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2244 Publications

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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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    03/15/23 | Cristae formation is a mechanical buckling event controlled by the inner membrane lipidome
    Kailash Venkatraman , Christopher T Lee , Guadalupe C. Garcia , Arijit Mahapatra , Guy Perkins , Keun-Young Kim , Hilda Amalia Pasolli , Sebastien Phan , Jennifer Lippincott-Schwartz , Mark Ellisman , Padmini Rangamani , Itay Budin
    bioRxiv. 2023 Mar 15:. doi: 10.1101/2023.03.13.532310

    The inner mitochondrial membrane (IMM) is the site of bulk ATP generation in cells and has a broadly conserved lipid composition enriched in unsaturated phospholipids and cardiolipin (CL). While proteins that shape the IMM and its characteristic cristae membranes (CM) have been defined, specific mechanisms by which mitochondrial lipids dictate its structure and function have yet to be elucidated. Here we combine experimental lipidome dissection with multi-scale modeling to investigate how lipid interactions shape CM morphology and ATP generation. When modulating fatty acid unsaturation in engineered yeast strains, we observed that loss of di-unsaturated phospholipids (PLs) led to a breakpoint in IMM topology and respiratory capacity. We found that PL unsaturation modulates the organization of ATP synthases that shape cristae ridges. Based on molecular modeling of mitochondrial-specific membrane adaptations, we hypothesized that conical lipids like CL buffer against the effects of saturation on the IMM. In cells, we discovered that loss of CL collapses the IMM at intermediate levels of PL saturation, an effect that is independent of ATP synthase oligomerization. To explain this interaction, we employed a continuum modeling approach, finding that lipid and protein-mediated curvatures are predicted to act in concert to form curved membranes in the IMM. The model highlighted a snapthrough instability in cristae tubule formation, which could drive IMM collapse upon small changes in composition. The interaction between CL and di-unsaturated PLs suggests that growth conditions that alter the fatty acid pool, such as oxygen availability, could define CL function. While loss of CL only has a minimal phenotype under standard laboratory conditions, we show that its synthesis is essential under microaerobic conditions that better mimic natural yeast fermentation. Lipid and protein-mediated mechanisms of curvature generation can thus act together to support mitochondrial architecture under changing environments.

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    03/13/23 | Connectome-constrained deep mechanistic networks predict neural responses across the fly visual system at single-neuron resolution
    Janne K. Lappalainen , Fabian D. Tschopp , Sridhama Prakhya , Mason McGill , Aljoscha Nern , Kazunori Shinomiya , Shin-ya Takemura , Eyal Gruntman , Jakob H. Macke , Srinivas C. Turaga
    bioRxiv. 2023 Mar 13:. doi: 10.1101/2023.03.11.532232

    We can now measure the connectivity of every neuron in a neural circuit, but we are still blind to other biological details, including the dynamical characteristics of each neuron. The degree to which connectivity measurements alone can inform understanding of neural computation is an open question. Here we show that with only measurements of the connectivity of a biological neural network, we can predict the neural activity underlying neural computation. We constructed a model neural network with the experimentally determined connectivity for 64 cell types in the motion pathways of the fruit fly optic lobe but with unknown parameters for the single neuron and single synapse properties. We then optimized the values of these unknown parameters using techniques from deep learning, to allow the model network to detect visual motion. Our mechanistic model makes detailed experimentally testable predictions for each neuron in the connectome. We found that model predictions agreed with experimental measurements of neural activity across 24 studies. Our work demonstrates a strategy for generating detailed hypotheses about the mechanisms of neural circuit function from connectivity measurements. We show that this strategy is more likely to be successful when neurons are sparsely connected—a universally observed feature of biological neural networks across species and brain regions.

