To understand neural computations, one would like to relate circuit dynamics to neuronal intrinsic excitability and connectivity. We developed tools for large-scale all-optical electrophysiology and applied them to approximately 300 layer 1 interneurons per mouse in vivo. Across two mice, targeted stimulation and voltage imaging identified 1,469 inhibitory and 5,752 directed electrical connections among 14,312 tested pairs. Presynaptic identity was more strongly associated with inhibitory post-synaptic potential (IPSP) amplitude, whereas postsynaptic identity was more strongly associated with IPSP decay time. Gap junctional and synaptic interactions had distinct spatiotemporal kernels, with corresponding signatures in spontaneous activity. Excitability measured under optogenetic stimulus predicted spiking responses to subthreshold voltage, depolarization rate, and spike history during spontaneous firing. Genetic subtypes also showed different behavioral-state-dependent voltage-to-spike relationships despite similar population-average subthreshold voltages. These measurements link cellular properties and pairwise interactions to spontaneous circuit dynamics, establishing an approach for functional circuit mapping in vivo.

Summary Fluorescent imaging in live cells is a cornerstone of life sciences. While natural fluorescent proteins have been engineered to enhance individual features, no existing tag combines ideal properties into a single system: high brightness, reversible binding, compact size, and stability across diverse conditions. Here, we achieve this through de novo design of rhodamine binders (Rhobin). To harness the broad repertoire of rhodamine fluorophores, we developed a generalizable design strategy for a pan-rhodamine binder compatible with diverse wavelengths and applications. Rhobin enables live- and fixed-cell imaging of various subcellular targets in mammalian cells, showing brightness surpassing existing tags. Its reversible fluorophore binding supports super-resolution stimulated emission depletion (STED) and live-cell single-molecule imaging for extended durations compared with HaloTag. Beyond conventional systems, Rhobin enables live imaging of the extremophile Sulfolobus acidocaldarius at 75°C, previously inaccessible with current tags. Together, these results establish Rhobin as a versatile platform for next-generation imaging and biosensor design.

To select behaviors appropriate to their circumstances and needs, animals integrate information about the external environment with information about the state of their bodies, derived from sensing and processing internal signals (interoception). However, the brain-wide circuit activity underlying interoception and its integration with sensorimotor processing remains unclear, partly because of technical barriers to accessing whole-brain activity at the cellular level during physiological perturbations. We developed an all-optical system for whole-brain neuronal imaging in behaving larval zebrafish during optical uncaging of gut- or bloodstream-targeted nutrients and visuo-motor stimulation. Widespread neural activity throughout the brain encoded nutrient delivery, unfolding on multiple timescales across many peripheral and central regions. Evoked activity depended on delivery location and occurred in response to both amino acids and D-glucose, but not L-glucose. Many gut responsive neurons also responded to swimming and visual stimuli, with brainstem areas primarily integrating gut and motor signals and midbrain regions integrating jointly gut, visual, and motor signals. This platform links body-brain communication studies to brain-wide neural computation in awake, behaving vertebrates.

Piconewton forces borne by individual proteins within complex assemblies underlie cell adhesion, migration, and tissue morphogenesis, yet remain difficult to image in living systems. Here, we introduce WHaloForce, a chemigenetic HaloTag-based tension sensor that converts force-dependent relief of tryptophan-mediated dye quenching into a fluorescence lifetime change. Optical tweezers revealed a switch-like unquenching transition near 5 pN, and the sensor responded reversibly to force changes in cells. WHaloForce enabled quantitative tension imaging of diverse force-bearing proteins (vinculin, E-cadherin, α-catenin, and laminin) in mammalian cells, mouse tissue, and C. elegans. Bright synthetic dyes made tension measurements possible at endogenous expression levels. In C. elegans, vinculin and laminin showed opposite tension patterns between tissues, revealing distinct force-transmission routes through adhesions and the extracellular matrix. During ovulation, laminin tension accumulated over repeated stretch-relaxation cycles, scaling with cumulative loading history. WHaloForce thus offers a modular platform for imaging spatiotemporal tension patterns in living systems.

