Understanding 3D genome organization by multidisciplinary methods

Nature Reviews Molecular Cell Biology, Journal Year: 2021, Volume and Issue: 22(8), P. 511 - 528

Published: May 5, 2021

Language: Английский

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A Review of Super-Resolution Single-Molecule Localization Microscopy Cluster Analysis and Quantification Methods

Patterns, Journal Year: 2020, Volume and Issue: 1(3), P. 100038 - 100038

Published: June 1, 2020

Recent developments in super-resolution SMLM imaging techniques enable researchers to study macromolecular structures at the nanometer scale. However, data quantification and interpretation methods have yet keep pace with rapid advancement of imaging. This article provides a balanced comprehensive review state-of-the-art image analysis ties disparate approaches together cohesive manner. Researchers are actively exploring new computational analyze data, including recent use data-driven machine-learning approaches. validation clustering remains an open challenge. Potential future directions using multi-modality (e.g., electron microscopy) might help validate quantitative methods. Single-molecule localization microscopy (SMLM) is relatively modality, winning 2014 Nobel Prize Chemistry, considered as one key techniques. resolution goes beyond diffraction limit light achieves on order 10–20 nm. thus enables single molecules low-level molecular interactions subcellular level. In contrast standard that produces 2D pixel or 3D voxel grid generates big point clouds millions localizations associated uncertainties. unprecedented breakthrough helps employ many fields within biology medicine, such studying cancerous cells cell-mediated immunity accelerating drug discovery. been for extract biosignatures various biological functions. this survey, we describe adopted quantify examine capabilities shortcomings surveyed We classify according (1) application (i.e., imaged molecules/structures), (2) acquisition (such dimension, resolution, number localizations), (3) details (2D versus 3D, field view region interest, multi-scale analysis, biosignature extraction, etc.). observe majority based second-order statistics sensitive noise artifacts, not applied do leverage formulations, scalable big-data analysis. Finally, summarize methodology, discuss some challenges, identify opportunities better modeling design integrated pipeline address challenges.

Language: Английский

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The ImageJ ecosystem: Open‐source software for image visualization, processing, and analysis

Protein Science, Journal Year: 2020, Volume and Issue: 30(1), P. 234 - 249

Published: Nov. 9, 2020

Abstract For decades, biologists have relied on software to visualize and interpret imaging data. As techniques for acquiring images increase in complexity, resulting larger multidimensional datasets, must adapt. ImageJ is an open‐source image analysis platform that has aided researchers with a variety of applications, driven mainly by engaged collaborative user developer communities. The close collaboration between programmers users resulted adaptations accommodate new challenges address the needs ImageJ's diverse base. consists many components, some relevant primarily developers vast collection user‐centric plugins. It available forms, including widely used Fiji distribution. We refer this entire codebase community as ecosystem. Here we review core features ecosystem highlight how responded technology advancements plugins tools recent years. These been developed several areas such visualization, segmentation, tracking biological entities large, complex datasets. Moreover, capabilities deep learning are being added ImageJ, reflecting shift bioimage towards exploiting artificial intelligence. facilitated profound architectural changes brought about ImageJ2 project. Therefore, also discuss contributions enhancing processing interoperability

Language: Английский

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MINFLUX nanometer-scale 3D imaging and microsecond-range tracking on a common fluorescence microscope

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: March 5, 2021

Abstract The recently introduced minimal photon fluxes (MINFLUX) concept pushed the resolution of fluorescence microscopy to molecular dimensions. Initial demonstrations relied on custom made, specialized microscopes, raising question method’s general availability. Here, we show that MINFLUX implemented with a standard microscope stand can attain 1–3 nm in three dimensions, rendering molecule-scale widely applicable. Advances, such as synchronized electro-optical and galvanometric beam steering stabilization locks sample position sub-nanometer precision respect stand, ensure nanometer-precise accurate real-time localization individually activated fluorophores. In our imaging cell- neurobiological samples, ~800 detected photons suffice 2.2 nm, whereas ~2500 yield precisions <1 (standard deviation). We further demonstrate 3D ~2.4 focal plane ~1.9 along optic axis. Localizing <20 within ~100 µs, establish this spatio-temporal single fluorophore tracking apply it diffusion labeled lipids lipid-bilayer model membranes.