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    03/10/23 | Drosophila antennae are dispensable for gravity orientation
    Nikolay Kladt , Michael B. Reiser
    bioRxiv. 2023 Mar 10:. doi: 10.1101/2023.03.08.531317

    The nearly constant downward force of gravity has powerfully shaped the behaviors of many organisms [1]. Walking flies readily orient against gravity in a behavior termed negative gravitaxis. In Drosophila this behavior is studied by observing the position of flies in vials [24] or simple mazes [59]. These assays have been used to conduct forward-genetic screens [568] and as simple tests of locomotion deficits [1012]. Despite this long history of investigation, the sensory basis of gravitaxis is largely unknown [1]. Recent studies have implicated the antennae as a major mechanosensory input [34], but many details remain unclear. Fly orientation behavior is expected to depend on the direction and amplitude of the gravitational pull, but little is known about the sensitivity of flies to these features of the environment. Here we directly measure the gravity-dependent orientation behavior of flies walking on an adjustable tilted platform, that is inspired by previous insect studies [1316]. In this arena, flies can freely orient with respect to gravity. Our findings indicate that flies are exquisitely sensitive to the direction of gravity’s pull. Surprisingly, this orientation behavior does not require antennal mechanosensory input, suggesting that other sensory structures must be involved.

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    03/10/23 | The connectome of an insect brain.
    Winding M, Pedigo BD, Barnes CL, Patsolic HG, Park Y, Kazimiers T, Fushiki A, Andrade IV, Khandelwal A, Valdes-Aleman J, Li F, Randel N, Barsotti E, Correia A, Fetter RD, Hartenstein V, Priebe CE, Vogelstein JT, Cardona A, Zlatic M
    Science. 2023 Mar 10;379(6636):eadd9330. doi: 10.1126/science.add9330

    Brains contain networks of interconnected neurons and so knowing the network architecture is essential for understanding brain function. We therefore mapped the synaptic-resolution connectome of an entire insect brain ( larva) with rich behavior, including learning, value computation, and action selection, comprising 3016 neurons and 548,000 synapses. We characterized neuron types, hubs, feedforward and feedback pathways, as well as cross-hemisphere and brain-nerve cord interactions. We found pervasive multisensory and interhemispheric integration, highly recurrent architecture, abundant feedback from descending neurons, and multiple novel circuit motifs. The brain's most recurrent circuits comprised the input and output neurons of the learning center. Some structural features, including multilayer shortcuts and nested recurrent loops, resembled state-of-the-art deep learning architectures. The identified brain architecture provides a basis for future experimental and theoretical studies of neural circuits.

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    03/09/23 | Smart Lattice Light Sheet Microscopy for imaging rare and complex cellular events
    Yu Shi , Jimmy S. Tabet , Daniel E. Milkie , Timothy A. Daugird , Chelsea Q. Yang , Andrea Giovannucci , Wesley R. Legant
    bioRxiv. 2023 Mar 09:. doi: 10.1101/2023.03.07.531517

    Light sheet microscopes enable rapid, high-resolution imaging of biological specimens; however, biological processes span a variety of spatiotemporal scales. Moreover, long-term phenotypes are often instigated by rare or fleeting biological events that are difficult to capture with a single imaging modality and constant imaging parameters. To overcome this limitation, we present smartLLSM, a microscope that incorporates AI-based instrument control to autonomously switch between epifluorescent inverted imaging and lattice light sheet microscopy. We apply this technology to two major scenarios. First, we demonstrate that the instrument provides population-level statistics of cell cycle states across thousands of cells on a coverslip. Second, we show that by using real-time image feedback to switch between imaging modes, the instrument autonomously captures multicolor 3D datasets or 4D time-lapse movies of dividing cells at rates that dramatically exceed human capabilities. Quantitative image analysis on high-content + high-throughput datasets reveal kinetochore and chromosome dynamics in dividing cells and determine the effects of drug perturbation on cells in specific mitotic stages. This new methodology enables efficient detection of rare events within a heterogeneous cell population and records these processes with high spatiotemporal 4D imaging over statistically significant replicates.

