The class B family of G-protein-coupled receptors (GPCRs) has long been a paradigm for peptide hormone recognition and signal transduction. One class B GPCR, the glucagon-like peptide-1 receptor (GLP-1R), has been considered as an anti-diabetes drug target and there are several peptidic drugs available for the treatment of this overwhelming disease. The previously determined structures of inactive GLP-1R in complex with two negative allosteric modulators include ten thermal-stabilizing mutations that were selected from a total of 98 designed mutations. Here we systematically summarize all 98 mutations we have tested and the results suggest that the mutagenesis strategy that strengthens inter-helical hydro­phobic interactions shows the highest success rate. We further investigate four back mutations by thermal-shift assay, crystallization and molecular dynamic simulations, and conclude that mutation I1962.66bF increases thermal stability intrinsically and that mutation S2714.47bA decreases crystal packing entropy extrinsically, while mutations S1932.63bC and M2333.36bC may be dispensable since these two cysteines are not di­sulfide-linked. Our results indicate intrinsic connections between different regions of GPCR transmembrane helices and the current data suggest a general mutagenesis principle for structural determination of GPCRs and other membrane proteins.

A series of Co2−xRuxMnSi (x = 0, 0.25, 0.5, 0.75, 1) Heusler compounds were successfully synthesized. The heat-treatment conditions were crucial to make the materials form a single phase with a Heusler structure. With increasing Ru content, the half-metallic gap, lattice parameters and magnetization are continuously adjustable in a wide range. The Co2−xRuxMnSi (x = 0, 0.25) compounds are rigorous half-metals and show a T3 dependence of resistance at low temperature. The Co2−xRuxMnSi (x = 0.5, 0.75, 1) Heusler compounds are the nearly half-metallic materials and show a semiconductive dependence of resistance at low temperature. The experimental magnetization is consistent with that in theory and follows the Slater–Pauling rule. The Curie temperature is higher than 750 K for all Co2−xRuxMnSi Heusler compounds.

The first ab initio aspherical structure refinement against experimental X-ray structure factors for polypeptides and proteins using a fragmentation approach to break up the protein into residues and solvent, thereby speeding up quantum-crystallographic Hirshfeld atom refinement (HAR) calculations, is described. It it found that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR on the complete unfragmented system when tested on dipeptides, tripeptides and hexapeptides. The largest changes are for the parameters describing H atoms involved in hydrogen-bond interactions, but it is shown that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speed-ups are observed for the larger systems. Using this approach, it is possible to perform a highly parallelized HAR in reasonable times for large systems. The method has been implemented in the TONTO software.

Small-angle scattering of X-rays and neutrons is a routine method for the determination of nanoparticle sizes. The so-called Guinier law represents the low-q approximation for the small-angle scattering curve from an assembly of particles. The Guinier law has originally been derived for nonmagnetic particle-matrix-type systems and it is successfully employed for the estimation of particle sizes in various scientific domains (e.g. soft-matter physics, biology, colloidal chemistry, materials science). An important prerequisite for it to apply is the presence of a discontinuous interface separating particles and matrix. Here, the Guinier law is introduced for the case of magnetic small-angle neutron scattering and its applicability is experimentally demonstrated for the example of nanocrystalline cobalt. It is well known that the magnetic microstructure of nanocrystalline ferromagnets is highly nonuniform on the nanometre length scale and characterized by a spectrum of continuously varying long-wavelength magnetization fluctuations, i.e. these systems do not manifest sharp interfaces in their magnetization profile. The magnetic Guinier radius depends on the applied magnetic field, on the magnetic interactions (exchange, magnetostatics) and on the magnetic anisotropy-field radius, which characterizes the size over which the magnetic anisotropy field is coherently aligned into the same direction. In contrast to the nonmagnetic conventional Guinier law, the magnetic version can be applied to fully dense random-anisotropy-type ferromagnets.

Methods are presented that detect three types of aberrations in single-particle cryo-EM data sets: symmetrical and antisymmetrical optical aberrations and magnification anisotropy. Because these methods only depend on the availability of a preliminary 3D reconstruction from the data, they can be used to correct for these aberrations for any given cryo-EM data set, a posteriori. Using five publicly available data sets, it is shown that considering these aberrations improves the resolution of the 3D reconstruction when these effects are present. The methods are implemented in version 3.1 of the open-source software package RELION.

