Fully integrated silicon probes for high-density recording of neural activity.

Sensory, motor and cognitive operations involve the coordinated action of large neuronal populations across multiple brain regions in both superficial and deep structures. Existing extracellular probes record neural activity with excellent spatial and temporal (sub-millisecond) resolution, but from only a few dozen neurons per shank. Optical Ca2+ imaging offers more coverage but lacks the temporal resolution needed to distinguish individual spikes reliably and does not measure local field potentials. Until now, no technology compatible with use in unrestrained animals has combined high spatiotemporal resolution with large volume coverage. Here we design, fabricate and test a new silicon probe known as Neuropixels to meet this need. Each probe has 384 recording channels that can programmably address 960 complementary metal-oxide-semiconductor (CMOS) processing-compatible low-impedance TiN sites that tile a single 10-mm long, 70 × 20-µm cross-section shank. The 6 × 9-mm probe base is fabricated with the shank on a single chip. Voltage signals are filtered, amplified, multiplexed and digitized on the base, allowing the direct transmission of noise-free digital data from the probe. The combination of dense recording sites and high channel count yielded well-isolated spiking activity from hundreds of neurons per probe implanted in mice and rats. Using two probes, more than 700 well-isolated single neurons were recorded simultaneously from five brain structures in an awake mouse. The fully integrated functionality and small size of Neuropixels probes allowed large populations of neurons from several brain structures to be recorded in freely moving animals. This combination of high-performance electrode technology and scalable chip fabrication methods opens a path towards recording of brain-wide neural activity during behaviour.

Laminar Localization and Projection-Specific Properties of Presubicular Neurons Targeting the Lateral Mammillary Nucleus, Thalamus, or Medial Entorhinal Cortex.

The presubiculum (PrS) is part of an interconnected network of distributed brain regions where individual neurons signal the animals heading direction. PrS sends axons to medial entorhinal cortex (MEC), it is reciprocally connected with anterior thalamic nuclei (ATNs), and it sends feedback projections to the lateral mammillary nucleus (LMN), involved in generating the head direction signal. The intrinsic properties of projecting neurons will influence the pathway-specific transmission of activity. Here, we used projection-specific labeling of presubicular neurons to identify MEC-, LMN-, and ATN-projecting neurons in mice. MEC-projecting neurons located in superficial layers II/III were mostly regular spiking pyramidal neurons, and we also identified a Martinotti-type GABAergic neuron. The cell bodies of LMN-projecting neurons were located in a well-delimited area in the middle portion of the PrS, which corresponds to layer IV. The physiology of LMN projecting, pyramidal neurons stood out with a tendency to fire in bursts of action potentials (APs) with rapid onset. These properties may be uniquely adapted to reliably transmit visual landmark information with short latency to upstream LMN. Neurons projecting to ATN were located in layers V/VI, and they were mostly regular spiking pyramidal neurons. Unsupervised cluster analysis of intrinsic properties suggested distinct physiological features for the different categories of projection neurons, with some similarities between MEC- and ATN-projecting neurons. Projection-specific subpopulations may serve separate functions in the PrS and may be engaged differently in transmitting head direction related information.

Mapping of a non-spatial dimension by the hippocampal-entorhinal circuit.

During spatial navigation, neural activity in the hippocampus and the medial entorhinal cortex (MEC) is correlated to navigational variables such as location, head direction, speed, and proximity to boundaries. These activity patterns are thought to provide a map-like representation of physical space. However, the hippocampal-entorhinal circuit is involved not only in spatial navigation, but also in a variety of memory-guided behaviours. The relationship between this general function and the specialized spatial activity patterns is unclear. A conceptual framework reconciling these views is that spatial representation is just one example of a more general mechanism for encoding continuous, task-relevant variables. Here we tested this idea by recording from hippocampal and entorhinal neurons during a task that required rats to use a joystick to manipulate sound along a continuous frequency axis. We found neural representation of the entire behavioural task, including activity that formed discrete firing fields at particular sound frequencies. Neurons involved in this representation overlapped with the known spatial cell types in the circuit, such as place cells and grid cells. These results suggest that common circuit mechanisms in the hippocampal-entorhinal system are used to represent diverse behavioural tasks, possibly supporting cognitive processes beyond spatial navigation.

Functional Architecture of the Rat Parasubiculum.

