Nejatbakhsh, A., et al. Extracting neural signals from semi-immobilized animals with deformable non-negative matrix factorization. bioRxiv (Submitted). PreprintAbstract
Extracting calcium traces from populations of neurons is a critical step in the study of the large-scale neural dynamics that govern behavior. Accurate activity extraction requires the correction of motion and movement-induced deformations as well as demixing of signals that may overlap spatially due to limitations in optical resolution. Traditionally, non-negative matrix factorization (NMF) methods have been successful in demixing and denoising cellular calcium activity in relatively motionless or pre-registered videos. However, standard NMF methods fail in animals undergoing significant non-rigid motion; similarly, standard image registration methods based on template matching can fail when large changes in activity lead to mismatches with the image template. To address these issues simultaneously, we introduce a deformable non-negative matrix factorization (dNMF) framework that jointly optimizes registration with signal demixing. On simulated data and real semi-immobilized C. elegans microscopy videos, dNMF outperforms traditional demixing methods that account for motion and demixing separately. Finally, following the extraction of neural traces from multiple imaging experiments, we develop a quantile regression time-series normalization technique to account for varying neural signal intensity baselines across different animals or different imaging setups. Open source code implementing this pipeline is available at
Yemini, E., et al. NeuroPAL: A Neuronal Polychromatic Atlas of Landmarks for Whole-Brain Imaging in C. elegans. bioRxiv (Submitted). PreprintAbstract
Comprehensively resolving single neurons and their cellular identities from whole-brain fluorescent images is a major challenge. We achieve this in C. elegans through the engineering and use of a multicolor transgene called NeuroPAL (a Neuronal Polychromatic Atlas of Landmarks). NeuroPAL worms share a stereotypical multicolor fluorescence map for the entire hermaphrodite nervous system that allows comprehensive determination of neuronal identities. Neurons labeled with NeuroPAL do not exhibit fluorescence in the green, cyan, or yellow emission channels, allowing the transgene to be used with numerous reporters of gene expression or neuronal dynamics. Here we showcase three studies that leverage NeuroPAL for nervous-system-wide neuronal identification. First, we determine the brainwide expression patterns of all metabotropic receptors for acetylcholine, GABA, and glutamate, completing a map of this communication network. Second, we uncover novel changes in cell fate caused by transcription factor mutations. Third, we record brainwide activity in response to attractive and repulsive chemosensory cues, characterizing multimodal coding and novel neuronal asymmetries for these stimuli. We present a software package that enables semi-automated determination of all neuronal identities based on color and positional information. The NeuroPAL framework and software provide a means to design landmark atlases for other tissues and organisms. In conclusion, we expect NeuroPAL to serve as an invaluable tool for gene expression analysis, neuronal fate studies, and for mapping whole-brain activity patterns.
Vogt, K., et al. Internal state configures olfactory behavior and early sensory processing in Drosophila larva. bioRxiv 1-19 (Submitted).Abstract
Animals can respond differently to a sensory cue when in different states. Here, we show that certain odors repel well-fed Drosophila larvae but attract food-deprived larvae and how feeding state flexibly alters neural processing in an early olfactory circuit, the antennal lobe, to determine the behavioral valence of a sensory cue. Odor valence is assigned by a neuronal architecture that controls a switch between two separate projection neuron output pathways that mediate opposite behavioral responses. A uniglomerular projection neuron pathway mediates odor attraction whereas a multiglomerular projection neuron pathway mediates odor repulsion. The serotonergic CSD neuron in the antennal lobe is a critical regulator of this neuronal and behavioral switch. CSD selects an appropriate behavior by shifting patterns of serotonergic modulation and glutamatergic inhibition onto each output pathway. The antennal lobe is a decision-making circuit for innate behavioral responses that uses feeding state to determine an odor’s valence.
