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2454 Janelia Publications

Showing 71-80 of 2454 results
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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01/15/24 | A neural circuit architecture for rapid behavioral flexibility in goal-directed navigation
Chuntao Dan , Brad K. Hulse , Ramya Kappagantula , Vivek Jayaraman , Ann M. Hermundstad
bioRxiv. 2024 Jan 15:. doi: 10.1101/2021.08.18.456004

Anchoring goals to spatial representations enables flexible navigation in both animals and artificial agents. However, using this strategy can be challenging in novel environments, when both spatial and goal representations must be acquired quickly and simultaneously. Here, we propose a framework for how Drosophila use their internal representation of head direction to build a goal heading representation upon selective thermal reinforcement. We show that flies in a well-established operant visual learning paradigm use stochastically generated fixations and directed saccades to express heading preferences, and that compass neurons, which represent flies’ head direction, are required to modify these preferences based on reinforcement. We describe how flies’ ability to quickly map their surroundings and adapt their behavior to the rules of their environment may rest on a behavioral policy whose parameters are flexible but whose form and dependence on head direction and goal representations are genetically encoded in the modular structure of their circuits. Using a symmetric visual setting, which predictably alters the dynamics of the head direction system, enabled us to describe how interactions between the evolving representations of head direction and goal impact behavior. We show how a policy tethered to these two internal representations can facilitate rapid learning of new goal headings, drive more exploitative behavior about stronger goal headings, and ensure that separate learning processes involved in mapping the environment and forming goals within that environment remain consistent with one another. Many of the mechanisms we outline may be broadly relevant for rapidly adaptive behavior driven by internal representations.

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01/11/24 | Bridging gaps in traditional research training with iBiology Courses.
Schnoes AM, Green NH, Nguyen TA, Vale RD, Goodwin SS, Behrman SL
PLoS Biology. 2024 Jan 11;22(1):e3002458. doi: 10.1371/journal.pbio.3002458

iBiology Courses provide trainees with just-in-time learning resources to become effective researchers. These courses can help scientists build core research skills, plan their research projects and careers, and learn from scientists with diverse backgrounds.

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01/11/24 | Epigenetic priming of embryonic lineages in the mammalian epiblast
Miquel Sendra , Katie McDole , Daniel Jimenez-Carretero , Juan de Dios Hourcade , Susana Temiño , Léo Guignard , Philipp J Keller , Fátima Sánchez-Cabo , Jorge N. Domínguez , Miguel Torres
bioRxiv. 2024 Jan 11:. doi: 10.1101/2024.01.11.575188

Understanding the diversification of mammalian cell lineages is an essential to embryonic development, organ regeneration and tissue engineering. Shortly after implantation in the uterus, the pluripotent cells of the mammalian epiblast generate the three germ layers: ectoderm, mesoderm and endoderm1. Although clonal analyses suggest early specification of epiblast cells towards particular cell lineages24, single-cell transcriptomes do not identify lineage-specific markers in the epiblast511 and thus, the molecular regulation of such specification remains unknow. Here, we studied the epigenetic landscape of single epiblast cells, which revealed lineage priming towards endoderm, ectoderm or mesoderm. Unexpectedly, epiblast cells with mesodermal priming show a strong signature for the endothelial/endocardial fate, suggesting early specification of this lineage aside from other mesoderm. Through clonal analysis and live imaging, we show that endothelial precursors show early lineage divergence from the rest of mesodermal derivatives. In particular, cardiomyocytes and endocardial cells show limited lineage relationship, despite being temporally and spatially co-recruited during gastrulation. Furthermore, analysing the live tracks of single cells through unsupervised classification of cell migratory activity, we found early behavioral divergence of endothelial precursors shortly after the onset of mesoderm migration towards the cardiogenic area. These results provide a new model for the phenotypically silent specification of mammalian cell lineages in pluripotent cells of the epiblast and modify current knowledge on the sequence and timing of cardiovascular lineages diversification.

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01/11/24 | Prediction of Cellular Identities from Trajectory and Cell Fate Information
Baiyang Dai , Jiamin Yang , Hari Shroff , Patrick La Riviere
arXiv. 2024 Jan 11:. doi: 10.48550/arXiv.2401.06182

Determining cell identities in imaging sequences is an important yet challenging task. The conventional method for cell identification is via cell tracking, which is complex and can be time-consuming. In this study, we propose an innovative approach to cell identification during early C. elegans embryogenesis using machine learning. We employed random forest, MLP, and LSTM models, and tested cell classification accuracy on 3D time-lapse confocal datasets spanning the first 4 hours of embryogenesis. By leveraging a small number of spatial-temporal features of individual cells, including cell trajectory and cell fate information, our models achieve an accuracy of over 90%, even with limited data. We also determine the most important feature contributions and can interpret these features in the context of biological knowledge. Our research demonstrates the success of predicting cell identities in 4D imaging sequences directly from simple spatio-temporal features.

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01/10/24 | Believing is seeing - the deceptive influence of bias in quantitative microscopy.
Lee RM, Eisenman LR, Khuon S, Aaron JS, Chew T
Journal of Cell Science. 2024 Jan 10;137(1):. doi: 10.1242/jcs.261567

The visual allure of microscopy makes it an intuitively powerful research tool. Intuition, however, can easily obscure or distort the reality of the information contained in an image. Common cognitive biases, combined with institutional pressures that reward positive research results, can quickly skew a microscopy project towards upholding, rather than rigorously challenging, a hypothesis. The impact of these biases on a variety of research topics is well known. What might be less appreciated are the many forms in which bias can permeate a microscopy experiment. Even well-intentioned researchers are susceptible to bias, which must therefore be actively recognized to be mitigated. Importantly, although image quantification has increasingly become an expectation, ostensibly to confront subtle biases, it is not a guarantee against bias and cannot alone shield an experiment from cognitive distortions. Here, we provide illustrative examples of the insidiously pervasive nature of bias in microscopy experiments - from initial experimental design to image acquisition, analysis and data interpretation. We then provide suggestions that can serve as guard rails against bias.

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