New measures of anisotropy of cryo-EM maps.

We propose two new measures of resolution anisotropy for cryogenic electron microscopy maps: Fourier shell occupancy (FSO), and the Bingham test (BT). FSO varies from 1 to 0, with 1 representing perfect isotropy, and lower values indicating increasing anisotropy. The threshold FSO = 0.5 occurs at Fourier shell correlation resolution. BT is a hypothesis test that complements the FSO to ensure the existence of anisotropy. FSO and BT allow visualization of resolution anisotropy. We illustrate their use with different experimental cryogenic electron microscopy maps.

Scipion3: A workflow engine for cryo-electron microscopy image processing and structural biology.

Image-processing pipelines require the design of complex workflows combining many different steps that bring the raw acquired data to a final result with biological meaning. In the image-processing domain of cryo-electron microscopy single-particle analysis (cryo-EM SPA), hundreds of steps must be performed to obtain the three-dimensional structure of a biological macromolecule by integrating data spread over thousands of micrographs containing millions of copies of allegedly the same macromolecule. The execution of such complicated workflows demands a specific tool to keep track of all these steps performed. Additionally, due to the extremely low signal-to-noise ratio (SNR), the estimation of any image parameter is heavily affected by noise resulting in a significant fraction of incorrect estimates. Although low SNR and processing millions of images by hundreds of sequential steps requiring substantial computational resources are specific to cryo-EM, these characteristics may be shared by other biological imaging domains. Here, we present Scipion, a Python generic open-source workflow engine specifically adapted for image processing. Its main characteristics are: (a) interoperability, (b) smart object model, (c) gluing operations, (d) comparison operations, (e) wide set of domain-specific operations, (f) execution in streaming, (g) smooth integration in high-performance computing environments, (h) execution with and without graphical capabilities, (i) flexible visualization, (j) user authentication and private access to private data, (k) scripting capabilities, (l) high performance, (m) traceability, (n) reproducibility, (o) self-reporting, (p) reusability, (q) extensibility, (r) software updates, and (s) non-restrictive software licensing.

Protective Strategies of Haberlea rhodopensis for Acquisition of Freezing Tolerance: Interaction between Dehydration and Low Temperature.

Resurrection plants are able to deal with complete dehydration of their leaves and then recover normal metabolic activity after rehydration. Only a few resurrection species are exposed to freezing temperatures in their natural environments, making them interesting models to study the key metabolic adjustments of freezing tolerances. Here, we investigate the effect of cold and freezing temperatures on physiological and biochemical changes in the leaves of Haberlea rhodopensis under natural and controlled environmental conditions. Our data shows that leaf water content affects its thermodynamical properties during vitrification under low temperatures. The changes in membrane lipid composition, accumulation of sugars, and synthesis of stress-induced proteins were significantly activated during the adaptation of H. rhodopensis to both cold and freezing temperatures. In particular, the freezing tolerance of H. rhodopensis relies on a sucrose/hexoses ratio in favor of hexoses during cold acclimation, while there is a shift in favor of sucrose upon exposure to freezing temperatures, especially evident when leaf desiccation is relevant. This pattern was paralleled by an elevated ratio of unsaturated/saturated fatty acids and significant quantitative and compositional changes in stress-induced proteins, namely dehydrins and early light-induced proteins (ELIPs). Taken together, our data indicate that common responses of H. rhodopensis plants to low temperature and desiccation involve the accumulation of sugars and upregulation of dehydrins/ELIP protein expression. Further studies on the molecular mechanisms underlying freezing tolerance (genes and genetic regulatory mechanisms) may help breeders to improve the resistance of crop plants.

Customized retarders based on waveplates.

Phase control is a critical parameter in polarization measurements. It is well known that a proper combination of wave plates allows to obtain achromatic phase shift, i.e., a constant retardation in certain spectral ranges. This paper is focused on a different, but more useful, goal, as it is to achieve customized variable retarders in broad spectral ranges. To do that, a merit function was used to measure the similarity between the overall phase shift of the wave plate combinations and the desired target. The control variables are the thicknesses and orientations of the wave plates. All possible combinations with four and five wave plates of quartz and MgF2 were analyzed, but our approach can be perfectly extended to deal with more wave plates. The result of an optimization process determines the thicknesses and orientations of the wave plates, which results in the closest retarder to the desired one. Numerical results show deviations below 10% between the target and the obtained retardation. These systems are of special interest in those fields and instruments in which polarization control plays a fundamental role.

