expression patterns along the visual pathway. The expression levels of testican-1 and testican-2 mRNAs as well as that of occ1 mRNA start of high in V1, progressively decrease along the ventral visual pathway, and end of low in the temporal areas. Complementary to them, the neuronal expression of SPARC mRNA is abundant in the association areas and scarce in V1. Whereas occ1, testican-1, and testican-2 mRNAs are preferentially distributed in thalamorecipient layers including “blobs,” SPARC mRNA expression avoids these layers. Neither SC1 nor testican-3 mRNA expression is selective to particular areas, but SC1 mRNA is abundantly observed in blobs. The expressions of occ1, testican-1, testican-2, and SC1 mRNA were downregulated after monocular tetrodotoxin injection. These results resonate with previous works on chemical and functional gradients along the primate occipitotemporal visual pathway and raise the possibility that these gradients and functional architecture may be related to the visual activity–dependent expression of these extracellular matrix glycoproteins.

Neurofilament protein and neuronal activity markers define regional architectonic parcellation in the mouse visual cortex

This study was designed to assess the chemoarchitectural organization and extent of the mouse visual cortex. We used nonphosphorylated neurofilament protein, a neuronal marker that exhibits region-specific cellular and laminar patterns, to delineate cortical subdivisions. A comprehensive analysis demonstrated that pyramidal and nonpyramidal neurons expressing neurofilament proteins display striking laminar and regional patterns in the mouse visual cortex permitting the delineation of the primary visual cortex (V1) and its monocular and binocular zones, 2 lateral, and 5 medial extrastriate cortical areas with clear anatomical boundaries and providing evidence that the mouse medial extrastriate cortex is not homogeneous. We also investigated the expression profiles of 2 neuronal activity markers, the immediate early genes c-fos and zif-268, following deprivation paradigms to ascertain the visual nature of all subdivisions caudal, medial, and lateral to V1. The present data indicate that neurochemically identifiable subdivisions of the mouse visual cortex exist laterally and medially to V1 and reveal specific anatomical and functional characteristics at the cellular and regional levels.