Choi, J., et al. Probing and manipulating embryogenesis via nanoscale thermometry and temperature control. Proceedings of the National Academy of Sciences (2020). Publisher's VersionAbstract
Temperature is a key control parameter of biological processes, but measuring and controlling temperatures on a cellular-length scale in living organisms remains an outstanding challenge. Applying nanoscale-thermometry techniques to early embryos, we study cell divisions in a highly controlled manner using local laser heating and real-time in vivo temperature readout. Nitrogen-vacancy centers in nanodiamonds, incorporated into the cells, allow us to map out the temperature distribution of a locally heated embryo with submicrometer spatial resolution and high sensitivity. The simultaneous cell-division imaging under controlled laser heating is used to achieve cell-cycle timing control and inversion, providing insights into timing-regulation mechanisms during early embryogenesis. Understanding the coordination of cell-division timing is one of the outstanding questions in the field of developmental biology. One active control parameter of the cell-cycle duration is temperature, as it can accelerate or decelerate the rate of biochemical reactions. However, controlled experiments at the cellular scale are challenging, due to the limited availability of biocompatible temperature sensors, as well as the lack of practical methods to systematically control local temperatures and cellular dynamics. Here, we demonstrate a method to probe and control the cell-division timing in Caenorhabditis elegans embryos using a combination of local laser heating and nanoscale thermometry. Local infrared laser illumination produces a temperature gradient across the embryo, which is precisely measured by in vivo nanoscale thermometry using quantum defects in nanodiamonds. These techniques enable selective, controlled acceleration of the cell divisions, even enabling an inversion of division order at the two-cell stage. Our data suggest that the cell-cycle timing asynchrony of the early embryonic development in C. elegans is determined independently by individual cells rather than via cell-to-cell communication. Our method can be used to control the development of multicellular organisms and to provide insights into the regulation of cell-division timings as a consequence of local perturbations.
Calarco, J.A. & Samuel, A.D.T. Imaging whole nervous systems: insights into behavior from brains inside bodies. Nature Methods 16, 14-15 (2019). Publisher's VersionAbstract
The development of systems combining rapid volumetric imaging with three-dimensional tracking has enabled the measurement of brain-wide dynamics in freely behaving animals such as worms, flies, and fish. These advances provide an exciting opportunity to understand the organization of neural circuits in the context of voluntary and natural behaviors. In this Comment, we highlight recent progress in this burgeoning area of research.
Budelli, G., et al. Ionotropic Receptors Specify the Morphogenesis of Phasic Sensors Controlling Rapid Thermal Preference in Drosophila. Neuron 101, 738-747 (2019). Publisher's VersionAbstract
Thermosensation is critical for avoiding thermal extremes and regulating body temperature. While thermosensors activated by noxious temperatures respond to hot or cold, many innocuous thermosensors exhibit robust baseline activity and lack discrete temperature thresholds, suggesting they are not simply warm and cool detectors. Here, we investigate how the aristal Cold Cells encode innocuous temperatures in Drosophila. We find they are not cold sensors but cooling-activated and warming-inhibited phasic thermosensors that operate similarly at warm and cool temperatures; we propose renaming them “Cooling Cells.” Unexpectedly, Cooling Cell thermosensing does not require the previously reported Brivido Transient Receptor Potential (TRP) channels. Instead, three Ionotropic Receptors (IRs), IR21a, IR25a, and IR93a, specify both the unique structure of Cooling Cell cilia endings and their thermosensitivity. Behaviorally, Cooling Cells promote both warm and cool avoidance. These findings reveal a morphogenetic role for IRs and demonstrate the central role of phasic thermosensing in innocuous thermosensation.
Si, G., et al. Structured Odorant Response Patterns across a Complete Olfactory Receptor Neuron Population. Neuron 101, 1-13 (2019). Publisher's VersionAbstract
Summary Odor perception allows animals to distinguish odors, recognize the same odor across concentrations, and determine concentration changes. How the activity patterns of primary olfactory receptor neurons (ORNs), at the individual and population levels, facilitate distinguishing these functions remains poorly understood. Here, we interrogate the complete ORN population of the Drosophila larva across a broadly sampled panel of odorants at varying concentrations. We find that the activity of each ORN scales with the concentration of any odorant via a fixed dose-response function with a variable sensitivity. Sensitivities across odorants and ORNs follow a power-law distribution. Much of receptor sensitivity to odorants is accounted for by a single geometrical property of molecular structure. Similarity in the shape of temporal response filters across odorants and ORNs extend these relationships to fluctuating environments. These results uncover shared individual- and population-level patterns that together lend structure to support odor perceptions.
Hawk, J.D., et al. Integration of plasticity mechanisms within a single sensory neuron of C. elegans actuates a memory. Neuron 97, 2, 356-367 (2018). Publisher's VersionAbstract
Neural plasticity, the ability of a neuron to change its cellular properties in response to past experiences, underpins the nervous system’s capacity to form memories and actuate behaviors. How different plasticity mechanisms act together in vivo and at a cellular level to transform sensory information into behavior is not well understood. Here we show that in the nematode C. elegans two plasticity mechanisms, sensory adaptation and presynaptic plasticity, act within a single cell to encode thermosensory information and actuate a temperature-preference memory. Sensory adaptation enables the primary thermosensory neuron, AFD, to adjust the temperature range of its sensitivity to the local environment, thereby optimizing its ability to detect temperature fluctuations associated with migration. Presynaptic plasticity transforms this thermosensory information into a behavioral preference by gating synaptic communication between sensory neuron AFD and its postsynaptic partner, AIY. The gating of synaptic communication is regulated at AFD presynaptic sites by the conserved kinase nPKC epsilon Bypassing or altering AFD presynaptic plasticity predictably changes the learned behavioral preferences without affecting sensory responses. Our findings indicate that two distinct and modular neuroplasticity mechanisms function together within a single sensory neuron to encode multiple components of information required to enact thermotactic behavior. The integration of these plasticity mechanisms result in a single-cell logic system that can both represent sensory stimuli and guide memory-based behavioral preference.
