scholarly journals Advances in cryo-EM and ED with a cold-field emission beam and energy filtration —Refinements of the CRYO ARM 300 system in RIKEN SPring-8 center—

Microscopy ◽  
2020 ◽  
Author(s):  
Saori Maki-Yonekura ◽  
Tasuku Hamaguchi ◽  
Hisashi Naitow ◽  
Kiyofumi Takaba ◽  
Koji Yonekura
Keyword(s):  
Field Emission ◽  
Direct Detection ◽  
Quality Data ◽  
Particle Analysis ◽  
High Quality Data ◽  
Camera Control ◽  
Cryo Electron Microscopy ◽  
Control Computer ◽  
Gpu Clusters ◽  
Resolution Single

Abstract We have designed and evaluated a cryo-electron microscopy (cryo-EM) system for higher-resolution single particle analysis and high-precision electron 3D crystallography. The system comprises a JEOL CRYO ARM 300 electron microscope—the first machine of this model—and a direct detection device camera, a scintillator-coupled camera, GPU clusters connected with a camera control computer and software for automated-data collection and efficient and accurate operation. The microscope provides parallel illumination of a highly coherent 300-kV electron beam to a sample from a cold-field emission gun and filters out energy-loss electrons through the sample with an in-column energy filter. The gun and filter are highly effective in improving imaging and diffraction, respectively, and have provided high quality data since July 2018. We here report on the characteristics of the cryo-EM system, updates, our progress and future plan for running such cryo-EM machines in RIKEN SPring-8 Center.

scholarly journals Cryo-EM single particle analysis with the Volta phase plate

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Radostin Danev ◽  
Wolfgang Baumeister
Keyword(s):  
Single Particle ◽  
Spherical Aberration ◽  
Quality Data ◽  
Particle Analysis ◽  
Limiting Factor ◽  
Phase Plate ◽  
Single Particle Analysis ◽  
High Quality Data ◽  
Size Heterogeneity ◽  
Resolution Single

We present a method for in-focus data acquisition with a phase plate that enables near-atomic resolution single particle reconstructions. Accurate focusing is the determining factor for obtaining high quality data. A double-area focusing strategy was implemented in order to achieve the required precision. With this approach we obtained a 3.2 Å resolution reconstruction of the Thermoplasma acidophilum 20S proteasome. The phase plate matches or slightly exceeds the performance of the conventional defocus approach. Spherical aberration becomes a limiting factor for achieving resolutions below 3 Å with in-focus phase plate images. The phase plate could enable single particle analysis of challenging samples in terms of small size, heterogeneity and flexibility that are difficult to solve by the conventional defocus approach.

scholarly journals Exploring high-resolution cryo-ET and subtomogram averaging capabilities of contemporary DEDs

2022 ◽  
Author(s):  
Martin Obr ◽  
Wim JH Hagen ◽  
Robert A Dick ◽  
Lingbo Yu ◽  
Abhay Kotecha ◽  
...  
Keyword(s):  
Field Emission ◽  
Electron Tomography ◽  
Particle Analysis ◽  
Energy Filtering ◽  
Cryo Electron Microscopy ◽  
Electron Detection ◽  
Thermo Fisher Scientific ◽  
Subtomogram Averaging ◽  
New Generation ◽  
Fisher Scientific

The potential of energy filtering and direct electron detection for cryo-electron microscopy (cryo- EM) image processing has been well documented for single particle analysis (SPA). Here, we assess the performance of recently introduced hardware for cryo-electron tomography (cryo-ET) and subtomogram averaging (STA), an increasingly popular structural determination method for complex 3D specimens. We acquired cryo-ET datasets of EIAV virus-like particles (VLPs) on two contemporary cryo-EM systems equipped with different energy filters and direct electron detectors (DED), specifically a Krios G4, equipped with a cold field emission gun (CFEG), Thermo Fisher Scientific Selectris X energy filter, and a Falcon 4 DED; and a Krios G3i, with a Schottky field emission gun (XFEG), a Gatan Bioquantum energy filter, and a K3 DED. We performed constrained cross-correlation-based STA on equally sized datasets acquired on the respective systems. The resulting EIAV CA hexamer reconstructions show that both systems perform comparably in the 4-6 Angstrom resolution range. In addition, by employing a recently introduced multiparticle refinement approach, we obtained a reconstruction of the EIAV CA hexamer at 2.9 Angstrom. Our results demonstrate the potential of the new generation of energy filters and DEDs for STA, and the effects of using different processing pipelines on their STA outcomes.

