scholarly journals Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

2020 ◽  
Author(s):  
Jonathan Bouvette ◽  
Hsuan-Fu Liu ◽  
Xiaochen Du ◽  
Ye Zhou ◽  
Andrew P. Sikkema ◽  
...  
Keyword(s):  
Data Collection ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Beam Image ◽  
Geometrical Constraints ◽  
Order Of Magnitude ◽  
Biological Environment ◽  
Map Resolution ◽  
Resolution Single

ABSTRACTTomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by an order of magnitude and improve map resolution by ~1-3 Å compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved.

scholarly journals Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Jonathan Bouvette ◽  
Hsuan-Fu Liu ◽  
Xiaochen Du ◽  
Ye Zhou ◽  
Andrew P. Sikkema ◽  
...  
Keyword(s):  
Data Collection ◽  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Beam Image ◽  
Geometrical Constraints ◽  
Order Of Magnitude ◽  
Biological Environment ◽  
Map Resolution ◽  
Resolution Single

AbstractTomographic reconstruction of cryopreserved specimens imaged in an electron microscope followed by extraction and averaging of sub-volumes has been successfully used to derive atomic models of macromolecules in their biological environment. Eliminating biochemical isolation steps required by other techniques, this method opens up the cell to in-situ structural studies. However, the need to compensate for errors in targeting introduced during mechanical navigation of the specimen significantly slows down tomographic data collection thus limiting its practical value. Here, we introduce protocols for tilt-series acquisition and processing that accelerate data collection speed by up to an order of magnitude and improve map resolution compared to existing approaches. We achieve this by using beam-image shift to multiply the number of areas imaged at each stage position, by integrating geometrical constraints during imaging to achieve high precision targeting, and by performing per-tilt astigmatic CTF estimation and data-driven exposure weighting to improve final map resolution. We validated our beam image-shift electron cryo-tomography (BISECT) approach by determining the structure of a low molecular weight target (~300 kDa) at 3.6 Å resolution where density for individual side chains is clearly resolved.

scholarly journals Beam image-shift accelerated data acquisition for near-atomic resolution single-particle cryo-electron tomography

2021 ◽  
Vol 77 (a1) ◽  
pp. a209-a209
Author(s):  
Jonathan Bouvette ◽  
Mario Borgnia ◽  
Hsuan-Fu Liu ◽  
Alberto Bartesaghi ◽  
Roel Schaaper ◽  
...  
Keyword(s):  
Data Acquisition ◽  
Single Particle ◽  
Electron Tomography ◽  
Atomic Resolution ◽  
Beam Image ◽  
Cryo Electron Tomography ◽  
Resolution Single

Automated electron tomography: from data collection to image processing

1995 ◽  
Vol 53 ◽  
pp. 26-27
Author(s):  
Weiping Liu ◽  
Jennifer Fung ◽  
W.J. de Ruijter ◽  
Hans Chen ◽  
John W. Sedat ◽  
...  
Keyword(s):  
Image Processing ◽  
Data Collection ◽  
Structural Information ◽  
Imaging Technique ◽  
Electron Tomography ◽  
Ccd Camera ◽  
Automated Data Collection ◽  
Full Control ◽  
Transmission Electron ◽  
Amorphous Structures

Electron tomography is a technique where many projections of an object are collected from the transmission electron microscope (TEM), and are then used to reconstruct the object in its entirety, allowing internal structure to be viewed. As vital as is the 3-D structural information and with no other 3-D imaging technique to compete in its resolution range, electron tomography of amorphous structures has been exercised only sporadically over the last ten years. Its general lack of popularity can be attributed to the tediousness of the entire process starting from the data collection, image processing for reconstruction, and extending to the 3-D image analysis. We have been investing effort to automate all aspects of electron tomography. Our systems of data collection and tomographic image processing will be briefly described.To date, we have developed a second generation automated data collection system based on an SGI workstation (Fig. 1) (The previous version used a micro VAX). The computer takes full control of the microscope operations with its graphical menu driven environment. This is made possible by the direct digital recording of images using the CCD camera.

Practical electron tomography

1995 ◽  
Vol 53 ◽  
pp. 742-743
Author(s):  
C.L. Woodcock
Keyword(s):  
Electron Tomography ◽  
Tomographic Reconstruction ◽  
Three Dimensional ◽  
3D Shape ◽  
Computational Resources ◽  
Shape Of Particles

Despite the potential of the technique, electron tomography has yet to be widely used by biologists. This is in part related to the rather daunting list of equipment and expertise that are required. Thanks to continuing advances in theory and instrumentation, tomography is now more feasible for the non-specialist. One barrier that has essentially disappeared is the expense of computational resources. In view of this progress, it is time to give more attention to practical issues that need to be considered when embarking on a tomographic project. The following recommendations and comments are derived from experience gained during two long-term collaborative projects.Tomographic reconstruction results in a three dimensional description of an individual EM specimen, most commonly a section, and is therefore applicable to problems in which ultrastructural details within the thickness of the specimen are obscured in single micrographs. Information that can be recovered using tomography includes the 3D shape of particles, and the arrangement and dispostion of overlapping fibrous and membranous structures.