X-ray imaging of soft materials is often difficult because of the low contrast of the components. This particularly applies to frozen hydrated biological cells where the feature of interest can have a similar density to the surroundings. As a consequence, a high dose is often required to achieve the desired resolution. However, the maximum dose that a specimen can tolerate is limited by radiation damage. Results from 3D coherent diffraction imaging (CDI) of frozen hydrated specimens have given resolutions of ∼80 nm compared with the expected resolution of 10 nm predicted from theoretical considerations for identifying a protein embedded in water. Possible explanations for this include the inapplicability of the dose-fractionation theorem, the difficulty of phase determination, an overall object-size dependence on the required fluence and dose, a low contrast within the biological cell, insufficient exposure, and a variety of practical difficulties such as scattering from surrounding material. A recent article [Villaneuva-Perez et al. (2018), Optica, 5, 450–457] concluded that imaging by Compton scattering gave a large dose advantage compared with CDI because of the object-size dependence for CDI. An object-size dependence would severely limit the applicability of CDI and perhaps related coherence-based methods for structural studies. This article specifically includes the overall object size in the analysis of the fluence and dose requirements for coherent imaging in order to investigate whether there is a dependence on object size. The applicability of the dose-fractionation theorem is also discussed. The analysis is extended to absorption-based imaging and imaging by incoherent scattering (Compton) and fluorescence. This article includes analysis of the dose required for imaging specific low-contrast cellular organelles as well as for protein against water. This article concludes that for both absorption-based and coherent diffraction imaging, the dose-fractionation theorem applies and the required dose is independent of the overall size of the object. For incoherent-imaging methods such as Compton scattering, the required dose depends on the X-ray path length through the specimen. For all three types of imaging, the dependence of fluence and dose on a resolution d goes as 1/d4 when imaging uniform-density voxels. The independence of CDI on object size means that there is no advantage for Compton scattering over coherent-based imaging methods. The most optimistic estimate of achievable resolution is 3 nm for imaging protein molecules in water/ice using lensless imaging methods in the water window. However, the attainable resolution depends on a variety of assumptions including the model for radiation damage as a function of resolution, the efficiency of any phase-retrieval process, the actual contrast of the feature of interest within the cell and the definition of resolution itself. There is insufficient observational information available regarding the most appropriate model for radiation damage in frozen hydrated biological material. It is advocated that, in order to compare theory with experiment, standard methods of reporting results covering parameters such as the feature examined (e.g. which cellular organelle), resolution, contrast, depth of the material (for 2D), estimate of noise and dose should be adopted.

A large amount of hydrogen circulates inside the Earth, which affects the long-term evolution of the planet. The majority of this hydrogen is stored in deep Earth within the crystal structures of dense minerals that are thermodynamically stable at high pressures and temperatures. To understand the reason for their stability under such extreme conditions, the chemical bonding geometry and cation exchange mechanism for including hydrogen were analyzed in a representative structure of such minerals (i.e. phase E of dense hydrous magnesium silicate) by using time-of-flight single-crystal neutron Laue diffraction. Phase E has a layered structure belonging to the space group R3m and a very large hydrogen capacity (up to 18% H2O weight fraction). It is stable at pressures of 13–18 GPa and temperatures of up to at least 1573 K. Deuterated high-quality crystals with the chemical formula Mg2.28Si1.32D2.15O6 were synthesized under the relevant high-pressure and high-temperature conditions. The nuclear density distribution obtained by neutron diffraction indicated that the O—D dipoles were directed towards neighboring O2− ions to form strong interlayer hydrogen bonds. This bonding plays a crucial role in stabilizing hydrogen within the mineral structure under such high-pressure and high-temperature conditions. It is considered that cation exchange occurs among Mg2+, D+ and Si4+ within this structure, making the hydrogen capacity flexible.

