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2449 Publications

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    02/01/24 | 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
    Nature Methods. 2024 Feb 01;21(2):301-310. doi: 10.1038/s41592-023-02126-0

    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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    02/01/24 | The density of regulatory information is a major determinant of evolutionary constraint on non-coding DNA in Drosophila
    Gonzalo Sabarís , Daniela M. Ortíz , Ian Laiker , Ignacio Mayansky , Sujay Naik , Giacomo Cavalli , David L. Stern , Ella Preger-Ben Noon , Nicolás Frankel
    Molecular Biology and Evolution. 2024 Feb 01;41(2):msae004. doi: 10.1093/molbev/msae004

    The density and distribution of regulatory information in non-coding DNA of eukaryotic genomes is largely unknown. Evolutionary analyses have estimated that ∼60% of nucleotides in intergenic regions of the D. melanogaster genome is functionally relevant. This estimate is difficult to reconcile with the commonly accepted idea that enhancers are compact regulatory elements that generally encompass less than 1 kilobase of DNA. Here, we approached this issue through a functional dissection of the regulatory region of the gene shavenbaby (svb). Most of the ∼90 kilobases of this large regulatory region is highly conserved in the genus Drosophila, though characterized enhancers occupy a small fraction of this region. By analyzing the regulation of svb in different contexts of Drosophila development, we found that the regulatory architecture that drives svb expression in the abdominal pupal epidermis is organized in a dramatically different way than the information that drives svb expression in the embryonic epidermis. While in the embryonic epidermis svb is activated by compact and dispersed enhancers, svb expression in the pupal epidermis is driven by large regions with enhancer activity, which occupy a great portion of the svb cis-regulatory DNA. We observed that other developmental genes also display a dense distribution of putative regulatory elements in their regulatory regions. Furthermore, we found that a large percentage of conserved non-coding DNA of the Drosophila genome is contained within putative regulatory DNA. These results suggest that part of the evolutionary constraint on non-coding DNA of Drosophila is explained by the density of regulatory information.

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    01/30/24 | Distributed fMRI dynamics predict distinct EEG rhythms across sleep and wakefulness.
    Leandro P. L. Jacob , Sydney M. Bailes , Stephanie D. Williams , Carsen Stringer , Laura D. Lewis
    bioRxiv. 2024 Jan 30:. doi: 10.1101/2024.01.29.577429

    The brain exhibits rich oscillatory dynamics that vary across tasks and states, such as the EEG oscillations that define sleep. These oscillations play critical roles in cognition and arousal, but the brainwide mechanisms underlying them are not yet described. Using simultaneous EEG and fast fMRI in subjects drifting between sleep and wakefulness, we developed a machine learning approach to investigate which brainwide fMRI dynamics predict alpha (8-12 Hz) and delta (1-4 Hz) rhythms. We predicted moment-by-moment EEG power from fMRI activity in held-out subjects, and found that information about alpha power was represented by a remarkably small set of regions, segregated in two distinct networks linked to arousal and visual systems. Conversely, delta rhythms were diffusely represented on a large spatial scale across the cortex. These results identify distributed networks that predict delta and alpha rhythms, and establish a computational framework for investigating fMRI brainwide dynamics underlying EEG oscillations.

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    01/25/24 | New genetic tools for mushroom body output neurons in Drosophila
    Rubin GM, Aso Y
    eLife. 2024 Jan 24:. doi: 10.7554/eLife.90523

    How memories of past events influence behavior is a key question in neuroscience. The major associative learning center in Drosophila, the Mushroom Body (MB), communicates to the rest of the brain through Mushroom Body Output Neurons (MBONs). While 21 MBON cell types have their dendrites confined to small compartments of the MB lobes, analysis of EM connectomes revealed the presence of an additional 14 MBON cell types that are atypical in having dendritic input both within the MB lobes and in adjacent brain regions. Genetic reagents for manipulating atypical MBONs and experimental data on their functions has been lacking. In this report we describe new cell-type-specific GAL4 drivers for many MBONs, including the majority of atypical MBONs. Using these genetic reagents, we conducted optogenetic activation screening to examine their ability to drive behaviors and learning. These reagents provide important new tools for the study of complex behaviors in Drosophila.