The parasubiculum is a major input structure of layer 2 of medial entorhinal cortex, where most grid cells are found. Here we investigated parasubicular circuits of the rat by anatomical analysis combined with juxtacellular recording/labeling and tetrode recordings during spatial exploration. In tangential sections, the parasubiculum appears as a linear structure flanking the medial entorhinal cortex mediodorsally. With a length of ∼5.2 mm and a width of only ∼0.3 mm (approximately one dendritic tree diameter), the parasubiculum is both one of the longest and narrowest cortical structures. Parasubicular neurons span the height of cortical layers 2 and 3, and we observed no obvious association of deep layers to this structure. The "superficial parasubiculum" (layers 2 and 1) divides into ∼15 patches, whereas deeper parasubicular sections (layer 3) form a continuous band of neurons. Anterograde tracing experiments show that parasubicular neurons extend long "circumcurrent" axons establishing a "global" internal connectivity. The parasubiculum is a prime target of GABAergic and cholinergic medial septal inputs. Other input structures include the subiculum, presubiculum, and anterior thalamus. Functional analysis of identified and unidentified parasubicular neurons shows strong theta rhythmicity of spiking, a large fraction of head-direction selectivity (50%, 34 of 68), and spatial responses (grid, border and irregular spatial cells, 57%, 39 of 68). Parasubicular output preferentially targets patches of calbindin-positive pyramidal neurons in layer 2 of medial entorhinal cortex, which might be relevant for grid cell function. These findings suggest the parasubiculum might shape entorhinal theta rhythmicity and the (dorsoventral) integration of information across grid scales. SIGNIFICANCE STATEMENT: Grid cells in medial entorhinal cortex (MEC) are crucial components of an internal navigation system of the mammalian brain. The parasubiculum is a major input structure of layer 2 of MEC, where most grid cells are found. Here we provide a functional and anatomical characterization of the parasubiculum and show that parasubicular neurons display unique features (i.e., strong theta rhythmicity of firing, prominent head-direction selectivity, and output selectively targeted to layer 2 pyramidal cell patches of MEC). These features could contribute to shaping the temporal and spatial code of downstream grid cells in entorhinal cortex.

Impaired path integration and grid cell spatial periodicity in mice lacking GluA1-containing AMPA receptors.

The hippocampus and the parahippocampal region have been proposed to contribute to path integration. Mice lacking GluA1-containing AMPA receptors (GluA1(-/-) mice) were previously shown to exhibit impaired hippocampal place cell selectivity. Here we investigated whether path integration performance and the activity of grid cells of the medial entorhinal cortex (MEC) are affected in these mice. We first tested GluA1(-/-) mice on a standard food-carrying homing task and found that they were impaired in processing idiothetic cues. To corroborate these findings, we developed an L-maze task that is less complex and is performed entirely in darkness, thereby reducing numerous confounding variables when testing path integration. Also in this task, the performance of GluA1(-/-) mice was impaired. Next, we performed in vivo recordings in the MEC of GluA1(-/-) mice. MEC neurons exhibited altered grid cell spatial periodicity and reduced spatial selectivity, whereas head direction tuning and speed modulation were not affected. The firing associations between pairs of neurons in GluA1(-/-) mice were stable, both in time and space, indicating that attractor states were still present despite the lack of grid periodicity. Together, these results support the hypothesis that spatial representations in the hippocampal-entorhinal network contribute to path integration.

Hypothalamic and other connections with dorsal CA2 area of the mouse hippocampus.

The CA2 area is an important, although relatively unexplored, component of the hippocampus. We used various tracers to provide a comprehensive analysis of CA2 connections in C57BL/6J mice. Using various adeno-associated viruses that express fluorescent proteins, we found a vasopressinergic projection from the paraventricular nuclei of the hypothalamus (PVN) to the CA2 as well as a projection from pyramidal neurons of the CA2 to the supramammillary nuclei. These projections were confirmed by retrograde tracing. As expected, we observed CA2 afferent projections from neurons in ipsilateral entorhinal cortical layer II as well as from bilateral dorsal CA2 and CA3 using retrograde tracers. Additionally, we saw CA2 neuronal input from bilateral medial septal nuclei, vertical and horizontal limbs of the nucleus of diagonal band of Broca, supramammillary nuclei (SUM), and median raphe nucleus. Dorsal CA2 injections of adeno-associated virus expressing green fluorescent protein revealed axonal projections primarily to dorsal CA1, CA2, and CA3 bilaterally. No projection was detected to the entorhinal cortex from the dorsal CA2. These results are consistent with recent observations that the dorsal CA2 forms disynaptic connections with the entorhinal cortex to influence dynamic memory processing. Mouse dorsal CA2 neurons send bilateral projections to the medial and lateral septal nuclei, vertical and horizontal limbs of the diagonal band of Broca, and SUM. Novel connections from the PVN and to the SUM suggest important regulatory roles for CA2 in mediating social and emotional input for memory processing.

