18Neocortex contains a multitude of cell types segregated into layers and functionally distinct regions. To 19investigate the diversity of cell types across the mouse neocortex, we analyzed 12,714 cells from the 20 primary visual cortex (VISp), and 9,035 cells from the anterior lateral motor cortex (ALM) by deep single-21cell RNA-sequencing (scRNA-seq), identifying 116 transcriptomic cell types. These two regions represent 22 distant poles of the neocortex and perform distinct functions. We define 50 inhibitory transcriptomic cell 23 types, all of which are shared across both cortical regions. In contrast, 49 of 52 excitatory transcriptomic 24 types were found in either VISp or ALM, with only three present in both. By combining single cell RNA-25 seq and retrograde labeling, we demonstrate correspondence between excitatory transcriptomic types and 26 their region-specific long-range target specificity. This study establishes a combined transcriptomic and 27projectional taxonomy of cortical cell types from functionally distinct regions of the mouse cortex. 28 29 1

Single-wavelength fluorescent reporters allow visualization of specific neurotransmitters with high spatial and temporal resolution. We report variants of the glutamate sensor iGluSnFR that are functionally brighter, detect sub-micromolar to millimolar glutamate, and have blue, cyan, green, or yellow emission profiles. These variants allow in vivo imaging where original iGluSnFR was too dim, can resolve glutamate transients in dendritic spines and axonal boutons, and permit kilohertz imaging.

Neuroscience is at a crossroads. Great effort is being invested into deciphering specific neural interactions and circuits. At the same time, there exist few general theories or principles that explain brain function. We attribute this disparity, in part, to limitations in current methodologies. Traditional neurophysiological approaches record the activities of one neuron or a few neurons at a time. Neurochemical approaches focus on single neurotransmitters. Yet, there is an increasing realization that neural circuits operate at emergent levels, where the interactions between hundreds or thousands of neurons, utilizing multiple chemical transmitters, generate functional states. Brains function at the nanoscale, so tools to study brains must ultimately operate at this scale, as well. Nanoscience and nanotechnology are poised to provide a rich toolkit of novel methods to explore brain function by enabling simultaneous measurement and manipulation of activity of thousands or even millions of neurons. We and others refer to this goal as the Brain Activity Mapping Project. In this Nano Focus, we discuss how recent developments in nanoscale analysis tools and in the design and synthesis of nanomaterials have generated optical, electrical, and chemical methods that can readily be adapted for use in neuroscience. These approaches represent exciting areas of technical development and research. Moreover, unique opportunities exist for nanoscientists, nanotechnologists, and other physical scientists and engineers to contribute to tackling the challenging problems involved in understanding the fundamentals of brain function.

Ionic flux in defined cell populations mediates essential physiological and behavioral functions. Cell type-specific activators of diverse ionic conductances are needed for probing these relationships. We combined chemistry and protein engineering to enable systematic creation of a toolbox of ligand-gated ion channels (LGICs) with orthogonal pharmacologic selectivity and divergent functional properties. The LGICs and their small molecule effectors can activate a range of ionic conductances in genetically-specified cell types.LGICs constructed for neuronal perturbation can be used to selectively manipulate neuron activity in mammalian brains in vivo.The diversity of ion channel tools accessible from this approach will be useful for examining the relationship between neuronal activity and animal behavior, as well as for cell biological and physiological applications requiring chemical control of ion conductance.Ion channels are complex molecular machines with critical cell biological functions. Ligandgated ion channels (LGICs) provide rapid, remote control over conductances for different ions. In neurons, LGICs can be exploited for stimulation or silencing to examine causal relationships between electrical activity and animal behavior. Several neuron manipulation tools have been derived fromLGICs and G-protein coupled receptors (1-4) that can be genetically targeted and are reported to be orthogonal to endogenous systems. These tools are useful (5-7) but also face limitations such as ligand instability and lack of brain access (2), slow pharmacokinetics (6), the need to knockout endogenous alleles (3), or reliance on complex intracellular signaling pathways (4). Optogenetic tools (8-10) activate conductances with millisecond precision, but optimization of ion conductance properties has been limited and light targeting is invasive.To overcome these limitations, we have developed a strategy to create chimeric LGICs with distinct conductance properties derived from modular combinations of pharmacologicallyselective ligand binding domains (LBDs) and functionally diverse ion pore domains (IPDs). Within the Cys-loop receptor superfamily, the LBD of the α7 nicotinic acetylcholine receptor (nAChR) behaves as an independent actuator module that can be transplanted onto the IPDs of other Cys-loop receptors (11,12). These include at least 43 ion channel subunits in vertebrates (13), and many additional invertebrate (14) and prokaryotic (15) subunits. Distinct IPDs confer selectivity for chloride or calcium as well as nonspecific cations. For example, splicing the α7 nAChR LBD to the IPDs of the serotonin receptor 3a or the glycine receptor produces chimeric channels (α7-5HT3 or α7-GlyR) with α7 nAChR pharmacology and cation or chloride conductance properties, respectively (11,12). This modular property is a strong foundation for tailoring functional characteristics. However, the † To whom correspondence should be addressed. sternsons@janelia.hhmi.org (S.M.S.), HHMI Author ManuscriptHHMI Author Manuscript HHMI Auth...