The structure of a decagonal quasicrystal in the Zn58Mg40Y2 (at.%) alloy was studied using electron diffraction and atomic resolution Z-contrast imaging techniques. This stable Frank–Kasper Zn–Mg–Y decagonal quasicrystal has an atomic structure which can be modeled with a rhombic/hexagonal tiling decorated with icosahedral units at each vertex. No perfect decagonal clusters were observed in the Zn–Mg–Y decagonal quasicrystal, which differs from the Zn–Mg–Dy decagonal crystal with the same space group P10/mmm. Y atoms occupy the center of `dented decagon' motifs consisting of three fat rhombic and two flattened hexagonal tiles. About 75% of fat rhombic tiles are arranged in groups of five forming star motifs, while the others connect with each other in a `zigzag' configuration. This decagonal quasicrystal has a composition of Zn68.3Mg29.1Y2.6 (at.%) with a valence electron concentration (e/a) of about 2.03, which is in accord with the Hume–Rothery criterion for the formation of the Zn-based quasicrystal phase (e/a = 2.0–2.15).

Two commonly encountered bottlenecks in the structure determination of a protein by X-ray crystallography are screening for conditions that give high-quality crystals and, in the case of novel structures, finding derivatization conditions for experimental phasing. In this study, the phasing molecule 5-amino-2,4,6-triiodoisophthalic acid (I3C) was added to a random microseed matrix screen to generate high-quality crystals derivatized with I3C in a single optimization experiment. I3C, often referred to as the magic triangle, contains an aromatic ring scaffold with three bound I atoms. This approach was applied to efficiently phase the structures of hen egg-white lysozyme and the N-terminal domain of the Orf11 protein from Staphylococcus phage P68 (Orf11 NTD) using SAD phasing. The structure of Orf11 NTD suggests that it may play a role as a virion-associated lysin or endolysin.

For the extraction of the best possible X-ray diffraction data from macromolecular crystals, accurate positioning of the crystals with respect to the X-ray beam is crucial. In addition, information about the shape and internal defects of crystals allows the optimization of data-collection strategies. Here, it is demonstrated that the X-ray beam available on the macromolecular crystallo­graphy beamline P14 at the high-brilliance synchrotron-radiation source PETRA III at DESY, Hamburg, Germany can be used for high-energy phase-contrast microtomography of protein crystals mounted in an optically opaque lipidic cubic phase matrix. Three-dimensional tomograms have been obtained at X-ray doses that are substantially smaller and on time scales that are substantially shorter than those used for diffraction-scanning approaches that display protein crystals at micrometre resolution. Adding a compound refractive lens as an objective to the imaging setup, two-dimensional imaging at sub-micrometre resolution has been achieved. All experiments were performed on a standard macromolecular crystallography beamline and are compatible with standard diffraction data-collection workflows and apparatus. Phase-contrast X-ray imaging of macromolecular crystals could find wide application at existing and upcoming low-emittance synchrotron-radiation sources.

Electron microscopy of macromolecular structures is an approach that is in increasing demand in the field of structural biology. The automation of image acquisition has greatly increased the potential throughput of electron microscopy. Here, the focus is on the possibilities in Scipion to implement flexible and robust image-processing workflows that allow the electron-microscope operator and the user to monitor the quality of image acquisition, assessing very simple acquisition measures or obtaining a first estimate of the initial volume, or the data resolution and heterogeneity, without any need for programming skills. These workflows can implement intelligent automatic decisions and they can warn the user of possible acquisition failures. These concepts are illustrated by analysis of the well known 2.2 Å resolution β-galactosidase data set.

As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.

Apoptosis is a crucial process by which multicellular organisms control tissue growth, removal and inflammation. Disruption of the normal apoptotic function is often observed in cancer, where cell death is avoided by the overexpression of anti-apoptotic proteins of the Bcl-2 (B-cell lymphoma 2) family, including Mcl-1 (myeloid cell leukaemia 1). This makes Mcl-1 a potential target for drug therapy, through which normal apoptosis may be restored by inhibiting the protective function of Mcl-1. Here, the discovery and biophysical properties of an anti-Mcl-1 antibody fragment are described and the utility of both the scFv and Fab are demonstrated in generating an Mcl-1 crystal system amenable to iterative structure-guided drug design.

