Researchers develop an MS shotgun proteomic method to tackle small numbers of cancer cells in blood.

If you are wondering when to apply which design methods, this mind map may help you.

Small-animal physiology studies are typically complicated, but the level of complexity is greatly increased when performing live-animal X-ray imaging studies at synchrotron and compact light sources. This group has extensive experience in these types of studies at the SPring-8 and Australian synchrotrons, as well as the Munich Compact Light Source. These experimental settings produce unique challenges. Experiments are always performed in an isolated radiation enclosure not specifically designed for live-animal imaging. This requires equipment adapted to physiological monitoring and test-substance delivery, as well as shuttering to reduce the radiation dose. Experiment designs must also take into account the fixed location, size and orientation of the X-ray beam. This article describes the techniques developed to overcome the challenges involved in respiratory X-ray imaging of live animals at synchrotrons, now enabling increasingly sophisticated imaging protocols.

Rietveld/MEM analysis applied to synchrotron powder X-ray diffraction data of dehydrated CHA zeolites with catalytically active Cu2+ reveals Cu2+ in both the six- and eight-membered rings in the CHA framework, providing the first complete structural model that accounts for all Cu2+. Density functional theory calculations are used to corroborate the experimental structure and to discuss the Cu2+ coordination in terms of the Al distribution in the framework.

From solutions of prehnitene and the ternary halides (SnCl)[MCl4] (M = Al, Ga) in chloro­benzene, the new cationic SnII–π-arene complexes catena-poly[[chlorido­aluminate(III)]-tri-μ-chlorido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetra­meth­yl­benzene)­tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-3:4κ4Cl-[chlorido­aluminate(III)]-μ-chlorido-4:1'κ2Cl], [Al2Sn2Cl10(C10H14)2]n, (1) and catena-poly[[chlorido­gallate(III)]-tri-μ-chlor­ido-4':1κ2Cl,1:2κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-2:3κ4Cl-[(η6-1,2,3,4-tetra­methyl­benzene)­tin(II)]-di-μ-chlorido-3:4κ4Cl-[chlor­ido­gallate(III)]-μ-chlorido-4:1'κ2Cl], [Ga2Sn2Cl10(C10H14)2]n, (2), were isolated. In these first main-group metal–prehnitene complexes, the distorted η6 arene π-bonding to the tin atoms of the Sn2Cl22+ moieties in the centre of [{1,2,3,4-(CH3)4C6H2}2Sn2Cl2][MCl4]2 repeating units (site symmetry overline{1}) is characterized by: (i) a significant ring slippage of ca 0.4 Å indicated by the dispersion of Sn—C distances [1: 2.881 (2)–3.216 (2) Å; 2: 2.891 (3)–3.214 (3) Å]; (ii) the non-methyl-substituted arene C atoms positioned closest to the SnII central atom; (iii) a pronounced tilt of the plane of the arene ligand against the plane of the central (Sn2Cl2)2+ four-membered ring species [1: 15.59 (11)°, 2: 15.69 (9)°]; (iv) metal–arene bonding of medium strength as illustrated by application of the bond-valence method in an indirect manner, defining the π-arene bonding inter­action of the SnII central atoms as s(SnII—arene) = 2 − Σs(SnII—Cl), that gives s(SnII—arene) = 0.37 and 0.38 valence units for the aluminate and the gallate, respectively, indicating that comparatively strong main-group metal–arene bonding is present and in line with the expectation that [AlCl4]− is the slightly weaker coordinating anion as compared to [GaCl4]−.

The title compound, C22H22O2S2, 1, represents an example of an ortho-vanillin-based functionalized di­thio­ether, which could be useful as a potential chelating ligand or bridging ligand for coordination chemistry. This di­thio­acetal 1 crystallizes in the ortho­rhom­bic space group Pbca. The phenyl rings of the benzyl groups and that of the vanillin unit form dihedral angles of 35.38 (6) and 79.77 (6)°, respectively. The crystal structure, recorded at 100 K, displays both weak intra­molecular O—H⋯O and inter­molecular O—H⋯S hydrogen bonding.

Exact and approximate mathematical formulas of equatorial aberration for powder diffraction data collected with an Si strip X-ray detector in continuous-scan integration mode are presented. An approximate formula is applied to treat the experimental data measured with a commercial powder diffractometer.