He, L., Si, G., Huang, J., Samuel, A.D.T. & Perrimon, N. Mechanical regulation of stem-cell differentiation by the stretch-activated Piezo channel. Nature (2018). Publisher's VersionAbstract
Stem cells of the Drosophila midgut sense mechanical signals in vivo through the stretch-activated ion channel Piezo, which is expressed on previously unidentified enteroendocrine precursor cells.
Klein, M., et al. Exploratory search during directed navigation in C. elegans and Drosophila larva. eLife 6, (2017). Publisher's VersionAbstract
Many organisms—from bacteria to nematodes to insect larvae—navigate their environments by biasing random movements. In these organisms, navigation in isotropic environments can be characterized as an essentially diffusive and undirected process. In stimulus gradients, movement decisions are biased to drive directed navigation toward favorable environments. How does directed navigation in a gradient modulate random exploration either parallel or orthogonal to the gradient? Here, we introduce methods originally used for analyzing protein folding trajectories to study the trajectories of the nematode Caenorhabditis elegans and the Drosophila larva in isotropic environments, as well as in thermal and chemical gradients. We find that the statistics of random exploration in any direction are little affected by directed movement along a stimulus gradient. A key constraint on the behavioral strategies of these organisms appears to be the preservation of their capacity to continuously explore their environments in all directions even while moving toward favorable conditions.
Lim, M.A., et al. Neuroendocrine Modulation Sustains the C. elegans Forward Motor State. eLIFE (2016). Publisher's VersionAbstract
Neuromodulators shape neural circuit dynamics. Combining electron microscopy, genetics, transcriptome profiling, calcium imaging, and optogenetics, we discovered a peptidergic neuron that modulates C. elegans motor circuit dynamics. The Six/SO-family homeobox transcription factor UNC-39 governs lineage-specific neurogenesis to give rise to a neuron RID. RID bears the anatomic hallmarks of a specialized endocrine neuron: it harbors near-exclusive dense core vesicles that cluster periodically along the axon, and expresses multiple neuropeptides, including the FMRF-amide-related FLP-14. RID activity increases during forward movement. Ablating RID reduces the sustainability of forward movement, a phenotype partially recapitulated by removing FLP-14. Optogenetic depolarization of RID prolongs forward movement, an effect reduced in the absence of FLP-14. Together, these results establish the role of a neuroendocrine cell RID in sustaining a specific behavioral state in C. elegans.
Narayan, A., et al. Contrasting responses within a single neuron class enable sex- specific attraction in C. elegans. Proceedings of the National Academy of Sciences USA (2016).Abstract
Animals find mates and food, and avoid predators by navigating to regions within a favorable range of available sensory cues. How are these ranges set and recognized? Here we show that male C. elegans exhibit strong concentration preferences for sex- specific small molecule cues secreted by hermaphrodites, and that these preferences emerge from the collective dynamics of a single male-specific class of neurons, the CEMs. Within a single worm, CEM responses are dissimilar, not determined by anatomical classification and can be excitatory or inhibitory. Response kinetics vary by concentration, suggesting a mechanism for establishing preferences. CEM responses are enhanced in the absence of synaptic transmission, and worms with only one intact CEM show non-preferential attraction to all concentrations of ascaroside for which CEM is the primary sensor, suggesting that synaptic modulation of CEM responses is necessary for establishing preferences. A heterogeneous concentration-dependent sensory representation thus appears to allow a single neural class to set behavioral preferences and recognize ranges of sensory cues. 