Reversible First-Order Single Crystal to Single Crystal Thermal Phase Transition in [(CH3)3CNH3]4[V4O12].

The well-known compound tetrakis(tert-butylammonium)-cyclo-tetrametavanadate (V), [(CH3)3CNH3]4[V4O12] (1h_RT), which crystallizes in the tetragonal I4/m space group, undergoes an irreversible solid state transformation upon heating, constituting one of the few examples in which the initial and the final stages are structurally characterized by sc-XRD. Now, we observed the ability of the same compound to undergo an additional single-crystal-to-single-crystal (SCSC) transformation upon thermal stimuli, but this time at low temperatures (153 K). Compound 1h_RT contains a discrete unprotonated [V4O12]4- tetrahedral anion in which V and O bridging atoms are coplanar. In both phases, these tetrameric anions are linked through tert-butylammonium cations in an extensive network of hydrogen bonds, but at low temperatures, this phase loses its characteristic O-V-O coplanarity, with the resulting rearrangement of the crystal packing and hydrogen-bond network which provide its reversibility at low temperatures. Again, the initial and final stages have been characterized structurally by sc-XRD.

Emerging Themes in CryoEM─Single Particle Analysis Image Processing.

Cryo-electron microscopy (CryoEM) has become a vital technique in structural biology. It is an interdisciplinary field that takes advantage of advances in biochemistry, physics, and image processing, among other disciplines. Innovations in these three basic pillars have contributed to the boosting of CryoEM in the past decade. This work reviews the main contributions in image processing to the current reconstruction workflow of single particle analysis (SPA) by CryoEM. Our review emphasizes the time evolution of the algorithms across the different steps of the workflow differentiating between two groups of approaches: analytical methods and deep learning algorithms. We present an analysis of the current state of the art. Finally, we discuss the emerging problems and challenges still to be addressed in the evolution of CryoEM image processing methods in SPA.

Continuous flexibility analysis of SARS-CoV-2 spike prefusion structures.

Using a new consensus-based image-processing approach together with principal component analysis, the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state have been analysed. These studies revealed concerted motions involving the receptor-binding domain (RBD), N-terminal domain, and subdomains 1 and 2 around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. It is shown that in this data set there are not well defined, stable spike conformations, but virtually a continuum of states. An ensemble map was obtained with minimum bias, from which the extremes of the change along the direction of maximal variance were modeled by flexible fitting. The results provide a warning of the potential image-processing classification instability of these complicated data sets, which has a direct impact on the interpretability of the results.

Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures.

With the help of novel processing workflows and algorithms, we have obtained a better understanding of the flexibility and conformational dynamics of the SARS-CoV-2 spike in the prefusion state. We have re-analyzed previous cryo-EM data combining 3D clustering approaches with ways to explore a continuous flexibility space based on 3D Principal Component Analysis. These advanced analyses revealed a concerted motion involving the receptor-binding domain (RBD), N-terminal domain (NTD), and subdomain 1 and 2 (SD1 & SD2) around the previously characterized 1-RBD-up state, which have been modeled as elastic deformations. We show that in this dataset there are not well-defined, stable, spike conformations, but virtually a continuum of states moving in a concerted fashion. We obtained an improved resolution ensemble map with minimum bias, from which we model by flexible fitting the extremes of the change along the direction of maximal variance. Moreover, a high-resolution structure of a recently described biochemically stabilized form of the spike is shown to greatly reduce the dynamics observed for the wild-type spike. Our results provide new detailed avenues to potentially restrain the spike dynamics for structure-based drug and vaccine design and at the same time give a warning of the potential image processing classification instability of these complicated datasets, having a direct impact on the interpretability of the results.

Measuring local-directional resolution and local anisotropy in cryo-EM maps.