In this article, a method is presented to estimate a new local quality measure for 3D cryoEM maps that adopts the form of a `local resolution' type of information. The algorithm (DeepRes) is based on deep-learning 3D feature detection. DeepRes is fully automatic and parameter-free, and avoids the issues of most current methods, such as their insensitivity to enhancements owing to B-factor sharpening (unless the 3D mask is changed), among others, which is an issue that has been virtually neglected in the cryoEM field until now. In this way, DeepRes can be applied to any map, detecting subtle changes in local quality after applying enhancement processes such as isotropic filters or substantially more complex procedures, such as model-based local sharpening, non-model-based methods or denoising, that may be very difficult to follow using current methods. It performs as a human observer expects. The comparison with traditional local resolution indicators is also addressed.

Innovative new crystallographic methods are facilitating structural studies from ever smaller crystals of biological macromolecules. In particular, serial X-ray crystallography and microcrystal electron diffraction (MicroED) have emerged as useful methods for obtaining structural information from crystals on the nanometre to micrometre scale. Despite the utility of these methods, their implementation can often be difficult, as they present many challenges that are not encountered in traditional macromolecular crystallography experiments. Here, XFEL serial crystallography experiments and MicroED experiments using batch-grown microcrystals of the enzyme cyclophilin A are described. The results provide a roadmap for researchers hoping to design macromolecular microcrystallography experiments, and they highlight the strengths and weaknesses of the two methods. Specifically, we focus on how the different physical conditions imposed by the sample-preparation and delivery methods required for each type of experiment affect the crystal structure of the enzyme.

Developing methods to determine high-resolution structures from micrometre- or even submicrometre-sized protein crystals has become increasingly important in recent years. This applies to both large protein complexes and membrane proteins, where protein production and the subsequent growth of large homogeneous crystals is often challenging, and to samples which yield only micro- or nanocrystals such as amyloid or viral polyhedrin proteins. The versatile macromolecular crystallography microfocus (VMXm) beamline at Diamond Light Source specializes in X-ray diffraction measurements from micro- and nanocrystals. Because of the possibility of measuring data from crystalline samples that approach the resolution limit of visible-light microscopy, the beamline design includes a scanning electron microscope (SEM) to visualize, locate and accurately centre crystals for X-ray diffraction experiments. To ensure that scanning electron microscopy is an appropriate method for sample visualization, tests were carried out to assess the effect of SEM radiation on diffraction quality. Cytoplasmic polyhedrosis virus polyhedrin protein crystals cryocooled on electron-microscopy grids were exposed to SEM radiation before X-ray diffraction data were collected. After processing the data with DIALS, no statistically significant difference in data quality was found between datasets collected from crystals exposed and not exposed to SEM radiation. This study supports the use of an SEM as a tool for the visualization of protein crystals and as an integrated visualization tool on the VMXm beamline.

Recent developments have resulted in electron cryo-microscopy (cryo-EM) becoming a useful tool for the structure determination of biological macromolecules. For samples containing inherent flexibility, heterogeneity or preferred orientation, the collection of extensive cryo-EM data using several conditions and microscopes is often required. In such a scenario, merging cryo-EM data sets is advantageous because it allows improved three-dimensional reconstructions to be obtained. Since data sets are not always collected with the same pixel size, merging data can be challenging. Here, two methods to combine cryo-EM data are described. Both involve the calculation of a rescaling factor from independent data sets. The effects of errors in the scaling factor on the results of data merging are also estimated. The methods described here provide a guideline for cryo-EM users who wish to combine data sets from the same type of microscope and detector.

The room-temperature experiment has been revisited for macromolecular crystallography. Despite being limited by radiation damage, such experiments reveal structural differences depending on temperature, and it is expected that they will be able to probe structures that are physiologically alive. For such experiments, the humid-air and glue-coating (HAG) method for humidity-controlled experiments is proposed. The HAG method improves the stability of most crystals in capillary-free experiments and is applicable at both cryogenic and ambient temperatures. To expand the thermal versatility of the HAG method, a new humidifier and a protein-crystal-handling workbench have been developed. The devices provide temperatures down to 4°C and successfully maintain growth at that temperature of bovine cytochrome c oxidase crystals, which are highly sensitive to temperature variation. Hence, the humidifier and protein-crystal-handling workbench have proved useful for temperature-sensitive samples and will help reveal temperature-dependent variations in protein structures.