Knecht, Z.A., et al. Distinct combinations of variant ionotropic glutamate receptors mediate thermosensation and hygrosensation in Drosophila. eLife (2016). Publisher's VersionAbstract
Ionotropic Receptors (IRs) are a large subfamily of variant ionotropicglutamate receptors present across Protostomia. While these receptors are mostextensively studied for their roles in chemosensory detection in insects, recent work has implicated two family members, IR21a and IR25a, in thermosensation in Drosophila. Here we characterize one of the most deeply conserved receptors, IR93a, and show that it is co-expressed and functions with IR21a and IR25a to mediate physiological and behavioral responses to cool temperatures. IR93a is also co-expressed with IR25a and a distinct receptor, IR40a, in a discrete population of sensory neurons in the sacculus, a multi-chambered pocket within the antenna. We demonstrate that this combination of receptors is important for neuronal responses to dry air and behavioral discrimination of humidity differences. Our results identify IR93a as a common component of molecularlyand cellularly distinct IR pathways underlying thermosensation and hygrosensation in insects. 
Shen, Y., et al. An extrasynaptic GABAergic signal modulates a pattern of forward movement in Caenorhabditis elegans. eLife 5, e14197 (2016). Publisher's VersionAbstract
As a common neurotransmitter in the nervous system, γ-aminobutyric acid (GABA) modulates locomotory patterns in both vertebrates and invertebrates. However, the signaling mechanisms underlying the behavioral effects of GABAergic modulation are not completely understood. Here, we demonstrate that a GABAergic signal in C. elegans modulates the amplitude of undulatory head bending through extrasynaptic neurotransmission and conserved metabotropic receptors. We show that the GABAergic RME head motor neurons generate undulatory activity patterns that correlate with head bending and the activity of RME causally links with head bending amplitude. The undulatory activity of RME is regulated by a pair of cholinergic head motor neurons SMD, which facilitate head bending, and inhibits SMD to limit head bending. The extrasynaptic neurotransmission between SMD and RME provides a gain control system to set head bending amplitude to a value correlated with optimal efficiency of forward movement.
Ni, L., et al. The Ionotropic Receptors IR21a and IR25a mediate cool sensing in Drosophila. eLife 5, e13254 (2016). Publisher's VersionAbstract
Animals rely on highly sensitive thermoreceptors to seek out optimal temperatures, but the molecular mechanisms of thermosensing are not well understood. The Dorsal Organ Cool Cells (DOCCs) of the Drosophila larva are a set of exceptionally thermosensitive neurons critical for larval cool avoidance. Here we show that DOCC cool-sensing is mediated by Ionotropic Receptors (IRs), a family of sensory receptors widely studied in invertebrate chemical sensing. We find that two IRs, IR21a and IR25a, are required to mediate DOCC responses to cooling and are required for cool avoidance behavior. Furthermore, we find that ectopic expression of IR21a can confer cool-responsiveness in an Ir25a-dependent manner, suggesting an instructive role for IR21a in thermosensing. Together, these data show that IR family receptors can function together to mediate thermosensation of exquisite sensitivity.
van Giesen, L., et al. Multimodal stimulus coding by a gustatory sensory neuron in Drosophila larvae. Nature Communications 7, 10687 (2016).Abstract
Accurate perception of taste information is crucial for animal survival. In adult Drosophila, gustatory receptor neurons (GRNs) perceive chemical stimuli of one specific gustatory modality associated with a stereotyped behavioural response, such as aversion or attraction. We show that GRNs of Drosophila larvae employ a surprisingly different mode of gustatory information coding. Using a novel method for calcium imaging in the larval gustatory system, we identify a multimodal GRN that responds to chemicals of different taste modalities with opposing valence, such as sweet sucrose and bitter denatonium, reliant on different sensory receptors. This multimodal neuron is essential for bitter compound avoidance, and its artificial activation is sufficient to mediate aversion. However, the neuron is also essential for the integration of taste blends. Our findings support a model for taste coding in larvae, in which distinct receptor proteins mediate different responses within the same, multimodal GRN. 
Lim, M.A., et al. Neuroendocrine Modulation Sustains the C. elegans Forward Motor State. eLIFE (2016). Publisher's VersionAbstract
Neuromodulators shape neural circuit dynamics. Combining electron microscopy, genetics, transcriptome profiling, calcium imaging, and optogenetics, we discovered a peptidergic neuron that modulates C. elegans motor circuit dynamics. The Six/SO-family homeobox transcription factor UNC-39 governs lineage-specific neurogenesis to give rise to a neuron RID. RID bears the anatomic hallmarks of a specialized endocrine neuron: it harbors near-exclusive dense core vesicles that cluster periodically along the axon, and expresses multiple neuropeptides, including the FMRF-amide-related FLP-14. RID activity increases during forward movement. Ablating RID reduces the sustainability of forward movement, a phenotype partially recapitulated by removing FLP-14. Optogenetic depolarization of RID prolongs forward movement, an effect reduced in the absence of FLP-14. Together, these results establish the role of a neuroendocrine cell RID in sustaining a specific behavioral state in C. elegans.
