ElectronStructuresCrystallographyTomographyBiologicalCryoEMExperimental dataMicrographsMethodsMolecularRCSB Protein DataBiochemicalFluorescenceResolutionMacromoleculesCharacterizeCorrectionImagingProcedureResearchersTechniquesAcquisitionBiomedical dataFunctionalComplexesAnalyzePreliminary dataCollectionSetsMutationAnalysisReconstruction
Electron46
- Cryo-electron microscopy structures of the N501Y SARS-CoV-2. (ubc.ca)
- We present a 2.9-Å resolution cryo-electron microscopy (cryo-EM) structure of the complex between the ACE2 receptor and N501Y spike protein ectodomains that shows Y501 inserted into a cavity at the binding interface near Y41 of ACE2. (ubc.ca)
- The EM Data Bank or Electron Microscopy Data Bank (EMDB) collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. (wikipedia.org)
- EMBL Heidelberg hosts a cryo-electron microscopy (cryo-EM) service platform, available for use by external scientists with both single particle and tomography projects. (embl.org)
- The Cryo-Electron Microscopy Service Platform at EMBL Heidelberg is now offering remote service to all interested users, including the COVID-19-related projects (single-particle analysis and cryo-electron tomography). (embl.org)
- The topic of this thesis is the development of new reconstruction methods for cryo-electron microscopy (cryo-EM). (epfl.ch)
- They used a cutting-edge technique called cryo-electron microscopy and combined it with supercomputer analysis. (insidehpc.com)
- Over 1.4 million 'freeze frames' of the human preinitiation complex, or PIC, were obtained with cryo-electron microscopy. (insidehpc.com)
- Among the most exciting of these newly deposited PDB structures are those coming from singleparticle cryo-electron microscopy (EM) and cryo-electron tomography (ET). (iscb.org)
- Recent technical advances in sample preparation, electron optics, direct electron detection, and data processing software have created a perfect storm for the PDB. (iscb.org)
- Scientists used x-ray crystallography and Cryo-electron microscopy to obtain the protein's structure. (isaaa.org)
- Here we report the cryo-electron microscopy structure of human ALDP with nominal resolution at 3.4 Å. (elifesciences.org)
- D ) Cryo-electron microscopy structure of ALDP. (elifesciences.org)
- The scientists used cryo-electron microscopy to validate their technique. (scienceboard.net)
- Another well-studied and practically important example is cryo-electron microscopy, Bresler says. (mit.edu)
- Cryogenic electron microscopy (cryo-EM) has revolutionized biology and life science as a powerful alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination. (ucla.edu)
- Here, an automatic procedure requiring only sequence information and crystallo-graphic data is presented that uses AlphaFold predictions to produce an electron-density map and a structural model. (iucr.org)
- Within the TEM field, cryo-electron microscopy (cryo-EM) allows visualization of intact molecules/complexes under near native conditions. (utmb.edu)
- Further, the development of cryo-electron microscopy tomographic techniques (cryo-ET) has made it possible to image structurally heterogeneous objects such as cells and organelles to nanometer resolution. (utmb.edu)
- This course is for the student to develop an understanding of the principles of electron microscopy as applied to the study of biological macromolecules and tissues. (utmb.edu)
- Knowledge of these principles will provide a foundation for gaining practical experience and training in biological transmission electron microscopy. (utmb.edu)
- In transmission electron microscopy (TEM), a high-energy electron beam is used to examine the structures of molecules, down to the level of atomic details. (case.edu)
- Cryogenic Electron Microscopy (Cryo-EM) is an approach that allows the observation of hydrated biological specimens in their native environment at cryogenic temperatures in TEM. (case.edu)
- The FEI Talos Arctica is a 200keV high- performance automated transmission electron microscope designed specifically for cryo-electron microscopy. (edu.au)
- The cryo-electron microscopy structure reveals domain organization and structural details of the Nf1 exon 23a splicing 3 isoform 2 in a closed, self-inhibited, Zn-stabilized state and an open state. (nature.com)
- Our high-resolution single particle cryo-electron microscopy (EM) structures reveal the domain organization and structural details of the full-length Nf1-23a isoform 2 dimer (Fig. 1a-c , Extended Data Figs. 1 - 3 ). (nature.com)
- NCCAT is housed at the Simons Electron Microscopy Center at the New York Structural Biology Center in New York City, New York. (cryoemcenters.org)
- This course covers the fundamental principles underlying cryo-electron microscopy starting with the basic anatomy of electron microscopes, an introduction to Fourier transforms, and the principles of image formation. (freevideolectures.com)
- In the study, Grotjahn's team put together a computational toolkit to process imaging data from a microscopy technique called cryo-electron tomography (cryo-ET)-which essentially images biological samples in three dimensions, using electrons instead of light. (scripps.edu)