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    01/24/24 | Mapping of multiple neurotransmitter receptor subtypes and distinct protein complexes to the connectome.
    Sanfilippo P, Kim AJ, Bhukel A, Yoo J, Mirshahidi PS, Pandey V, Bevir H, Yuen A, Mirshahidi PS, Guo P, Li H, Wohlschlegel JA, Aso Y, Zipursky SL
    Neuron. 2024 Jan 24:. doi: 10.1016/j.neuron.2023.12.014

    Neurons express various combinations of neurotransmitter receptor (NR) subunits and receive inputs from multiple neuron types expressing different neurotransmitters. Localizing NR subunits to specific synaptic inputs has been challenging. Here, we use epitope-tagged endogenous NR subunits, expansion light-sheet microscopy, and electron microscopy (EM) connectomics to molecularly characterize synapses in Drosophila. We show that in directionally selective motion-sensitive neurons, different multiple NRs elaborated a highly stereotyped molecular topography with NR localized to specific domains receiving cell-type-specific inputs. Developmental studies suggested that NRs or complexes of them with other membrane proteins determine patterns of synaptic inputs. In support of this model, we identify a transmembrane protein selectively associated with a subset of spatially restricted synapses and demonstrate its requirement for synapse formation through genetic analysis. We propose that mechanisms that regulate the precise spatial distribution of NRs provide a molecular cartography specifying the patterns of synaptic connections onto dendrites.

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    01/24/24 | Mechanical stretch regulates macropinocytosis in Hydra vulgaris.
    Skokan TD, Hobmayer B, McKinley KL, Vale RD
    Molecular Biology of the Cell. 2024 Jan 24:mbcE22020065. doi: 10.1091/mbc.E22-02-0065

    Cells rely on a diverse array of engulfment processes to sense, exploit, and adapt to their environments. Among these, macropinocytosis enables indiscriminate and rapid uptake of large volumes of fluid and membrane, rendering it a highly versatile engulfment strategy. Much of the molecular machinery required for macropinocytosis has been well established, yet how this process is regulated in the context of organs and organisms remains poorly understood. Here, we report the discovery of extensive macropinocytosis in the outer epithelium of the cnidarian . Exploiting 's relatively simple body plan, we developed approaches to visualize macropinocytosis over extended periods of time, revealing constitutive engulfment across the entire body axis. We show that the direct application of planar stretch leads to calcium influx and the inhibition of macropinocytosis. Finally, we establish a role for stretch-activated channels in inhibiting this process. Together, our approaches provide a platform for the mechanistic dissection of constitutive macropinocytosis in physiological contexts and highlight a potential role for macropinocytosis in responding to cell surface tension. [Media: see text] [Media: see text] [Media: see text] [Media: see text].

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    01/24/24 | Motion of VAPB molecules reveals ER-mitochondria contact site subdomains.
    Obara CJ, Nixon-Abell J, Moore AS, Riccio F, Hoffman DP, Shtengel G, Xu CS, Schaefer K, Pasolli HA, Masson J, Hess HF, Calderon CP, Blackstone C, Lippincott-Schwartz J
    Nature. 2024 Jan 24;626(7997):169-176. doi: 10.1038/s41586-023-06956-y

    To coordinate cellular physiology, eukaryotic cells rely on the rapid exchange of molecules at specialized organelle-organelle contact sites. Endoplasmic reticulum-mitochondrial contact sites (ERMCSs) are particularly vital communication hubs, playing key roles in the exchange of signalling molecules, lipids and metabolites. ERMCSs are maintained by interactions between complementary tethering molecules on the surface of each organelle. However, due to the extreme sensitivity of these membrane interfaces to experimental perturbation, a clear understanding of their nanoscale organization and regulation is still lacking. Here we combine three-dimensional electron microscopy with high-speed molecular tracking of a model organelle tether, Vesicle-associated membrane protein (VAMP)-associated protein B (VAPB), to map the structure and diffusion landscape of ERMCSs. We uncovered dynamic subdomains within VAPB contact sites that correlate with ER membrane curvature and undergo rapid remodelling. We show that VAPB molecules enter and leave ERMCSs within seconds, despite the contact site itself remaining stable over much longer time scales. This metastability allows ERMCSs to remodel with changes in the physiological environment to accommodate metabolic needs of the cell. An amyotrophic lateral sclerosis-associated mutation in VAPB perturbs these subdomains, likely impairing their remodelling capacity and resulting in impaired interorganelle communication. These results establish high-speed single-molecule imaging as a new tool for mapping the structure of contact site interfaces and reveal that the diffusion landscape of VAPB at contact sites is a crucial component of ERMCS homeostasis.