Repeatability, Reproducibility, and Calibration of the MyotonPro® on Tissue Mimicking Phantoms

2013 ◽  
Author(s):  
John Dougherty ◽  
Emily Schaefer ◽  
Kalyani Nair ◽  
Joseph Kelly ◽  
Alfonse Masi
Keyword(s):  
Data Collection ◽  
Dynamic Stiffness ◽  
Correlation Study ◽  
Living Tissue ◽  
Polymeric Gel ◽  
Stiffness Properties ◽  
Tissue Phantoms ◽  
Repeatability And Reproducibility ◽  
Living Tissues

The MyotonPro® (Myoton AS, Tallinn, Estonia) is commonly used to quantify stiffness properties of living tissues in situ. Current studies quantify the dynamic stiffness properties of living tissues, but do not validate or compare these measurements to a standardized method. Additionally, living tissue, being dynamic in nature, presents much variability in data collection. To address these issues this study focuses on the repeatability and reproducibility of the MyotonPro® on polymeric gel-based tissue phantoms. In addition, a correlation study is also performed to translate dynamic stiffness to a more standardized property, Young’s modulus. Such studies help to confirm the reliability of the measurements obtained in situ.

Cryo electron tomography of vitrified fibroblasts: Microtubule plus ends in situ

2008 ◽  
Vol 161 (3) ◽  
pp. 459-468 ◽  
Author(s):  
Roman I. Koning ◽  
Sandra Zovko ◽  
Montserrat Bárcena ◽  
Gert T. Oostergetel ◽  
Henk K. Koerten ◽  
...  
Keyword(s):  
Electron Tomography ◽  
Cryo Electron Tomography

scholarly journals Tunable In Situ 3D-Printed PVDF-TrFE Piezoelectric Arrays

Sensors ◽  
2021 ◽  
Vol 21 (15) ◽  
pp. 5032
Author(s):  
Alec Ikei ◽  
James Wissman ◽  
Kaushik Sampath ◽  
Gregory Yesner ◽  
Syed N. Qadri
Keyword(s):  
3D Printing ◽  
Polyvinylidene Fluoride ◽  
Vinylidene Fluoride ◽  
Mechanical Strain ◽  
Pressure Sensors ◽  
Strain Ratio ◽  
Ex Situ ◽  
Order Of Magnitude ◽  
3D Printed

In the functional 3D-printing field, poly(vinylidene fluoride-co-trifluoroethylene) (PVDF-TrFE) has been shown to be a more promising choice of material over polyvinylidene fluoride (PVDF), due to its ability to be poled to a high level of piezoelectric performance without a large mechanical strain ratio. In this work, a novel presentation of in situ 3D printing and poling of PVDF-TrFE is shown with a d33 performance of up to 18 pC N−1, more than an order of magnitude larger than previously reported in situ poled polymer piezoelectrics. This finding paves the way forward for pressure sensors with much higher sensitivity and accuracy. In addition, the ability of in situ pole sensors to demonstrate different performance levels is shown in a fully 3D-printed five-element sensor array, accelerating and increasing the design space for complex sensing arrays. The in situ poled sample performance was compared to the performance of samples prepared through an ex situ corona poling process.

scholarly journals Magmatic flare-up causes crustal thickening at the transition from subduction to continental collision

2021 ◽  
Vol 2 (1) ◽  
Author(s):  
Carlos E. Ganade ◽  
Pierre Lanari ◽  
Daniela Rubatto ◽  
Joerg Hermann ◽  
Roberto F. Weinberg ◽  
...  
Keyword(s):  
Production Rate ◽  
Continental Margin ◽  
Subduction Zones ◽  
Continental Collision ◽  
Crustal Thickening ◽  
Time Intervals ◽  
West Gondwana ◽  
Continental Arc ◽  
Order Of Magnitude

AbstractAbove subduction zones, magma production rate and crustal generation can increase by an order of magnitude during narrow time intervals known as magmatic flare-ups. However, the consequences of these events in the deep arc environment remain poorly understood. Here we use petrological and in-situ zircon dating techniques to investigate the root of a continental arc within the collisional West Gondwana Orogen that is now exposed in the Kabyé Massif, Togo. We show that gabbros intruded 670 million years ago at 20–25 km depth were transformed to eclogites by 620 million years ago at 65–70 km depth. This was coeval with extensive magmatism at 20–40 km depth, indicative of a flare-up event which peaked just prior to the subduction of the continental margin. We propose that increased H2O flux from subduction of serpentinized mantle in the hyper-extended margin of the approaching continent was responsible for the increased magma productivity and crustal thickening.

Estimation and Scaling of the Near-Saturated Hydraulic Conductivity

1999 ◽  
Vol 30 (3) ◽  
pp. 177-190 ◽  
Author(s):  
Per Atle Olsen
Keyword(s):  
Hydraulic Conductivity ◽  
Saturated Hydraulic Conductivity ◽  
Scaling Analysis ◽  
Laboratory Measurements ◽  
Estimation Errors ◽  
Geometric Means ◽  
Top Soil ◽  
Structured Soils ◽  
Order Of Magnitude

The hydraulic conductivity in structured soils is known to increase drastically when approaching saturation. Tension infiltration allows in situ infiltration of water at predetermined matric potentials, thus allowing exploration of the hydraulic properties near saturation. In this study, the near saturated (ψ≥-0.15 m) hydraulic conductivity was estimated both in the top- and sub-soil of three Norwegian soils. A priory analysis of estimation errors due to measurement uncertainties was conducted. In order to facilitate the comparison between soils and depths, scaling analysis was applied. It was found that the increase in hydraulic conductivity with increasing matric potentials (increasing water content) was steeper in the sub-soil than in the top-soil. The estimated field saturated hydraulic conductivity was compared with laboratory measurements of the saturated hydraulic conductivity. The geometric means of the laboratory measurements was in the same order of magnitude as the field estimates. The variability of the field estimates of the hydraulic conductivity from one of the soils was also assessed. The variability of the field estimates was generally smaller than the laboratory measurements of the saturated hydraulic conductivity.

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