- Furthermore, our cryo-electron microscopy (cryo-EM) structure of the 50S·ObgE·GMPPNP complex indicates that the evolutionarily conserved N-terminal domain (NTD) of ObgE is a tRNA structural mimic, with specific interactions with peptidyl-transferase center, displaying a marked resemblance to Class I release factors. (rcsb.org)
- We use state-of-the-art facilities in X-ray crystallography, NMR spectroscopy, mass spectrometry, cryo-electron microscopy, imaging, biophysical and biochemical analysis, molecular and cell biology. (ucl.ac.uk)
- She continued her training at the University of Texas Health Science Center in Houston, where she received a Master of Science and PhD degree in Health Informatics for her work in biomolecular structural data integration of cryo-electron micrographs and X-ray crystallography models. (stanford.edu)
- Over the last several years, he has successfully used techniques developed in these areas to solve problems in electronic structure calculations, nuclear structure calculations, cavity design for accelerator models, single-particle analysis for cryo-electron microscopy, single molecular diffractive imaging, phase retrieval, ptychography, etc. (lbl.gov)
- The FEI Titan Krios is a 300keV ultra-high- performance, automated, three condenser transmission electron microscope is designed specifically for cryo electron microscopy and is capable of delivering 1.8Angstrom atomic resolution structures. (edu.au)
- Correction of electron beam-induced sample motion is one of the major factors contributing to the recent resolution breakthroughs in cryo-electron microscopy. (biorxiv.org)
- Previous electron tomography data of Arp2/3 complexes bound to actin filaments in a test-tube environment was too imprecise, making it impossible to unambiguously tell where the individual elements of the complex must be located,' explained Florian Fäßler, a postdoctoral researcher in the lab of IST Austria professor Florian Schur. (labroots.com)
- The researchers used powerful cryo-electron microscopy tools to rapidly freeze the cells in place, then image them from many angles. (labroots.com)
- We shall achieve these results using cryo-electron microscopy. (ukri.org)
- Surface plasmon resonance, x-ray crystallography, and cryo-electron microscopy determined binding kinetics and structural data. (bvsalud.org)
- Cryo-electron microscopy reveals a planar and roughly symmetrical complex formed by REGN5713/14/15 bound to Bet v 1. (bvsalud.org)
- In addition to low-resolution models of the intact T3SS core from cryo-electron microscopy, several high-resolution structures of monomeric T3SS components have been determined. (lu.se)
- Here we report the reconstruction using single-particle cryo-electron microscopy of the complex between subunits BchD and BchI of Rhodobacter capsulatus Mg-chelatase in the presence of ADP, the nonhydrolyzable ATP analog AMPPNP, and ATP at 7.5 A, 14 A, and 13 A resolution, respectively. (lu.se)
- For a subset of interactions essential for the virus life cycle, the authors determined the cryo-electron microscopy structures and mined patient data to understand how targeting host factors may be relevant to clinical outcomes. (cdc.gov)
- In the last years there has been an explosion of the cryo electron microscopy single particle technique to get high-resolution structures of protein complexes. (lu.se)
- Facilities for 3D optical imaging and electron microscopy at Materials Engineering with instruments including E-SEM FEI Quanta 200 MKII with analytical system Pegasus (EBSD+EDS) from EDAX and optical microscope Keyence VHX-6000. (lu.se)
- Electron microscopy in which the ELECTRONS or their reaction products that pass down through the specimen are imaged below the plane of the specimen. (bvsalud.org)
Structures6
- The next wave of exciting new structures will come from so-called integrative/hybrid methods, which typically combine cryo-EM or -ET data with data from chemical cross-linking, fluorescence resonance energy transfer, and homology models to produce multi-scale structures of even larger biomolecular machines. (iscb.org)
- This procedure was applied to X-ray data for 215 structures released by the Protein Data Bank in a recent six-month period. (iucr.org)
- With improvements of data acquisition hardware and image processing software, it is now possible to determine three-dimensional structures of structurally homogeneous biological macromolecules to near-atomic resolution. (utmb.edu)
- The laboratory will offer hands-on experience in recording signals from single neurons, examining neural structures, and analysis of whole-brain functional brain imaging data. (princeton.edu)
- Previous work in this area has been on modeling the assembly structure of the type III secretion system and prediction of the high-resolution structures of homo-oligomeric proteins using limited experimental data from Nuclear Magnetic Resonance (NMR) in order to speed up the process of structure determination. (lu.se)
- In fact, getting a nice sample for optimal imaging and processing the data to obtain correct and most informative structures, still requires specialists' skills. (lu.se)
Crystallography1
- Cryoelectron microscopy and x-ray crystallography analyses of NoV VLPs identified the shell (S) and protruding domains (subdomains P1-1, P1-2, and P2) ( 18 ). (cdc.gov)
Tomography1
