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2224 Publications

Showing 1-10 of 2224 results
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    12/16/22 | En bloc preparation of Drosophila brains enables high-throughput FIB-SEM connectomics.
    Lu Z, Xu CS, Hayworth KJ, Pang S, Shinomiya K, Plaza SM, Scheffer LK, Rubin GM, Hess HF, Rivlin PK, Meinertzhagen IA
    Frontiers in Neural Circuits. 2022 Dec 16;16:917251. doi: 10.3389/fncir.2022.917251

    Deriving the detailed synaptic connections of an entire nervous system is the unrealized goal of the nascent field of connectomics. For the fruit fly , in particular, we need to dissect the brain, connectives, and ventral nerve cord as a single continuous unit, fix and stain it, and undertake automated segmentation of neuron membranes. To achieve this, we designed a protocol using progressive lowering of temperature dehydration (PLT), a technique routinely used to preserve cellular structure and antigenicity. We combined PLT with low temperature staining (LTS) and recover fixed neurons as round profiles with darkly stained synapses, suitable for machine segmentation and automatic synapse detection. Here we report three different PLT-LTS methods designed to meet the requirements for FIB-SEM imaging of the brain. These requirements include: good preservation of ultrastructural detail, high level of staining, artifact-free microdissection, and smooth hot-knife cutting to reduce the brain to dimensions suited to FIB-SEM. In addition to PLT-LTS, we designed a jig to microdissect and pre-fix the fly's delicate brain and central nervous system. Collectively these methods optimize morphological preservation, allow us to image the brain usually at 8 nm per voxel, and simultaneously speed the formerly slow rate of FIB-SEM imaging.

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    01/24/23 | Hierarchical architecture of dopaminergic circuits enables second-order conditioning in Drosophila
    Daichi Yamada , Daniel Bushey , Li Feng , Karen Hibbard , Megan Sammons , Jan Funke , Ashok Litwin-Kumar , Toshihide Hige , Yoshinori Aso
    eLife. 2023 Jan 24:. doi: 10.7554/eLife.79042

    Dopaminergic neurons with distinct projection patterns and physiological properties compose memory subsystems in a brain. However, it is poorly understood whether or how they interact during complex learning. Here, we identify a feedforward circuit formed between dopamine subsystems and show that it is essential for second-order conditioning, an ethologically important form of higher-order associative learning. The Drosophila mushroom body comprises a series of dopaminergic compartments, each of which exhibits distinct memory dynamics. We find that a slow and stable memory compartment can serve as an effective “teacher” by instructing other faster and transient memory compartments via a single key interneuron, which we identify by connectome analysis and neurotransmitter prediction. This excitatory interneuron acquires enhanced response to reward-predicting odor after first-order conditioning and, upon activation, evokes dopamine release in the “student” compartments. These hierarchical connections between dopamine subsystems explain distinct properties of first- and second-order memory long known by behavioral psychologists.

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    01/20/23 | How microscopic epistasis and clonal interference shape the fitness trajectory in a spin glass model of microbial long-term evolution
    Nicholas M. Boffi , Yipei Guo , Chris H. Rycroft , Ariel Amir
    bioRxiv. 2023 Jan 20:. doi: 10.1101/2023.

    The adaptive dynamics of evolving microbial populations takes place on a complex fitness landscape generated by epistatic interactions. The population generically consists of multiple competing strains, a phenomenon known as clonal interference. Microscopic epistasis and clonal interference are central aspects of evolution in microbes, but their combined effects on the functional form of the population’s mean fitness are poorly understood. Here, we develop a computational method that resolves the full microscopic complexity of an evolving population subject to a standard serial dilution protocol. We find that stronger microscopic epistasis gives rise to fitness trajectories with slower growth independent of the number of competing strains, which we quantify with power-law fits and understand mechanistically via a random walk model that neglects dynamical correlations between genes. We show that clonal interference leads to fitness trajectories with faster growth (in functional form) without microscopic epistasis, but has a negligible effect when epistasis is sufficiently strong, indicating that the role of clonal interference depends intimately on the underlying fitness landscape.

