Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem

Schodt, David W.; Lidke, Keith A.

doi:10.3389/fbinf.2021.724325

Cited by 5 publications

(1 citation statement)

References 23 publications

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“…A 5 × 5 μm 2 region of data was selected. Localizations were frameconnected 36 and those not connected to anything were removed. The localizations were further filtered by the NND filter.…”

Section: Dna-paint Data Analysis Of Kindlinmentioning

confidence: 99%

High-precision estimation of emitter positions using Bayesian grouping of localizations

et al. 2022

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Single-molecule localization microscopy super-resolution methods rely on stochastic blinking/binding events, which often occur multiple times from each emitter over the course of data acquisition. Typically, the blinking/binding events from each emitter are treated as independent events, without an attempt to assign them to a particular emitter. Here, we describe a Bayesian method of inferring the positions of the tagged molecules by exploring the possible grouping and combination of localizations from multiple blinking/binding events. The results are position estimates of the tagged molecules that have improved localization precision and facilitate nanoscale structural insights. The Bayesian framework uses the localization precisions to learn the statistical distribution of the number of blinking/binding events per emitter and infer the number and position of emitters. We demonstrate the method on a range of synthetic data with various emitter densities, DNA origami constructs and biological structures using DNA-PAINT and dSTORM data. We show that under some experimental conditions it is possible to achieve sub-nanometer precision.

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Section: Dna-paint Data Analysis Of Kindlinmentioning

confidence: 99%

High-precision estimation of emitter positions using Bayesian grouping of localizations

et al. 2022

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Multiparatopic antibodies induce targeted downregulation of programmed death-ligand 1

Ludwig,

Meksiriporn,

Tan

et al. 2024

Cell Chemical Biology

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Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes

Rinaldi,

Kanagy,

Kaye

et al. 2023

Preprint

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Immunoreceptor tyrosine-based activation motif (ITAM)-containing Fc receptors are critical components of the innate and adaptive immune systems. FcεRI mediates the allergic response via crosslinking of IgE-bound receptors by multivalent antigens. Yet, the underlying molecular mechanisms that govern the response of FcεRI to specific antigens remain poorly understood. We compared responses induced by two antigens with distinct geometries, high valency DNP-BSA and trivalent DF3, and found unique secretion and receptor phosphorylation profiles that are due to differential recruitment of Lyn and SHIP1. To understand how these two antigens can cause such markedly different outcomes, we used direct stochastic optical reconstruction microscopy (dSTORM) super-resolution imaging combined with Bayesian Grouping of Localizations (BaGoL) analysis to compare the nanoscale characteristics of FcεRI aggregates. DF3 aggregates were found to be smaller and more densely packed than DNP-BSA aggregates. Using lifetime-based Förster resonance energy transfer (FRET) measurements, we discovered that FcεRI subunits undergo structural rearrangements upon crosslinking with either antigen, and in response to interaction with monovalent antigen presented on a supported lipid bilayer. The extent of conformational change is positively correlated with signaling efficiency. Finally, we provide evidence for forces in optimizing FcεRI signaling, such that immobilizing DF3 on a rigid surface promoted degranulation while increasing DNP-BSA flexibility lowered degranulation. These results provide a link between the physical attributes of allergens, including size, shape, valency, and flexibility, and FcεRI signaling strength. Thus, the antigen modulates mast cell outcomes by creating unique aggregate geometries that tune FcεRI conformation, phosphorylation and signaling partner recruitment.Statement of SignificanceThis work elucidates the molecular mechanisms underlying differential FcεRI signaling responses induced by antigens of distinct geometries. By combining super-resolution imaging and biophysical techniques, we demonstrate that the physical attributes of allergens, including shape, flexibility, and valency, modulate mast cell signaling outcomes by altering FcεRI aggregate organization and conformational states. This provides novel insights into the structure-function relationships governing FcεRI signal transduction and its role in mast cell activation. Overall, this work establishes a link between allergen physical properties and immune receptor signaling at the molecular level, with important implications for understanding and regulating allergic responses.

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Spatiotemporal Clustering of Repeated Super-Resolution Localizations via Linear Assignment Problem

Cited by 5 publications

References 23 publications

High-precision estimation of emitter positions using Bayesian grouping of localizations

High-precision estimation of emitter positions using Bayesian grouping of localizations

Multiparatopic antibodies induce targeted downregulation of programmed death-ligand 1

Antigen Geometry Tunes Mast Cell Signaling Through Distinct FcεRI Aggregation and Structural Changes

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