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2368 Publications

Showing 11-20 of 2368 results
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    11/06/23 | A complete reconstruction of the early visual system of an adult insect.
    Chua NJ, Makarova AA, Gunn P, Villani S, Cohen B, Thasin M, Wu J, Shefter D, Pang S, Xu CS, Hess HF, Polilov AA, Chklovskii DB
    Current Biology. 2023 Nov 06;33(21):4611-4623. doi: 10.1016/j.cub.2023.09.021

    For most model organisms in neuroscience, research into visual processing in the brain is difficult because of a lack of high-resolution maps that capture complex neuronal circuitry. The microinsect Megaphragma viggianii, because of its small size and non-trivial behavior, provides a unique opportunity for tractable whole-organism connectomics. We image its whole head using serial electron microscopy. We reconstruct its compound eye and analyze the optical properties of the ommatidia as well as the connectome of the first visual neuropil-the lamina. Compared with the fruit fly and the honeybee, Megaphragma visual system is highly simplified: it has 29 ommatidia per eye and 6 lamina neuron types. We report features that are both stereotypical among most ommatidia and specialized to some. By identifying the "barebones" circuits critical for flying insects, our results will facilitate constructing computational models of visual processing in insects.

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    11/03/23 | Volitional activation of remote place representations with a hippocampal brain-machine interface.
    Lai C, Tanaka S, Harris TD, Lee AK
    Science. 2023 Nov 03;382(6670):566-573. doi: 10.1126/science.adh5206

    The hippocampus is critical for recollecting and imagining experiences. This is believed to involve voluntarily drawing from hippocampal memory representations of people, events, and places, including maplike representations of familiar environments. However, whether representations in such "cognitive maps" can be volitionally accessed is unknown. We developed a brain-machine interface to test whether rats can do so by controlling their hippocampal activity in a flexible, goal-directed, and model-based manner. We found that rats can efficiently navigate or direct objects to arbitrary goal locations within a virtual reality arena solely by activating and sustaining appropriate hippocampal representations of remote places. This provides insight into the mechanisms underlying episodic memory recall, mental simulation and planning, and imagination and opens up possibilities for high-level neural prosthetics that use hippocampal representations.

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    11/01/23 | Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover
    Carolyn M Ott , Russel Torres , Tung-Sheng Kuan , Aaron T Kuan , JoAnn Buchanan , Leila Elabbady , Sharmishtaa Seshamani , Agnes L Bodor , Forrest C Collman , Davi D Bock , Wei-Chung Allen Lee , Nuno Macarico da Costa , Jennifer Lippincott-Schwartz
    bioRxiv. 2023 Nov 01:. doi: 10.1101/2023.10.31.564838

    A primary cilium is a thin membrane-bound extension off a cell surface that contains receptors for perceiving and transmitting signals that modulate cell state and activity. While many cell types have a primary cilium, little is known about primary cilia in the brain, where they are less accessible than cilia on cultured cells or epithelial tissues and protrude from cell bodies into a deep, dense network of glial and neuronal processes. Here, we investigated cilia frequency, internal structure, shape, and position in large, high-resolution transmission electron microscopy volumes of mouse primary visual cortex. Cilia extended from the cell bodies of nearly all excitatory and inhibitory neurons, astrocytes, and oligodendrocyte precursor cells (OPCs), but were absent from oligodendrocytes and microglia. Structural comparisons revealed that the membrane structure at the base of the cilium and the microtubule organization differed between neurons and glia. OPC cilia were distinct in that they were the shortest and contained pervasive internal vesicles only occasionally observed in neuron and astrocyte cilia. Investigating cilia-proximal features revealed that many cilia were directly adjacent to synapses, suggesting cilia are well poised to encounter locally released signaling molecules. The internal anatomy, including microtubule changes and centriole location, defined key structural features including cilium placement and shape. Together, the anatomical insights both within and around neuron and glia cilia provide new insights into cilia formation and function across cell types in the brain.

