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Neural implants with large numbers of electrodes have become an important tool for examining brain functions. However, these devices typically displace a large intracranial volume compared with the neurons they record. This large size limits the density of implants, provokes tissue reactions that degrade chronic performance, and impedes the ability to accurately visualize recording sites within intact circuits. Here we report next-generation silicon-based neural probes at a cellular scale (5 × 10 µm cross section), with ultra-high-density packing (as little as 66 µm between shanks) and 64 or 256 closely spaced recording sites per probe. We show that these probes can be inserted into superficial or deep brain structures and record large spikes in freely behaving rats for many weeks. Finally, we demonstrate a slice-in-place approach for the precise registration of recording sites relative to nearby neurons and anatomical features, including striatal µ-opioid receptor patches. This scalable technology provides a valuable tool for examining information processing within neural circuits and potentially for human brain-machine interfaces. NEW & NOTEWORTHY Devices with many electrodes penetrating into the brain are an important tool for investigating neural information processing, but they are typically large compared with neurons. This results in substantial damage and makes it harder to reconstruct recording locations within brain circuits. This paper presents high-channel-count silicon probes with much smaller features and a method for slicing through probe, brain, and skull all together. This allows probe tips to be directly observed relative to immunohistochemical markers.

Sleep has been implicated in both memory consolidation and forgetting of experiences. However, it is unclear what governs the balance between consolidation and forgetting. Here, we tested how activity-dependent processing during sleep might differentially regulate these two processes. We specifically examined how neural reactivations during non-rapid eye movement (NREM) sleep were causally linked to consolidation versus weakening of the neural correlates of neuroprosthetic skill. Strikingly, we found that slow oscillations (SOs) and delta (δ) waves have dissociable and competing roles in consolidation versus forgetting. By modulating cortical spiking linked to SOs or δ waves using closed-loop optogenetic methods, we could, respectively, weaken or strengthen consolidation and thereby bidirectionally modulate sleep-dependent performance gains. We further found that changes in the temporal coupling of spindles to SOs relative to δ waves could account for such effects. Thus, our results indicate that neural activity driven by SOs and δ waves have competing roles in sleep-dependent memory consolidation., (Published by Elsevier Inc.)

Much progress has been made in understanding how behavioral experience and neural activity can modify the structure and function of neural circuits during development and in the adult brain. Studies of physiological and molecular mechanisms underlying activity-dependent plasticity in animal models have suggested potential therapeutic approaches for a wide range of brain disorders in humans. Physiological and electrical stimulations as well as plasticity-modifying molecular agents may facilitate functional recovery by selectively enhancing existing neural circuits or promoting the formation of new functional circuits. Here, we review the advances in basic studies of neural plasticity mechanisms in developing and adult nervous systems and current clinical treatments that harness neural plasticity, and we offer perspectives on future development of plasticity-based therapy., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Memory formation requires learning-based molecular and structural changes in neurons, whereas matrix metalloproteinase (MMP) 9 is involved in the synaptic plasticity by cleaving extracellular matrix proteins and, thus, is associated with learning processes in the mammalian brain. Because the mechanisms of MMP-9 transcription in the brain are poorly understood, this study aimed to elucidate regulation of MMP-9 gene expression in the mouse brain after fear learning. We show here that contextual fear conditioning markedly increases MMP-9 transcription, followed by enhanced enzymatic levels in the three major brain structures implicated in fear learning, i.e. the amygdala, hippocampus, and prefrontal cortex. To reveal the role of AP-1 transcription factor in MMP-9 gene expression, we have used reporter gene constructs with specifically mutated AP-1 gene promoter sites. The constructs were introduced into the medial prefrontal cortex of neonatal mouse pups by electroporation, and the regulation of MMP-9 transcription was studied after contextual fear conditioning in the adult animals. Specifically, -42/-50- and -478/-486-bp AP-1 binding motifs of the mouse MMP-9 promoter sequence have been found to play a major role in MMP-9 gene activation. Furthermore, increases in MMP-9 gene promoter binding by the AP-1 transcription factor proteins c-Fos and c-Jun have been demonstrated in all three brain structures under investigation. Hence, our results suggest that AP-1 acts as a positive regulator of MMP-9 transcription in the brain following fear learning.

Oscillatory phase coupling within large-scale brain networks is a topic of increasing interest within systems, cognitive, and theoretical neuroscience. Evidence shows that brain rhythms play a role in controlling neuronal excitability and response modulation (Haider B, McCormick D. Neuron 62: 171-189, 2009) and regulate the efficacy of communication between cortical regions (Fries P. Trends Cogn Sci 9: 474-480, 2005) and distinct spatiotemporal scales (Canolty RT, Knight RT. Trends Cogn Sci 14: 506-515, 2010). In this view, anatomically connected brain areas form the scaffolding upon which neuronal oscillations rapidly create and dissolve transient functional networks (Lakatos P, Karmos G, Mehta A, Ulbert I, Schroeder C. Science 320: 110-113, 2008). Importantly, testing these hypotheses requires methods designed to accurately reflect dynamic changes in multivariate phase coupling within brain networks. Unfortunately, phase coupling between neurophysiological signals is commonly investigated using suboptimal techniques. Here we describe how a recently developed probabilistic model, phase coupling estimation (PCE; Cadieu C, Koepsell K Neural Comput 44: 3107-3126, 2010), can be used to investigate changes in multivariate phase coupling, and we detail the advantages of this model over the commonly employed phase-locking value (PLV; Lachaux JP, Rodriguez E, Martinerie J, Varela F. Human Brain Map 8: 194-208, 1999). We show that the N-dimensional PCE is a natural generalization of the inherently bivariate PLV. Using simulations, we show that PCE accurately captures both direct and indirect (network mediated) coupling between network elements in situations where PLV produces erroneous results. We present empirical results on recordings from humans and nonhuman primates and show that the PCE-estimated coupling values are different from those using the bivariate PLV. Critically on these empirical recordings, PCE output tends to be sparser than the PLVs, indicating fewer significant interactions and perhaps a more parsimonious description of the data. Finally, the physical interpretation of PCE parameters is straightforward: the PCE parameters correspond to interaction terms in a network of coupled oscillators. Forward modeling of a network of coupled oscillators with parameters estimated by PCE generates synthetic data with statistical characteristics identical to empirical signals. Given these advantages over the PLV, PCE is a useful tool for investigating multivariate phase coupling in distributed brain networks.

Understanding the principles governing the dynamic coordination of functional brain networks remains an important unmet goal within neuroscience. How do distributed ensembles of neurons transiently coordinate their activity across a variety of spatial and temporal scales? While a complete mechanistic account of this process remains elusive, evidence suggests that neuronal oscillations may play a key role in this process, with different rhythms influencing both local computation and long-range communication. To investigate this question, we recorded multiple single unit and local field potential (LFP) activity from microelectrode arrays implanted bilaterally in macaque motor areas. Monkeys performed a delayed center-out reach task either manually using their natural arm (Manual Control, MC) or under direct neural control through a brain-machine interface (Brain Control, BC). In accord with prior work, we found that the spiking activity of individual neurons is coupled to multiple aspects of the ongoing motor beta rhythm (10-45 Hz) during both MC and BC, with neurons exhibiting a diversity of coupling preferences. However, here we show that for identified single neurons, this beta-to-rate mapping can change in a reversible and task-dependent way. For example, as beta power increases, a given neuron may increase spiking during MC but decrease spiking during BC, or exhibit a reversible shift in the preferred phase of firing. The within-task stability of coupling, combined with the reversible cross-task changes in coupling, suggest that task-dependent changes in the beta-to-rate mapping play a role in the transient functional reorganization of neural ensembles. We characterize the range of task-dependent changes in the mapping from beta amplitude, phase, and inter-hemispheric phase differences to the spike rates of an ensemble of simultaneously-recorded neurons, and discuss the potential implications that dynamic remapping from oscillatory activity to spike rate and timing may hold for models of computation and communication in distributed functional brain networks.

Objective: Pediatric ischemic stroke is a poorly understood, yet clinically important, problem. The sole approved treatment for acute stroke is tissue-type plasminogen activator. However, tissue plasminogen activator vasoactivity aggravates hypoxia/ischemia-induced impairment of cerebrovasodilation in response to hypercapnia and hypotension in newborn pigs. Mitogen-activated protein kinase (a family of 3 kinases, extracellular signal-related kinase, p38, and c-Jun-N-terminal kinase) is upregulated after hypoxia/ischemia. Coupling of tissue plasminogen activator to red blood cells prevented hypoxia/ischemia-induced impairment of dilation and suppressed extracellular signal-related kinase mitogen-activated protein kinase activation. This study investigated the differential roles of mitogen-activated protein kinase isoforms in the effects of red blood cells-tissue plasminogen activator on cerebrovasodilation in a translationally relevant injury model, photothrombosis., Design: Prospective, randomized animal study., Setting: : University laboratory., Subjects: Newborn (1- to 5-day-old) pigs., Interventions: Cerebral blood flow and pial artery diameter were determined before and after photothrombotic injury (laser 532 nm and erythrosine B) was produced in piglets equipped with a closed cranial window. Cerebral blood flow extracellular signal-related kinase, p38, and c-Jun-N-terminal kinase mitogen-activated protein kinase were determined by enzyme-linked immunosorbent assay., Measurements and Main Results: Tissue plasminogen activator and red blood cells-tissue plasminogen activator alleviated reduction of cerebral blood flow after photothrombotic injury. Cerebrovasodilation was blunted by photothrombotic injury, reversed to vasoconstriction by tissue plasminogen activator, but dilation was maintained by red blood cells-tissue plasminogen activator. Cerebral blood flow c-Jun-N-terminal kinase and p38 mitogen-activated protein kinase but not extracellular signal-related kinase mitogen-activated protein kinase was elevated by photothrombotic injury, an effect potentiated by tissue plasminogen activator. Red blood cells-tissue plasminogen activator blocked c-Jun-N-terminal kinase but potentiated p38 mitogen-activated protein kinase upregulation after photothrombotic injury. A c-Jun-N-terminal kinase mitogen-activated protein kinase antagonist prevented, a p38 mitogen-activated protein kinase antagonist potentiated, whereas an extracellular signal-related kinase mitogen-activated protein kinase antagonist had no effect on dilator impairment after photothrombotic injury., Conclusions: These data indicate that in addition to restoring perfusion, red blood cells-tissue plasminogen activator prevents impairment of cerebrovasodilation after photothrombotic injury through blockade of c-Jun-N-terminal kinase and potentiation of p38 mitogen-activated protein kinase. These data suggest tissue plasminogen activator coupling to red blood cells offers a novel approach to increase the benefit/risk ratio of thrombolytic therapy to treat central nervous system ischemic disorders.

Hebb proposed that neuronal cell assemblies are critical for effective perception, cognition, and action. However, evidence for brain mechanisms that coordinate multiple coactive assemblies remains lacking. Neuronal oscillations have been suggested as one possible mechanism for cell assembly coordination. Prior studies have shown that spike timing depends upon local field potential (LFP) phase proximal to the cell body, but few studies have examined the dependence of spiking on distal LFP phases in other brain areas far from the neuron or the influence of LFP-LFP phase coupling between distal areas on spiking. We investigated these interactions by recording LFPs and single-unit activity using multiple microelectrode arrays in several brain areas and then used a unique probabilistic multivariate phase distribution to model the dependence of spike timing on the full pattern of proximal LFP phases, distal LFP phases, and LFP-LFP phase coupling between electrodes. Here we show that spiking activity in single neurons and neuronal ensembles depends on dynamic patterns of oscillatory phase coupling between multiple brain areas, in addition to the effects of proximal LFP phase. Neurons that prefer similar patterns of phase coupling exhibit similar changes in spike rates, whereas neurons with different preferences show divergent responses, providing a basic mechanism to bind different neurons together into coordinated cell assemblies. Surprisingly, phase-coupling-based rate correlations are independent of interneuron distance. Phase-coupling preferences correlate with behavior and neural function and remain stable over multiple days. These findings suggest that neuronal oscillations enable selective and dynamic control of distributed functional cell assemblies.

