A5043619276- Advanced Electron Microscopy Techniques and Applications
- Electron and X-Ray Spectroscopy Techniques
- Advanced X-ray Imaging Techniques
- Cell Image Analysis Techniques
- Enzyme Structure and Function
- Machine Learning in Materials Science
- Advanced Fluorescence Microscopy Techniques
- Virus-based gene therapy research
- Medical Imaging Techniques and Applications
- Bacteriophages and microbial interactions
- Image Processing Techniques and Applications
- Viral gastroenteritis research and epidemiology
- RNA and protein synthesis mechanisms
- Distributed and Parallel Computing Systems
- Molecular Biology Techniques and Applications
- Force Microscopy Techniques and Applications
- Integrated Circuits and Semiconductor Failure Analysis
- Genomics and Phylogenetic Studies
- Viral Infections and Immunology Research
- Advanced MRI Techniques and Applications
- Scientific Computing and Data Management
- Radiation Detection and Scintillator Technologies
- Animal Virus Infections Studies
- Protein Structure and Dynamics
- RNA modifications and cancer
Universidad Autónoma de Madrid
2014-2023
Centro Nacional de Biotecnología
2009-2023
Consejo Superior de Investigaciones Científicas
1994-2021
Biocom
2021
Diamond Light Source
2018
Tel Aviv University
2013
Universidad San Pablo CEU
2004
City University of New York
2001-2003
The Graduate Center, CUNY
2001-2003
Temple University
2001
Recent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow once cryo-EM map has been calculated, sharpening process is usually performed to enhance visualization, step that proven very important in key task structural modeling. However, approaches, general, neglects local quality map, which clearly suboptimal.Here, new method for density proposed. The algorithm, named...
Algebraic reconstruction techniques (ART) are iterative procedures for solving systems of linear equations. They have been used in tomography to recover objects from their projections. In this work we apply an ART approach which the basis functions describe not based on voxels, but much smoother named "blobs". The data collection studied follows so-called "conical tilt geometry" that is commonly many applications three-dimensional electron microscopy biological macromolecules. performance...
Abstract Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. Achieving high-resolution structural details with electron microscopy requires identification a large number (up to hundreds thousands) single particles from micrographs, which is laborious task if it has be manually done and constitutes hurdle towards high-throughput. Automatic particle selection in micrographs far being settled new more...
The MRC binary file format is widely used in the three-dimensional electron microscopy field for storing image and volume data. Files contain a header which describes kind of data held, together with other important metadata. In response to advances techniques, number variants have emerged useful additional data, but limit interoperability between different software packages. Following extensive discussions, authors, who represent leading packages field, propose set extensions standard...
Abstract Motivation: Structural information of macromolecular complexes provides key insights into the way they carry out their biological functions. The reconstruction process leading to final 3D map requires an approximate initial model. Generation model is still open and challenging problem in single-particle analysis. Results: We present a fast efficient approach obtain reliable, low-resolution estimation structure macromolecule, without any priori knowledge, addressing well-known issue...
Full field soft X-ray microscopy is becoming a powerful imaging technique to analyze whole cells preserved under cryo conditions. Images obtained in these microscopes can be combined by tomographic reconstruction quantitatively estimate the three-dimensional (3D) distribution of absorption coefficients inside cell. The impulse response an system one factors that limits quality microscope reconstructions. main goal this work experimentally measure 3D and assess optical resolution depth...
Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) microscopy (cryoEM) was few years ago. Its data workflows are far from being well defined and the user experience still not smooth. Moreover, file formats of different software packages their associated metadata standardized, mainly since developed by groups, focusing on steps pipeline. The Scipion framework, originally for SPA (de la Rosa-Trevín et al., 2016), has...
Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of SARS-CoV-2 spike in prefusion state have been analysed. These studies revealed concerted motions involving receptor-binding domain (RBD), N-terminal domain, subdomains 1 2 around previously characterized 1-RBD-up state, which modeled as elastic deformations. It is shown that this data set there are not well defined, stable conformations, but...
Abstract In recent years, advances in cryoEM have dramatically increased the resolution of reconstructions and, with it, number solved atomic models. It is widely accepted that quality maps varies locally; therefore, evaluation maps-derived structural models must be done locally as well. this article, a method for local analysis map-to-model fit presented. The algorithm uses comparison two maps. first FSC (Fourier shell correlation) between full map and model, while second calculated half...
Cryo-electron microscopy (cryoEM) has become a well established technique to elucidate the 3D structures of biological macromolecules. Projection images from thousands macromolecules that are assumed be structurally identical combined into single map representing Coulomb potential macromolecule under study. This article discusses possible caveats along image-processing path and how avoid them obtain reliable structure. Some these problems very known in community. These may referred as...
ABSTRACT Adenovirus is one of the most complex icosahedral, nonenveloped viruses. Even after its structure was solved at near-atomic resolution by both cryo-electron microscopy and X-ray crystallography, location minor coat proteins still a subject debate. The elaborated capsid architecture product correspondingly assembly process, about which many aspects remain unknown. Genome encapsidation involves concerted action five virus proteins, proteolytic processing protease needed to prime...