scholarly journals Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age

2019 ◽  
Vol 75 (1) ◽  
pp. 3-11 ◽  
Author(s):  
Alok K. Mitra
Keyword(s):  
Electron Microscopy ◽  
Structural Biology ◽  
Atomic Resolution ◽  
Particle Analysis ◽  
Biological Macromolecules ◽  
Single Particles ◽  
Cryo Electron Microscopy ◽  
Electron Microscopes ◽  
Resolution Single ◽  
Resolution Structure

Structural biology is going through a revolution as a result of transformational advances in the field of cryo-electron microscopy (cryo-EM) driven by the development of direct electron detectors and ultrastable electron microscopes. High-resolution cryo-EM images of isolated biomolecules (single particles) suspended in a thin layer of vitrified buffer are subjected to powerful image-processing algorithms, enabling near-atomic resolution structures to be determined in unprecedented numbers. Prior to these advances, electron crystallography of two-dimensional crystals and helical assemblies of proteins had established the feasibility of atomic resolution structure determination using cryo-EM. Atomic resolution single-particle analysis, without the need for crystals, now promises to resolve problems in structural biology that were intractable just a few years ago.

What Can Digitization Do For Formulated Product Innovation and Development

2020 ◽  
Author(s):  
James McDonagh ◽  
William Swope ◽  
Richard L. Anderson ◽  
Michael Johnston ◽  
David J. Bray
Keyword(s):  
High Performance ◽  
Quality Data ◽  
High Quality Data ◽  
Base Level ◽  
Hybrid Approaches ◽  
Digital Ecosystem ◽  
Recent Developments ◽  
Chemical Simulation ◽  
High Level ◽  
Physical And Chemical

Digitization offers significant opportunities for the formulated product industry to transform the way it works and develop new methods of business. R&D is one area of operation that is challenging to take advantage of these technologies due to its high level of domain specialisation and creativity but the benefits could be significant. Recent developments of base level technologies such as artificial intelligence (AI)/machine learning (ML), robotics and high performance computing (HPC), to name a few, present disruptive and transformative technologies which could offer new insights, discovery methods and enhanced chemical control when combined in a digital ecosystem of connectivity, distributive services and decentralisation. At the fundamental level, research in these technologies has shown that new physical and chemical insights can be gained, which in turn can augment experimental R&D approaches through physics-based chemical simulation, data driven models and hybrid approaches. In all of these cases, high quality data is required to build and validate models in addition to the skills and expertise to exploit such methods. In this article we give an overview of some of the digital technology demonstrators we have developed for formulated product R&D. We discuss the challenges in building and deploying these demonstrators.<br>

Collecting High-Quality Data

2018 ◽  
Author(s):  
Mary Kay Gugerty ◽  
Dean Karlan
Keyword(s):  
Data Collection ◽  
Social Desirability ◽  
Measurement Errors ◽  
Monitoring And Evaluation ◽  
Quality Data ◽  
Social Desirability Bias ◽  
High Quality ◽  
High Quality Data ◽  
Evaluation Systems ◽  
Demand Effect

Without high-quality data, even the best-designed monitoring and evaluation systems will collapse. Chapter 7 introduces some the basics of collecting high-quality data and discusses how to address challenges that frequently arise. High-quality data must be clearly defined and have an indicator that validly and reliably measures the intended concept. The chapter then explains how to avoid common biases and measurement errors like anchoring, social desirability bias, the experimenter demand effect, unclear wording, long recall periods, and translation context. It then guides organizations on how to find indicators, test data collection instruments, manage surveys, and train staff appropriately for data collection and entry.

scholarly journals Cryo–electron microscopy structure of the antidiuretic hormone arginine-vasopressin V2 receptor signaling complex

2021 ◽  
Vol 7 (21) ◽  
pp. eabg5628
Author(s):  
Julien Bous ◽  
Hélène Orcel ◽  
Nicolas Floquet ◽  
Cédric Leyrat ◽  
Joséphine Lai-Kee-Him ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Antidiuretic Hormone ◽  
Arginine Vasopressin ◽  
Molecular Mechanisms ◽  
Particle Analysis ◽  
Resonance Spectroscopy ◽  
Gpcr Signaling ◽  
Signaling Complex ◽  
Cryo Electron Microscopy ◽  
V2 Receptor

The antidiuretic hormone arginine-vasopressin (AVP) forms a signaling complex with the V2 receptor (V2R) and the Gs protein, promoting kidney water reabsorption. Molecular mechanisms underlying activation of this critical G protein–coupled receptor (GPCR) signaling system are still unknown. To fill this gap of knowledge, we report here the cryo–electron microscopy structure of the AVP-V2R-Gs complex. Single-particle analysis revealed the presence of three different states. The two best maps were combined with computational and nuclear magnetic resonance spectroscopy constraints to reconstruct two structures of the ternary complex. These structures differ in AVP and Gs binding modes. They reveal an original receptor-Gs interface in which the Gαs subunit penetrates deep into the active V2R. The structures help to explain how V2R R137H or R137L/C variants can lead to two severe genetic diseases. Our study provides important structural insights into the function of this clinically relevant GPCR signaling complex.

scholarly journals Velocity Analysis Using Separated Diffractions for Lunar Penetrating Radar Obtained by Yutu-2 Rover

2021 ◽  
Vol 13 (7) ◽  
pp. 1387
Author(s):  
Chao Li ◽  
Jinhai Zhang
Keyword(s):  
Dielectric Permittivity ◽  
Lunar Regolith ◽  
Velocity Model ◽  
Velocity Estimation ◽  
Quality Data ◽  
High Quality Data ◽  
Shallow Subsurface ◽  
Subsurface Structures ◽  
Ground Penetrating ◽  
Permittivity Model

The high-frequency channel of lunar penetrating radar (LPR) onboard Yutu-2 rover successfully collected high quality data on the far side of the Moon, which provide a chance for us to detect the shallow subsurface structures and thickness of lunar regolith. However, traditional methods cannot obtain reliable dielectric permittivity model, especially in the presence of high mix between diffractions and reflections, which is essential for understanding and interpreting the composition of lunar subsurface materials. In this paper, we introduce an effective method to construct a reliable velocity model by separating diffractions from reflections and perform focusing analysis using separated diffractions. We first used the plane-wave destruction method to extract weak-energy diffractions interfered by strong reflections, and the LPR data are separated into two parts: diffractions and reflections. Then, we construct a macro-velocity model of lunar subsurface by focusing analysis on separated diffractions. Both the synthetic ground penetrating radar (GPR) and LPR data shows that the migration results of separated reflections have much clearer subsurface structures, compared with the migration results of un-separated data. Our results produce accurate velocity estimation, which is vital for high-precision migration; additionally, the accurate velocity estimation directly provides solid constraints on the dielectric permittivity at different depth.

scholarly journals Redistribution Preferences, Inequality Information, and Partisan Motivated Reasoning in the United States

Societies ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 65
Author(s):  
Clem Brooks ◽  
Elijah Harter
Keyword(s):  
Party Identification ◽  
Motivated Reasoning ◽  
The United States ◽  
Quality Data ◽  
Historical Time ◽  
High Quality Data ◽  
Redistributive Policies ◽  
Election Studies ◽  
New Evidence ◽  
The U.S

In an era of rising inequality, the U.S. public’s relatively modest support for redistributive policies has been a puzzle for scholars. Deepening the paradox is recent evidence that presenting information about inequality increases subjects’ support for redistributive policies by only a small amount. What explains inequality information’s limited effects? We extend partisan motivated reasoning scholarship to investigate whether political party identification confounds individuals’ processing of inequality information. Our study considers a much larger number of redistribution preference measures (12) than past scholarship. We offer a second novelty by bringing the dimension of historical time into hypothesis testing. Analyzing high-quality data from four American National Election Studies surveys, we find new evidence that partisanship confounds the interrelationship of inequality information and redistribution preferences. Further, our analyses find the effects of partisanship on redistribution preferences grew in magnitude from 2004 through 2016. We discuss implications for scholarship on information, motivated reasoning, and attitudes towards redistribution.

Developmental Impacts of Remittances on Migrant-Sending Households: Micro-Level Evidence from Punjab, Pakistan

2019 ◽  
Vol 14 (3) ◽  
pp. 338-366
Author(s):  
Kashif Imran ◽  
Evelyn S. Devadason ◽  
Cheong Kee Cheok
Keyword(s):  
Human Development ◽  
Human Development Index ◽  
Quality Data ◽  
High Quality ◽  
High Quality Data ◽  
Development Index ◽  
Policy Interventions ◽  
Education And Health ◽  
Micro Level ◽  
The Government

This article analyzes the overall and type of developmental impacts of remittances for migrant-sending households (HHs) in districts of Punjab, Pakistan. For this purpose, an HH-based human development index is constructed based on the dimensions of education, health and housing, with a view to enrich insights into interactions between remittances and HH development. Using high-quality data from a HH micro-survey for Punjab, the study finds that most migrant-sending HHs are better off than the HHs without this stream of income. More importantly, migrant HHs have significantly higher development in terms of housing in most districts of Punjab relative to non-migrant HHs. Thus, the government would need policy interventions focusing on housing to address inequalities in human development at the district-HH level, and subsequently balance its current focus on the provision of education and health.

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