Closed-loop operation of a brain-machine interface (BMI) relies on the subject's ability to learn an inverse transformation of the plant to be controlled. In this paper, we propose a model of the learning process that undergoes closed-loop BMI operation. We first explore the properties of the model and show that it is able to learn an inverse model of the controlled plant. Then, we compare the model predictions to actual experimental neural and behavioral data from nonhuman primates operating a BMI, which demonstrate high accordance of the model with the experimental data. Applying tools from control theory to this learning model will help in the design of a new generation of neural information decoders which will maximize learning speed for BMI users.

Babies experience hypoxia (H) and ischemia (I) from stroke. The only approved treatment for stroke is fibrinolytic therapy with tissue-type plasminogen activator (tPA). However, tPA potentiates H/I-induced impairment of responses to cerebrovasodilators such as hypercapnia and hypotension, and blockade of tPA-mediated vasoactivity prevents this deleterious effect. Coupling of tPA to red blood cells (RBCs) reduces its central nervous system (CNS) toxicity through spatially confining the drug to the vasculature. Mitogen-activated protein kinase (MAPK), a family of at least three kinases, is upregulated after H/I. In this study we determined whether RBC-tPA given before or after cerebral H/I would preserve responses to cerebrovasodilators and prevent neuronal injury mediated through the extracellular signal-related kinase (ERK) MAPK pathway. Animals given RBC-tPA maintained responses to cerebrovasodilators at levels equivalent to pre-H/I values. cerebrospinal fluid and brain parenchymal ERK MAPK was elevated by H/I and this upregulation was potentiated by tPA, but blunted by RBC-tPA. U0126, an ERK MAPK antagonist, also maintained cerebrovasodilation post H/I. Neuronal degeneration in CA1 hippocampus after H/I was not improved by tPA, but was ameliorated by RBC-tPA and U0126. These data suggest that coupling of tPA to RBCs offers a novel approach toward increasing the benefit/risk ratio of thrombolytic therapy for CNS disorders associated with H/I.

Purpose: O377 was identified as a new dominant cataract mutation in mice after radiation experiments. The purpose of this study was to genetically characterize the mutation and to analyze its biological consequences., Methods: Linkage analysis of the O377 mouse mutant was performed; candidate genes including Crybb2 were sequenced. The authors analyzed eyes and brains of the mutants by histology and the expression domains of Crybb2 by in situ hybridization and immunohistochemistry. RNA was isolated from whole brains of heterozygous and homozygous O377 mutants, and differential expression arrays were performed. All studies were compared with age- and strain-matched wild-type mice., Results: The mutation was mapped to chromosome 5 and characterized as an A-->T substitution at the end of intron 5 of the Crybb2 gene. It led to alternative splicing with a 57-bp insertion in the mRNA and to 19 additional amino acids in the protein. In the brain, betaB2-crystallin was expressed in the cerebellum, olfactory bulb, cerebral cortex, and hippocampus. The only morphologic difference in the brain is the increased number of Purkinje cells in the cerebellum of homozygous strain-matched mutants. Differential expression analysis revealed the upregulation of calpain-3 in the brain of homozygous mutants, which was confirmed by quantitative real-time PCR., Conclusions: These results confirm the third allele of Crybb2 in the mouse that also affected exon 6 and the fourth Greek key motif. Moreover, expression analysis of Crybb2 identified for the first time distinct regions of expression in the brain, and the differential expression analysis points to the participation of Ca2+ in the corresponding pathologic processes.