Venkatachalam, V., et al. Panneuronal Imaging in Roaming C. elegans. Proceedings of the National Academy of Sciences USA 113, E1082-1088 (2016). Publisher's VersionAbstract
We present an imaging system for pan-neuronal recording in crawling Caenorhabditis elegans. A spinning disk confocal microscope, modified for automated tracking of the C. elegans head ganglia, simultaneously records the activity and position of \~80 neurons that coexpress cytoplasmic calcium indicator GCaMP6s and nuclear localized red fluorescent protein at 10 volumes per second. We developed a behavioral analysis algorithm that maps the movements of the head ganglia to the animal’s posture and locomotion. Image registration and analysis software automatically assigns an index to each nucleus and calculates the corresponding calcium signal. Neurons with highly stereotyped positions can be associated with unique indexes and subsequently identified using an atlas of the worm nervous system. To test our system, we analyzed the brainwide activity patterns of moving worms subjected to thermosensory inputs. We demonstrate that our setup is able to uncover representations of sensory input and motor output of individual neurons from brainwide dynamics. Our imaging setup and analysis pipeline should facilitate mapping circuits for sensory to motor transformation in transparent behaving animals such as C. elegans and Drosophila larva.
Berck, M., et al. The wiring diagram of a glomerular olfactory system. eLife 5, e14859 (2016). Publisher's VersionAbstract
The sense of smell enables animals to detect and react to long-distance cues according to internalized valences. Odors evoke responses from olfactory receptor neurons (ORNs), whose activities are integrated and processed in olfactory glomeruli and then relayed by projection neurons (PNs) to higher brain centers. The wiring diagram with synaptic resolution, which is unknown for any glomerular olfactory system, would enable the formulation of circuit function hypotheses to explain physiological and behavioral observations. Here, we have mapped with electron microscopy the complete wiring diagram of the left and right antennal lobes of Drosophila larva, an olfactory neuropil similar to the vertebrate olfactory bulb. We found two parallel circuits processing ORN inputs. First, a canonical circuit that consists of uniglomerular PNs that relay gain-controlled ORN inputs to the learning and memory center (mushroom body) and the center for innate behaviors (lateral horn). Second, a novel circuit where multiglomerular PNs and hierarchically structured local neurons (LNs) extract complex features from odor space and relay them to multiple brain areas. We found two types of panglomerular inhibitory LNs: one primarily providing presynaptic inhibition (onto ORNs) and another also providing postsynaptic inhibition (onto PNs), indicating that these two functionally different types of inhibition are susceptible to independent modulation. The wiring diagram revealed an LN circuit that putatively implements a bistable gain control mechanism, which either computes odor saliency through panglomerular inhibition, or allows a subset of glomeruli to respond to faint aversive odors in the presence of strong appetitive odor concentrations. This switch between operational modes is regulated by both neuromodulatory neurons and non-olfactory sensory neurons. Descending neurons from higher brain areas further indicate the context-dependent nature of early olfactory processing. The complete wiring diagram of the first olfactory neuropil of a genetically tractable organism will support detailed experimental and theoretical studies of circuit function towards bridging the gap between circuits and behavior.
Kain, J.S., Zhang, S., Klein, M., Samuel, A. & de Bivort, B. Bet-hedging, seasons and the evolution of behavioral diversity in Drosophila. Evolution 69, 3171-3186 (2015). Publisher's VersionAbstract
Organisms use various strategies to cope with fluctuating environmental conditions. In diversified bet-hedging, a single genotype exhibits phenotypic heterogeneity with the expectation that some individuals will survive transient selective pressures. To date, empirical evidence for bet-hedging is scarce. Here, we observe that individual Drosophila melanogaster flies exhibit striking variation in light- and temperature-preference behaviors. With a modeling approach that combines real world weather and climate data to simulate temperature preference-dependent survival and reproduction, we find that a bet-hedging strategy may underlie the observed interindividual behavioral diversity. Specifically, bet-hedging outcompetes strategies in which individualthermal preferences are heritable. Animals employing bet-hedging refrain from adapting to the coolness of spring with increased  warm-seeking that inevitably becomes counterproductive in the hot summer. This strategy is particularly valuable when mean seasonal temperatures are typical, or when there is considerable fluctuation in temperature within the season. The model predicts, and we experimentally verify, that the behaviors of individual flies are not heritable. Finally, we model the effects of historical weather data, climate change, and geographic seasonal variation on the optimal strategies underlying behavioral variation between individuals, characterizing the regimes in which bet-hedging is advantageous.