- The Falcon 3 direct detection device's counting mode and drift correction produce high signal-to-noise and high-resolution images for tomography and single-particle data. (edu.au)
Biological5
- or use data science methods and tools to deduce information about biological systems. (nih.gov)
- Biostatistics areas of interest include development of advanced statistical techniques and methodologies for design of biological experiments, collection and analysis of the data from those experiments and interpretation of, and inference from, the results. (nih.gov)
- Of interest are development of computational and mathematical algorithms and tools, modeling techniques and approaches for understanding the complexity of biological systems, and utilization of big datasets and data science methods for model construction. (nih.gov)
- Prior to joining Stanford, Dr. Rusu was a Lead Engineer and Medical Image Analysis Scientist at GE Global Research Niskayuna NY where she was involved in the development of analytic methods to characterize biological samples in microscopy images and pathologic conditions in MRI or CT. (stanford.edu)
- Our goal is to use high-resolution structural modeling techniques guided by constraints taken from lower resolution experimental data to generate structural models of important biological protein assemblies for which high resolution structural determination is unfeasible. (lu.se)
CryoEM3
- Under the NIH Unified Data Resource for CryoEM, the Research Collaboration for Structural Biology (RCSB) also acts as a deposition, data processing and distribution center for EMDB data, while the National Center for Macromolecular Imaging (NCMI) is a collaborative partner in providing services and tools concerning the EMDB. (wikipedia.org)
- We provide services and training in all aspects of cryoEM sample preparation, screening and high-resolution data collection. (unc.edu)
- The CryoEM centers provide access to instrumentation for data collection (primarily, but not exclusively, high-end microscopes) as well as focused training programs to help labs become independent cryoEM practitioners. (cryoemcenters.org)
Experimental data1
- Resarchers developed methods to determine the CTF from experimental data and to obtain a CTF-corrected 3D reconstruction. (harvard.edu)
Micrographs1
- Zhu J, Penczek PA, Schröder R, Frank J. Three-dimensional reconstruction with contrast transfer function correction from energy-filtered cryoelectron micrographs: procedure and application to the 70S Escherichia coli ribosome. (harvard.edu)
Methods4
- We are pioneering both multi-disciplinary approaches aimed to bridge across the scales of biology, and methods to integrate disparate data across the disciplines. (ucl.ac.uk)
- The PIMed Laboratory has a multi-disciplinary direction and focuses on developing analytic methods for biomedical data integration, with a particular interest in radiology-pathology fusion to facilitate radiology image labeling. (stanford.edu)
- Dr. Mirabela Rusu focuses on developing analytic methods for biomedical data integration, with a particular interest in radiology-pathology fusion. (stanford.edu)
- Major efforts are also devoted to the inventions of new methods for sample preparation and for automation of both cryo-EM data acquisition and image processing. (lu.se)
Molecular3
- Discovered 25 years ago, scientists have finally gathered its structural data that is crucial in explaining how the protein works to govern plant protection on a molecular level. (isaaa.org)
- while data is stored in Richland, Washington at PNNL in the Environmental Molecular Sciences Laboratory. (cryoemcenters.org)
- probes, molecular reporters and fluorescent indicators for structural or functional imaging or microscopy/nanoscopy. (nih.gov)
RCSB Protein Data1
- Credit: RCSB Protein Data Bank. (nih.gov)
Biochemical1
- The structural data rationalizes previous biochemical and genetic evidence regarding the initiation mechanism of the HCV and other related IRESs. (nih.gov)
Fluorescence1
- Cellomics Platform at MultiParkThe Cellomics ArrayScan VTI HCS Reader enables automated acquisition, visualization and quantification of a large number of images, with an automated fluorescence and brightfield microscopy allowing extraction of quantitative data from intensity and area measurement in high-throughput format. (lu.se)
Resolution6
- We provide researchers from Europe and beyond with a synergistic portfolio of imaging services including cryo-EM, super-resolution and intravital microscopy to enable new ground-breaking research that crosses the scales of biology. (embl.org)
- Advances in algorithms for data and image processing and in hardware for image acquisition have made cryo-EM a routine method to determine the 3D structure of suitable macromolecules with identical or similar conformations at near-atomic resolution. (ucla.edu)
- Around 20 % of the sample are ready for high resolution data collection with already prepared grids that have been pre-screened on Glacios microscopes. (eudat.eu)
- Yet, for these systems ample non-structural data is typically available providing a wealth of lower resolution information. (lu.se)
- These low and high-resolution data sets originates from T3SSes from different species and can also be collected from other structurally homologous systems, such as the flagella. (lu.se)
