Three-dimensional reconstruction for coherent diffraction patterns obtained by XFEL

The three-dimensional (3D) structural analysis of single particles using an X-ray free-electron laser (XFEL) is a new structural biology technique that enables observations of molecules that are difficult to crystallize, such as flexible biomolecular complexes and living tissue in the state close to physiological conditions. In order to restore the 3D structure from the diffraction patterns obtained by the XFEL, computational algorithms are necessary as the orientation of the incident beam with respect to the sample needs to be estimated. A program package for XFEL single-particle analysis based on the Xmipp software package, that is commonly used for image processing in 3D cryo-electron microscopy, has been developed. The reconstruction program has been tested using diffraction patterns of an aerosol nanoparticle obtained by tomographic coherent X-ray diffraction microscopy.The developed reconstruction method can successfully identify the orientations of coherent X-ray diffraction patterns of an aerosol nanoparticle. ? 2017 Miki Nakano et al.112Ysciescopu

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewedThe authors would like to acknowledge support from the Spanish Ministry of Economy and Competitiveness through grants BIO2013-44647-R and BIO2016-76400-R (AEI/ FEDER, UE), Comunidad Autonoma de Madrid through grant S2017/BMD-3817, Instituto de Salud Carlos III through grants PT13 /0001/0009 and PT17/0009/0010,the European Union (EU) and Horizon 2020 through West-Life (EINFRA- 2015-1, Proposal 675858), CORBEL (INFRADEV-1-2014-1, Proposal 654248), ELIXIR–EXCELERATE (INFRADEV-3- 2015, Proposal 676559), iNEXT (INFRAIA-1-2014-2015, Proposal 653706), EOSCpilot (INFRADEV-04-2016, Proposal 739563) and the National Institutes of Health (P41 GM 103712) (IB

Advances in Xmipp for cryo-electron microscopy: from Xmipp to Scipion

Xmipp is an open-source software package consisting of multiple programs for processing data originating from electron microscopy and electron tomography, designed and managed by the Biocomputing Unit of the Spanish National Center for Biotechnology, although with contributions from many other developers over the world. During its 25 years of existence, Xmipp underwent multiple changes and updates. While there were many publications related to new programs and functionality added to Xmipp, there is no single publication on the Xmipp as a package since 2013. In this article, we give an overview of the changes and new work since 2013, describe technologies and techniques used during the development, and take a peek at the future of the package

Protein structure determination by electron cryo-microscopy.

Transmission electron cryo-microscopy (cryoEM) is a versatile tool in the structural analysis of proteins and biological macromolecular assemblies. In this review, we present a brief survey of the methods used in cryoEM, and their current developments. These latest advances provide exciting opportunities for the three-dimensional structural determination of macromolecular complexes that are either too large or too heterogeneous to be investigated by conventional X-ray crystallography or nuclear magnetic resonance (NMR). The endeavour of understanding the function of protein or macromolecular complex is often helped by combining data from electron microscopy and X-ray crystallography. We will thus provide a brief overview of the computational techniques involved in combining data from different techniques for the interpretation of the EM structure

A novel method for improvement of visualization of power spectra for sorting cryo-electron micrographs and their local areas

International audienceIn a context of automation of cryo-electron microscopy, we developed a novel method for improving visibility of diffraction rings in the power spectra of cryo-electron micrographs of vitreous ice (without carbon film or high concentration of diffracting material). We used these enhanced spectra to semi-automatically detect and remove micrographs and/or local areas introducing errors in the global 3D map (drifted and charged areas) or those unable to increase global signal-to-noise ratio (non-diffracting areas). Our strategy also allows a detection of micrographs/areas with a strong astigmatism. These images should be removed when using algorithms that do not correct astigmatism. Our sorting method is simple and fast since it uses the normalized cross-correlation between enhanced spectra and their copies rotated by 90. It owes its success mainly to the novel pre-processing of power spectra. The improved visibility also allows an easier visual check of accuracy of sorting. We show that our algorithm can even improve the visibility of diffraction rings of cryo-electron micrographs of pure water. Moreover, we show that this visibility depends strongly on ice thickness. This algorithm is implemented in the Xmipp (open-source image processing package) and is freely available for implementation in any other software package

A dynamic personal medical record improvement: pilot study for diabetes self-management in Serbia

In this study, we investigate the potential for improving the control of patient’s health status, by giving them a specific role in the management of their condition. In particular, we study the aspect of patient cooperation in facilitating the self-control of their health status, by combining relevant medical data with environment data, using telecom and IT services. The main question is related to patients’ willingness to keep an updated personal medical record, making it dynamic, and to share the record with other health care institutions and their staff in case of travelling. The hypothesis is that regular feedback to the patient from the dynamic medical record would improve the life style, diet and correct doses of medicines for controlling the health condition. The study was conducted on 62 randomly selected individuals with diabetes, from the medical practice database in Belgrade, Serbia. The results showed that 56% of participants preferred SMS as a mean of communication, followed by phone calls (18%), and email (16%). Also, the study showed that 68% of participants were willing to allow access to their medical record, whilst the rest of participants were worried about data protection issues. The results of this study showed current poor control of patient condition, regardless of the fact that regular advice was given by the family doctor on a three months basis