The human brain online: an open resource for advancing brain research

Cross-modality synthesis of EM time series and live fluorescence imaging

Analyses across imaging modalities allow the integration of complementary spatiotemporal information about brain development, structure, and function. However, systematic atlasing across modalities is limited by challenges to effective image alignment. We combine highly spatially resolved electron microscopy (EM) and highly temporally resolved time-lapse fluorescence microscopy (FM) to examine the emergence of a complex nervous system in Caenorhabditis elegans embryogenesis. We generate an EM time series at four classic developmental stages and create a landmark-based co-optimization algorithm for cross-modality image alignment, which handles developmental heterochrony among datasets to achieve accurate single-cell level alignment. Synthesis based on the EM series and time-lapse FM series carrying different cell-specific markers reveals critical dynamic behaviors across scales of identifiable individual cells in the emergence of the primary neuropil, the nerve ring, as well as a major sensory organ, the amphid. Our study paves the way for systematic cross-modality data synthesis in C. elegans and demonstrates a powerful approach that may be applied broadly.

The neurobiological basis of sex differences in learned fear and its inhibition

Learning that certain cues or environments predict threat enhances survival by promoting appropriate fear and the resulting defensive responses. Adapting to changing stimulus contingencies by learning that such cues no longer predict threat, or distinguishing between these threat-related and other innocuous stimuli, also enhances survival by limiting fear responding in an appropriate manner to conserve resources. Importantly, a failure to inhibit fear in response to harmless stimuli is a feature of certain anxiety and trauma-related disorders, which are also associated with dysfunction of the neural circuitry underlying learned fear and its inhibition. Interestingly, these disorders are up to twice as common in women, compared to men. Despite this striking sex difference in disease prevalence, the neurobiological factors involved remain poorly understood. This is due in part to the majority of relevant preclinical studies having neglected to include female subjects alongside males, which has greatly hindered progress in this field. However, more recent studies have begun to redress this imbalance and emerging evidence indicates that there are significant sex differences in the inhibition of learned fear and associated neural circuit function. This paper provides a narrative review on sex differences in learned fear and its inhibition through extinction and discrimination, along with the key gonadal hormone and brain mechanisms involved. Understanding the endocrine and neural basis of sex differences in learned fear inhibition may lead to novel insights on the neurobiological mechanisms underlying the enhanced vulnerability to develop anxiety-related disorders that are observed in women.

Extracellular voltage thresholds for maximizing information extraction in primate auditory cortex: implications for a brain computer interface

OBJECTIVE

Research by Oby et al (2016) demonstrated that the optimal threshold for extracting information from visual and motor cortices may differ from the optimal threshold for identifying single neurons via spike sorting methods. The optimal threshold for extracting information from auditory cortex has yet to be identified, nor has the optimal temporal scale for representing auditory cortical activity. Here, we describe a procedure to jointly optimize the extracellular threshold and bin size with respect to the decoding accuracy achieved by a linear classifier for a diverse set of auditory stimuli.

APPROACH

We used linear multichannel arrays to record extracellular neural activity from the auditory cortex of awake squirrel monkeys passively listening to both simple and complex sounds. We executed a grid search of the coordinate space defined by the voltage threshold (in units of standard deviation) and the bin size (in units of milliseconds), and computed decoding accuracy at each point.

MAIN RESULTS

The optimal threshold for information extraction was consistently near two standard deviations below the voltage trace mean, which falls significantly below the range of three to five standard deviations typically used as inputs to spike sorting algorithms in basic research and in brain-computer interface (BCI) applications. The optimal binwidth was minimized at the optimal voltage threshold, particularly for acoustic stimuli dominated by temporally dynamic features, indicating that permissive thresholding permits readout of cortical responses with temporal precision on the order of a few milliseconds.

SIGNIFICANCE

The improvements in decoding accuracy we observed for optimal readout parameters suggest that standard thresholding methods substantially underestimate the information present in auditory cortical spiking patterns. The fact that optimal thresholds were relatively low indicates that local populations of cortical neurons exhibit high temporal coherence that could be leveraged in service of future auditory BCI applications.