Fluorescent proteins and small-molecule dyes offer complementary advantages for biological imaging: Proteins are amenable to genetic tagging, whereas dyes provide superior brightness and photostability. To combine these strengths, we used de novo protein design to generate small, nanomolar-affinity, high-selectivity binders (NovoTags) for three cell-permeable dyes spanning the visible spectrum. We show that the NovoTag fluorescent lifetimes can be tuned and demonstrate their application in lifetime- and wavelength-based multiplexed fluorescence imaging. We also designed a two-chain version (NovoSplit) that functions as a chemically induced dimerization system with fluorescent readout in living cells or as a minimally perturbing proximity probe in fixed cells. Our approach combines the advantages of fluorescent proteins and small-molecule dyes, thus expanding the toolkit for cellular imaging.

Expansion microscopy (ExM) enables nanoscale fluorescence imaging on standard microscopes, but its combination with single-molecule localization microscopy (SMLM) remains challenging due to the incompatibility of expanded hydrogels with photoswitching buffers. Here, we introduce a single-step expansion microscopy approach that enables SMLM using spontaneously blinking dyes in 6–14× expanded samples, without re-embedding or buffer exchange. Using this approach, we achieve nanometer-scale spatial resolution by resolving the organization of the nuclear pore complex and the molecular structure of recombinant homotrimeric proliferating cell nuclear antigen.

Cells depend on the spatial organization of proteins, RNA, and DNA into discrete subcellular compartments. Previous methods have largely centered on measuring spatial organization based on only one of these biomolecular classes at a time. Here, we demonstrate that POCA photocatalytic proximity labeling can serve as a unified photosensitizer-based platform for profiling the proximal proteomes of protein, RNA, and DNA targets within a single experimental framework. We show that POCA can harness standard immunofluorescence or in situ hybridization workflows to specifically target organic fluorophore photosensitizers to intracellular targets for proximity labeling in fixed cells. POCA-targeted proximity labeling requires minimal cellular input and does not require genetic engineering. Additionally, POCA photosensitizers are selected to also be fluorescent, enabling direct confirmation of on-target localization by imaging prior to proteomic analysis. To demonstrate broad utility, we apply POCA across multiple molecular targets spanning protein, RNA, and genomic DNA, including components of the nuclear pore complex, nucleolus, nuclear speckles, telomeres, and pericentromeric heterochromatin. By anchoring proximity labeling to both a protein and an RNA within the same nuclear compartment, we resolve shared and distinct proximal proteomes from orthogonal molecular perspectives.Competing Interest StatementD.K.S. is a collaborator with Thermo Fisher Scientific, Genentech, Calico Labs, Matchpoint Therapeutics, and AI Proteins. K.M.B is a collaborator with Thermo Fisher Scientific and on the advisory board for Matchpoint Therapeutics. B.J.B. has filed a patent application covering aspects of this work (US Patent App. 18/728,937). B.J.B. is listed as an inventor on patent applications related to the SABER technology related to this work (US Patent 11,492,661; US Patent App. 18/607,269). E.L.H. also collaborates with Thermo Fisher Scientific, Genentech, and Xaira Therapeutics and consults for Calico Labs, Matchpoint Therapeutics, and Flagship Pioneering. Patents and patent applications covering azetidine-containing rhodamine dyes (with inventors J.B.G. and L.D.L.) are assigned to HHMI. L.D.L. is a scientific cofounder, consultant, and shareholder of Eikon Therapeutics. The other authors declare no conflicts.National Institutes of Health, R35GM137916, R35GM150919, DP2GM146246, P30 CA015704, U24HG006673, T32HL007093W. M. Keck Foundation, https://ror.org/000dswa46Pew Charitable Trusts, https://ror.org/02xhk2825Andy Hill CARE FoundationDavid and Lucile Packard Foundation, https://ror.org/032atxq54Damon Runyon Cancer Research Foundation, https://ror.org/01gd7b947

Spontaneously blinking fluorophores toggle between nonfluorescent and fluorescent forms without caging groups or redox buffers, enabling super-resolution imaging. The intrinsic blinking of such dyes is governed by molecular structure and modulated by environment; there is no one-size-fits-all fluorophore suitable for every imaging context. We report dyes with tuned on:off ratios that enable single-molecule localization microscopy and super-resolution optical fluctuation imaging of biomolecular structures in vitro and in cells.

