scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

2015 ◽  
Author(s):  
Michael A. Cianfrocco ◽  
Andres E. Leschziner
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Cost Effective ◽  
Cryo Electron Microscopy ◽  
Software Packages ◽  
Electron Microscopes ◽  
Microscopy Data ◽  
New Generation

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. However, calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon’s elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters that can range in size from 16 to 480+ CPUs. Importantly, these computing clusters are also cost-effective, as we illustrate here by determining a near-atomic resolution structure of the 80S yeast ribosome for $28.89 USD in ~10 hours.

scholarly journals Low cost, high performance processing of single particle cryo-electron microscopy data in the cloud

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Michael A Cianfrocco ◽  
Andres E Leschziner
Keyword(s):  
Electron Microscopy ◽  
Cloud Computing ◽  
High Resolution ◽  
Single Particle ◽  
High Performance ◽  
Low Cost ◽  
Computing Environment ◽  
Cryo Electron Microscopy ◽  
Electron Microscopes ◽  
Microscopy Data

The advent of a new generation of electron microscopes and direct electron detectors has realized the potential of single particle cryo-electron microscopy (cryo-EM) as a technique to generate high-resolution structures. Calculating these structures requires high performance computing clusters, a resource that may be limiting to many likely cryo-EM users. To address this limitation and facilitate the spread of cryo-EM, we developed a publicly available ‘off-the-shelf’ computing environment on Amazon's elastic cloud computing infrastructure. This environment provides users with single particle cryo-EM software packages and the ability to create computing clusters with 16–480+ CPUs. We tested our computing environment using a publicly available 80S yeast ribosome dataset and estimate that laboratories could determine high-resolution cryo-EM structures for $50 to $1500 per structure within a timeframe comparable to local clusters. Our analysis shows that Amazon's cloud computing environment may offer a viable computing environment for cryo-EM.

scholarly journals Synthetic self-assembling ADDomer platform for highly efficient vaccination by genetically encoded multiepitope display

2019 ◽  
Vol 5 (9) ◽  
pp. eaaw2853 ◽  
Author(s):  
Charles Vragniau ◽  
Joshua C. Bufton ◽  
Frédéric Garzoni ◽  
Emilie Stermann ◽  
Fruzsina Rabi ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Electron Microscopy ◽  
High Performance ◽  
Vaccine Candidate ◽  
Cost Effective ◽  
Atomic Resolution ◽  
Self Assembling ◽  
Cryo Electron Microscopy ◽  
Architectural Features ◽  
Multimeric Protein

Self-assembling virus-like particles represent highly attractive tools for developing next-generation vaccines and protein therapeutics. We created ADDomer, an adenovirus-derived multimeric protein-based self-assembling nanoparticle scaffold engineered to facilitate plug-and-play display of multiple immunogenic epitopes from pathogens. We used cryo–electron microscopy at near-atomic resolution and implemented novel, cost-effective, high-performance cloud computing to reveal architectural features in unprecedented detail. We analyzed ADDomer interaction with components of the immune system and developed a promising first-in-kind ADDomer-based vaccine candidate to combat emerging Chikungunya infectious disease, exemplifying the potential of our approach.

scholarly journals Towards on-the-fly Cryo-Electron Microscopy Data Processing by High Performance Data Analysis

2018 ◽  
Vol 955 ◽  
pp. 012005 ◽  
Author(s):  
Evgeny Pichkur ◽  
Timur Baimukhametov ◽  
Anton Teslyuk ◽  
Anton Orekhov ◽  
Roman Kamyshinsky ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Data Analysis ◽  
Data Processing ◽  
High Performance ◽  
Performance Data ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Live Analysis and Reconstruction of Single-Particle Cryo-Electron Microscopy Data with CryoFLARE

2020 ◽  
Vol 60 (5) ◽  
pp. 2561-2569 ◽  
Author(s):  
Andreas D. Schenk ◽  
Simone Cavadini ◽  
Nicolas H. Thomä ◽  
Christel Genoud
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Cryo Electron Microscopy ◽  
Electron Microscopy Data ◽  
Microscopy Data

scholarly journals Conformations of macromolecules and their complexes from heterogeneous datasets

2014 ◽  
Vol 369 (1647) ◽  
pp. 20130567 ◽  
Author(s):  
P. Schwander ◽  
R. Fung ◽  
A. Ourmazd
Keyword(s):  
Electron Microscopy ◽  
Prior Knowledge ◽  
Single Particle ◽  
Conformational Heterogeneity ◽  
X Ray ◽  
Cryo Electron Microscopy ◽  
Heterogeneous Datasets ◽  
Large Ensembles ◽  
New Generation ◽  
Image Datasets

We describe a new generation of algorithms capable of mapping the structure and conformations of macromolecules and their complexes from large ensembles of heterogeneous snapshots, and demonstrate the feasibility of determining both discrete and continuous macromolecular conformational spectra. These algorithms naturally incorporate conformational heterogeneity without resort to sorting and classification, or prior knowledge of the type of heterogeneity present. They are applicable to single-particle diffraction and image datasets produced by X-ray lasers and cryo-electron microscopy, respectively, and particularly suitable for systems not easily amenable to purification or crystallization.

scholarly journals Vitrification after multiple rounds of sample application and blotting improves particle density on cryo-electron microscopy grids

2016 ◽  
Author(s):  
Joost Snijder ◽  
Andrew J. Borst ◽  
Annie Dosey ◽  
Alexandra C. Walls ◽  
Anika Burrell ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Single Particle ◽  
Particle Density ◽  
Protein Complexes ◽  
Cost Effective ◽  
Carbon Support ◽  
Cryo Electron Microscopy ◽  
Sample Application ◽  
Single Field

Single particle cryo-electron microscopy (cryoEM) is becoming widely adopted as a tool for structural characterization of biomolecules at near-atomic resolution. Vitrification of the sample to obtain a dense distribution of particles within a single field of view remains a major bottleneck for the success of such experiments. Here, we describe a simple and cost-effective method to increase the density of frozen-hydrated particles on grids with holey carbon support films. It relies on performing multiple rounds of sample application and blotting prior to plunge freezing in liquid ethane. We show that this approach is generally applicable and significantly increases particle density for a range of samples, such as small protein complexes, viruses and filamentous assemblies. The method is versatile, easy to implement, minimizes sample requirements and can enable characterization of samples that would otherwise resist structural studies using single particle cryoEM.

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