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199 Publications

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    02/24/22 | Neuromuscular embodiment of feedback control elements in Drosophila flight.
    Samuel C Whitehead , Sofia Leone , Theodore Lindsay , Matthew R Meiselman , Noah Cowan , Michael H Dickinson , Nilay Yapici , David Stern , Troy Shirangi , Itai Cohen
    bioRxiv. 2022 Feb 24:. doi: 10.1101/2022.02.22.481344

    While insects like Drosophila are flying, aerodynamic instabilities require that they make millisecond-timescale adjustments to their wing motion to stay aloft and on course. These stabilization reflexes can be modeled as a proportional-integral (PI) controller; however, it is unclear how such control might be instantiated in insects at the level of muscles and neurons. Here, we show that the b1 and b2 motor units—prominent components of the fly's steering muscles system—modulate specific elements of the PI controller: the angular displacement (integral, I) and angular velocity (proportional, P), respectively. Moreover, these effects are observed only during the stabilization of pitch. Our results provide evidence for an organizational principle in which each muscle contributes to a specific functional role in flight control, a finding that highlights the power of using top-down behavioral modeling to guide bottom-up cellular manipulation studies.

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    02/23/22 | The importance of accounting for movement when relating neuronal activity to sensory and cognitive processes.
    Edward Zagha , Jeffrey C Erlich , Soohyun Lee , Gyorgy Lur , Daniel H O'Connor , Nicholas A Steinmetz , Carsen Stringer , Hongdian Yang
    Journal of Neuroscience: The Official Journal of the Society for Neuroscience. 2022 Feb 23;42(8):1375-1382. doi: 10.1523/JNEUROSCI.1919-21.2021

    A surprising finding of recent studies in mouse is the dominance of widespread movement-related activity throughout the brain, including in early sensory areas. In awake subjects, failing to account for movement risks misattributing movement-related activity to other (e.g., sensory or cognitive) processes. In this article, we 1) review task designs for separating task-related and movement-related activity, 2) review three 'case studies' in which not considering movement would have resulted in critically different interpretations of neuronal function, and 3) discuss functional couplings that may prevent us from ever fully isolating sensory, motor, and cognitive-related activity. Our main thesis is that neural signals related to movement are ubiquitous, and therefore ought to be considered first and foremost when attempting to correlate neuronal activity with task-related processes.

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    Romani LabSvoboda Lab
    02/22/22 | Neural Algorithms and Circuits for Motor Planning.
    Inagaki HK, Chen S, Daie K, Finklestein A, Fontolan L, Romani S, Svoboda K
    Annual Reviews Neuroscience. 2022 Feb 22:. doi: 10.1146/annurev-neuro-092021-121730

    The brain plans and executes volitional movements. The underlying patterns of neural population activity have been explored in the context of movements of the eyes, limbs, tongue, and head in nonhuman primates and rodents. How do networks of neurons produce the slow neural dynamics that prepare specific movements and the fast dynamics that ultimately initiate these movements? Recent work exploits rapid and calibrated perturbations of neural activity to test specific dynamical systems models that are capable of producing the observed neural activity. These joint experimental and computational studies show that cortical dynamics during motor planning reflect fixed points of neural activity (attractors). Subcortical control signals reshape and move attractors over multiple timescales, causing commitment to specific actions and rapid transitions to movement execution. Experiments in rodents are beginning to reveal how these algorithms are implemented at the level of brain-wide neural circuits. Expected final online publication date for the , Volume 45 is July 2022. Please see for revised estimates.

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    Looger Lab
    02/19/22 | Volume-transmitted GABA waves drive epileptiform rhythms in the hippocampal network.
    Vincent Magloire , Leonid P. Savtchenko , Sergyi Sylantyev , Thomas P. Jensen , Nicholas Cole , Jonathan S. Marvin , Loren L. Looger , Dimitri M. Kullmann , Matthew C. Walker , Ivan Pavlov , Dmitri A. Rusakov
    bioRxiv. 2022 Feb 19:. doi: 10.1101/2021.03.25.437016

    Synchronised rhythmic activity of the brain is thought to arise from neuronal network behaviours that rely on synaptic signalling between individual cells. This notion has been a basis to explain periodic epileptiform discharges that are driven by interneuronal networks. However, interneuronal discharges not only engage cell-cell GABAergic transmission but also control the extracellular GABA concentration ([GABA]e) and thus tonic GABAA receptor conductance (Gtonic) across the cell population. At the same time, the firing activity of interneurons shows a bell-shaped dependence on Gtonic, suggesting an innate susceptibility to self-sustained oscillations. Here, we employ patch-clamp GABA ‘sniffer’ and fast two-photon excitation imaging of GABA sensor to show that periodic epileptiform discharges are preceded by a region-wide, rising wave of extracellular GABA. Neural network simulations based on such observations reveal that it is the volume-transmitted, extrasynaptic actions of GABA targeting multiple off-target cells that drives synchronised interneuronal spiking prompting periodic epileptiform bursts. We validate this hypothesis using simultaneous patch-clamp recordings from multiple nerve cells, selective optogenetic stimulation of fast-spiking interneurons, and by revealing the role of GABA uptake. Our findings thus unveil a key role of extrasynaptic, volume-transmitted GABA actions in enabling and pacing regenerative rhythmic activity in brain networks.