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    01/22/24 | KMT2 family of H3K4 methyltransferases: enzymatic activity-dependent and -independent functions.
    Van HT, Xie G, Dong P, Liu Z, Ge K
    Journal of Molecular Biology. 2024 Jan 22:168453. doi: 10.1016/j.jmb.2024.168453

    Histone-lysine N-methyltransferase 2 (KMT2) methyltransferases play critical roles in gene regulation, cell differentiation, animal development, and human diseases. KMT2 biological roles are often attributed to their methyltransferase activities on lysine 4 of histone H3 (H3K4). However, recent data indicate that KMT2 proteins also possess non-enzymatic functions. In this review, we discuss the current understanding of KMT2 family, with a focus on their enzymatic activity-dependent and -independent functions. Six mammalian KMT2 proteins of three subgroups, KMT2A/B (MLL1/2), KMT2C/D (MLL3/4), and KMT2F/G (SETD1A/B or SET1A/B), have shared and distinct protein domains, catalytic substrates, genomic localizations, and associated complex subunits. Recent studies have revealed the central role of KMT2C/D in enhancer regulation, differentiation, and development and have highlighted KMT2C/D enzymatic activity-dependent and independent roles in mouse embryonic development and cell differentiation. Catalytic dependent and independent roles for KMT2A/B and KMT2F/G in gene regulation, differentiation, and development are less understood. Finally, we provide our perspectives and lay out future research directions that may help advance the investigation on enzymatic activity-dependent and -independent biological roles and working mechanisms of KMT2 methyltransferases.

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    01/19/24 | Organelle proteomic profiling reveals lysosomal heterogeneity in association with longevity
    Yong Yu , Shihong M. Gao , Youchen Guan , Pei-Wen Hu , Qinghao Zhang , Jiaming Liu , Bentian Jing , Qian Zhao , David M Sabatini , Monther Abu-Remaileh , Sung Yun Jung , Meng C. Wang
    eLife. 2024 Jan 19:. doi: 10.7554/eLife.85214

    Lysosomes are active sites to integrate cellular metabolism and signal transduction. A collection of proteins enriched at lysosomes mediate these metabolic and signaling functions. Both lysosomal metabolism and lysosomal signaling have been linked with longevity regulation; however, how lysosomes adjust their protein composition to accommodate this regulation remains unclear. Using large-scale proteomic profiling, we systemically profiled lysosome- enriched proteomes in association with different longevity mechanisms. We further discovered the lysosomal recruitment of AMPK and nucleoporin proteins and their requirements for longevity in response to increased lysosomal lipolysis. Through comparative proteomic analyses of lysosomes from different tissues and labeled with different markers, we discovered lysosomal heterogeneity across tissues as well as the specific enrichment of the Ragulator complex on Cystinosin positive lysosomes. Together, this work uncovers lysosomal proteome heterogeneity at different levels and provides resources for understanding the contribution of lysosomal proteome dynamics in modulating signal transduction, organelle crosstalk and organism longevity.

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    01/18/24 | Failure to mate enhances investment in behaviors that may promote mating reward and impairs the ability to cope with stressors via a subpopulation of Neuropeptide F receptor neurons.
    Ryvkin J, Omesi L, Kim Y, Levi M, Pozeilov H, Barak-Buchris L, Agranovich B, Abramovich I, Gottlieb E, Jacob A, Nässel DR, Heberlein U, Shohat-Ophir G
    PLoS Genetics. 2024 Jan 18;20(1):e1011054. doi: 10.1371/journal.pgen.1011054

    Living in dynamic environments such as the social domain, where interaction with others determines the reproductive success of individuals, requires the ability to recognize opportunities to obtain natural rewards and cope with challenges that are associated with achieving them. As such, actions that promote survival and reproduction are reinforced by the brain reward system, whereas coping with the challenges associated with obtaining these rewards is mediated by stress-response pathways, the activation of which can impair health and shorten lifespan. While much research has been devoted to understanding mechanisms underlying the way by which natural rewards are processed by the reward system, less attention has been given to the consequences of failure to obtain a desirable reward. As a model system to study the impact of failure to obtain a natural reward, we used the well-established courtship suppression paradigm in Drosophila melanogaster as means to induce repeated failures to obtain sexual reward in male flies. We discovered that beyond the known reduction in courtship actions caused by interaction with non-receptive females, repeated failures to mate induce a stress response characterized by persistent motivation to obtain the sexual reward, reduced male-male social interaction, and enhanced aggression. This frustrative-like state caused by the conflict between high motivation to obtain sexual reward and the inability to fulfill their mating drive impairs the capacity of rejected males to tolerate stressors such as starvation and oxidative stress. We further show that sensitivity to starvation and enhanced social arousal is mediated by the disinhibition of a small population of neurons that express receptors for the fly homologue of neuropeptide Y. Our findings demonstrate for the first time the existence of social stress in flies and offers a framework to study mechanisms underlying the crosstalk between reward, stress, and reproduction in a simple nervous system that is highly amenable to genetic manipulation.

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