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    03/02/23 | Brain-wide neural activity underlying memory-guided movement
    Susu Chen , Yi Liu , Ziyue Wang , Jennifer Colonell , Liu D. Liu , Han Hou , Nai-Wen Tien , Tim Wang , Timothy Harris , Shaul Druckmann , Nuo Li , Karel Svoboda
    bioRxiv. 2023 Mar 02:. doi: 10.1101/2023.03.01.530520

    Behavior requires neural activity across the brain, but most experiments probe neurons in a single area at a time. Here we used multiple Neuropixels probes to record neural activity simultaneously in brain-wide circuits, in mice performing a memory-guided directional licking task. We targeted brain areas that form multi-regional loops with anterior lateral motor cortex (ALM), a key circuit node mediating the behavior. Neurons encoding sensory stimuli, choice, and actions were distributed across the brain. However, in addition to ALM, coding of choice was concentrated in subcortical areas receiving input from ALM, in an ALM-dependent manner. Choice signals were first detected in ALM and the midbrain, followed by the thalamus, and other brain areas. At the time of movement initiation, choice-selective activity collapsed across the brain, followed by new activity patterns driving specific actions. Our experiments provide the foundation for neural circuit models of decision-making and movement initiation.

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    Looger Lab
    03/02/23 | Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane.
    Nichols AL, Blumenfeld Z, Luebbert L, Knox HJ, Muthusamy AK, Marvin JS, Kim CH, Grant SN, Walton DP, Cohen BN, Hammar R, Looger L, Artursson P, Dougherty DA, Lester HA
    Journal of Neuroscience. 2023 Mar 02:. doi: 10.1523/JNEUROSCI.1519-22.2022

    Selective serotonin reuptake inhibitors (SSRIs) are the most prescribed treatment for individuals experiencing major depressive disorder (MDD). The therapeutic mechanisms that take place before, during, or after SSRIs bind the serotonin transporter (SERT) are poorly understood, partially because no studies exist of the cellular and subcellular pharmacokinetic properties of SSRIs in living cells. We studied escitalopram and fluoxetine using new intensity-based drug-sensing fluorescent reporters ("iDrugSnFRs") targeted to the plasma membrane (PM), cytoplasm, or endoplasmic reticulum (ER) of cultured neurons and mammalian cell lines. We also employed chemical detection of drug within cells and phospholipid membranes. The drugs attain equilibrium in neuronal cytoplasm and ER, at approximately the same concentration as the externally applied solution, with time constants of a few s (escitalopram) or 200-300 s (fluoxetine). Simultaneously, the drugs accumulate within lipid membranes by ≥ 18-fold (escitalopram) or 180-fold (fluoxetine), and possibly by much larger factors. Both drugs leave cytoplasm, lumen, and membranes just as quickly during washout. We synthesized membrane-impermeant quaternary amine derivatives of the two SSRIs. The quaternary derivatives are substantially excluded from membrane, cytoplasm, and ER for > 2.4 h. They inhibit SERT transport-associated currents 6- or 11-fold less potently than the SSRIs (escitalopram or fluoxetine derivative, respectively), providing useful probes for distinguishing compartmentalized SSRI effects. Although our measurements are orders of magnitude faster than the "therapeutic lag" of SSRIs, these data suggest that SSRI-SERT interactions within organelles or membranes may play roles during either the therapeutic effects or the "antidepressant discontinuation syndrome".Selective serotonin reuptake inhibitors stabilize mood in several disorders. In general, these drugs bind to the serotonin (5-hydroxytryptamine) transporter (SERT), which clears serotonin from CNS and peripheral tissues. SERT ligands are effective and relatively safe; primary care practitioners often prescribe them. However, they have several side effects and require 2 to 6 weeks of continuous administration until they act effectively. How they work remains perplexing, contrasting with earlier assumptions that the therapeutic mechanism involves SERT inhibition followed by increased extracellular serotonin levels. This study establishes that two SERT ligands, fluoxetine and escitalopram, enter neurons within minutes, while simultaneously accumulating in many membranes. Such knowledge will motivate future research, hopefully revealing where and how SERT ligands "engage" their therapeutic target(s).