The introduction of local resolution has enormously helped the understanding of cryo-EM maps. Still, for any given pixel it is a global, aggregated value, that makes impossible the individual analysis of the contribution of the different projection directions. We introduce MonoDir, a fully automatic, parameter-free method that, starting only from the final cryo-EM map, decomposes local resolution into the different projection directions, providing a detailed level of analysis of the final map. Many applications of directional local resolution are possible, and we concentrate here on map quality and validation.

Automatic local resolution-based sharpening of cryo-EM maps.

MOTIVATION: Recent technological advances and computational developments have allowed the reconstruction of Cryo-Electron Microscopy (cryo-EM) maps at near-atomic resolution. On a typical workflow and once the cryo-EM map has been calculated, a sharpening process is usually performed to enhance map visualization, a step that has proven very important in the key task of structural modeling. However, sharpening approaches, in general, neglects the local quality of the map, which is clearly suboptimal. RESULTS: Here, a new method for local sharpening of cryo-EM density maps is proposed. The algorithm, named LocalDeblur, is based on a local resolution-guided Wiener restoration approach of the original map. The method is fully automatic and, from the user point of view, virtually parameter-free, without requiring either a starting model or introducing any additional structure factor correction or boosting. Results clearly show a significant impact on map interpretability, greatly helping modeling. In particular, this local sharpening approach is especially suitable for maps that present a broad resolution range, as is often the case for membrane proteins or macromolecules with high flexibility, all of them otherwise very suitable and interesting specimens for cryo-EM. To our knowledge, and leaving out the use of local filters, it represents the first application of local resolution in cryo-EM sharpening. AVAILABILITY AND IMPLEMENTATION: The source code (LocalDeblur) can be found at https://github.com/I2PC/xmipp and can be run using Scipion (http://scipion.cnb.csic.es) (release numbers greater than or equal 1.2.1). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Novel Antibacterial and Toughened Carbon-Fibre/Epoxy Composites by the Incorporation of TiO2 Nanoparticles Modified Electrospun Nanofibre Veils.

The inclusion of electrospun nanofiber veils was revealed as an effective method for enhancing the mechanical properties of fiber-reinforced epoxy resin composites. These veils will eventually allow the incorporation of nanomaterials not only for mechanical reinforcement but also in multifunctional applications. Therefore, this paper investigates the effect of electrospun nanofibrous veils made of polyamide 6 modified with TiO2 nanoparticles on the mechanical properties of a carbon-fiber/epoxy composite. The nanofibers were included in the carbon-fiber/epoxy composite as a single structure. The effect of positioning these veils in different composite positions was investigated. Compared to the reference, the use of unmodified and TiO2 modified veils increased the flexural stress at failure and the fracture toughness of composites. When TiO2 modified veils were incorporated, new antibacterial properties were achieved due to the photocatalytic properties of the veils, widening the application area of these composites.

TiO2-Doped Electrospun Nanofibrous Membrane for Photocatalytic Water Treatment.

This work has been focused on the one-step fabrication by electrospinning of polyamide 6 (PA6) nanofibre membranes modified with titanium dioxide nanoparticles (TiO2), where these TiO2 nanoparticles aggregates could induce a photocatalytic activity. The main potential application of these membranes could be the purification of contaminated water. Thus, it is important to analyse the contaminant degradation capability since in these membranes this is based on their photocatalytic activity. In this work, the effect of the photocatalysis has been studied both on the degradation of an organic model contaminant and on the removal of Escherichia coli and other coliform bacteria. As a result, it was observed that these membranes present excellent photocatalytic activity when they are irradiated under UV light, allowing a 70% reduction of an organic model pollutant after 240 min. In addition, these membranes successfully removed Escherichia coli and other coliform bacteria in artificially inoculated water after 24 h of contact with them. Moreover, the stand-alone structure of the membranes allowed for the reusing of the immobilized catalyst. The experimental evidence indicated that developed nanofibre membranes are a fast and efficient solution for polluted water decontamination based on photocatalysis. Their use could contribute to guarantee a fresh water level and quality, mitigating the water scarcity problem worldwide.

