Spatial Sequencing: A Perspective.

Fluorescent spatial sequencing brings next-generation sequencing into a new realm capable of identifying nucleic acids in the cell's natural environment. For the first time, scientists are able to multiplex the assignment of specific locations to hundreds of transcriptional targets and lay the foundation for understanding how genetic changes control the fate of each cell within the tissue microenvironment. In this perspective, we discuss the capabilities of fluorescent spatial sequencing in the context of other spatial imaging technologies and describe how these new technologies offer a data-rich, multiomic solution to many research applications. Fluorescent spatial sequencing has opened options for exploring many fundamental questions in biology, helping us gain a better understanding of cell and tissue development and disease progression.

From evoked potentials to cortical currents: Resolving V1 and V2 components using retinotopy constrained source estimation without fMRI.

Despite evoked potentials' (EP) ubiquity in research and clinical medicine, insights are limited to gross brain dynamics as it remains challenging to map surface potentials to their sources in specific cortical regions. Multiple sources cancellation due to cortical folding and cross-talk obscures close sources, e.g. between visual areas V1 and V2. Recently retinotopic functional magnetic resonance imaging (fMRI) responses were used to constrain source locations to assist separating close sources and to determine cortical current generators. However, an fMRI is largely infeasible for routine EP investigation. We developed a novel method that replaces the fMRI derived retinotopic layout (RL) by an approach where the retinotopy and current estimates are generated from EEG or MEG signals and a standard clinical T1-weighted anatomical MRI. Using the EEG-RL, sources were localized to within 2 mm of the fMRI-RL constrained localized sources. The EEG-RL also produced V1 and V2 current waveforms that closely matched the fMRI-RL's (n = 2) r(1,198) = 0.99, P < 0.0001. Applying the method to subjects without fMRI (n = 4) demonstrates it generates waveforms that agree closely with the literature. Our advance allows investigators with their current EEG or MEG systems to create a library of brain models tuned to individual subjects' cortical folding in retinotopic maps, and should be applicable to auditory and somatosensory maps. The novel method developed expands EP's ability to study specific brain areas, revitalizing this well-worn technique. Hum Brain Mapp 37:1696-1709, 2016. © 2016 Wiley Periodicals, Inc.

Highly multiplexed subcellular RNA sequencing in situ.

Understanding the spatial organization of gene expression with single-nucleotide resolution requires localizing the sequences of expressed RNA transcripts within a cell in situ. Here, we describe fluorescent in situ RNA sequencing (FISSEQ), in which stably cross-linked complementary DNA (cDNA) amplicons are sequenced within a biological sample. Using 30-base reads from 8102 genes in situ, we examined RNA expression and localization in human primary fibroblasts with a simulated wound-healing assay. FISSEQ is compatible with tissue sections and whole-mount embryos and reduces the limitations of optical resolution and noisy signals on single-molecule detection. Our platform enables massively parallel detection of genetic elements, including gene transcripts and molecular barcodes, and can be used to investigate cellular phenotype, gene regulation, and environment in situ.

Adult neurogenesis produces neurons with unique GABAergic synapses in the olfactory bulb.

Neuronal regeneration occurs naturally in a few restricted mammalian brain regions, but its functional significance remains debated. Here we search for unique features in the synaptic outputs made by adult-born granule cell interneurons in the mouse olfactory bulb using optogenetic targeting of specific neuronal ages. We find that adult-born interneurons are resistant to presynaptic GABA(B)-mediated depression of GABA release compared with interneurons born just after birth that exhibit strong GABA(B) neuromodulation. Correlated with this functional change, we found altered localization of the GGABA(B)R1 protein within adult-born granule cells. These results suggest that adult neurogenesis produces a population of functionally unique GABAergic synapses in the olfactory bulb.

Changing the P300 brain computer interface.

Brain-computer interfaces (BCIs) are now feasible for use as an alternative control option for those with severe motor impairments. The P300 component of the evoked potential has proven useful as a control signal. Individuals do not need to be trained to produce the signal, and it is fairly stable and has a large evoked potential. Even with recent signal classification advances, on-line experiments with P300-based BCIs remain far from perfect. We present two potential methods for improving control accuracy. Experimental results in an evoked potential BCI, used to control items in a virtual apartment, show a reduced response exists when items are accidentally controlled. The presence of a P300-like signal in response to goal items means that it can be used for automatic error correction. Preliminary results from an interface experiment using three different button configurations for a yes/no BCI task show that the configuration of buttons may affect on-line signal classification. These results will be discussed in light of the special considerations needed when working with an amyotrophic lateral sclerosis (ALS) patient.