Dietary intake of unsaturated fatty acids modulates physiological properties of entorhinal cortex neurons in mice.

Dietary lipids modify brain fatty acid profile, but evidence of their direct effect on neuronal function is sparse. The enthorinal cortex (EC) neurons connecting to the hippocampus play a critical role in learning and memory. Here, we have exposed mice to diets based on canola:soybean oils (40 : 10, g/kg) or safflower : corn oils (25 : 25, g/kg) to investigate the relationship between the lipid profile of brain fatty acids and the intrinsic properties of EC neurons. Consumption of canola : soybean oil-enriched diet led to the increase of the monounsaturated fatty acid oleic acid and to a decrease of arachidonic acid in ethanolamine glycerophospholipids of the white matter. We also found an important rise in docosahexaenoic acid (DHA) within ethanolamine glycerophospholipids and phosphatidylserine of gray matter. The canola:soybean oil treatment led to a shorter duration of action potential (-21%), a reduction in the duration of postsynaptic response (-21%) and increased firing activity (+43%). Data from additional experiments with animals fed DHA alone or DHA with canola oil suggested that dietary monounsaturated fatty acid may have contributed to these effects on EC neuron physiology. Since neuronal function within the enthorhinal-hippocampal loop is critical to learning and memory processes, the present data may provide a functional basis for the beneficial cognitive effects of canola oil-based diets.

Afferent and efferent connections of the cortical and medial nuclei of the amygdala in sheep.

The cortical (CoA) and the medial (MeA) nuclei of the amygdala are involved in the processing of olfactory information relevant to social recognition in the ewe. To better understand the neural pathways responsible for these effects, the connections of both CoA and MeA with the telencephalic and diencephalic regions were studied by injecting an anterograde (Biotin-Dextran-Amine, BDA) or a retrograde (Fluorogold, FG) neuronal tracer into either the CoA or the MeA. Concerning the primary olfactory structures, the CoA receives inputs from both the main olfactory bulb and the accessory olfactory bulb (AOB), while the MeA is innervated by cells only from the AOB. Among the other olfactory structures, only the entorhinal cortex and the tenia tecta are connected with both the CoA and the MeA. With respect to the other secondary olfactory structures, the connections with the CoA and the MeA show segregating neuronal routes. The CoA is connected with the accessory olfactory nucleus, the piriform, the endopiriform and the orbitofrontal cortices while the MeA exhibited connections with the nucleus of the lateral olfactory tract, the perirhinal and the insular cortices. Concerning the diencephalic structures, only the MeA receives projections from the PVN and the MBH. On the other hand, we showed that the BNST is the major site of connection with both the CoA and the MeA. Reciprocal projections were observed between the CoA and the MeA and between both nuclei and the basal or the lateral nuclei of the amygdala with the exception of the CoA which does not send inputs to the lateral nucleus. These data are discussed in relation with olfactory learning in the context of sexual and maternal behavior in sheep.

Origin of calretinin-containing, vesicular glutamate transporter 2-coexpressing fiber terminals in the entorhinal cortex of the rat.