- Capable of two-color STED microscopy with lateral resolution ~50nm with excitation wavelengths 561nm and 640nm. (lu.se)
Macromolecules1
- Cryoelectron microscopy provides the means of studying macromolecules in their native state. (harvard.edu)
Characterize1
- The field of regulatory genomics has recently witnessed significantly increased interest in the three-dimensional structure of DNA in the nucleus, catalyzed by the availability of chromosome conformation capture (3C) data sets that characterize the 3D organization of chromatin at a genome-wide scale. (iscb.org)
Correction1
- The CTF correction and 3D reconstruction accomplished in one step made it easy to combine different defocus data sets and decrease the error accumulation in the computation. (harvard.edu)
Imaging2
- Experts are on hand to help and support researchers during microscope handling, data acquisition and optimisation of imaging conditions. (embl.org)
- During her postdoctoral training at Rutgers and Case Western Reserve University, Dr. Rusu has developed computational tools for the integration and interpretation of multi-modal medical imaging data and focused on studying prostate and lung cancers. (stanford.edu)
Procedure1
- By contrast, the central philosophy of data-driven approaches is to let the reconstruction algorithm be guided by the measured data through some learning procedure. (epfl.ch)
Researchers3
- The conference brings together leading experts and young researchers to share their expertise and discuss current trends as well as newly discovered findings in the field of microscopy. (chemistryviews.org)
- Using the data cloud for scientific discovery will allow researchers to achieve breakthroughs faster than ever before. (scienceboard.net)
- Recently, his biggest focus has been trying to unveil fundamental phenomena that are broadly responsible for determining the computational complexity of statistics problems - and finding the "sweet spot" where available data and computation resources enable researchers to effectively solve a problem. (mit.edu)
Techniques2
- Guy Bresler, a newly-tenured associate professor in the Department of Electrical Engineering and Computer Science, studies computational complexity and researches techniques to learn models from data. (mit.edu)
- The scope of studies ranges from those focused-on sequencing, mass spectrometry, bioimaging and other high-through-put techniques in data to medicine, pharmacology, and populational studies. (nih.gov)
Acquisition1
- Both microscopes are equipped with an automatic sample loading system and configured for automatic data acquisition. (embl.org)
Biomedical data1
- Dr. Rusu is an Assistant Professor, in the Department of Radiology, and, by courtesy, Department of Urology and Biomedical Data Science, at Stanford University, where she leads the Personalized Integrative Medicine Laboratory (PIMed). (stanford.edu)
Functional1
- These structural data might define ObgE as a specialized translation factor related to stress responses, and provide a framework towards future elucidation of functional interplay between ObgE and ribosome-associated (p)ppGpp regulators. (rcsb.org)
Complexes1
- This generated enough data to reconstruct three-dimensional images of 10,000 different, active Arp2/3 complexes. (labroots.com)
Analyze1
- With the emergence of these new data types, there is an increasingly growing demand for computational tools that can systematically analyze these data. (iscb.org)
Preliminary data2
- Preliminary data and grids can be used to apply for General Access. (cryoemcenters.org)
- To demonstrate we can produce the deliverables stated in the proposal we have collected preliminary data on the inner-membrane assembly platform and produced a preliminary structure of the ATPase. (ukri.org)
Collection1
- The multi-GPU accelerated program, MotionCor2, is sufficiently fast to keep up with automated data collection. (biorxiv.org)
Sets2
- We were able to process the large data sets obtained by the microscope on the cloud in a fraction of the time and at much lower cost than previously thought possible" said Christopher Woods, IT specialist at the University of Bristol. (scienceboard.net)
- The result is an exceptionally robust strategy that can work on a wide range of data sets, including those very close to focus or with very short integration times, obviating the need for particle polishing. (biorxiv.org)
Mutation1
- Other sources of experimental information include X-ray diffraction, biotinylation, sequence mutation and deletion, solution binding and chemical cross-linking data. (lu.se)
Analysis2
- These tools range from data processing issues (e.g. mapping and normalization) to data analysis issues, such as predicting chromosomal organizational units (e.g. (iscb.org)
- His core expertise is in numerical linear algebra, optimization, large-scale data analysis, and high performance computing. (lbl.gov)
Reconstruction3
- In this thesis, we investigated two reconstruction paradigms: model-based and data-driven. (epfl.ch)
- Finally, we developed a completely new paradigm for SPA reconstruction that leverages the remarkable capability of deep neural networks to capture data distribution. (epfl.ch)
- The image data for the 3D reconstruction were acquired exclusively from a CCD camera. (rcsb.org)