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    01/20/23 | Multimodal mapping of cell types and projections in the central nucleus of the amygdala
    Yuhan Wang , Sabine Krabbe , Mark Eddison , Fredrick E. Henry , Greg Fleishman , Andrew L. Lemire , Lihua Wang , Wyatt Korff , Paul W. Tillberg , Andreas Lüthi , Scott M. Sternson
    eLife. 2023 Jan 20:. doi: 10.7554/eLife.84262

    The central nucleus of the amygdala (CEA) is a brain region that integrates external and internal sensory information and executes innate and adaptive behaviors through distinct output pathways. Despite its complex functions, the diversity of molecularly defined neuronal types in the CEA and their contributions to major axonal projection targets have not been examined systematically. Here, we performed single-cell RNA-sequencing (scRNA-Seq) to classify molecularly defined cell types in the CEA and identified marker-genes to map the location of these neuronal types using expansion assisted iterative fluorescence in situ hybridization (EASI-FISH). We developed new methods to integrate EASI-FISH with 5-plex retrograde axonal labeling to determine the spatial, morphological, and connectivity properties of ∼30,000 molecularly defined CEA neurons. Our study revealed spatio-molecular organization of the CEA, with medial and lateral CEA associated with distinct cell families. We also found a long-range axon projection network from the CEA, where target regions receive inputs from multiple molecularly defined cell types. Axon collateralization was found primarily among projections to hindbrain targets, which are distinct from forebrain projections. This resource reports marker-gene combinations for molecularly defined cell types and axon-projection types, which will be useful for selective interrogation of these neuronal populations to study their contributions to the diverse functions of the CEA.

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    01/18/23 | Functional specialization and structured representations for space and time in prefrontal cortex
    Claudia Böhm , Albert K. Lee
    bioRxiv. 2023 Jan 18:. doi: 10.1101/2023.01.16.524214

    Individual neurons in prefrontal cortex – a key brain area involved in cognitive functions – are selective for variables such as space or time, as well as more cognitive aspects of tasks, such as learned categories. Many neurons exhibit mixed selectivity, that is, they show selectivity for multiple variables. A fundamental question is whether neurons are functionally specialized for particular variables and how selectivity for different variables intersects across the population. Here, we analyzed neural correlates of space and time in rats performing a navigational task with two behaviorally important categories – starts and goals. Using simultaneous recordings of many medial prefrontal cortex (mPFC) neurons during behavior, we found that population codes for elapsed time were invariant to different locations within categories, and subsets of neurons had functional preferences for time or space across categories. Thus, mPFC exhibits structured selectivity, which may facilitate complex behaviors by efficiently generating informative representations of multiple variables.

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    01/18/23 | Mesolimbic dopamine adapts the rate of learning from action.
    Coddington LT, Lindo SE, Dudman JT
    Nature. 2023 Jan 18:. doi: 10.1038/s41586-022-05614-z

    Recent success in training artificial agents and robots derives from a combination of direct learning of behavioural policies and indirect learning through value functions. Policy learning and value learning use distinct algorithms that optimize behavioural performance and reward prediction, respectively. In animals, behavioural learning and the role of mesolimbic dopamine signalling have been extensively evaluated with respect to reward prediction; however, so far there has been little consideration of how direct policy learning might inform our understanding. Here we used a comprehensive dataset of orofacial and body movements to understand how behavioural policies evolved as naive, head-restrained mice learned a trace conditioning paradigm. Individual differences in initial dopaminergic reward responses correlated with the emergence of learned behavioural policy, but not the emergence of putative value encoding for a predictive cue. Likewise, physiologically calibrated manipulations of mesolimbic dopamine produced several effects inconsistent with value learning but predicted by a neural-network-based model that used dopamine signals to set an adaptive rate, not an error signal, for behavioural policy learning. This work provides strong evidence that phasic dopamine activity can regulate direct learning of behavioural policies, expanding the explanatory power of reinforcement learning models for animal learning.

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    01/07/23 | Solving the spike sorting problem with Kilosort
    Marius Pachitariu , Shashwat Sridhar , Carsen Stringer
    bioRxiv. 2023 Jan 07:. doi: 10.1101/2023.01.07.523036

    Spike sorting is the computational process of extracting the firing times of single neurons from recordings of local electrical fields. This is an important but hard problem in neuroscience, complicated by the non-stationarity of the recordings and the dense overlap in electrical fields between nearby neurons. To solve the spike sorting problem, we have continuously developed over the past eight years a framework known as Kilosort. This paper describes the various algorithmic steps introduced in different versions of Kilosort. We also report the development of Kilosort4, a new version with substantially improved performance due to new clustering algorithms inspired by graph-based approaches. To test the performance of Kilosort, we developed a realistic simulation framework which uses densely sampled electrical fields from real experiments to generate non-stationary spike waveforms and realistic noise. We find that nearly all versions of Kilosort outperform other algorithms on a variety of simulated conditions, and Kilosort4 performs best in all cases, correctly identifying even neurons with low amplitudes and small spatial extents in high drift conditions.