Mesenchymal stem cell derived secretome and extracellular vesicles for acute lung injury and other inflammatory lung diseases

INTRODUCTION

Acute respiratory distress syndrome is a major cause of respiratory failure in critically ill patients. Despite extensive research into its pathophysiology, mortality remains high. No effective pharmacotherapy exists. Based largely on numerous preclinical studies, administration of mesenchymal stem or stromal cell (MSC) as a therapeutic for acute lung injury holds great promise, and clinical trials are currently underway. However, concern for the use of stem cells, specifically the risk of iatrogenic tumor formation, remains unresolved. Accumulating evidence now suggest that novel cell-free therapies including MSC-derived conditioned medium and extracellular vesicles released from MSCs might constitute compelling alternatives.

AREAS COVERED

The current review summarizes the preclinical studies testing MSC conditioned medium and/or MSC extracellular vesicles as treatment for acute lung injury and other inflammatory lung diseases.

EXPERT OPINION

While certain logistical obstacles limit the clinical applications of MSC conditioned medium such as the volume required for treatment, the therapeutic application of MSC extracellular vesicles remains promising, primarily due to ability of extracellular vesicles to maintain the functional phenotype of the parent cell. However, utilization of MSC extracellular vesicles will require large-scale production and standardization concerning identification, characterization and quantification.

Fabrication and initial testing of the μDBS: a novel Deep Brain Stimulation electrode with thousands of individually controllable contacts

High frequency electrical stimulation of deep brain structures such as the subthalamic nucleus in Parkinson's disease or thalamus for essential tremor is used clinically to reduce symptom severity. Deep brain stimulation activates neurons in specific brain structures and connection pathways, overriding aberrant neural activity associated with symptoms. While optimal deep brain stimulation might activate a particular neural structure precisely, existing deep brain stimulation can only generate roughly-spherical regions of activation that do not overlap with any target anatomy. Additionally, side effects linked to stimulation may be the result of limited control over placement of stimulation and its subsequent spread out of optimal target boundaries. We propose a novel lead with thousands of individually controllable contacts capable of asymmetric stimulation profiles. Here we outline the design motivation, manufacturing process, and initial testing of this new electrode design, placing it on track for further directional stimulation studies.

The evolution of Homo sapiens denisova and Homo sapiens neanderthalensis miRNA targeting genes in the prenatal and postnatal brain

BACKGROUND

As the evolution of miRNA genes has been found to be one of the important factors in formation of the modern type of man, we performed a comparative analysis of the evolution of miRNA genes in two archaic hominines, Homo sapiens neanderthalensis and Homo sapiens denisova, and elucidated the expression of their target mRNAs in bain.

RESULTS

A comparative analysis of the genomes of primates, including species in the genus Homo, identified a group of miRNA genes having fixed substitutions with important implications for the evolution of Homo sapiens neanderthalensis and Homo sapiens denisova. The mRNAs targeted by miRNAs with mutations specific for Homo sapiens denisova exhibited enhanced expression during postnatal brain development in modern humans. By contrast, the expression of mRNAs targeted by miRNAs bearing variations specific for Homo sapiens neanderthalensis was shown to be enhanced in prenatal brain development.

CONCLUSIONS

Our results highlight the importance of changes in miRNA gene sequences in the course of Homo sapiens denisova and Homo sapiens neanderthalensis evolution. The genetic alterations of miRNAs regulating the spatiotemporal expression of multiple genes in the prenatal and postnatal brain may contribute to the progressive evolution of brain function, which is consistent with the observations of fine technical and typological properties of tools and decorative items reported from archaeological Denisovan sites. The data also suggest that differential spatial-temporal regulation of gene products promoted by the subspecies-specific mutations in the miRNA genes might have occurred in the brains of Homo sapiens denisova and Homo sapiens neanderthalensis, potentially contributing to the cultural differences between these two archaic hominines.