The entorhinal cortex of the rat (EC) contains a dense fiber plexus that expresses the calcium-binding protein calretinin (CR). Some CR fibers contain vesicular glutamate transporter 2 (VGluT2, associated with glutamatergic neurotransmission). CR-VGluT2 coexpressing fibers may have an extrinsic origin, for instance, the midline thalamic nucleus reuniens. Alternatively, they may belong to cortical interneurons. We studied the first possibility with anterograde and retrograde neuroanatomical tracing methods combined with CR and VGluT2 immunofluorescence and confocal laser scanning. The alternative possibility was studied with in situ hybridization fluorescence histochemistry for VGluT2 mRNA combined with CR immunofluorescence. In the anterograde tracing experiments, we observed many labeled reuniens fibers in EC expressing CR. Some of these labeled fibers contained immunoreactivity for VGluT2 and CR. In the complementary retrograde tracing experiments, we found retrogradely labeled cell bodies in nucleus reuniens of the thalamus that coexpressed CR. We also examined the colocalization of VGluT2 and CR in the entorhinal cortex by using in situ hybridization and CR immunofluorescence. In these experiments, we observed CR-immunopositive cortical neurons that coexpressed VGluT2. For the same sections, with CR as the principal marker and parvalbumin as a control marker, we found that parvalbumin neurons were negative for VGluT2 mRNA. Thus, CR-VGluT2-expressing axon terminals in EC belong to two sources: projection fibers from the thalamus and axon collaterals of local interneurons. VGluT2 expression is linked to the synaptic transmission of the excitatory neurotransmitter glutamate, so these thalamic CR-VGluT2 projection neurons and entorhinal CR-VGluT2 interneurons should be regarded as excitatory.

The majority of brain mast cells in B10.PL mice is present in the hippocampal formation.

In the healthy mammalian CNS, mast cells (MCs) are thought to be located mostly in the thalamus. In this study, we have systematically assessed the presence of MCs in the hippocampal formation (HF) and in the thalamus of normal male and female B10.PL mice. Giemsa(+) and Toluidine Blue(+) MCs were detected by histomorphometric analyses at perivascular and intraparenchymal sites of both the hippocampus and the entorhinal cortex. We found a mean number of 4.4 MCs in the HF of female and 3.3 MCs in male B10.PL mice. In contrast to the HF, no MCs were present in the thalamus of these mice. Notably, all HF-MCs showed immunoreactivity for Kit, the receptor for the MC growth and maturation factor SCF, as assessed by FITC-avidin/Kit double labelling. We demonstrate that the majority of brain MCs is found in the hippocampus and entorhinal cortex of B10.PL mice, though the total number of MCs is small compared to other mouse strains or rats. The presence of most brain MCs in the HF of B10.PL mice suggests a potential role of MCs in hippocampal physiology and pathology.

Localization of M2 muscarinic receptor protein in parvalbumin and calretinin containing cells of the adult rat entorhinal cortex using two complementary methods.

We investigated parvalbumin (PV) and calretinin (CR) containing interneurons in the rat entorhinal cortex. RNA amplification following single cell dissection of immunohistochemically labeled cells from layers II to VI revealed that PV cells, in contrast to CR cells, express the m2 muscarinic receptor (M2AchR) protein. Double immunostaining to confirm the results of RNA amplification indicated that the majority of PV cells contain M2AchR protein, whereas only a small proportion of CR cells do. In contrast, a large number of layer I CR cells, which are mostly Cajal-Retzius cells, were positive for M2AchR. RNA amplification following dissection of these cells also revealed that they contain the M2AchR protein. These findings emphasize that there are significant differences in the expression of different proteins, even among similar neuronal types in the same brain region. This highlights the importance of accurately collecting single cells, and knowledge of anatomical details in molecular biological studies.

A neuronal glutamate transporter contributes to neurotransmitter GABA synthesis and epilepsy.

The predominant neuronal glutamate transporter, EAAC1 (for excitatory amino acid carrier-1), is localized to the dendrites and somata of many neurons. Rare presynaptic localization is restricted to GABA terminals. Because glutamate is a precursor for GABA synthesis, we hypothesized that EAAC1 may play a role in regulating GABA synthesis and, thus, could cause epilepsy in rats when inactivated. Reduced expression of EAAC1 by antisense treatment led to behavioral abnormalities, including staring-freezing episodes and electrographic (EEG) seizures. Extracellular hippocampal and thalamocortical slice recordings showed excessive excitability in antisense-treated rats. Patch-clamp recordings of miniature IPSCs (mIPSCs) conducted in CA1 pyramidal neurons in slices from EAAC1 antisense-treated animals demonstrated a significant decrease in mIPSC amplitude, indicating decreased tonic inhibition. There was a 50% loss of hippocampal GABA levels associated with knockdown of EAAC1, and newly synthesized GABA from extracellular glutamate was significantly impaired by reduction of EAAC1 expression. EAAC1 may participate in normal GABA neurosynthesis and limbic hyperexcitability, whereas epilepsy can result from a disruption of the interaction between EAAC1 and GABA metabolism.

