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从粒子轨迹中学习连续二维扩散映射,无需数据分箱。

Learning Continuous 2D Diffusion Maps from Particle Trajectories without Data Binning.

作者信息

Kumar Vishesh, Shepard Bryan J, Rojewski Alex, Manzo Carlo, Pressé Steve

机构信息

Center for Biological Physics, Arizona State University, USA.

Department of Physics, Arizona State University, USA.

出版信息

bioRxiv. 2024 Feb 29:2024.02.27.582378. doi: 10.1101/2024.02.27.582378.

DOI:10.1101/2024.02.27.582378
PMID:38464131
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10925201/
Abstract

Diffusion coefficients often vary across regions, such as cellular membranes, and quantifying their variation can provide valuable insight into local membrane properties such as composition and stiffness. Toward quantifying diffusion coefficient spatial maps and uncertainties from particle tracks, we use a Bayesian method and place Gaussian Process (GP) Priors on the maps. For the sake of computational efficiency, we leverage inducing point methods on GPs arising from the mathematical structure of the data giving rise to non-conjugate likelihood-prior pairs. We analyze both synthetic data, where ground truth is known, as well as data drawn from live-cell single-molecule imaging of membrane proteins. The resulting tool provides an unsupervised method to rigorously map diffusion coefficients continuously across membranes without data binning.

摘要

扩散系数通常在不同区域有所变化,比如细胞膜,量化其变化可以为诸如组成和硬度等局部膜特性提供有价值的见解。为了从粒子轨迹量化扩散系数空间图和不确定性,我们使用一种贝叶斯方法,并在这些图上放置高斯过程(GP)先验。出于计算效率的考虑,我们利用诱导点方法处理由数据的数学结构产生的高斯过程,这些数据会产生非共轭似然 - 先验对。我们分析了合成数据(其真实情况已知)以及从膜蛋白的活细胞单分子成像中获取的数据。由此产生的工具提供了一种无监督方法,可在不进行数据分箱的情况下,严格地在整个膜上连续绘制扩散系数图。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/4b20d496e14b/nihpp-2024.02.27.582378v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/d07228172f91/nihpp-2024.02.27.582378v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/ae4417300b28/nihpp-2024.02.27.582378v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/f4f1b339bf97/nihpp-2024.02.27.582378v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/4b20d496e14b/nihpp-2024.02.27.582378v1-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/d07228172f91/nihpp-2024.02.27.582378v1-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/ae4417300b28/nihpp-2024.02.27.582378v1-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/f4f1b339bf97/nihpp-2024.02.27.582378v1-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/8c46/10925201/4b20d496e14b/nihpp-2024.02.27.582378v1-f0004.jpg

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本文引用的文献

1
BNP-Track: a framework for superresolved tracking.BNP-Track:用于超分辨率跟踪的框架。
Nat Methods. 2024 Sep;21(9):1716-1724. doi: 10.1038/s41592-024-02349-9. Epub 2024 Jul 22.
2
Visualizing Intramolecular Dynamics of Membrane Proteins.可视化膜蛋白的分子内动力学。
Int J Mol Sci. 2022 Nov 22;23(23):14539. doi: 10.3390/ijms232314539.
3
Structure and dynamics of membrane protein in SARS-CoV-2.新冠病毒膜蛋白的结构与动力学
J Biomol Struct Dyn. 2022 Jul;40(10):4725-4738. doi: 10.1080/07391102.2020.1861983. Epub 2020 Dec 22.
4
Inferring effective forces for Langevin dynamics using Gaussian processes.使用高斯过程推断朗之万动力学的有效力。
J Chem Phys. 2020 Mar 31;152(12):124106. doi: 10.1063/1.5144523.
5
High-throughput, single-particle tracking reveals nested membrane domains that dictate KRas diffusion and trafficking.高通量、单颗粒追踪揭示了决定 KRas 扩散和运输的嵌套膜域。
Elife. 2019 Nov 1;8:e46393. doi: 10.7554/eLife.46393.
6
Membrane Lipid Composition: Effect on Membrane and Organelle Structure, Function and Compartmentalization and Therapeutic Avenues.膜脂组成:对膜和细胞器结构、功能和区室化的影响及治疗途径。
Int J Mol Sci. 2019 May 1;20(9):2167. doi: 10.3390/ijms20092167.
7
The Lateral Organization and Mobility of Plasma Membrane Components.质膜成分的侧向组织和流动性。
Cell. 2019 May 2;177(4):806-819. doi: 10.1016/j.cell.2019.04.018.
8
A method for single molecule tracking using a conventional single-focus confocal setup.一种使用传统单聚焦共焦设置进行单分子跟踪的方法。
J Chem Phys. 2019 Mar 21;150(11):114108. doi: 10.1063/1.5083869.
9
Biological Membrane Organization and Cellular Signaling.生物膜组织与细胞信号转导。
Chem Rev. 2019 May 8;119(9):5849-5880. doi: 10.1021/acs.chemrev.8b00439. Epub 2019 Feb 12.
10
Inferring diffusion dynamics from FCS in heterogeneous nuclear environments.从异质核环境中的荧光相关光谱推断扩散动力学。
Biophys J. 2015 Jul 7;109(1):7-17. doi: 10.1016/j.bpj.2015.05.035.