(Invited) Neuroengineering Overview

Neuroengineering, the field of creating new tools for neuroscience, is an emerging field which includes the invention of technologies to activate and silence electrical activity in the brain, technologies to read out electrical activity from cells in the brain, and tools for mapping the brain. In this talk I will give an overview of technologies that recently emerged from our lab. First, recent optogenetic tools have begun to reach the physical limits of performance. The optogenetic molecules (opsins) Chronos and Chrimson enable activation of distinct neural populations with multiple colors of light, and Jaws is a red shifted inhibitor of neural activity that enables noninvasive neural silencing. Since opsins express all along cell membranes, light focused on one cell body will result in artifactual activation of multiple cells, whose processes are physically touching the neuron of interest. To tackle this problem, we designed a class of somatic opsins that express mainly at the cell body. This, in combination with holographic stimulation enables single cell optogenetics at millisecond temporal resolution. Activity sensors represent an area of great interest in neuroengineering. The voltage sensor Archon is an archaerhodopsin-based molecule with a high voltage sensitivity and brightness compared to its predecessors. The aforementioned cross talk problem also pertains to sensors: since cell-processes are touching cell bodies, the signal coming from a cell body could in principle originate from nearby cells. To solve this problem we developed a GCaMP6f molecule that is retained in the cell body only, called somaGCaMP6f. This molecule enables low crosstalk physiological imaging in mice and fish. Lastly, we have developed a technology that greatly facilitates the mapping of the brain. Optical super-resolution techniques are slow and costly, and accordingly do not scale well to large-scale brain circuitry. Instead of improving the resolving power of the microscope, we have found a way to physically expand biological specimens 4x-20x in linear dimension, in an isotropic fashion. This method, which we call expansion microscopy (ExM), enables the mapping of molecules of interest across cells and tissues of extended scale, and thus facilitates the analysis of neural circuits across scales of relevance to understanding brain function. </jats:p

Machine Learning Analysis of Naïve B-Cell Receptor Repertoires Stratifies Celiac Disease Patients and Controls

Celiac disease (CeD) is a common autoimmune disorder caused by an abnormal immune response to dietary gluten proteins. The disease has high heritability. HLA is the major susceptibility factor, and the HLA effect is mediated via presentation of deamidated gluten peptides by disease-associated HLA-DQ variants to CD4+ T cells. In addition to gluten-specific CD4+ T cells the patients have antibodies to transglutaminase 2 (autoantigen) and deamidated gluten peptides. These disease-specific antibodies recognize defined epitopes and they display common usage of specific heavy and light chains across patients. Interactions between T cells and B cells are likely central in the pathogenesis, but how the repertoires of naïve T and B cells relate to the pathogenic effector cells is unexplored. To this end, we applied machine learning classification models to naïve B cell receptor (BCR) repertoires from CeD patients and healthy controls. Strikingly, we obtained a promising classification performance with an F1 score of 85%. Clusters of heavy and light chain sequences were inferred and used as features for the model, and signatures associated with the disease were then characterized. These signatures included amino acid (AA) 3-mers with distinct bio-physiochemical characteristics and enriched V and J genes. We found that CeD-associated clusters can be identified and that common motifs can be characterized from naïve BCR repertoires. The results may indicate a genetic influence by BCR encoding genes in CeD. Analysis of naïve BCRs as presented here may become an important part of assessing the risk of individuals to develop CeD. Our model demonstrates the potential of using BCR repertoires and in particular, naïve BCR repertoires, as disease susceptibility markers.</jats:p

Temporally precise single-cell-resolution optogenetics

© 2017 The Author(s). Optogenetic control of individual neurons with high temporal precision within intact mammalian brain circuitry would enable powerful explorations of how neural circuits operate. Two-photon computer-generated holography enables precise sculpting of light and could in principle enable simultaneous illumination of many neurons in a network, with the requisite temporal precision to simulate accurate neural codes. We designed a high-efficacy soma-targeted opsin, finding that fusing the N-terminal 150 residues of kainate receptor subunit 2 (KA2) to the recently discovered high-photocurrent channelrhodopsin CoChR restricted expression of this opsin primarily to the cell body of mammalian cortical neurons. In combination with two-photon holographic stimulation, we found that this somatic CoChR (soCoChR) enabled photostimulation of individual cells in mouse cortical brain slices with single-cell resolution and <1-ms temporal precision. We used soCoChR to perform connectivity mapping on intact cortical circuits