Dataset Information

Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms.

ABSTRACT: In nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact bacterial biofilms. µCT is a vital tool for visualizing bacterial communities that can provide insights into the relationship between bacterial biofilm structure and function. Our results imply that dense and structured calcium carbonate lamina forms a diffusion barrier sheltering the inner cell mass of the biofilm colony. Therefore, µCT can be employed in clinical settings to predict the permeability of the biofilms. It is demonstrated that chemical interference with urease, a key enzyme in biomineralization, inhibits the assembly of complex bacterial structures, prevents the formation of mineral diffusion barriers and increases biofilm permeability. Therefore, biomineralization enzymes emerge as novel therapeutic targets for highly resistant infections.

SUBMITTER: Keren-Paz A

PROVIDER: S-EPMC5904145 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms.

Keren-Paz Alona A Brumfeld Vlad V Oppenheimer-Shaanan Yaara Y Kolodkin-Gal Ilana I

NPJ biofilms and microbiomes 20180417

In nature, bacteria predominantly exist as highly structured biofilms, which are held together by extracellular polymeric substance and protect their residents from environmental insults, such as antibiotics. The mechanisms supporting this phenotypic resistance are poorly understood. Recently, we identified a new mechanism maintaining biofilms - an active production of calcite minerals. In this work, a high-resolution and robust µCT technique is used to study the mineralized areas within intact ...[more]

PMID: 29675263

Similar Datasets

Project description:Micro-CT is widely used for small animal imaging in preclinical studies of cardiopulmonary disease, but further development is needed to improve spatial resolution, temporal resolution, and material contrast. We present a technique for visualizing the changing distribution of iodine in the cardiac cycle with dual source micro-CT.The approach entails a retrospectively gated dual energy scan with optimized filters and voltages, and a series of computational operations to reconstruct the data. Projection interpolation and five-dimensional bilateral filtration (three spatial dimensions + time + energy) are used to reduce noise and artifacts associated with retrospective gating. We reconstruct separate volumes corresponding to different cardiac phases and apply a linear transformation to decompose these volumes into components representing concentrations of water and iodine. Since the resulting material images are still compromised by noise, we improve their quality in an iterative process that minimizes the discrepancy between the original acquired projections and the projections predicted by the reconstructed volumes. The values in the voxels of each of the reconstructed volumes represent the coefficients of linear combinations of basis functions over time and energy. We have implemented the reconstruction algorithm on a graphics processing unit (GPU) with CUDA. We tested the utility of the technique in simulations and applied the technique in an in vivo scan of a C57BL∕6 mouse injected with blood pool contrast agent at a dose of 0.01 ml∕g body weight. Postreconstruction, at each cardiac phase in the iodine images, we segmented the left ventricle and computed its volume. Using the maximum and minimum volumes in the left ventricle, we calculated the stroke volume, the ejection fraction, and the cardiac output.Our proposed method produces five-dimensional volumetric images that distinguish different materials at different points in time, and can be used to segment regions containing iodinated blood and compute measures of cardiac function.We believe this combined spectral and temporal imaging technique will be useful for future studies of cardiopulmonary disease in small animals.

Project description:A novel motion correction algorithm for X-ray lung CT imaging has been developed recently. It was designed to perform for routine chest or thorax CT scans without gating, namely axial or helical scans with pitch around 1.0. The algorithm makes use of two conjugate partial angle reconstruction images for motion estimation via non-rigid registration which is followed by a motion compensated reconstruction. Differently from other conventional approaches, no segmentation is adopted in motion estimation. This makes motion estimation of various fine lung structures possible. The aim of this study is to explore the performance of the proposed method in correcting the lung motion artifacts which arise even under routine CT scans with breath-hold. The artifacts are known to mimic various lung diseases, so it is of great interest to address the problem. For that purpose, a moving phantom experiment and clinical study (seven cases) were conducted. We selected the entropy and positivity as figure of merits to compare the reconstructed images before and after the motion correction. Results of both phantom and clinical studies showed a statistically significant improvement by the proposed method, namely up to 53.6% (p < 0.05) and up to 35.5% (p < 0.05) improvement by means of the positivity measure, respectively. Images of the proposed method show significantly reduced motion artifacts of various lung structures such as lung parenchyma, pulmonary vessels, and airways which are prominent in FBP images. Results of two exemplary cases also showed great potential of the proposed method in correcting motion artifacts of the aorta which is known to mimic aortic dissection. Compared to other approaches, the proposed method provides an excellent performance and a fully automatic workflow. In addition, it has a great potential to handle motions in wide range of organs such as lung structures and the aorta. We expect that this would pave a way toward innovations in chest and thorax CT imaging.

Dataset Information

Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms.

Publications

Micro-CT X-ray imaging exposes structured diffusion barriers within biofilms.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets