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Error-Speed Correlations in Biopolymer Synthesis.

ABSTRACT: Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. The performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this Letter, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal conditions, polymers that are synthesized faster due to a fluctuation tend to have either better or worse errors than the average. The error-correction mechanism implemented by the enzyme determines which of the two cases holds. For example, discrimination in the forward reaction rates tends to grant smaller errors to polymers with faster synthesis. The opposite occurs for discrimination in monomer rejection rates. Our results provide an experimentally feasible way to identify error-correction mechanisms by measuring the error-speed correlations.

SUBMITTER: Chiuchiu D

PROVIDER: S-EPMC7402413 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Error-Speed Correlations in Biopolymer Synthesis.

Chiuchiú Davide D Tu Yuhai Y Pigolotti Simone S

Physical review letters 20190701 3

Synthesis of biopolymers such as DNA, RNA, and proteins are biophysical processes aided by enzymes. The performance of these enzymes is usually characterized in terms of their average error rate and speed. However, because of thermal fluctuations in these single-molecule processes, both error and speed are inherently stochastic quantities. In this Letter, we study fluctuations of error and speed in biopolymer synthesis and show that they are in general correlated. This means that, under equal co ...[more]

PMID: 31386470

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Project description:RATIONALE AND OBJECTIVES:The purpose of this work is to determine if the speed of sound value of a breast cyst can aid in the clinical management of breast masses. Breast macrocysts are defined as fluid-filled tissue masses >1 cm in diameter and are thought to be aberrations of normal development and involution, often associated with apocrine metaplasia. The benign natural history of breast cysts is well known, and it is important to obtain high specificity in breast imaging to avoid unnecessary biopsies in women who have benign diseases, particularly those with dense breast tissue. Transmission ultrasound is a tomographic imaging modality that generates high-resolution, 3D speed of sound maps that could be used to identify breast tissue types and act as a biomarker to differentiate lesions. We performed this study to investigate the microanatomy of macrocysts observed using transmission ultrasound, as well as assess the relationship of speed of sound to the physical and biochemical parameters of cyst fluids. MATERIALS AND METHODS:Cyst fluid samples were obtained from 37 patients as part of a case-collection study for ultrasound imaging of the breast. The speed of sound of each sample was measured using a quantitative transmission ultrasound scanner in vivo. Electrolytes, protein, cholesterol, viscosity, and specific gravity were also measured (in the aspirated cyst fluid) to assess their relationship to the speed of sound values obtained during breast imaging. RESULTS:We found positive correlations between viscosity and cholesterol (r?=?0.71) and viscosity and total protein?×?cholesterol (r?=?0.78). Additionally, we performed direct cell counts on cyst fluids and confirmed a positive correlation of number of cells with speed of sound (r?=?0.74). The speed of sound of breast macrocysts, as observed using transmission ultrasound, correlated with the cytological features of intracystic cell clumps. CONCLUSION:On the basis of our work with speed as a classifier, we propose a spectrum of breast macrocysts from fluid-filled to highly cellular. Our results suggest high-speed cysts are mature macrocysts with high cell counts and many cellular clumps that correlate with cyst microanatomy as seen by transmission ultrasound. Further studies are needed to confirm our findings and to assess the clinical value of speed of sound measurements in breast imaging using transmission ultrasound.

Dataset Information

Error-Speed Correlations in Biopolymer Synthesis.

Publications

Error-Speed Correlations in Biopolymer Synthesis.

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