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    02/18/22 | Visualizing cellular and tissue ultrastructure using Ten-fold Robust Expansion Microscopy (TREx)
    Hugo G.J. Damstra , Boaz Mohar , Mark Eddison , Anna Akhmanova , Lukas C. Kapitein , Paul W. Tillberg
    eLife. 2022 Feb 18:. doi:

    Expansion microscopy (ExM) is a powerful technique to overcome the diffraction limit of light microscopy that can be applied in both tissues and cells. In ExM, samples are embedded in a swellable polymer gel to physically expand the sample and isotropically increase resolution in x, y and z. The maximum resolution increase is limited by the expansion factor of the polymer gel, which is four-fold for the original ExM protocol. Variations on the original ExM method have been reported that allow for greater expansion factors, for example using iterative expansion, but at the cost of ease of adoption or versatility. Here, we systematically explore the ExM recipe space and present a novel method termed Ten-fold Robust Expansion Microscopy (TREx) that, like the original ExM method, requires no specialized equipment or procedures to carry out. We demonstrate that TREx gels expand ten-fold, can be handled easily, and can be applied to both thick tissue sections and cells enabling high-resolution subcellular imaging in a single expansion step. We show that applying TREx on antibody-stained samples can be combined with off-the-shelf small molecule stains for both total protein and membranes to provide ultrastructural context to subcellular protein localization.

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    02/15/22 | Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission
    Abhi Aggarwal , Rui Liu , Yang Chen , Amelia J Ralowicz , Samuel J Bergerson , Filip Tomaska , Timothy L Hanson , Jeremy P Hasseman , Daniel Reep , Getahun Tsegaye , Pantong Yao , Xiang Ji , Marinus Kloos , Deepika Walpita , Ronak Patel , Paul W Tilberg , Boaz Mohar , GENIE , Loren L Looger , Jonathan S Marvin , Michael B Hoppa , Arthur Konnerth , David Kleinfeld , Eric R Schreiter , Kaspar Podgorski
    bioRxiv PrePrint. 2022 Feb 15:. doi: 10.1101/2022.02.13.480251

    The fluorescent glutamate indicator iGluSnFR enables imaging of neurotransmission with genetic and molecular specificity. However, existing iGluSnFR variants exhibit saturating activation kinetics and are excluded from post-synaptic densities, limiting their ability to distinguish synaptic from extrasynaptic glutamate. Using a multi-assay screen in bacteria, soluble protein, and cultured neurons, we generated novel variants with improved kinetics and signal-to-noise ratios. We also developed surface display constructs that improve iGluSnFR’s nanoscopic localization to post-synapses. The resulting indicator, iGluSnFR3, exhibits rapid non-saturating activation kinetics and reports synaptic glutamate release with improved linearity and increased specificity versus extrasynaptic signals in cultured neurons. In mouse visual cortex, imaging of iGluSnFR3 at individual boutons reported single electrophysiologically-observed action potentials with high specificity versus non-synaptic transients. In vibrissal sensory cortex Layer 4, we used iGluSnFR3 to characterize distinct patterns of touch-evoked feedforward input from thalamocortical boutons and both feedforward and recurrent input onto L4 cortical neuron dendritic spines.

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    02/13/22 | Structured random receptive fields enable informative sensory encodings
    Biraj Pandey , Marius Pachitariu , Bingni W. Brunton , Kameron Decker Harris
    bioRxiv. 2022 Feb 13:. doi: 10.1101/2021.09.09.459651

    Brains must represent the outside world so that animals survive and thrive. In early sensory systems, neural populations have diverse receptive fields structured to detect important features in inputs, yet significant variability has been ignored in classical models of sensory neurons. We model neuronal receptive fields as random, variable samples from parametrized distributions in two sensory modalities, using data from insect mechanosensors and neurons of mammalian primary visual cortex. We show that these random feature neurons perform a randomized wavelet transform on inputs which removes high frequency noise and boosts the signal. Our result makes a significant theoretical connection between the foundational concepts of receptive fields in neuroscience and random features in artificial neural networks. Further, these random feature neurons enable learning from fewer training samples and with smaller networks in artificial tasks. This structured random model of receptive fields provides a unifying, mathematically tractable framework to understand sensory encodings across both spatial and temporal domains.