Nanoporous anodic aluminium oxide (AAO) membranes are promising host systems for confinement of condensed matter. Characterizing their structure and composition is thus of primary importance for studying the behavior of confined objects. Here a novel methodology to extract quantitative information on the structure and composition of well defined AAO membranes by combining small-angle neutron scattering (SANS) measurements and scanning electron microscopy (SEM) imaging is reported. In particular, (i) information about the pore hexagonal arrangement is extracted from SEM analysis, (ii) the best SANS experimental conditions to perform reliable measurements are determined and (iii) a detailed fitting method is proposed, in which the probed length in the fitting model is a critical parameter related to the longitudinal pore ordering. Finally, to validate this strategy, it is applied to characterize AAOs prepared under different conditions and it is shown that the experimental SANS data can be fully reproduced by a core/shell model, indicating the existence of a contaminated shell. This original approach, based on a detailed and complete description of the SANS data, can be applied to a variety of confining media and will allow the further investigation of condensed matter under confinement.

Clays and soils produce strong small-angle X-ray scattering (SAXS) because they contain large numbers of nanoparticles, namely allophane and ferrihydrite. These nanoparticles are amorphous and have approximately spherical shape with a size of around 3–10 nm. The weight ratios of these nanoparticles will affect the properties of the clays and soils. However, the nanoparticles in clays and soils are not generally quantified and are sometimes ignored because there is no standard method to quantify them. This paper describes a method to quantify nanoparticles in clays and soils with SAXS. This is achieved by deriving normalized SAXS intensities from unit weight of the sample, which are not affected by absorption. By integrating the normalized SAXS intensities over the reciprocal space, one obtains a value that is proportional to the weight ratio of the nanoparticles, proportional to the square of the difference of density between the nanoparticles and the liquid surrounding the nanoparticles, and inversely proportional to the density of the nanoparticles. If the density of the nanoparticles is known, the weight ratio of the nanoparticles can be calculated from the SAXS intensities. The density of nanoparticles was estimated from the chemical composition of the sample. Nanoparticles in colloidal silica, silica gels, mixtures of silica gel and α-aluminium oxide, and synthetic clays have been quantified with the integral SAXS method. The results show that the errors of the weight ratios of nanoparticles are around 25% of the weight ratio. It is also shown that some natural clays contain large fractions of nanoparticles; montmorillonite clay from the Mikawa deposit, pyrophillite clay from the Shokozan deposit and kaolinite clay from the Kanpaku deposit contain 25 (7), 10 (2) and 19 (5) wt% nanoparticles, respectively, where errors are shown in parentheses.

A new temperature-controllable humidifier for X-ray diffraction has been developed. It is shown that the humidifier can successfully maintain protein crystal growth at a temperature lower than room temperature.

The sin2ψ and cosα methods are compared via diffracting-grain identification from electron backscatter diffraction maps. Artificial textures created by the X-ray diffraction measurements are plotted and X-ray elastic constants of the diffracting-grain sets are computed.

Exact and approximate formulas for equatorial aberration of a continuous-scan Si strip detector are compared.

The diffraction response of a single crystal to electric field measured by X-ray diffraction by angles close to π. Such schemes allow one to determine with high (~ 10–5–10–6) accuracy the relative changes in the lattice constant.

The title compound, C11H11NO5, has a nearly planar geometry. In the crystal, the molecules are assembled into chains parallel to the [overline{1}11] direction by O—H...O and C—H...O hydrogen bonds.

New research by astrophysicist David Kipping has revealed that in some special cases, a star can be weighed directly. Such a star must have a planet orbiting it with a moon orbiting the planet.

The post Harvard-Smithsonian astrophysicist discovers new method to weigh some distant stars appeared first on Smithsonian Insider.

The most widely used methods for calculating species extinction rates are "fundamentally flawed" and overestimate extinction rates by as much as 160 percent, life scientists report May 19 in the journal Nature.

The post Methods for calculating species extinction rates overestimate extinction, says Smithsonian scientist appeared first on Smithsonian Insider.

Detecting alien worlds presents a significant challenge since they are small, faint, and close to their stars. The two most prolific techniques for finding exoplanets […]

The post New method of finding planets scores first discovery appeared first on Smithsonian Insider.