Language: Английский

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A New Class of NIR‐II Gold Nanocluster‐Based Protein Biolabels for In Vivo Tumor‐Targeted Imaging

Angewandte Chemie International Edition, Journal Year: 2020, Volume and Issue: 60(3), P. 1306 - 1312

Published: Sept. 17, 2020

Abstract The design of bright NIR‐II luminescent nanomaterials that enable efficient labelling proteins without disturbing their physiological properties in vivo is challenging. We developed an strategy to synthesize gold nanoclusters (Au NCs) protected by biocompatible cyclodextrin (CD). Leveraging the ultrasmall size Au NCs (<2 nm) and strong macrocycle‐based host–guest chemistry, as‐synthesized CD‐Au can readily label proteins/antibodies. Moreover, labelled proteins/antibodies highly tracking during blood circulation, biodistribution tumor targeting ability, thus leading a sensitive tumor‐targeted imaging. are stable harsh biological environment show good biocompatibility high renal clearance efficiency. Therefore, biolabels this study provide promising platform monitor behavior biomolecules living organisms.

Language: Английский

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Modified aptamers enable quantitative sub-10-nm cellular DNA-PAINT imaging

Nature Methods, Journal Year: 2018, Volume and Issue: 15(9), P. 685 - 688

Published: Aug. 17, 2018

Language: Английский

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An introduction to optical super-resolution microscopy for the adventurous biologist

Methods and Applications in Fluorescence, Journal Year: 2018, Volume and Issue: 6(2), P. 022003 - 022003

Published: Feb. 9, 2018

Ever since the inception of light microscopy, laws physics have seemingly thwarted every attempt to visualize processes life at its most fundamental, sub-cellular, level. The diffraction limit has restricted our view length scales well above 250 nm and in doing so, severely compromised ability gain true insights into many biological systems. Fortunately, continuous advancements optics, electronics mathematics provided means once again make work advantage. Even though some fundamental concepts enabling super-resolution microscopy been known for quite time, practically feasible implementations long remained elusive. It should therefore not come as a surprise that 2014 Nobel Prize Chemistry was awarded scientists who, each their own way, contributed transforming from technological tour de force staple biologist's toolkit. By overcoming barrier, could be established an indispensable tool age where importance understanding molecular level cannot overstated. This review strives provide aspiring science researcher with introduction optical starting governing compound fluorescent confocal current state-of-the-art techniques applications.

Language: Английский

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Live-cell STED nanoscopy of mitochondrial cristae

Scientific Reports, Journal Year: 2019, Volume and Issue: 9(1)

Published: Aug. 27, 2019

Abstract Mitochondria are highly dynamic organelles that exhibit a complex inner architecture. They smooth outer membrane and convoluted forms invaginations called cristae. Imaging cristae in living cells poses formidable challenge for super-resolution light microscopy. Relying on cell line stably expressing the mitochondrial protein COX8A fused to SNAP-tag using STED ( st imulated e mission d epletion) nanoscopy, we demonstrate visualization of dynamics cultivated human cells. We show HeLa lamellar often arranged groups separated by voids generally occupied nucleoids.

Language: Английский

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Atomic Force Microscopy-Based Force Spectroscopy and Multiparametric Imaging of Biomolecular and Cellular Systems

Chemical Reviews, Journal Year: 2020, Volume and Issue: 121(19), P. 11701 - 11725

Published: Nov. 9, 2020

During the last three decades, a series of key technological improvements turned atomic force microscopy (AFM) into nanoscopic laboratory to directly observe and chemically characterize molecular cell biological systems under physiological conditions. Here, we review that have established AFM as an analytical tool quantify native from micro- nanoscale. Native include living tissues, cells, cellular components such single or complexed proteins, nucleic acids, lipids, sugars. We showcase procedures customize chemical laboratories by functionalizing tips outline advantages limitations in applying different modes image, sense, manipulate biosystems at (sub)nanometer spatial millisecond temporal resolution. further discuss theoretical approaches extract kinetic thermodynamic parameters specific biomolecular interactions detected for bonds extend discussion multiple bonds. Finally, highlight potential combining with optical spectroscopy address full complexity tackle fundamental challenges life sciences.

Language: Английский

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MINFLUX monitors rapid molecular jumps with superior spatiotemporal resolution

Proceedings of the National Academy of Sciences, Journal Year: 2018, Volume and Issue: 115(24), P. 6117 - 6122

Published: May 29, 2018

Significance Popular localization of single molecules through calculating the centroid diffraction pattern produced by molecular fluorescence on a camera is typically limited to spatiotemporal resolutions >10 nm per milliseconds. By requiring at least 10–100 times fewer detected photons and being free bias due orientation, concept called MINFLUX propels tracking hitherto-unachievable regime single-digit nanometer precision within substantially less than millisecond. Our experiments herald feasibility detect interactions conformational changes microsecond timescales.

Language: Английский

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