Proteins essential for signaling, morphogenesis, and migration traverse the complex intracellular landscape via vesicular trafficking, microtubule-based transport, and diffusion. However, the precise mechanisms guiding soluble proteins toward their functional destinations have remained elusive. Here, we demonstrate that soluble proteins are directed toward the cell's advancing edge through advection-diffusion enhanced by intracellular fluid flow. We reveal that advective transport occurs within a specialized compartment at the cell's leading edge, separated from the rest of the cytoplasm by an actin-myosin condensate barrier. The barrier limits protein mixing between the compartment and the rest of the cytoplasm, maintaining localized protein concentrations. Contraction at the barrier generates a molecularly non-specific fluid flow that drives the forward movement of treadmilling actin monomers, actin-binding proteins, adhesion molecules, and even inert proteins. Dynamic changes in the local curvature of the barrier steer the fluid flow to direct proteins toward protrusive regions of the leading edge. This advective mechanism synchronizes protein distribution with local changes in cell morphology. Outside this compartment, diffusion dominates as the principal mode of soluble protein transport. Our findings uncover previously unrecognized compartmentalization strategies that regulate soluble protein concentrations and coordinate their efficient distribution for homeostasis, protrusion, and adhesion.

Mitochondria utilize calcium to increase ATP synthesis. However, excessive matrix calcium activates the mitochondrial permeability transition (mPT), a process that permeabilizes the mitochondrial inner membrane and leads to cell death. While initially characterized 50 y ago, the proteins underlying the process are unclear, although integral membrane proteins were expected to be the porous entities during calcium overload. Here, we designed two assays to study the mPT using high-throughput methodologies. By surveying 19,113 proteins in human cells, we identified four proteins that sensitize the human mPT, but only one that was essential for mPT activation, mitochondrial-localized NRLX1. Surprisingly, NLRX1 is not an integral membrane protein, and our work did not identify any essential integral membrane proteins for the human mPT. The mitochondrial permeability transition (mPT) is an evolutionarily conserved destructive process that permeabilizes the inner mitochondrial membrane in response to calcium overload. The molecular mechanism underlying the mPT is not established. To unambiguously identify essential proteins, we designed two phenotypic assays for mitochondrial calcium overload and applied them to FACS-based CRISPR screening in human cells, ultimately evaluating 19,113 genes. The first screen studied mitochondrial membrane potential (MMP) collapse in response to calcium overload. Top-ranked genes were the essential proteins of the mitochondrial calcium uniporter complex, MCU and EMRE, reflecting that the calcium-induced MMP collapse results from mitochondrial calcium entry and not the mPT. The second screen measured the permeability of the inner mitochondrial membrane. Here, the fluorescent interaction of a membrane impermeant 600 Da dye and a mitochondrial-targeted HaloTag protein was studied under mPT activating conditions; calcium overload and the thiol-reactive molecule phenylarsine oxide. With secondary validation, we identified four protein-encoding genes that delayed or prevented the mPT under knockout: NF2, REST, BPTF, and NRLX1. Knockout of the nonmitochondrial proteins BPTF, NF2, or REST increased mitochondrial calcium retention capacity (CRC). However, calcium release or sensitivity to cyclosporin A (CsA) persisted, indicative of mPT sensitizers. Only knockout of the mitochondrial matrix protein, NLRX1, increased CRC, abolished calcium release, and was CsA-insensitive. This top-ranked hit of the mitochondrial permeability screen meets the definition of an essential mPT activator. Integral membrane proteins, including all previously proposed mPT candidates, were not essential activators.