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    02/25/23 | OME-Zarr: a cloud-optimized bioimaging file format with international community support.
    Josh Moore , Daniela Basurto-Lozada , Sébastien Besson , John Bogovic , Eva M. Brown , Jean-Marie Burel , Gustavo de Medeiros , Erin E. Diel , David Gault , Satrajit S. Ghosh , Ilan Gold , Yaroslav O. Halchenko , Matthew Hartley , Dave Horsfall , Mark S. Keller , Mark Kittisopikul , Gabor Kovacs , Aybüke Küpcü Yoldaş , Albane le Tournoulx de la Villegeorges , Tong Li , Prisca Liberali , Melissa Linkert , Dominik Lindner , Joel Lüthi , Jeremy Maitin-Shepard , Trevor Manz , Matthew McCormick , Khaled Mohamed , William Moore , Bugra Özdemir , Constantin Pape , Lucas Pelkmans , Martin Prete , Tobias Pietzsch , Stephan Preibisch , Norman Rzepka , David R. Stirling , Jonathan Striebel , Christian Tischer , Daniel Toloudis , Petr Walczysko , Alan M. Watson , Frances Wong , Kevin A. Yamauchi , Omer Bayraktar , Muzlifah Haniffa , Stephan Saalfeld , Jason R. Swedlow
    bioRxiv. 2023 Feb 25:. doi: 10.1101/2023.02.17.528834

    A growing community is constructing a next-generation file format (NGFF) for bioimaging to overcome problems of scalability and heterogeneity. Organized by the Open Microscopy Environment (OME), individuals and institutes across diverse modalities facing these problems have designed a format specification process (OME-NGFF) to address these needs. This paper brings together a wide range of those community members to describe the format itself – OME-Zarr – along with tools and data resources available today to increase FAIR access and remove barriers in the scientific process. The current momentum offers an opportunity to unify a key component of the bioimaging domain — the file format that underlies so many personal, institutional, and global data management and analysis tasks.

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    02/23/23 | A searchable image resource of Drosophila GAL4-driver expression patterns with single neuron resolution.
    Meissner GW, Nern A, Dorman Z, Depasquale GM, Forster K, Gibney T, Hausenfluck JH, He Y, Iyer NA, Jeter J, Johnson L, Johnston RM, Lee K, Melton B, Yarbrough B, Zugates CT, Clements J, Goina C, Otsuna H, Rokicki K, Svirskas RR, Aso Y, Card GM, Dickson BJ, Ehrhardt E, Goldammer J, Ito M, Kainmueller D, Korff W, Mais L, minegishi r, Namiki S, Rubin GM, Sterne GR, Wolff T, Malkesman O
    eLife. 2023 Feb 23;12:. doi: 10.7554/eLife.80660

    Precise, repeatable genetic access to specific neurons via GAL4/UAS and related methods is a key advantage of Drosophila neuroscience. Neuronal targeting is typically documented using light microscopy of full GAL4 expression patterns, which generally lack the single-cell resolution required for reliable cell type identification. Here we use stochastic GAL4 labeling with the MultiColor FlpOut approach to generate cellular resolution confocal images at large scale. We are releasing aligned images of 74,000 such adult central nervous systems. An anticipated use of this resource is to bridge the gap between neurons identified by electron or light microscopy. Identifying individual neurons that make up each GAL4 expression pattern improves the prediction of split-GAL4 combinations targeting particular neurons. To this end we have made the images searchable on the NeuronBridge website. We demonstrate the potential of NeuronBridge to rapidly and effectively identify neuron matches based on morphology across imaging modalities and datasets.

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