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    11/01/23 | Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope.
    Lovelace JW, Ma J, Yadav S, Chhabria K, Shen H, Pang Z, Qi T, Sehgal R, Zhang Y, Bali T, Vaissiere T, Tan S, Liu Y, Rumbaugh G, Ye L, Kleinfeld D, Stringer C, Augustine V
    Nature. 2023 Nov 01;623(7986):387-396. doi: 10.1038/s41586-023-06680-7

    Visceral sensory pathways mediate homeostatic reflexes, the dysfunction of which leads to many neurological disorders. The Bezold-Jarisch reflex (BJR), first described in 1867, is a cardioinhibitory reflex that is speculated to be mediated by vagal sensory neurons (VSNs) that also triggers syncope. However, the molecular identity, anatomical organization, physiological characteristics and behavioural influence of cardiac VSNs remain mostly unknown. Here we leveraged single-cell RNA-sequencing data and HYBRiD tissue clearing to show that VSNs that express neuropeptide Y receptor Y2 (NPY2R) predominately connect the heart ventricular wall to the area postrema. Optogenetic activation of NPY2R VSNs elicits the classic triad of BJR responses-hypotension, bradycardia and suppressed respiration-and causes an animal to faint. Photostimulation during high-resolution echocardiography and laser Doppler flowmetry with behavioural observation revealed a range of phenotypes reflected in clinical syncope, including reduced cardiac output, cerebral hypoperfusion, pupil dilation and eye-roll. Large-scale Neuropixels brain recordings and machine-learning-based modelling showed that this manipulation causes the suppression of activity across a large distributed neuronal population that is not explained by changes in spontaneous behavioural movements. Additionally, bidirectional manipulation of the periventricular zone had a push-pull effect, with inhibition leading to longer syncope periods and activation inducing arousal. Finally, ablating NPY2R VSNs specifically abolished the BJR. Combined, these results demonstrate a genetically defined cardiac reflex that recapitulates characteristics of human syncope at physiological, behavioural and neural network levels.

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    10/31/23 | Effects of stochastic coding on olfactory discrimination in flies and mice.
    Srinivasan S, Daste S, Modi MN, Turner GC, Fleischmann A, Navlakha S
    PLoS Biology. 2023 Oct 31;21(10):e3002206. doi: 10.1371/journal.pbio.3002206

    Sparse coding can improve discrimination of sensory stimuli by reducing overlap between their representations. Two factors, however, can offset sparse coding's benefits: similar sensory stimuli have significant overlap and responses vary across trials. To elucidate the effects of these 2 factors, we analyzed odor responses in the fly and mouse olfactory regions implicated in learning and discrimination-the mushroom body (MB) and the piriform cortex (PCx). We found that neuronal responses fall along a continuum from extremely reliable across trials to extremely variable or stochastic. Computationally, we show that the observed variability arises from noise within central circuits rather than sensory noise. We propose this coding scheme to be advantageous for coarse- and fine-odor discrimination. More reliable cells enable quick discrimination between dissimilar odors. For similar odors, however, these cells overlap and do not provide distinguishing information. By contrast, more unreliable cells are decorrelated for similar odors, providing distinguishing information, though these benefits only accrue with extended training with more trials. Overall, we have uncovered a conserved, stochastic coding scheme in vertebrates and invertebrates, and we identify a candidate mechanism, based on variability in a winner-take-all (WTA) inhibitory circuit, that improves discrimination with training.