Fos imaging reveals differential neuronal activation of areas of rat temporal cortex by novel and familiar sounds.

To provide information about the possible regions involved in auditory recognition memory, this study employed an imaging technique that has proved valuable in the study of visual recognition memory. The technique was used to image populations of neurons that are differentially activated by novel and familiar auditory stimuli, thereby paralleling previous studies of visual familiarity discrimination. Differences evoked by novel and familiar sounds in the activation of neurons were measured in different parts of the rat auditory pathway by immunohistochemistry for the protein product (Fos) of the immediate early gene c-fos. Significantly higher counts of stained neuronal nuclei (266 +/- 21/mm2) were evoked by novel than by familiar sounds (192 +/- 17/mm2) in the auditory association cortex (area Te3; AudA). No such significant differences were found for the inferior colliculus, primary auditory cortex, postrhinal cortex, perirhinal cortex (PRH), entorhinal cortex, amygdala or hippocampus. These findings are discussed in relation to the results of lesion studies and what is known of areas involved in familiarity discrimination for visual stimuli. Differential activation is produced by novel and familiar individual stimuli in sensory association cortex for both auditory and visual stimuli, whereas the PRH is differentially activated by visual but not auditory stimuli. It is suggested that this latter difference is related to the nature of the particular auditory and visual stimuli used.

Expression of the cannabinoid receptor CB1 in distinct neuronal subpopulations in the adult mouse forebrain.

Cannabinoids can modulate motor behaviour, learning and memory, cognition and pain perception. These effects correlate with the expression of the cannabinoid receptor 1 (CB1) and with the presence of endogenous cannabinoids in the brain. In trying to obtain further insights into the mechanisms underlying the modulatory effects of cannabinoids, CB1-positive neurons were determined in the murine forebrain at a single cell resolution. We performed a double in situ hybridization study to detect mRNA of CB1 in combination with mRNA of glutamic acid decarboxylase 65k, neuropeptide cholecystokinin (CCK), parvalbumin, calretinin and calbindin D28k, respectively. Our results revealed that CB1-expressing cells can be divided into distinct neuronal subpopulations. There is a clear distinction between neurons containing CB1 mRNA either at high levels or low levels. The majority of high CB1-expressing cells are GABAergic (gamma-aminobutyric acid) neurons belonging mainly to the cholecystokinin-positive and parvalbumin-negative type of interneurons (basket cells) and, to a lower extent, to the calbindin D28k-positive mid-proximal dendritic inhibitory interneurons. Only a fraction of low CB1-expressing cells is GABAergic. In the hippocampus, amygdala and entorhinal cortex area, CB1 mRNA is present at low but significant levels in many non-GABAergic cells that can be considered as projecting principal neurons. Thus, a complex mechanism appears to underlie the modulatory effects of cannabinoids. They might act on principal glutamatergic circuits as well as modulate local GABAergic inhibitory circuits. CB1 is very highly coexpressed with CCK. It is known that cannabinoids and CCK often have opposite effects on behaviour and physiology. Therefore, we suggest that a putative cross-talk between cannabinoids and CCK might exist and will be relevant to better understanding of physiology and pharmacology of the cannabinoid system.

Alumina gel injections into the temporal lobe of rhesus monkeys cause complex partial seizures and morphological changes found in human temporal lobe epilepsy.