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    02/01/22 | Organization of translating secretome mRNAS on endoplasmic reticulum
    Choi H, Liao Y, Yoon YJ, Grimm J, Lavis LD, Singer RH, Lippincott-Schwartz J
    Biophysical Journal. 2022 Feb 01;121(3):33a. doi: 10.1016/j.bpj.2021.11.2550

    The endoplasmic reticulum (ER) has a complex morphology comprised of stacked sheets, tubules, and three-way junctions, which together function as a platform for protein synthesis of membrane and secretory proteins. Specific ER subdomains are thought to be spatially organized to enable protein synthesis activity, but precisely where these domains are localized is unclear, especially relative to the plethora of organelle interactions taking place on the ER. Here, we use single-molecule tracking of ribosomes and mRNA in combination with simultaneous imaging of ER to assess the sites of membrane protein synthesis on the ER. We found that ribosomes were widely distributed throughout different ER morphologies, but the synthesis of membrane proteins (including Type I, II, and multi-spanning) and an ER luminal protein (Calreticulin) occurred primarily at three-way junctions. Lunapark played a key role in stabilizing transmembrane protein mRNA at three-way junctions. We additionally found that translating mRNAs coding for transmembrane proteins are in the vicinity of lysosomes and translate through a cap-independent but eIF2-dependent mechanism. These results support the idea that discrete ER subdomains co-exist with lysosomes to support specific types of protein synthesis activities, with ER-lysosome interactions playing an important role in the translation of secretome mRNAs.

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    Perhaps the most valuable single set of resources for genetic studies of Drosophila melanogaster is the collection of multiply-inverted chromosomes commonly known as balancer chromosomes. Balancers prevent the recovery of recombination exchange products within genomic regions included in inversions and allow perpetual maintenance of deleterious alleles in living stocks and the execution of complex genetic crosses. Balancer chromosomes have been generated traditionally by exposing animals to ionizing radiation and screening for altered chromosome structure or for unusual marker segregation patterns. These approaches are tedious and unpredictable, and have failed to produce the desired products in some species. Here I describe transgenic tools that allow targeted chromosome rearrangements in Drosophila species. The key new resources are engineered reporter genes containing introns with yeast recombination sites and enhancers that drive fluorescent reporter genes in multiple body regions. These tools were used to generate a doubly-inverted chromosome 3R in D. simulans that serves as an effective balancer chromosome.

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    02/09/22 | Ascending neurons convey behavioral state to integrative sensory and action selection centers in the brain
    Chin-Lin Chen , Florian Aymanns , Ryo Minegishi , Victor D. V. Matsuda , Nicolas Talabot , Semih Günel , Barry J. Dickson , Pavan Ramdya
    bioRxiv. 2022 Feb 09:. doi: 10.1101/2022.02.09.479566

    Knowledge of one’s own behavioral state—whether one is walking, grooming, or resting—is critical for contextualizing sensory cues including interpreting visual motion and tracking odor sources. Additionally, awareness of one’s own posture is important to avoid initiating destabilizing or physically impossible actions. Ascending neurons (ANs), interneurons in the vertebrate spinal cord or insect ventral nerve cord (VNC) that project to the brain, may provide such high-fidelity behavioral state signals. However, little is known about what ANs encode and where they convey signals in any brain. To address this gap, we performed a large-scale functional screen of AN movement encoding, brain targeting, and motor system patterning in the adult fly, Drosophila melanogaster. Using a new library of AN sparse driver lines, we measured the functional properties of 247 genetically-identifiable ANs by performing two-photon microscopy recordings of neural activity in tethered, behaving flies. Quantitative, deep network-based neural and behavioral analyses revealed that ANs nearly exclusively encode high-level behaviors—primarily walking as well as resting and grooming—rather than low-level joint or limb movements. ANs that convey self-motion—resting, walking, and responses to gust-like puff stimuli—project to the brain’s anterior ventrolateral protocerebrum (AVLP), a multimodal, integrative sensory hub, while those that encode discrete actions—eye grooming, turning, and proboscis extension—project to the brain’s gnathal ganglion (GNG), a locus for action selection. The structure and polarity of AN projections within the VNC are predictive of their functional encoding and imply that ANs participate in motor computations while also relaying state signals to the brain. Illustrative of this are ANs that temporally integrate proboscis extensions over tens-of-seconds, likely through recurrent interconnectivity. Thus, in line with long-held theoretical predictions, ascending populations convey high-level behavioral state signals almost exclusively to brain regions implicated in sensory feature contextualization and action selection.

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