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    10/31/23 | Tensor formalism for predicting synaptic connections with ensemble modeling or optimization.
    Tirthabir Biswas , Tianzhi Lambus Li , James E. Fitzgerald
    arXiv. 2023 Oct 31:. doi: 10.48550/arXiv.2310.20309

    Theoretical neuroscientists often try to understand how the structure of a neural network relates to its function by focusing on structural features that would either follow from optimization or occur consistently across possible implementations. Both optimization theories and ensemble modeling approaches have repeatedly proven their worth, and it would simplify theory building considerably if predictions from both theory types could be derived and tested simultaneously. Here we show how tensor formalism from theoretical physics can be used to unify and solve many optimization and ensemble modeling approaches to predicting synaptic connectivity from neuronal responses. We specifically focus on analyzing the solution space of synaptic weights that allow a thresholdlinear neural network to respond in a prescribed way to a limited number of input conditions. For optimization purposes, we compute the synaptic weight vector that minimizes an arbitrary quadratic loss function. For ensemble modeling, we identify synaptic weight features that occur consistently across all solutions bounded by an arbitrary quadratic function. We derive a common solution to this suite of nonlinear problems by showing how each of them reduces to an equivalent linear problem that can be solved analytically. Although identifying the equivalent linear problem is nontrivial, our tensor formalism provides an elegant geometrical perspective that allows us to solve the problem numerically. The final algorithm is applicable to a wide range of interesting neuroscience problems, and the associated geometric insights may carry over to other scientific problems that require constrained optimization.

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    10/27/23 | Lactate biosensors for spectrally and spatially multiplexed fluorescence imaging.
    Nasu Y, Aggarwal A, Le GN, Vo CT, Kambe Y, Wang X, Beinlich FR, Lee AB, Ram TR, Wang F, Gorzo KA, Kamijo Y, Boisvert M, Nishinami S, Kawamura G, Ozawa T, Toda H, Gordon GR, Ge S, Hirase H, Nedergaard M, Paquet M, Drobizhev M, Podgorski K, Campbell RE
    Nature Communications. 2023 Oct 27;14(1):6598. doi: 10.1038/s41467-023-42230-5

    L-Lactate is increasingly appreciated as a key metabolite and signaling molecule in mammals. However, investigations of the inter- and intra-cellular dynamics of L-lactate are currently hampered by the limited selection and performance of L-lactate-specific genetically encoded biosensors. Here we now report a spectrally and functionally orthogonal pair of high-performance genetically encoded biosensors: a green fluorescent extracellular L-lactate biosensor, designated eLACCO2.1, and a red fluorescent intracellular L-lactate biosensor, designated R-iLACCO1. eLACCO2.1 exhibits excellent membrane localization and robust fluorescence response. To the best of our knowledge, R-iLACCO1 and its affinity variants exhibit larger fluorescence responses than any previously reported intracellular L-lactate biosensor. We demonstrate spectrally and spatially multiplexed imaging of L-lactate dynamics by coexpression of eLACCO2.1 and R-iLACCO1 in cultured cells, and in vivo imaging of extracellular and intracellular L-lactate dynamics in mice.

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    10/27/23 | Nanoscale imaging reveals the mechanisms of ER-to-Golgi transport via a dynamic tubular-vesicular network
    Luis Wong-Dilworth , Gresy Bregu , Steffen Restel , Carmen Rodilla-Ramirez , Svenja Ebeling , Shelly Harel , Paula Leupold , Jonathan Grimm , Luke D. Lavis , Jessica Angulo-Capel , Felix Campelo , Francesca Bottanelli
    bioRxiv. 2023 Oct 27:. doi: 10.1101/2023.10.27.563951