Stroke and the connectome: how connectivity guides therapeutic intervention

Connections between neurons are affected within 3 min of stroke onset by massive ischemic depolarization and then delayed cell death. Some connections can recover with prompt reperfusion; others associated with the dying infarct do not. Disruption in functional connectivity is due to direct tissue loss and indirect disconnections of remote areas known as diaschisis. Stroke is devastating, yet given the brain's redundant design, collateral surviving networks and their connections are well-positioned to compensate. Our perspective is that new treatments for stroke may involve a rational functional and structural connections-based approach. Surviving, affected, and at-risk networks can be identified and targeted with scenario-specific treatments. Strategies for recovery may include functional inhibition of the intact hemisphere, rerouting of connections, or setpoint-mediated network plasticity. These approaches may be guided by brain imaging and enabled by patient- and injury-specific brain stimulation, rehabilitation, and potential molecule-based strategies to enable new connections.

Hypomethylation of the paternally inherited LRRTM1 promoter linked to schizophrenia

Epigenetic effects on psychiatric traits remain relatively under-studied, and it remains unclear what the sizes of individual epigenetic effects may be, or how they vary between different clinical populations. The gene LRRTM1 (chromosome 2p12) has previously been linked and associated with schizophrenia in a parent-of-origin manner in a set of affected siblings (LOD = 4.72), indirectly suggesting a disruption of paternal imprinting at this locus in these families. From the same set of siblings that originally showed strong linkage at this locus, we analyzed 99 individuals using 454-bisulfite sequencing, from whole blood DNA, to measure the level of DNA methylation in the promoter region of LRRTM1. We also assessed seven additional loci that would be informative to compare. Paternal identity-by-descent sharing at LRRTM1, within sibling pairs, was linked to their similarity of methylation at the gene's promoter. Reduced methylation at the promoter showed a significant association with schizophrenia. Sibling pairs concordant for schizophrenia showed more similar methylation levels at the LRRTM1 promoter than diagnostically discordant pairs. The alleles of common SNPs spanning the locus did not explain this epigenetic linkage, which can therefore be considered as largely independent of DNA sequence variation and would not be detected in standard genetic association analysis. Our data suggest that hypomethylation at the LRRTM1 promoter, particularly of the paternally inherited allele, was a risk factor for the development of schizophrenia in this set of siblings affected with familial schizophrenia, and that had previously showed linkage at this locus in an affected-sib-pair context.

Functional associations among G protein-coupled neurotransmitter receptors in the human brain

Background

The activity of neurons is controlled by groups of neurotransmitter receptors rather than by individual receptors. Experimental studies have investigated some receptor interactions, but currently little information is available about transcriptional associations among receptors at the whole-brain level.

Results

A total of 4950 correlations between 100 G protein-coupled neurotransmitter receptors were examined across 169 brain regions in the human brain using expression data published in the Allen Human Brain Atlas. A large number of highly significant correlations were found, many of which have not been investigated in hypothesis-driven studies. The highest positive and negative correlations of each receptor are reported, which can facilitate the construction of receptor sets likely to be affected by altered transcription of one receptor (such sets always exist, but their members are difficult to predict). A graph analysis isolated two large receptor communities, within each of which receptor mRNA levels were strongly cross-correlated.

Conclusions

The presented systematic analysis shows that the mRNA levels of many G protein-coupled receptors are interdependent. This finding is not unexpected, since the brain is a highly integrated complex system. However, the analysis also revealed two novel properties of global brain structure. First, receptor correlations are described by a simple statistical distribution, which suggests that receptor interactions may be guided by qualitatively similar processes. Second, receptors appear to form two large functional communities, which might be differentially affected in brain disorders.

Brain banking for neurological disorders

Brain banks are used to gather, store, and provide human brain tissue for research and have been fundamental to improving our knowledge of the brain in health and disease. To maintain this role, the legal and ethical issues relevant to the operations of brain banks need to be more widely understood. In recent years, researchers have reported that shortages of high-quality brain tissue samples from both healthy and diseased people have impaired their efforts. Closer collaborations between brain banks and improved strategies for brain donation programmes will be essential to overcome these problems as the demand for brain tissue increases and new research techniques become more widespread, with the potential for substantial scientific advances in increasingly common neurological disorders.