How did the universe begin? And what came before the Big Bang? Cosmologists have asked these questions ever since discovering that our universe is expanding. […]

The post Theorists Propose a New Method to Probe the Beginning of the Universe appeared first on Smithsonian Insider.

Oysters are keystone organisms in estuaries around the world, influencing water quality, constructing habitat and providing food for humans and wildlife. Yet their populations in […]

The post Ancient Native-American methods may be key to sustainable oyster harvests appeared first on Smithsonian Insider.

Structural investigations of amorphous and nanocrystalline phases forming in solution are historically challenging. Few methods are capable of in situ atomic structural analysis and rigorous control of the system. A mixed-flow reactor (MFR) is used for total X-ray scattering experiments to examine the short- and long-range structure of phases in situ with pair distribution function (PDF) analysis. The adaptable experimental setup enables data collection for a range of different system chemistries, initial supersaturations and residence times. The age of the sample during analysis is controlled by adjusting the flow rate. Faster rates allow for younger samples to be examined, but if flow is too fast not enough data are acquired to average out excess signal noise. Slower flow rates form older samples, but at very slow speeds particles settle and block flow, clogging the system. Proper background collection and subtraction is critical for data optimization. Overall, this MFR method is an ideal scheme for analyzing the in situ structures of phases that form during crystal growth in solution. As a proof of concept, high-resolution total X-ray scattering data of amorphous and crystalline calcium phosphates and amorphous calcium carbonate were collected for PDF analysis.

Crystal structure identification of thin organic films entails a number of technical and methodological challenges. In particular, if molecular crystals are epitaxially grown on single-crystalline substrates a complex scenario of multiple preferred orientations of the adsorbate, several symmetry-related in-plane alignments and the occurrence of unknown polymorphs is frequently observed. In theory, the parameters of the reduced unit cell and its orientation can simply be obtained from the matrix of three linearly independent reciprocal-space vectors. However, if the sample exhibits unit cells in various orientations and/or with different lattice parameters, it is necessary to assign all experimentally obtained reflections to their associated individual origin. In the present work, an effective algorithm is described to accomplish this task in order to determine the unit-cell parameters of complex systems comprising different orientations and polymorphs. This method is applied to a polycrystalline thin film of the conjugated organic material 6,13-pentacene­quinone (PQ) epitaxially grown on an Ag(111) surface. All reciprocal vectors can be allocated to unit cells of the same lattice constants but grown in various orientations [sixfold rotational symmetry for the contact planes (102) and (102)]. The as-determined unit cell is identical to that reported in a previous study determined for a fibre-textured PQ film. Preliminary results further indicate that the algorithm is especially effective in analysing epitaxially grown crystallites not only for various orientations, but also if different polymorphs are present in the film.

Recent developments of two-color operation modes at X-ray free-electron laser facilities provide new research opportunities, such as X-ray pump/X-ray probe experiments and multiple-wavelength anomalous dispersion phasing methods. However, most existing indexing methods were developed for indexing diffraction data from monochromatic X-ray beams. Here, a new algorithm is presented for indexing two-color diffraction data, as an extension of the sparse-pattern indexing algorithm SPIND, which has been demonstrated to be capable of indexing diffraction patterns with as few as five peaks. The principle and implementation of the two-color indexing method, SPIND-TC, are reported in this paper. The algorithm was tested on both simulated and experimental data of protein crystals. The results show that the diffraction data can be accurately indexed in both cases. Source codes are publicly available at https://github.com/lixx11/SPIND-TC.

The standard method of joint probability distribution functions, so crucial for the development of direct methods, has been revisited and updated. It consists of three steps: identification of the reflections which may contribute to the estimation of a given structure invariant or seminvariant, calculation of the corresponding joint probability distribution, and derivation of the conditional distribution of the invariant or seminvariant phase given the values of some diffracted amplitudes. In this article the conditional distributions are derived directly without passing through the second step. A good feature of direct methods is that they may work in the absence of any prior information: that is also their weakness. Different types of prior information have been taken into consideration: interatomic distances, interatomic vectors, Patterson peaks, structural model. The method of directly deriving the conditional distributions has been applied to those cases. Some new formulas have been obtained estimating two-, three- and four-phase invariants. Special attention has been dedicated to the practical aspects of the new formulas, in order to simplify their possible use in direct phasing procedures.