    The endoplasmic reticulum (ER) and the Golgi apparatus are the first sorting stations along the secretory pathway of mammalian cells and have a crucial role in protein quality control and cellular homeostasis. While machinery components mediating ER-to-Golgi transport have been mapped, it is unclear how exchange between the two closely juxtaposed organelles is coordinated in living cells. Here, using gene editing to tag machinery components, live-cell confocal and stimulated emission depletion (STED) super-resolution microscopy, we show that ER-to-Golgi transport occurs via a dynamic network of tubules positive for the small GTPase ARF4. swCOPI machinery is tightly associated to this network and moves with tubular-vesicular structures. Strikingly, the ARF4 network appears to be continuous with the ER and ARF4 tubules remodel around static ER exit sites (ERES) defined by COPII machinery. We were further able to dissect the steps of ER-to-Golgi transport with functional trafficking assays. A wave of cargo released from the ER percolates through peripheral and Golgi-tethered ARF4 structures before filling the cis-Golgi. Perturbation via acute degradation of ARF4 shows an active regulatory role for the GTPase and COPI in anterograde transport. Our data supports a model in which anterograde ER-to-Golgi transport occurs via an ARF4 tubular-vesicular network directly connecting the ER and Golgi-associated pre-cisternae.

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    10/26/23 | Neural-circuit basis of song preference learning in fruit flies
    Keisuke Imoto , Yuki Ishikawa , Yoshinori Aso , Jan Funke , Ryoya Tanaka , Azusa Kamikouchi
    bioRxiv. 2023 Oct 26:. doi: 10.1101/2023.10.24.563693

    As observed in human language learning and song learning in birds, the fruit fly Drosophila melanogaster changes its' auditory behaviors according to prior sound experiences. Female flies that have heard male courtship songs of the same species are less responsive to courtship songs of different species. This phenomenon, known as song preference learning in flies, requires GABAergic input to pC1 neurons in the central brain, with these neurons playing a key role in mating behavior by integrating multimodal sensory and internal information. The neural circuit basis of this GABAergic input, however, has not yet been identified. Here, we find that pCd-2 neurons, totaling four cells per hemibrain and expressing the sex-determination gene doublesex, provide the GABAergic input to pC1 neurons for song preference learning. First, RNAi-mediated knockdown of GABA production in pCd-2 neurons abolished song preference learning. Second, pCd-2 neurons directly, and in many cases mutually, connect with pC1 neurons, suggesting the existence of reciprocal circuits between pC1 and pCd-2 neurons. Finally, GABAergic and dopaminergic inputs to pCd-2 neurons are necessary for song preference learning. Together, this study suggests that reciprocal circuits between pC1 and pCd-2 neurons serve as a sensory and internal state-integrated hub, allowing flexible control over female copulation. Consequently, this provides a neural circuit model that underlies experience-dependent auditory plasticity.

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    10/25/23 | Optimized Red-Absorbing Dyes for Imaging and Sensing.
    Grimm JB, Tkachuk AN, Patel R, Hennigan ST, Gutu A, Dong P, Gandin V, Osowski AM, Holland KL, Liu ZJ, Brown TA, Lavis LD
    Journal of the American Chemical Society. 2023 Oct 25;145(42):23000-23013. doi: 10.1021/jacs.3c05273

    Rhodamine dyes are excellent scaffolds for developing a broad range of fluorescent probes. A key property of rhodamines is their equilibrium between a colorless lactone and fluorescent zwitterion. Tuning the lactone-zwitterion equilibrium constant () can optimize dye properties for specific biological applications. Here, we use known and novel organic chemistry to prepare a comprehensive collection of rhodamine dyes to elucidate the structure-activity relationships that govern . We discovered that the auxochrome substituent strongly affects the lactone-zwitterion equilibrium, providing a roadmap for the rational design of improved rhodamine dyes. Electron-donating auxochromes, such as julolidine, work in tandem with fluorinated pendant phenyl rings to yield bright, red-shifted fluorophores for live-cell single-particle tracking (SPT) and multicolor imaging. The -aryl auxochrome combined with fluorination yields red-shifted Förster resonance energy transfer (FRET) quencher dyes useful for creating a new semisynthetic indicator to sense cAMP using fluorescence lifetime imaging microscopy (FLIM). Together, this work expands the synthetic methods available for rhodamine synthesis, generates new reagents for advanced fluorescence imaging experiments, and describes structure-activity relationships that will guide the design of future probes.

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