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Objective quantification of nanoscale protein distributions.

ABSTRACT: Nanoscale distribution of molecules within small subcellular compartments of neurons critically influences their functional roles. Although, numerous ways of analyzing the spatial arrangement of proteins have been described, a thorough comparison of their effectiveness is missing. Here we present an open source software, GoldExt, with a plethora of measures for quantification of the nanoscale distribution of proteins in subcellular compartments (e.g. synapses) of nerve cells. First, we compared the ability of five different measures to distinguish artificial uniform and clustered patterns from random point patterns. Then, the performance of a set of clustering algorithms was evaluated on simulated datasets with predefined number of clusters. Finally, we applied the best performing methods to experimental data, and analyzed the nanoscale distribution of different pre- and postsynaptic proteins, revealing random, uniform and clustered sub-synaptic distribution patterns. Our results reveal that application of a single measure is sufficient to distinguish between different distributions.

SUBMITTER: Szoboszlay M

PROVIDER: S-EPMC5681686 | biostudies-literature | 2017 Nov

REPOSITORIES: biostudies-literature

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Objective quantification of nanoscale protein distributions.

Szoboszlay Miklos M Kirizs Tekla T Nusser Zoltan Z

Scientific reports 20171110 1

Nanoscale distribution of molecules within small subcellular compartments of neurons critically influences their functional roles. Although, numerous ways of analyzing the spatial arrangement of proteins have been described, a thorough comparison of their effectiveness is missing. Here we present an open source software, GoldExt, with a plethora of measures for quantification of the nanoscale distribution of proteins in subcellular compartments (e.g. synapses) of nerve cells. First, we compared ...[more]

PMID: 29127366

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Project description:PurposeThis study aimed to apply open-source analysis code to raw habitual physical activity data from wrist-worn monitors to: 1) objectively, unobtrusively, and accurately discriminate between "running" and "nonrunning" days; and 2) develop and compare simple accelerometer-derived metrics of external training load with existing self-report measures.MethodsSeven-day wrist-worn accelerometer (GENEActiv; Activinsights Ltd, Kimbolton, UK) data obtained from 35 experienced runners (age, 41.9 ± 11.4 yr; height, 1.72 ± 0.08 m; mass, 68.5 ± 9.7 kg; body mass index, 23.2 ± 2.2 kg·m; 19 [54%] women) every other week over 9 to 18 wk were date-matched with self-reported training log data. Receiver operating characteristic analyses were applied to accelerometer metrics ("Average Acceleration," "Most Active-30mins," "Mins≥400 mg") to discriminate between "running" and "nonrunning" days and cross-validated (leave one out cross-validation). Variance explained in training log criterion metrics (miles, duration, training load) by accelerometer metrics (Mins≥400 mg, "workload (WL) 400-4000 mg") was examined using linear regression with leave one out cross-validation.ResultsMost Active-30mins and Mins≥400 mg had >94% accuracy for correctly classifying "running" and "nonrunning" days, with validation indicating robustness. Variance explained in miles, duration, and training load by Mins≥400 mg (67%-76%) and WL400-4000 mg (55%-69%) was high, with validation indicating robustness.ConclusionsWrist-worn accelerometer metrics can be used to objectively, unobtrusively, and accurately identify running training days in runners, reducing the need for training logs or user input in future prospective research or commercial activity tracking. The high percentage of variance explained in existing self-reported measures of training load by simple, accelerometer-derived metrics of external training load supports the future use of accelerometry for prospective, preventative, and prescriptive monitoring purposes in runners.

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Objective quantification of nanoscale protein distributions.

Publications

Objective quantification of nanoscale protein distributions.

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