The brain’s capabilities rely on both the molecular properties of individual cells and their interactions across brain-wide networks. However, relating gene expression to activity in individual neurons across the entire brain remains elusive. Here we developed an experimental-computational platform, WARP, for whole-brain imaging of neuronal activity during behavior, expansion-assisted spatial transcriptomics, and cellular-level registration of these two modalities. Through joint analysis of whole-brain neuronal activity during multiple behaviors, cellular gene expression, and anatomy, we identified functions of molecularly defined populations — including luminance coding in a cckb-pou4f2 midbrain population and task-structured activity in pvalb7-eomesa hippocampal-like neurons — and defined over 2,000 other function-gene-anatomy subpopulations. Analysis of this unprecedented multimodal dataset also revealed that most gene-matched neurons showed stronger activity correlations, highlighting a brain-wide role for gene expression in functional organization. WARP establishes a foundational platform and open-access dataset for cross-experiment discovery, high-throughput function-to-gene mapping, unification of cell biology and systems neuroscience, and scalable circuit modeling at the whole-brain scale.

Neural recordings using optical methods have improved dramatically. For example, we demonstrate here recordings of over 100,000 neurons from the mouse cortex obtained with a standard commercial microscope. To process such large datasets, we developed Suite2p, a collection of efficient algorithms for motion correction, cell detection, activity extraction and quality control. We also developed new approaches to benchmark performance on these tasks. Our GPU-accelerated non-rigid motion correction substantially outperforms alternative methods, while running over five times faster. For cell detection, Suite2p outperforms the CNMF algorithm in Caiman and Fiola, finding more cells and producing fewer false positives, while running in a fraction of the time. We also introduce quality control steps for users to evaluate performance on their own data, while offering alternative algorithms for specialized types of recordings such as those from one-photon and voltage imaging.

Cortical neurogenesis proceeds through a precise temporal program in which radial glia sequentially generate distinct neuronal subtypes and later glia, yet how post-transcriptional regulators coordinate these transitions remain poorly understood. We previously identified that a decreasing temporal gradient of the RNA-binding protein Imp encodes neural stem cell age in Drosophila. In this work, we extend our investigation to Imp1, a mammalian homologue of Imp, and its role in murine neocortical development. Using TEMPO to track birth-order dynamics, we demonstrate that sustained Imp1 overexpression during early neurogenesis arrests temporal fate progression, shifting neuronal populations toward deeper cortical layers V-VI. Immunostaining with layer-specific transcription factors Cux1 and Ctip2 confirmed that laminar repositioning results from genuine changes in neuronal identity rather than migratory defects, with neurons adopting molecular identities matching their final positions. Temporal window-specific manipulations reveal distinct stage-specific effects where early-stage Imp1 induction produces cascading effects on fate specification and moderately delays the neuronal-to-gliogenic transition, while mid-stage induction induces neuronal accumulation in the subplate region. Live imaging of organotypic cultures reveals continuous neuronal recruitment within intermediate and ventricular zones, with mid-stage-born neurons accumulating at significantly faster rates than earlier cohorts. Strikingly, mid-stage Imp1 overexpression also induces ectopic glial-like foci distributed throughout the cortical plate, featuring dramatic cellular expansion and morphological heterogeneity. These findings establish Imp1 as a dosage- and stage-dependent temporal rheostat orchestrating developmental transitions in radial glial progenitors, controlling neuronal fate decisions and spatial organization. This work advances our understanding of molecular timing mechanisms governing neuronal diversity in the mammalian cortex.

Animals rapidly adapt to changing circumstances by shifting how they perceive, integrate, and act. Such flexibility is often attributed to transitions between internal states that exert widespread influence across the brain. Yet the mechanisms that drive state transitions and how they reconfigure brainwide computation remain unclear. Larval zebrafish, when actions are rendered futile by decoupling visual flow feedback from swimming in virtual reality, enter a temporary passive, energy-preserving state. In this state, astrocyte calcium levels are elevated, and swim reinitiation requires greater accumulated visual motion. Using whole-brain, cellular-resolution activity imaging, we observed widespread circuit alterations underlying this disengaged state: neuronal visual responses weakened, visual motion integration over time became dramatically leakier, motor inhibition increased, and motor preparation slowed, together suppressing conversion of sensory evidence into action. Astrocyte calcium rose during futile swimming, tracked the emergence and resolution of these brainwide changes, and was both necessary and sufficient to drive them. Thus, astrocytes orchestrate internal states that profoundly reshape neural computations, most powerfully at intermediate integrative processing stages, to meet changing demands.

Stem cells rapidly proliferate after injury to repair damaged tissue, and chronic injury predisposes to cancer. However, injury-activated mitogens, the mechanisms that keep them inactive until injury, and their role in cancer are not understood. Here we identify Igf2 as the injury-activated mitogen for neuroendocrine stem cells, a facultative airway stem cell and origin of small cell lung cancer. Igf2 is constitutively produced by the stem cells but sequestered in inactive form by co-expressed Igf binding proteins. Injury releases Igf2 and induces proliferation by activating its receptors and repressing Rb tumor suppressor, which normally enforces stem cell quiescence. Persistent pathway activation initiates oncogenesis. Thus, in addition to its classical hormonal roles in physiology, growth, and aging, Igf operates locally with Igf binding proteins and Rb to control injury-induced stem cell activation and cancer. This pathway may also control related stem cells and cancers of the body and brain.