The goal of the present study was to determine whether alumina gel injections into temporal lobe structures cause complex partial seizures (CPS) and pathological changes observed in human temporal lobe epilepsy. Rhesus monkeys with alumina gel injections in the amygdala, perirhinal and entorhinal cortices, or Ammon's horn and dentate gyrus all initially displayed focal pathological electroencephalographic (EEG) slowing limited to the site of injection. After clinical seizures developed, they also displayed widespread pathological EEG slowing over both hemispheres, interictal and ictal epileptiform EEG abnormalities limited to the mesial-inferior temporal lobe on the side of injection, and different degrees of spread to other ipsilateral and contralateral structures. Noninjected control and nonepileptic monkeys with injections into the middle and inferior temporal gyri displayed no hippocampal neuronal loss or mossy fiber sprouting. When alumina gel was injected into the amygdala, CPS began within 3-6 weeks and degeneration of neurons and gliosis occurred in the perirhinal cortex or the hippocampus, with consequent sprouting of mossy fibers in the dentate gyrus. Dispersion of the granule cell layer was also observed. Other monkeys with alumina gel in the perirhinal and entorhinal cortices developed CPS within 2-3 weeks after the injections and displayed mossy fiber sprouting only after 4 weeks after the injections. Alumina gel in Ammon's horn and the dentate gyrus also induced CPS, but mossy fiber sprouting was limited to sites immediately adjacent to the injection, probably because none survived more than 4 weeks after the injections. This nonhuman primate model of CPS displayed similar anatomical, behavioral, and EEG features as observed in human temporal lobe epilepsy and provides opportunities to analyze the chronological sequence of epileptogenesis and to test potential therapies.

PACSIN, a brain protein that is upregulated upon differentiation into neuronal cells.

To identify genes that are differentially expressed during self-repair processes in mouse brain, we screened a subtracted cDNA library enriched for brain-specific clones. One of these clones, H74, detected a 4.4-kb mRNA predominantly expressed in brain and dorsal root ganglia neurons. Expression increased continuously during the lifespan and the state of differentiation, but decreased after entorhinal-cortex lesion. A full-length cDNA clone was isolated from a cerebellum cDNA library and characterized. Sequence analysis and database search revealed high sequence similarity to FAP52, a protein expressed in focal-adhesion contacts, and uncharacterized Echinococcus and Caenorhabditis elegans gene products. Furthermore, peptide sequences derived from human cDNA fragments showed up to 65% sequence identity at the amino acid level. The presence of a C-terminal src homology 3 (SH3) domain and its phosphorylation by casein kinase 2 (CK2) and protein kinase C (PKC) imply a role in signaling. Here we demonstrate that the gene encodes a phosphoprotein, referred to as PACSIN, with a restricted spatial and temporal expression pattern.

The distribution of two calcium binding proteins, calbindin D-28K and parvalbumin, in the entorhinal cortex of the adult mouse.

The immunohistochemical localization of two specific calcium binding proteins, parvalbumin (PV) and calbindin D-28K (CB), were examined in the entorhinal cortex (EC) of the adult mouse. The PV and CB immunoreactivities exhibited a conspicuous regional and laminar distribution in the EC. The overall immunostaining pattern of PV and CB appeared to be complementary in the EC, especially in the medial entorhinal area (MEA). In the dorsal MEA, although layer 2 showed intense PV and CB immunostaining, the PV immunoreactivity was denser in layers 3, 5 and 6a than in layers 4 and 6b, whereas the CB immunoreactivity was denser in layers 4 and 6b than in layers 3, 5 and 6a. Moreover, we recognized the dorsoventral gradation of the PV and CB staining that is, in the dorsal to ventral direction, the intensity of the PV immunostaining in layers 2, 3, 5 and 6a gradually decreased whereas that of the CB immunostaining in those layers gradually increased. In addition, a similar dorsoventral gradation was also observed in the number of PV immunoreactive (PV-IR) and CB-IR neurons in layer 3. In layer 2 of the MEA, the CB-IR neurons were clustered, while displaying a patch-like pattern which could not be recognized in either Nissl staining or PV staining. In contrast, layer 2 of the LEA was separated into two sublayers, the superficial sublayer 2a and the deeper sublayer 2b; both of these sublayers consisted of cell clusters recognized by Nissl staining. These sublayers showed a prominent difference in their CB immunoreactivity; the cells in the layer 2a clusters were CB negative, whereas the cells in the layer 2b clusters were CB-IR. Furthermore, we also recognized a particular region at the most medial part of the MEA, where layer 2 was different from the other portion of the MEA regarding CB immunoreactivity and the cells containing another calcium binding protein, calretinin, were clustered in layer 3. Both the adjacent section technique and the fluorescent double-staining technique clearly revealed that a relatively large number of presumable interneurons contained both PV and CB immunoreactivities. Furthermore, the three neuron groups that were immunoreactive for both PV and CB, immunoreactive for PV alone and immunoreactive for CB alone were heterogeneous in their structural features such as shape and size, and no particular difference was found in their structural features among these three groups.