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    Card LabFly Functional ConnectomeDrosophila Resources
    01/04/23 | Synaptic gradients transform object location to action.
    Dombrovski M, Peek MY, Park J, Vaccari A, Sumathipala M, Morrow C, Breads P, Zhao A, Kurmangaliyev YZ, Sanfilippo P, Rehan A, Polsky J, Alghailani S, Tenshaw E, Namiki S, Zipursky SL, Card GM
    Nature. 2023 Jan 04;613(7944):534-42. doi: 10.1038/s41586-022-05562-8

    To survive, animals must convert sensory information into appropriate behaviours. Vision is a common sense for locating ethologically relevant stimuli and guiding motor responses. How circuitry converts object location in retinal coordinates to movement direction in body coordinates remains largely unknown. Here we show through behaviour, physiology, anatomy and connectomics in Drosophila that visuomotor transformation occurs by conversion of topographic maps formed by the dendrites of feature-detecting visual projection neurons (VPNs) into synaptic weight gradients of VPN outputs onto central brain neurons. We demonstrate how this gradient motif transforms the anteroposterior location of a visual looming stimulus into the fly's directional escape. Specifically, we discover that two neurons postsynaptic to a looming-responsive VPN type promote opposite takeoff directions. Opposite synaptic weight gradients onto these neurons from looming VPNs in different visual field regions convert localized looming threats into correctly oriented escapes. For a second looming-responsive VPN type, we demonstrate graded responses along the dorsoventral axis. We show that this synaptic gradient motif generalizes across all 20 primary VPN cell types and most often arises without VPN axon topography. Synaptic gradients may thus be a general mechanism for conveying spatial features of sensory information into directed motor outputs.

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    01/02/23 | In situ cryo-electron tomography reveals the asymmetric architecture of mammalian sperm axonemes.
    Chen Z, Greenan GA, Shiozaki M, Liu Y, Skinner WM, Zhao X, Zhao S, Yan R, Yu Z, Lishko PV, Agard DA, Vale RD
    Nature Structural & Molecular Biology. 2023 Jan 02:. doi: 10.1038/s41594-022-00861-0

    The flagella of mammalian sperm display non-planar, asymmetric beating, in contrast to the planar, symmetric beating of flagella from sea urchin sperm and unicellular organisms. The molecular basis of this difference is unclear. Here, we perform in situ cryo-electron tomography of mouse and human sperm, providing the highest-resolution structural information to date. Our subtomogram averages reveal mammalian sperm-specific protein complexes within the microtubules, the radial spokes and nexin-dynein regulatory complexes. The locations and structures of these complexes suggest potential roles in enhancing the mechanical strength of mammalian sperm axonemes and regulating dynein-based axonemal bending. Intriguingly, we find that each of the nine outer microtubule doublets is decorated with a distinct combination of sperm-specific complexes. We propose that this asymmetric distribution of proteins differentially regulates the sliding of each microtubule doublet and may underlie the asymmetric beating of mammalian sperm.

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    01/02/23 | Time-tagged ticker tapes for intracellular recordings.
    Lin D, Li X, Moult E, Park P, Tang B, Shen H, Grimm JB, Falco N, Jia BZ, Baker D, Lavis LD, Cohen AE
    Nature Biotechnology. 2023 Jan 02:. doi: 10.1038/s41587-022-01524-7

    Recording transcriptional histories of a cell would enable deeper understanding of cellular developmental trajectories and responses to external perturbations. Here we describe an engineered protein fiber that incorporates diverse fluorescent marks during its growth to store a ticker tape-like history. An embedded HaloTag reporter incorporates user-supplied dyes, leading to colored stripes that map the growth of each individual fiber to wall clock time. A co-expressed eGFP tag driven by a promoter of interest records a history of transcriptional activation. High-resolution multi-spectral imaging on fixed samples reads the cellular histories, and interpolation of eGFP marks relative to HaloTag timestamps provides accurate absolute timing. We demonstrate recordings of doxycycline-induced transcription in HEK cells and cFos promoter activation in cultured neurons, with a single-cell absolute accuracy of 30-40 minutes over a 12-hour recording. The protein-based ticker tape design we present here could be generalized to achieve massively parallel single-cell recordings of diverse physiological modalities.

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