Animals reprioritize behavioral goals in response to internal physiological states. Using larval zebrafish, we investigated whether engagement with a visuomotor task, the optomotor response (OMR), is coupled to cardiac dynamics. We discovered that threats lead to tachycardia that is synchronized with behavioral suppression. The change in heart rate is represented in the activity of specific neuronal populations. Severing the input to the sympathetic ganglia or ablating the vagus nerve revealed that the threat-related changes to behavioral state do not require interoceptive pathways. Direct tachycardic optopacing of the heart similarly suppressed the OMR response, but by reducing cardiac filling during diastole, thereby impacting oxygen delivery to the CNS. Optopacing also changed the activity of specific brain regions but in neurons distinct from those associated with threat-induced tachycardia. These cardiac function-associated central changes may have relevance to autonomic imbalances in anxiety, stress, and orthostatic disorders.

Assigning valence-appeal or aversion-to gustatory stimuli and relaying it to higher-order brain regions to guide flexible behaviors is crucial to survival. Yet the neural circuits that transform taste into motivationally relevant signals remain poorly defined in any model system. In Drosophila melanogaster, substantial progress has been made in mapping the sensorimotor pathways encoding intrinsic valence for feeding and the architecture of the dopaminergic reinforcement system. However, where and how "effective" (i.e., real-time) valence is first imposed on a taste has long been a mystery. Here, we identified a pair of subesophageal zone interneurons in Drosophila, termed Fox, that impart reinforcing positive valence to sweet taste and convey this signal to the mushroom body, the fly's associative learning center. We show that Fox neuron activity is necessary and sufficient to drive appetitive behaviors and can override a tastant's intrinsic neutral or aversive valence without impairing taste quality discrimination. Furthermore, Fox neurons relay the positive valence to specific dopaminergic neurons that mediate appetitive memory formation. Our findings reveal a circuit mechanism through which effective valence is bestowed upon sweet sensation and transformed into a reinforcing signal that supports learned sugar responses. The Fox neurons form a convergent-divergent "hourglass" circuit motif, acting as a bottleneck for valence assignment and distributing motivational signals to higher-order centers. This architecture confers both robustness and flexibility in reward processing-an organizational principle that may generalize across species.

Insecticides remain indispensable for crop protection and food security, yet their widespread use may contribute to the global decline of beneficial insect populations. Efforts to mitigate these impacts are hampered by a fragmented understanding of how insects metabolise insecticides and how sublethal exposures affect physiology, behaviour, and fitness. Here, we synthesise current understanding of metabolic detoxification and highlight critical gaps: the tissue- and time-dependent dynamics of insecticide entry and processing, the triggers and architecture of xenobiotic transcriptional responses, the role of rapid non-transcriptional regulation, and the population-level consequences of sublethal effects. We also outline emerging experimental strategies for addressing these questions and propose a next-generation research pipeline centred on multi-endpoint phenomics across life stages and sentinel species, integrated with AI-driven predictive toxicology, as a framework for identifying safer chemicals. We propose an integrated framework unifying molecular, physiological, and ecological responses to sublethal exposure to guide the design of insecticides that maintain effective pest control while safeguarding insect biodiversity and the ecosystems it underpins.

The cell cycle is tightly regulated by checkpoint mechanisms that ensure faithful duplication and segregation of the genome. Here, we induced cell-cell fusion between mitotic and interphase cells to study how nuclei from different cell cycle stages behave in a shared cytoplasm. We found that mitosis is a dominant cell cycle state: the mitotic cytoplasm can drive interphase nuclei into mitosis, whereas, in high ratios of interphase versus mitotic nuclei, fusion forced mitotic nuclei to exit mitosis. Both outcomes represent checkpoint override events with impactful consequences. Interphase nuclei forced into mitosis form aberrant mitotic spindles, show partially condensed DNA and ultimately undergo mitotic catastrophe. Conversely, forced mitotic exit resulted in reformation of nuclear envelope membranes around condensed chromosomes, forming nuclei with a defective nuclear import machinery. Altogether, cell-cell fusion revealed an unexpected plasticity in cell cycle control and highlight cell-cell fusion experiments as a powerful experimental system to study how competing cytoplasmic states are integrated in a shared cytoplasm.

Dendrites transform local electrical activity into intracellular Ca2+ signals that drive plasticity1,2, yet the voltage→Ca2+ mapping during natural behavior remains poorly defined. Here, we measure this transfer function via simultaneous voltage and Ca2+ imaging throughout the dendritic arbors of hippocampal CA2 pyramidal neurons in behaving mice. Dendritic Ca2+ exhibited a hierarchical activation pattern dominated by back-propagating action potentials: simple spikes primarily drove somatic and proximal Ca2+, whereas complex spikes produced larger somatic Ca2+ signals and propagated farther into distal dendrites, sometimes in a branch-selective manner. Dendrite-restricted co-activation of voltage and Ca2+ without concurrent somatic events was rare. A biophysics-inspired model accurately predicted local Ca2+ transients from local voltage waveforms. Our data and model provide a quantitative understanding of when – and why – dendritic Ca2+ signals in CA2 pyramidal cells arise during behavior.