Fragment-based molecular-replacement methods can solve a macromolecular structure quasi-ab initio. ARCIMBOLDO, using a common secondary-structure or tertiary-structure template or a library of folds, locates these with Phaser and reveals the rest of the structure by density modification and autotracing in SHELXE. The latter stage is challenging when dealing with diffraction data at lower resolution, low solvent content, high β-sheet composition or situations in which the initial fragments represent a low fraction of the total scattering or where their accuracy is low. SEQUENCE SLIDER aims to overcome these complications by extending the initial polyalanine fragment with side chains in a multisolution framework. Its use is illustrated on test cases and previously unknown structures. The selection and order of fragments to be extended follows the decrease in log-likelihood gain (LLG) calculated with Phaser upon the omission of each single fragment. When the starting substructure is derived from a remote homolog, sequence assignment to fragments is restricted by the original alignment. Otherwise, the secondary-structure prediction is matched to that found in fragments and traces. Sequence hypotheses are trialled in a brute-force approach through side-chain building and refinement. Scoring the refined models through their LLG in Phaser may allow discrimination of the correct sequence or filter the best partial structures for further density modification and autotracing. The default limits for the number of models to pursue are hardware dependent. In its most economic implementation, suitable for a single laptop, the main-chain trace is extended as polyserine rather than trialling models with different sequence assignments, which requires a grid or multicore machine. SEQUENCE SLIDER has been instrumental in solving two novel structures: that of MltC from 2.7 Å resolution data and that of a pneumococcal lipoprotein with 638 residues and 35% solvent content.

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide additional insight. ALIXE can be used to exhaustively analyse all partial solutions produced or to complement those already selected for expansion, and also to reduce the number of redundant solutions, which is particularly relevant to the case of coiled coils, or to combine partial solutions from different programs. In each case parallelization and optimization to provide speedup makes its use amenable to typical hardware found in crystallography. ARCIMBOLDO_BORGES and ARCIMBOLDO_SHREDDER now call on ALIXE by default.

The analysis of large structural databases reveals general features and relationships among proteins, providing useful insight. A different approach is required to characterize ubiquitous secondary-structure elements, where flexibility is essential in order to capture small local differences. The ALEPH software is optimized for the analysis and the extraction of small protein folds by relying on their geometry rather than on their sequence. The annotation of the structural variability of a given fold provides valuable information for fragment-based molecular-replacement methods, in which testing alternative model hypotheses can succeed in solving difficult structures when no homology models are available or are successful. ARCIMBOLDO_BORGES combines the use of composite secondary-structure elements as a search model with density modification and tracing to reveal the rest of the structure when both steps are successful. This phasing method relies on general fold libraries describing variations around a given pattern of β-sheets and helices extracted using ALEPH. The program introduces characteristic vectors defined from the main-chain atoms as a way to describe the geometrical properties of the structure. ALEPH encodes structural properties in a graph network, the exploration of which allows secondary-structure annotation, decomposition of a structure into small compact folds, generation of libraries of models representing a variation of a given fold and finally superposition of these folds onto a target structure. These functions are available through a graphical interface designed to interactively show the results of structure manipulation, annotation, fold decomposition, clustering and library generation. ALEPH can produce pictures of the graphs, structures and folds for publication purposes.

Cryo-electron microscopy (cryo-EM) has rapidly expanded with the introduction of direct electron detectors, improved image-processing software and automated image acquisition. Its recent adoption by industry, particularly in structure-based drug design, creates new requirements in terms of reliability, reproducibility and throughput. In 2016, Thermo Fisher Scientific (then FEI) partnered with the Medical Research Council Laboratory of Molecular Biology, the University of Cambridge Nanoscience Centre and five pharmaceutical companies [Astex Pharmaceuticals, AstraZeneca, GSK, Sosei Heptares and Union Chimique Belge (UCB)] to form the Cambridge Pharmaceutical Cryo-EM Consortium to share the risks of exploring cryo-EM for early-stage drug discovery. The Consortium expanded with a second Themo Scientific Krios Cryo-EM at the University of Cambridge Department of Materials Science and Metallurgy. Several Consortium members have set up in-house facilities, and a full service cryo-EM facility with Krios and Glacios has been created with the Electron Bio-Imaging Centre for Industry (eBIC for Industry) at Diamond Light Source (DLS), UK. This paper will cover the lessons learned during the setting up of these facilities, including two Consortium Krios microscopes and preparation laboratories, several Glacios microscopes at Consortium member sites, and a Krios and Glacios at eBIC for Industry, regarding site evaluation and selection for high-resolution cryo-EM microscopes, the installation process, scheduling, the operation and maintenance of the microscopes and preparation laboratories, and image processing.

In processing X-ray diffraction data, the intensities obtained from integration of the diffraction images must be corrected for experimental effects in order to place all intensities on a common scale both within and between data collections. Scaling corrects for effects such as changes in sample illumination, absorption and, to some extent, global radiation damage that cause the measured intensities of symmetry-equivalent observations to differ throughout a data set. This necessarily requires a prior evaluation of the point-group symmetry of the crystal. This paper describes and evaluates the scaling algorithms implemented within the DIALS data-processing package and demonstrates the effectiveness and key features of the implementation on example macromolecular crystallographic rotation data. In particular, the scaling algorithms enable new workflows for the scaling of multi-crystal or multi-sweep data sets, providing the analysis required to support current trends towards collecting data from ever-smaller samples. In addition, the implementation of a free-set validation method is discussed, which allows the quantification of the suitability of scaling-model and algorithm choices.

Different approaches of 2D lens arrays as Shack–Hartmann sensors for hard X-rays are compared. For the first time, a combination of Shack–Hartmann sensors for hard X-rays (SHSX) with a super-resolution imaging approach to perform multi-contrast imaging is demonstrated. A diamond lens is employed as a well known test object. The interleaving approach has great potential to overcome the 2D lens array limitation given by the two-photon polymerization lithography. Finally, the radiation damage induced by continuous exposure of an SHSX prototype with a white beam was studied showing a good performance of several hours. The shape modification and influence in the final image quality are presented.

A lipid droplet (LD) core of a cell consists mainly of neutral lipids, triacylglycerols and/or steryl esters (SEs). The structuration of these lipids inside the core is still under debate. Lipid segregation inside LDs has been observed but is sometimes suggested to be an artefact of LD isolation and chemical fixation. LD imaging in their native state and in unaltered cellular environments appears essential to overcome these possible technical pitfalls. Here, imaging techniques for ultrastructural study of native LDs in cellulo are provided and it is shown that LDs are organized structures. Cryo soft X-ray tomography and deep-ultraviolet (DUV) transmittance imaging are showing a partitioning of SEs at the periphery of the LD core. Furthermore, DUV transmittance and tryptophan/tyrosine auto-fluorescence imaging on living cells are combined to obtain complementary information on cell chemical contents. This multimodal approach paves the way for a new label-free organelle imaging technique in living cells.

Anaerobic ammonium-oxidizing (anammox) bacteria play a key role in the global nitrogen cycle and in nitrogenous wastewater treatment. The anammox bacteria ultrastructure is unique and distinctly different from that of other prokaryotic cells. The morphological structure of an organism is related to its function; however, research on the ultrastructure of intact anammox bacteria is lacking. In this study, in situ three-dimensional nondestructive ultrastructure imaging of a whole anammox cell was performed using synchrotron soft X-ray tomography (SXT) and the total variation-based simultaneous algebraic reconstruction technique (TV-SART). Statistical and quantitative analyses of the intact anammox bacteria were performed. High soft X-ray absorption composition inside anammoxosome was detected and verified to be relevant to iron-binding protein. On this basis, the shape adaptation of the anammox bacteria response to iron was explored.

The laser annealing process for AuNi nanoparticles has been visualized using coherent X-ray diffraction imaging (CXDI). AuNi bimetallic alloy nanoparticles, originally phase separated due to the miscibility gap, transform to metastable mixed alloy particles with rounded surface as they are irradiated by laser pulses. A three-dimensional CXDI shows that the internal part of the AuNi particles is in the mixed phase with preferred compositions at ∼29 at% of Au and ∼90 at% of Au.

A dedicated X-ray imaging detector for 200 keV high-energy X-ray microtomography was developed to realize high-efficiency high-resolution imaging while keeping the field of view wide.

Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

Grazing-incidence small-angle X-ray scattering (GISAXS) coupled with computed tomography (CT) has enabled the visualization of the spatial distribution of nanostructures in thin films. 2D GISAXS images are obtained by scanning along the direction perpendicular to the X-ray beam at each rotation angle. Because the intensities at the q positions contain nanostructural information, the reconstructed CT images individually represent the spatial distributions of this information (e.g. size, shape, surface, characteristic length). These images are reconstructed from the intensities acquired at angular intervals over 180°, but the total measurement time is prolonged. This increase in the radiation dosage can cause damage to the sample. One way to reduce the overall measurement time is to perform a scanning GISAXS measurement along the direction perpendicular to the X-ray beam with a limited interval angle. Using filtered back-projection (FBP), CT images are reconstructed from sinograms with limited interval angles from 3 to 48° (FBP-CT images). However, these images are blurred and have a low image quality. In this study, to optimize the CT image quality, total variation (TV) regularization is introduced to minimize sinogram image noise and artifacts. It is proposed that the TV method can be applied to downsampling of sinograms in order to improve the CT images in comparison with the FBP-CT images.

BornAgain is a free and open-source multi-platform software framework for simulating and fitting X-ray and neutron reflectometry, off-specular scattering, and grazing-incidence small-angle scattering (GISAS). This paper concentrates on GISAS. Support for reflectometry and off-specular scattering has been added more recently, is still under intense development and will be described in a later publication. BornAgain supports neutron polarization and magnetic scattering. Users can define sample and instrument models through Python scripting. A large subset of the functionality is also available through a graphical user interface. This paper describes the software in terms of the realized non-functional and functional requirements. The web site https://www.bornagainproject.org/ provides further documentation.

Two methods for reconstructing intragranular strain fields are developed for scanning three-dimensional X-ray diffraction (3DXRD). The methods are compared with a third approach where voxels are reconstructed independently of their neighbours [Hayashi, Setoyama & Seno (2017). Mater. Sci. Forum, 905, 157–164]. The 3D strain field of a tin grain, located within a sample of approximately 70 grains, is analysed and compared across reconstruction methods. Implicit assumptions of sub-problem independence, made in the independent voxel reconstruction method, are demonstrated to introduce bias and reduce reconstruction accuracy. It is verified that the two proposed methods remedy these problems by taking the spatial properties of the inverse problem into account. Improvements in reconstruction quality achieved by the two proposed methods are further supported by reconstructions using synthetic diffraction data.

BEATRIX, is a new tool for performing data analysis of energy-resolved neutron-imaging experiments involving intense fitting procedures of multi-channel spectra. The use of BEATRIX is illustrated for a test specimen, providing spatially resolved 2D maps for residual strains and Bragg edge heights.

The unique nucleating and phasing capabilities of the crystallophore, Tb-Xo4, are illustrated through challenging cases.

The effects of relative humidity on a tetragonal crystal form of hen egg white lysozyme are studied via in situ laboratory X-ray powder diffraction.

Dynamical X-ray diffraction simulations of very asymmetric diffraction from single crystals of silicon were made to accompany an experimental rocking-curve topography study reported in a seperate paper. Effects on rocking curves were found and are reported. The development of Uragami [(1969), J. Phys. Soc. Jpn, 27, 147–154] for Takagi–Taupin simulations was followed and applied to the case of both convex and concave surface undulations.

Neutron crystal structure analysis of hen egg-white lysozyme hydrogen/deuterium exchanged before crystallization were performed by the joint X-ray and neutron refinement. The differences in hydrogen/deuterium exchange behavior between this study and previous ones were observed.

Described here are instructions for building and using an inexpensive automated microscope (AMi) that has been specifically designed for viewing and imaging the contents of multi-well plates. The X, Y, Z translation stage is controlled through dedicated software (AMiGUI) that is being made freely available. Movements are controlled by an Arduino-based board running grbl, and the graphical user interface and image acquisition are controlled via a Raspberry Pi microcomputer running Python. Images can be written to the Raspberry Pi or to a remote disk. Plates with multiple sample wells at each row/column position are supported, and a script file for automated z-stack depth-of-field enhancement is written along with the images. The graphical user interface and real-time imaging also make it easy to manually inspect and capture images of individual samples.

Immunoglobulin E (IgE) plays a central role in the allergic response, in which cross-linking of allergen by Fc∊RI-bound IgE triggers mast cell and basophil degranulation and the release of inflammatory mediators. The high-affinity interaction between IgE and Fc∊RI is a long-standing target for therapeutic intervention in allergic disease. Omalizumab is a clinically approved anti-IgE monoclonal antibody that binds to free IgE, also with high affinity, preventing its interaction with Fc∊RI. All attempts to crystallize the pre-formed complex between the omalizumab Fab and the Fc region of IgE (IgE-Fc), to understand the structural basis for its mechanism of action, surprisingly failed. Instead, the Fab alone selectively crystallized in different crystal forms, but their structures revealed intermolecular Fab/Fab interactions that were clearly strong enough to disrupt the Fab/IgE-Fc complexes. Some of these interactions were common to other Fab crystal structures. Mutations were therefore designed to disrupt two recurring packing interactions observed in the omalizumab Fab crystal structures without interfering with the ability of the omalizumab Fab to recognize IgE-Fc; this led to the successful crystallization and subsequent structure determination of the Fab/IgE-Fc complex. The mutagenesis strategy adopted to achieve this result is applicable to other intractable Fab/antigen complexes or systems in which Fabs are used as crystallization chaperones.

A new Smithsonian study that examines 10 million years of the evolution of tiny coral-like organisms called cupuladriid bryzoans has revealed that some species of this organism lingered on earth for more than one million years after the event that ultimately caused their extinction: the rising of the Isthmus of Panama.

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In a series of ongoing experiments on Barro Colorado Island in the Panama Canal, Kays and other researchers are using camera traps, radio collars and palm nuts with tracking transmitters attached to them to take a closer look at the nut-hoarding strategies of the agouti.

The post Camera traps & radio collars reveal hoarding strategies of the South American agouti appeared first on Smithsonian Insider.

It’s not an exaggeration to say Hedrick was ecstatic when she peered into her inverted phase contrast microscope and found "Amphisolenia quadrispina" floating in her sample. “For 20 years I’ve been hoping to see something like this,” she says.

The post From the Bay of Bengal, a dinoflagellate makes its way to the Smithsonian appeared first on Smithsonian Insider.

Eleven bats remain in the National Zoo’s colony. The initial challenge the team faced was how to feed the animals. Virginia big-eared bats, which are a subspecies of the Townsend’s big-eared bat (Corynorhinuss townsendii), eat while flying.

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New world megafauna such as mammoths, bison and camelids that were alive at the end of the Pleistocene epoch (some 13,000 years ago) would have produced massive amounts of methane-rich flatulence and belching, thanks to the cellulose-digesting microbes in their guts.

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The Smithsonian Astrophysical Observatory is a major partner in the Atmospheric Imaging Assembly, which is a group of four telescopes on NASA's Solar Dynamics Observatory that photograph the sun in 10 different wavelength bands, or colors, once every 10 seconds.

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Describing a species is a serious undertaking. In the case of T. acutus, Coats and his collaborators documented its microscopic life cycle, conducted extensive DNA analysis and unearthed scientific papers dating back to 1873—when parasitic dinoflagellates were first noted by German scientist Ernst Haeckel.

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Researchers at the Smithsonian Conservation Biology Institute conducted three different kinds of genetics tests and all yielded the same result—the Galapagos seabirds have been genetically different from the magnificent frigatebirds elsewhere for more than half a million years.

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Darwin's bark spider cast giant webs across streams, rivers and lakes, suspending the web’s orb above water and attaching it to plants on each riverbank. Bridgelines of these water-spanning webs have been measured as long as 25 meters.

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The most puzzling characteristic of deep-sea dragonfishes (stromiids) is found where their backbone (or vertebral column) approaches the back of their skull. In the anterior region of the backbone, these […]

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A research team from The Smithsonian Environmental Research Center and Virginia's Old Dominion University will be awarded $110,999 to develop a tool to help seagrass restorers predict which places will be the best for planting seagrasses, the Virginia Sea Grant has announced.

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The new agreement, effective immediately through Dec. 5, 2015, stipulates that the Smithsonian's National Zoological Park will conduct research in the areas of giant panda breeding and cub behavior.

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The male’s fluke design helps it overcome the drag caused by their long tusks, the scientists determined. The female’s fluke design gives them increased speed for diving while foraging.

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Tiny Antarctic marine creatures collected 100 years ago by British Royal Navy explorer Robert Falcon Scott are giving scientists new clues about polar environmental change.

The post Tiny creatures collected 100 years ago confirm accelerating carbon uptake in Antarctic Ocean appeared first on Smithsonian Insider.

A remarkable 5,000-year-old deposit of bones representing an entire herd of Persian gazelles recently discovered in northeastern Syria is firm evidence, scientists say, of an ancient hunting practice largely responsible for the near extinction of gazelles in this region today.

The post Archaeological evidence confirms mass hunting of gazelles 5,000 years ago appeared first on Smithsonian Insider.

The National Aeronautics and Space Administration has made available to the public a new online collection of images that capture the excitement of planetary exploration and the journey to understand the origin and evolution of the solar system.

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