In the title compound, C17H27NO2, the piperidine ring has a chair conformation and is positioned normal to the benzene ring. In the crystal, molecules are linked by C—H...O hydrogen bonds, forming chains propagating along the c-axis direction.

An intuitive method is presented for detecting pseudosymmetries in Z' > 1 cases as a complement to well-proven strategies already available in the literature. It is based in the simple idea that the mid-points between equivalent atoms in symmetrically related mol­ecules are disposed according to simple well-known patterns, which are easily recognizable by optical inspection. A number of Z' = 4 cases in the literature are analyzed, which allows some of the potentialities of the method to be revealed.

A method is described for indexing grazing-incidence X-ray diffraction data of epitaxially grown thin films comprising various crystal orientations and/or polymorphs by measuring reciprocal-lattice vectors.

Several strong earthquakes around the world have resulted in a phenomenon called soil liquefaction, the seismic generation of excess porewater pressures and softening of granular soils, often to the point that they may not be able to support the foundations of buildings and other infrastructure.

Although individual anglers – people who fish recreationally – generally take small numbers of fish, collectively, a large number of them can have a substantial impact on the overall stock.

A new report from the National Academies of Sciences, Engineering, and Medicine outlines how to examine whether specific levels of nutrients or other food substances (NOFSs) can ameliorate the risk of chronic disease and recommends ways to develop dietary reference intakes (DRI) based on chronic disease outcomes.

Producing more precise county-level estimates of crops and farmland cash rents will require integrating multiple data sources using model-based predictions that are more transparent and reproducible, says a new report from the National Academies of Sciences, Engineering, and Medicine.

Perk Labs has formally launched new verticals and unveiled the...

Using 'gardening' techniques to actively restore endangered coral reefs is ecologically sound and economically feasible, according to recent research.

High quality landscape assessments of areas protected under the Natura 2000 network are critical for effective long-term management plans. In a recent study, scientists have presented a integrated assessment of a Natura 2000 site in Sicily, Italy, which not only considers preservation of environmental features, as required by Natura 2000, but also human features, such as places of historical interest or industrial activity.

A standardised method to help choose the most cost-effective measures to remediate contaminated sites has been developed by Austrian researchers. The method takes into account a wide range of factors, including the principles of sustainability.

A recent study has described a simple method to screen the toxicity of materials used in consumer products. Using utility meter products as examples, the study found, for example, that stainless steel and polyvinyl chloride (PVC) had high toxicity potentials and suggests less toxic, but equally effective and priced, alternatives that could be used instead.

High quality landscape assessments of areas protected under the Natura 2000 network are critical for effective long-term management plans. In a recent study, scientists have presented a integrated assessment of a Natura 2000 site in Sicily, Italy, which not only considers preservation of environmental features, as required by Natura 2000, but also human features, such as places of historical interest or industrial activity.

Storage of carbon in soil helps to keep land fertile and regulates the climate, and is therefore an important ecosystem service. However, mapping of soil carbon stocks currently uses unreliable measures. This study used data from a national survey of English grasslands to show that soil carbon stocks can be accurately predicted using simple measures of soil and climatic conditions.

The presence of plastics in aquatic environments is a growing concern across the EU. This study explored the amount of microplastic particles present in raw and treated water at three water-treatment plants in the Czech Republic. While treated water contained fewer particles than raw1 fresh water, the amount found in treated water was not negligible, and largely comprised tiny particles of <10 micrometres (μm) in diameter. Ways to filter microplastics from potable water must be identified and their risk to humans, sources and routes into drinking water determined, say the researchers.

New research has identified 25 variables that influence noise in urban areas. By combining these into an equation, the study produced an accurate tool to describe urban sound environments that could be useful in urban planning.

It is difficult to compare estimates of noise exposure across EU Member States because the methods used to produce the data vary between countries. A new study has investigated five methods of estimating noise exposure and identified some of the reasons for variation in the data they produce.

Methods for assessing the sustainability of tourist destinations have been developed. In a new Spanish study, researchers describe a framework for analysing sustainability that is designed for policymakers and tourism managers, and, as a case study, apply it to the region of Andalusia.