Thermostructural Behavior in a Series of Lanthanide-Containing Polyoxotungstate Hybrids with Copper(II) Complexes of the Tetraazamacrocycle Cyclam: A Single-Crystal-to-Single-Crystal Transformation Study.

A series of 14 isostructural [Cu(cyclam)]2[{Cu(cyclam)}4{(α-GeW11O39)Ln(H2O)(OAc)}2]·18H2O (1-Ln, where Ln = La-Lu; cyclam = 1,4,8,11-tetraazacyclotetradecane) polyoxometalate-based hybrids reported herein represent (i) the first example of a two-dimensional covalent hybrid lattice involving the [{(α-XW11O39)Ln(H2O)(OAc)}2] n- archetype and (ii) the first structural characterization of such a dimeric polyoxotungste for Ln = La and Pr as well as for the combination of X = Ge and Ln = Ce, Nd, Sm, or Lu. Compounds 1-Ln have been characterized by elemental analyses, infrared spectroscopy, and thermogravimetric analysis, and their thermostructural behavior has been monitored by powder and single-crystal X-ray diffraction. The title compounds undergo two single-crystal-to-single-crystal transformations triggered by thermal dehydration leading to the [{Cu(cyclam)}6{(α-GeW11O39)Ln(H2O)(OAc)}2]·4H2O intermediate (2-Ln, where Ln = Eu or Er) and [Cu(cyclam)]0.5[{Cu(cyclam)}5.5{(α-GeW11O39)Ln(OAc)}2] (3-Ln, where Ln = Ce or Eu) final anhydrous phases, the latter evidencing a coordinatively unsaturated derivative of the dimeric archetype for the first time. These transitions involve formation and disruption of Cu-OPOM bonds that result in different {Cu(cyclam)}2+ moieties grafting onto and being released from Keggin surfaces, which reduces the dimensionality of 1-Ln to one-dimensional covalent assemblies for 2-Ln and 3-Ln. While all 3-Ln phases rehydrate fully upon exposure to air for 24 h, the kinetics governing the crystal transitions back toward 1-Ln through 2-Ln depend on the nature of Ln. Under ambient moisture, the anhydrous structures fully revert back to the parent framework for Ln = La-Sm, while the samples containing Eu to Lu afford mixtures of 1-Ln and 2-Ln and require immersion in water for the structural reversion to reach completion. Single-crystal X-ray diffraction analyses of the rehydrated 1R-Ln samples (Ln = Ce, Eu, and Er) support these observations.

Validation of electron microscopy initial models via small angle X-ray scattering curves.

MOTIVATION: Cryo electron microscopy (EM) is currently one of the main tools to reveal the structural information of biological macromolecules. The re-construction of three-dimensional (3D) maps is typically carried out following an iterative process that requires an initial estimation of the 3D map to be refined in subsequent steps. Therefore, its determination is key in the quality of the final results, and there are cases in which it is still an open issue in single particle analysis (SPA). Small angle X-ray scattering (SAXS) is a well-known technique applied to structural biology. It is useful from small nanostructures up to macromolecular ensembles for its ability to obtain low resolution information of the biological sample measuring its X-ray scattering curve. These curves, together with further analysis, are able to yield information on the sizes, shapes and structures of the analyzed particles. RESULTS: In this paper, we show how the low resolution structural information revealed by SAXS is very useful for the validation of EM initial 3D models in SPA, helping the following refinement process to obtain more accurate 3D structures. For this purpose, we approximate the initial map by pseudo-atoms and predict the SAXS curve expected for this pseudo-atomic structure. The match between the predicted and experimental SAXS curves is considered as a good sign of the correctness of the EM initial map. AVAILABILITY AND IMPLEMENTATION: The algorithm is freely available as part of the Scipion 1.2 software at http://scipion.i2pc.es/.

Metal Nanoparticles Embedded in Cellulose Nanocrystal Based Films: Material Properties and Post-use Analysis.

