Dataset Information

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

ABSTRACT: Coadaptation between bacterial hosts and plasmids frequently results in adaptive changes restricted exclusively to host genome leaving plasmids unchanged. To better understand this remarkable stability, we transformed naïve Escherichia coli cells with a plasmid carrying an antibiotic-resistance gene and forced them to adapt in a turbidostat environment. We then drew population samples at regular intervals and subjected them to duplex sequencing-a technique specifically designed for identification of low-frequency mutations. Variants at ten sites implicated in plasmid copy number control emerged almost immediately, tracked consistently across the experiment's time points, and faded below detectable frequencies toward the end. This variation crash coincided with the emergence of mutations on the host chromosome. Mathematical modeling of trajectories for adaptive changes affecting plasmid copy number showed that such mutations cannot readily fix or even reach appreciable frequencies. We conclude that there is a strong selection against alterations of copy number even if it can provide a degree of growth advantage. This incentive is likely rooted in the complex interplay between mutated and wild-type plasmids constrained within a single cell and underscores the importance of understanding of intracellular plasmid variability.

SUBMITTER: Mei H

PROVIDER: S-EPMC6827461 | biostudies-literature | 2019 Oct

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

Mei Han H Arbeithuber Barbara B Cremona Marzia A MA DeGiorgio Michael M Nekrutenko Anton A

Genome biology and evolution 20191001 10

Coadaptation between bacterial hosts and plasmids frequently results in adaptive changes restricted exclusively to host genome leaving plasmids unchanged. To better understand this remarkable stability, we transformed naïve Escherichia coli cells with a plasmid carrying an antibiotic-resistance gene and forced them to adapt in a turbidostat environment. We then drew population samples at regular intervals and subjected them to duplex sequencing-a technique specifically designed for identificatio ...[more]

PMID: 31539047

Similar Datasets

Project description:Objective and Impact Statement: We developed a generalized computational approach to design uniform, high-intensity excitation light for low-cost, quantitative fluorescence imaging of in vitro, ex vivo, and in vivo samples with a single device. Introduction: Fluorescence imaging is a ubiquitous tool for biomedical applications. Researchers extensively modify existing systems for tissue imaging, increasing the time and effort needed for translational research and thick tissue imaging. These modifications are application-specific, requiring new designs to scale across sample types. Methods: We implemented a computational model to simulate light propagation from multiple sources. Using a global optimization algorithm and a custom cost function, we determined the spatial positioning of optical fibers to generate 2 illumination profiles. These results were implemented to image core needle biopsies, preclinical mammary tumors, or tumor-derived organoids. Samples were stained with molecular probes and imaged with uniform and nonuniform illumination. Results: Simulation results were faithfully translated to benchtop systems. We demonstrated that uniform illumination increased the reliability of intraimage analysis compared to nonuniform illumination and was concordant with traditional histological findings. The computational approach was used to optimize the illumination geometry for the purposes of imaging 3 different fluorophores through a mammary window chamber model. Illumination specifically designed for intravital tumor imaging generated higher image contrast compared to the case in which illumination originally optimized for biopsy images was used. Conclusion: We demonstrate the significance of using a computationally designed illumination for in vitro, ex vivo, and in vivo fluorescence imaging. Application-specific illumination increased the reliability of intraimage analysis and enhanced the local contrast of biological features. This approach is generalizable across light sources, biological applications, and detectors.

Project description:ObjectivesThis study was conducted in order to compare the effect of field of view (FOV) size on image quality between ultra-high-resolution CT (U-HRCT) and conventional high-resolution CT (HRCT).MethodsEleven cadaveric lungs were scanned with U-HRCT and conventional HRCT and reconstructed with five FOVs (40, 80, 160, 240, and 320 mm). Three radiologists evaluated and scored the images. Three image evaluations were performed, comparing the image quality with the five FOVs with respect to the 160-mm FOV. The first evaluation was performed on conventional HRCT images, and the second evaluation on U-HRCT images. Images were scored on normal structure, abnormal findings, and overall image quality. The third evaluation was a comparison of the images obtained with conventional HRCT and U-HRCT, with scoring performed on overall image quality. Quantitative evaluation of noise was performed by setting ROIs.ResultsIn conventional HRCT, image quality was improved when the FOV was reduced to 160 mm. In U-HRCT, image quality, except for noise, improved when the FOV was reduced to 80 mm. In the third evaluation, overall image quality was improved in U-HRCT over conventional HRCT at all FOVs. Noise of U-HRCT increased with respect to conventional HRCT when the FOV was reduced from 160 to 40 mm. However, at 240- and 320-mm FOVs, the noise of U-HRCT and conventional HRCT showed no differences.ConclusionsIn conventional HRCT, image quality did not improve when the FOV was reduced below 160 mm. However, in U-HRCT, image quality improved even when the FOV was reduced to 80 mm.Key points• Reducing the size of the field of view to 160 mm improves diagnostic imaging quality in high-resolution CT. • In ultra-high-resolution CT, improvements in image quality can be obtained by reducing the size of the field of view to 80 mm. • Ultra-high-resolution CT produces images of higher quality compared with conventional HRCT irrespective of the size of the field of view.

Dataset Information

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

Publications

A High-Resolution View of Adaptive Event Dynamics in a Plasmid.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets