Article
Multidisciplinary Sciences
Joshua B. R. White, Daniel P. Maskell, Andrew Howe, Martin Harrow, Daniel K. Clare, C. Alistair Siebert, Emma L. Hesketh, Rebecca F. Thompson
Summary: Cryo-electron microscopy is a powerful technique for structure determination of macromolecular complexes through single particle analysis, involving vitrification, specimen screening, data collection, and image processing, with options for user modification and common troubleshooting. Variations on imaging protocols to assist users in efficient operation and imaging when physical access to the microscope is limited are being developed due to remote microscope operation becoming standard.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS
(2021)
Article
Multidisciplinary Sciences
J. J. Erik Maris, Freddy T. Rabouw, Bert M. Weckhuysen, Florian Meirer
Summary: Single-particle tracking is a powerful method for studying the motion of individual molecules and particles. The DiffusionLab software package provides motion analysis tools for challenging data sets, allowing trajectory classification based on motion type and computation of diffusion constants.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
C. O. S. Sorzano, D. Semchonok, S-C Lin, Y-C Lo, J. L. Vilas, A. Jimenez-Moreno, M. Gragera, S. Vacca, D. Maluenda, M. Martinez, E. Ramirez-Aportela, R. Melero, A. Cuervo, J. J. Conesa, P. Conesa, P. Losana, L. Del Cano, J. Jimenez de la Morena, Y. C. Fonseca, R. Sanchez-Garcia, D. Strelak, E. Fernandez-Gimenez, F. de Isidro, D. Herreros, P. L. Kastritis, R. Marabini, B. D. Bruce, J. M. Carazo
Summary: The presence of preferred orientations in SPA by cryoEM poses a challenge for achieving high-resolution structures, but some image processing algorithms are more robust against these detrimental conditions.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Chemistry, Multidisciplinary
Nesrine Aissaoui, Josephine Lai-Kee-Him, Allan Mills, Nathalie Declerck, Zakia Morichaud, Konstantin Brodolin, Sonia Baconnais, Eric Le Cam, Jean Baptiste Charbonnier, Remy Sounier, Sebastien Granier, Virginie Ropars, Patrick Bron, Gaetan Bellot
Summary: Technological breakthroughs in electron microscopy have made it possible to study biological macromolecular complexes with novel challenges, such as sample preparation and heterogeneous macromolecular assemblies. In this study, a V-shaped DNA origami template was used to position proteins, demonstrating a new approach for characterizing mechanosensitive proteins and expanding the range of potential targets for single-particle EM investigation. Validation with RNAP protein showed compatibility with cryo-EM sample preparation.
Article
Biochemistry & Molecular Biology
D. Herreros, J. Kiska, E. Ramirez-Aportela, J. Filipovic, J. M. Carazo, C. O. S. Sorzano
Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Chemistry, Physical
Joel Ribis, Alexia Wu, Raphaelle Guillou, Jean-Christophe Brachet, Cedric Baumier, Aurelie Gentils, Marie Loyer-Prost
Summary: To improve the safety of nuclear power plants, a Cr protective layer is deposited on zirconium alloys to enhance oxidation resistance. However, the risk of Cr desquamation needs to be avoided for safe use of the Cr-coated zirconium alloys.
Article
Engineering, Multidisciplinary
Songjie Li, Mengyuan He, Guanjie Hu, Yun Tian, Chengduo Wang, Ben Jing, Dehai Ping
Summary: This study discusses the coarsening process of second-phase particles in a solid-phase matrix, emphasizing the importance of considering the microstructural evolution of the corresponding matrix phase. Experimental observations reveal that the aggregation of fine carbide particles and the shrinkage of cementite layers are key driving forces behind the coarsening of cementite particles and the development of pearlite structure in carbon steels.
COMPOSITES PART B-ENGINEERING
(2022)
Article
Nanoscience & Nanotechnology
Ivan S. Pavlov, Anna G. Ivanova, Vladimir P. Filonenko, Igor P. Zibrov, Alexei E. Voloshin, Pavel V. Zinin, Alexander L. Vasiliev
Summary: This study investigates the formation of boron carbide superhard particles through a liquid-phase reaction at high pressure and high temperature. The synthesized particles exhibit a rhombic hexecontahedron morphology with twelve five-vertex stars. Electron microscopy and X-ray diffraction were used to analyze the crystal structure of these particles, revealing multiple cycling twinning rather than quasi-crystalline symptoms. The specific shape of the particles is explained by the decrease of surface energy during formation at high pressure and high temperature.
SCRIPTA MATERIALIA
(2023)
Article
Chemistry, Physical
Jin-Hu Dou, Maxx Q. Arguilla, Yi Luo, Jian Li, Weizhe Zhang, Lei Sun, Jenna L. Mancuso, Luming Yang, Tianyang Chen, Lucas R. Parent, Grigorii Skorupskii, Nicole J. Libretto, Chenyue Sun, Min Chieh Yang, Phat Vinh Dip, Edward J. Brignole, Jeffrey T. Miller, Jing Kong, Christopher H. Hendon, Junliang Sun, Mircea Dinca
Summary: Researchers have successfully grown single crystals of 2D metal-organic frameworks up to 200 µm in size by balancing in-plane and out-of-plane interactions, revealing anisotropic transport and a clear correlation between conductivity and the nature of the metal cation in the sheets.
Article
Biochemistry & Molecular Biology
Jeison Mendez, Edgar Garduno, Jose Maria Carazo, Carlos Oscar S. Sorzano
Summary: An accurate assignment of orientations in single-particle analysis is crucial for high-quality 3D map production, yet the problem's complexity often leads to multiple local minima in optimized goal functions. Validation methods are therefore essential to confirm the angular assignment and improve the resolution of 3D maps. This study introduces a graph-signal-processing-based methodology that analyzes correlation landscapes to estimate the reliability of assigned orientations, allowing for the identification of low-reliability images that may negatively impact the final 3D reconstruction.
JOURNAL OF STRUCTURAL BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
J. Garcia Condado, A. Munoz-Barrutia, C. O. S. Sorzano
Summary: Single-Particle Analysis by Cryo-Electron Microscopy is a technique used to determine the 3D structure of biological macromolecules. This article introduces HaPi, a method that automatically determines the handedness of macromolecule electron density maps solved by CryoEM. HaPi utilizes convolutional neural networks and a consensus strategy to determine the hand of the maps.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Qingqing Sheng, Hao Chen, Wenting Mao, Congcong Cui, Shunai Che, Lu Han
Summary: This study reports the synthesis of a porous silica scaffold with a single-diamond-surface structure, revealing its unique framework. The formation of this structure is believed to be induced by structural transition and energetic change due to fluctuations of Gaussian curvature.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Materials Science, Multidisciplinary
E. Yuzuak
Summary: The substantial study discusses the structural and magnetic phase transitions in the Ni46.8Cu2.5Mn36.5Sn14.3 alloy through AC susceptibility and heat capacity measurements, revealing martensitic and magnetic phase transitions. The addition of Cu in the alloy may contribute to discrepancies in the results, possibly due to hybridization or ferromagnetic band splitting. The findings contribute to the existing literature and show similarities with previous research.
MATERIALS RESEARCH BULLETIN
(2021)
Article
Biochemical Research Methods
Vikram Kestens, Tsvetelina Gerganova, Gert Roebben, Andrea Held
Summary: A new certified reference material for size and shape analysis of elongated nanoparticles has been developed by the European Commission's Joint Research Centre. The certified values, traceable to the unit of length in the International System of Units, range from 4 to 6% relative expanded uncertainties and can be used for quality assurance and calibration of electron microscopy methods for nanoparticle size and shape analysis, relevant for EU legislation related to nanomaterials.
ANALYTICAL AND BIOANALYTICAL CHEMISTRY
(2021)
Article
Engineering, Environmental
Jinke Han, Xiaowei Liu, Meng Jiang, Zhaofeng Wang, Minghou Xu
Summary: By utilizing three fixed detectors, this study proposed a method to improve the accuracy of measuring PM mass concentration using laser angular scattering, based on the difference in particle size sensitivity. Correction of PMCS using the asymmetry factor significantly enhanced measurement precision.
JOURNAL OF HAZARDOUS MATERIALS
(2021)
Article
Biochemistry & Molecular Biology
J. Jimenez de la Morena, P. Conesa, Y. C. Fonseca, F. P. de Isidro-Gomez, D. Herreros, E. Fernandez-Gimenez, D. Strelak, E. Moebel, T. O. Buchholz, F. Jug, A. Martinez-Sanchez, M. Harastani, S. Jonic, J. J. Conesa, A. Cuervo, P. Losana, I. Sanchez, M. Iceta, L. del Cano, M. Gragera, R. Melero, G. Sharov, D. Castano-Diez, A. Koster, J. G. Piccirillo, J. L. Vilas, J. Oton, R. Marabini, C. O. S. Sorzano, J. M. Carazo
Summary: This article introduces the extension of Scipion framework, called ScipionTomo, aiming to simplify image processing and analysis in cryogenic electron tomography. Developed by a collaborative multidisciplinary team, it combines the knowledge of Scipion developers with functionalities requested by beta testers and integrates third-party software packages.
JOURNAL OF STRUCTURAL BIOLOGY
(2022)
Article
Biochemical Research Methods
C. O. S. Sorzano, A. Jimenez-Moreno, D. Maluenda, M. Martinez, E. Ramirez-Aportela, J. Krieger, R. Melero, A. Cuervo, J. Conesa, J. Filipovic, P. Conesa, L. del Cano, Y. C. Fonseca, J. Jimenez-de la Morena, P. Losana, R. Sanchez-Garcia, D. Strelak, E. Fernandez-Gimenez, F. P. de Isidro-Gomez, D. Herreros, J. L. Vilas, R. Marabini, J. M. Carazo
Summary: This article discusses potential problems in cryo-electron microscopy and provides solutions. These problems include sample-related issues and algorithm-related issues. Instabilities in estimating key parameters throughout the processing workflow can significantly affect the reliability of the entire process. The article also proposes a new method to detect parameter bias.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Erney Ramirez-Aportela, Jose M. Carazo, Carlos Oscar S. Sorzano
Summary: Single-particle cryo-electron microscopy is a powerful technique for determining the 3D structure of biological molecules. This article explores the use of deepEMhancer, a deep-learning approach, as a regularizer in the refinement process. The combination of deepEMhancer with RELION improves image quality and is particularly useful for studying membrane proteins.
Article
Biochemistry & Molecular Biology
Arkadiusz W. Kulczyk, Carlos Oscar S. Sorzano, Przemyslaw Grela, Marek Tchorzewski, Nilgun E. Tumer, Xiao-Ping Li
Summary: This study uses cryo-EM to determine the structure of Shiga toxin 2a (Stx2a) complexed with the ribosomal P-stalk. The findings reveal the dynamics of the Stx2a-P-stalk interaction and suggest that the binding interface between Stx2a and the P-stalk could be a potential target for drug discovery.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2023)
Article
Chemistry, Multidisciplinary
C. O. S. Sorzano, M. A. Perez-de-la-Cruz Moreno, J. L. Vilas
Summary: This article investigates the absorption models of drugs in the body, including carrier mediated transport and saturable absorption. By studying the exact solutions of different absorption models, the differences between these models can be illustrated.
PHARMACEUTICAL RESEARCH
(2023)
Article
Multidisciplinary Sciences
D. Herreros, R. R. Lederman, J. M. Krieger, A. Jimenez-Moreno, M. Martinez, D. Myska, D. Strelak, J. Filipovic, C. O. S. Sorzano, J. M. Carazo
Summary: The advancements in Cryo-EM Single Particle Analysis play a vital role in understanding the relationship between macromolecular structure and function in biological processes. Traditional approaches have limitations in fully characterizing the conformational landscape due to the small number of accurately reconstructed states. To overcome this, we propose an extension of the Zernike3D method that can extract continuous flexibility information directly from particle datasets. Additionally, the introduced ZART reconstruction algorithm minimizes blurring induced by molecular motions.
NATURE COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
D. Herreros, J. Kiska, E. Ramirez-Aportela, J. Filipovic, J. M. Carazo, C. O. S. Sorzano
Summary: The main purpose of CryoEM Single Particle Analysis is to reconstruct the three-dimensional structure of a macromolecule. ZART is a new Algebraic Reconstruction Technique that can include continuous flexibility information to improve resolution and reduce motion blurring.
JOURNAL OF MOLECULAR BIOLOGY
(2023)
Article
Biochemical Research Methods
Jose-Luis Vilas, Hemant D. Tagare
Summary: This paper introduces two new anisotropy metrics, Fourier shell occupancy (FSO) and the Bingham test (BT), for assessing the quality of cryogenic electron microscopy maps. FSO ranges from 1 to 0, with lower values indicating increasing anisotropy. The threshold FSO = 0.5 corresponds to Fourier shell correlation resolution. BT complements FSO to confirm the presence of anisotropy. FSO and BT enable visualization of resolution anisotropy and are demonstrated using different experimental cryogenic electron microscopy maps.
Article
Chemistry, Analytical
David Strelak, Daniel Marchan, Jose Maria Carazo, Carlos O. S. Sorzano
Summary: This article conducts a comparative analysis of the quality and performance of commonly used software for movie alignment in Cryo-EM. The tested software includes FlexAlign, MotionCor2, Relion MotionCor, Warp, and CryoSPARC. The alignment precision, power spectra density, and performance scaling were compared using generated phantom data and real datasets.
Article
Biochemistry & Molecular Biology
E. Fernandez-Gimenez, M. M. Martinez, R. Marabini, D. Strelak, R. Sanchez-Garcia, J. M. Carazo, C. O. S. Sorzano
Summary: Single particle analysis is widely used in cryo-electron microscopy to obtain the near-atomic structure of biological macromolecules. However, current projection subtraction methods have limitations in fully removing the signal of components that are not of interest. Therefore, we have developed a new and more precise projection subtraction method, which has shown improved performance compared to existing methods.
JOURNAL OF STRUCTURAL BIOLOGY
(2023)