The dispersion of nanoparticles having different size-, shape-, and composition-dependent properties is an exciting approach to design and synthesize multifunctional materials and devices. This work shows a detailed investigation of the preparation and properties of free-standing nanocomposite films based on cellulose nanocrystals (CNC) loaded with three different types of metal nanoparticles. CNC-based nanocomposites having zinc oxide (ZnO), titanium dioxide (TiO2), and silver oxide (Ag2O) have been obtained through evaporation-induced self-assembly (EISA) in acqueous solution. Morphological and optical characteristics, chemical properties, wettability, and antimicrobial assays of the produced films were conducted. Furthermore, disintegrability in composting condition of CNC based nanocomposites was here investigated for the first time. The morphological observations revealed the formation of a chiral nematic structure with uniformly distributed nanoparticles. The bionanocomposite films based on the metal nanoparticles had effective antimicrobial activity, killing both Escherichia coli RB ( E. coli RB) and Staphylococcus aureus 8325-4 ( S. aureus 8325-4). The simplicity method of film preparation, the large quantity of cellulose in the world, and the free-standing nature of the nanocomposite films offer highly advantageous characteristics that can for the new development of multifunctional materials.

Immobilization of Polyoxometalates on Tailored Polymeric Surfaces.

Herein we describe the preparation of hybrid polymer-inorganic interfaces by the immobilization of polyoxometalate nanoclusters on functionalized polymer surfaces. The polymeric surfaces were made of polystyrene-b-poly(acrylic acid)/polystyrene (PS-b-PAA/PS) blends by spin coating on a silicon wafer. The functionalization of the polymer film was obtained by interfacial migration of the amphiphilic block copolymer toward the interface upon water vapor annealing. The carboxylic acid functional groups contained in the PAA block were then employed to anchor the [LnIII(α-SiW11O39)]5- polyoxometalates (Ln: Ce, Er). This purpose was achieved by immersing the films in aqueous solutions of the in situ-formed inorganic nanoclusters. X-ray photoelectron and confocal Raman spectroscopies, together with atomic force microscopy, confirmed the immobilization of the inorganic species at the interface.

MonoRes: Automatic and Accurate Estimation of Local Resolution for Electron Microscopy Maps.

Since the beginning of electron microscopy, resolution has been a critical parameter. In this article, we propose a fully automatic, accurate method for determining the local resolution of a 3D map (MonoRes). The foundation of this algorithm is an extension of the concept of analytic signal, termed monogenic signal. The map is filtered at different frequencies and the amplitude of the monogenic signal is calculated, after which a criterion is applied to determine the resolution at each voxel. MonoRes is fully automatic without compulsory user parameters, with great accuracy in all tests, and is computationally more rapid than existing methods in the field. In addition, MonoRes offers the option of local filtering of the original map based on the calculated local resolution.

Effect of Different Types of Electrospun Polyamide 6 Nanofibres on the Mechanical Properties of Carbon Fibre/Epoxy Composites.

Delamination and brittle matrix fracture have long since been the biggest problems in fibre-reinforced composites. Recently, the incorporation of electrospun nanofibre veils has been shown to be an effective method for improving the mechanical properties of these composites, without causing process problems and negatively affecting other mechanical properties. Thus, these nanofibres have the potential to be used as thickness-reinforcing materials in composites. This paper investigates the effect of incorporating standalone electrospun nanofibre veils made of two different types of polyamide 6 (PA6) on the mechanical properties of carbon fibre/epoxy composites. The influence of positioning the electrospun veils at different interlaminar positions of the laminate has also been investigated.

Formulation of Carbopol®/Poly(2-ethyl-2-oxazoline)s Mucoadhesive Tablets for Buccal Delivery of Hydrocortisone.

Poly(2-ethyl-2-oxazoline) has become an excellent alternative to the use of poly(ethylene glycol) in pharmaceutical formulations due to its valuable physicochemical and biological properties. This work presents a formulation of poorly-water soluble drug, hydrocortisone, using interpolymer complexes and physical blends of poly(2-ethyl-2-oxazoline)s and two Carbopols® (Carbopol 974 and Carbopol 971) for oromucosal administration. The swelling, hydrocortisone release and mucoadhesive properties of a series of tablet formulations obtained by combination of different Carbopols with poly(2-ethyl-2-oxazoline)s of different molecular weights have been evaluated in vitro.