Generation of integer and fractional vortex beams based on liquid crystal electronically reconfigurable spiral phase plates.

The manufacturing and characterization of a large-size 72-electrode liquid crystal-based reconfigurable spiral phase plate (SPP) is presented. The SPP is addressed by a custom-made driver with 72 independent channels, which allows for the generation of any arbitrary integer or fractional optical vortex beam with topological charges ranging from -24 to +24. The 25 mm diameter device is fabricated using direct laser writing, leading to a fill factor over 99%.

Chaperonin CCT controls extracellular vesicle production and cell metabolism through kinesin dynamics.

Cell proteostasis includes gene transcription, protein translation, folding of de novo proteins, post-translational modifications, secretion, degradation and recycling. By profiling the proteome of extracellular vesicles (EVs) from T cells, we have found the chaperonin complex CCT, involved in the correct folding of particular proteins. By limiting CCT cell-content by siRNA, cells undergo altered lipid composition and metabolic rewiring towards a lipid-dependent metabolism, with increased activity of peroxisomes and mitochondria.

Comparative Study of 4-Aminophenol Removal from Aqueous Solutions by Emulsion Liquid Membranes Using Acid and Basic Type 1 Facilitations: Optimisation and Kinetics.

The molecule 4-aminophenol (4AP) is recognised as a serious environmental pollutant that enters the environment during the manufacture and processing of a variety of industrial processes and through the degradation of some pharmaceutical products. This paper describes a comparative study of 4AP removal from aqueous solutions by emulsion liquid membranes using acid and basic type 1-facilitated transports. The results are explained by analysing the stripping process through both the different relative acid/basic strength of the hydroxyl and amine groups of the 4AP molecule and the hydrogen-bonding capacity with water of the ionisation products generated by the reaction of 4AP with HCl or NaOH.

A Bayesian approach to single-particle electron cryo-tomography in RELION-4.0.

We present a new approach for macromolecular structure determination from multiple particles in electron cryo-tomography (cryo-ET) data sets. Whereas existing subtomogram averaging approaches are based on 3D data models, we propose to optimise a regularised likelihood target that approximates a function of the 2D experimental images. In addition, analogous to Bayesian polishing and contrast transfer function (CTF) refinement in single-particle analysis, we describe the approaches that exploit the increased signal-to-noise ratio in the averaged structure to optimise tilt-series alignments, beam-induced motions of the particles throughout the tilt-series acquisition, defoci of the individual particles, as well as higher-order optical aberrations of the microscope.

ScipionTomo: Towards cryo-electron tomography software integration, reproducibility, and validation.

Image processing in cryogenic electron tomography (cryoET) is currently at a similar state as Single Particle Analysis (SPA) in cryogenic electron microscopy (cryoEM) was a few years ago. Its data processing workflows are far from being well defined and the user experience is still not smooth. Moreover, file formats of different software packages and their associated metadata are not standardized, mainly since different packages are developed by different groups, focusing on different steps of the data processing pipeline.

Identification of dyes and matrices for dye doped polymer waveguide emitters covering the visible spectrum.

Polymer based photonic devices offer the possibility cost effective roll-to-roll manufacture of photonic devices. The incorporation of luminescent dopants within a solid polymer waveguide allows for the generation of light within the device avoiding tedious mechanical light coupling. However, when a dopant is embedded in a solid matrix, depending on its concentration and the nature of materials involved, the emitted light may be quenched due to aggregation effects.

The chaperonin CCT controls T cell receptor-driven 3D configuration of centrioles.

T lymphocyte activation requires the formation of immune synapses (IS) with antigen-presenting cells. The dynamics of membrane receptors, signaling scaffolds, microfilaments, and microtubules at the IS determine the potency of T cell activation and subsequent immune response. Here, we show that the cytosolic chaperonin CCT (chaperonin-containing TCP1) controls the changes in reciprocal orientation of the centrioles and polarization of the tubulin dynamics induced by T cell receptor in T lymphocytes forming an IS.

Structures and distributions of SARS-CoV-2 spike proteins on intact virions.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virions are surrounded by a lipid bilayer from which spike (S) protein trimers protrude. Heavily glycosylated S trimers bind to the angiotensin-converting enzyme 2 receptor and mediate entry of virions into target cells. S exhibits extensive conformational flexibility: it modulates exposure of its receptor-binding site and subsequently undergoes complete structural rearrangement to drive fusion of viral and cellular membranes.

Measurement of local resolution in electron tomography.

Resolution (global and local) is one of the most reported metrics of quality measurement in Single Particle Analysis (SPA). However, in electron tomography, the situation is different and its computation is not straightforward. Typically, resolution estimation is global and, therefore, reduces the assessment of a whole tomogram to a single number.

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries.

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled.

Liquid crystal tunable claddings for polymer integrated optical waveguides.

Optical waveguides in photonic integrated circuits are traditionally passive elements merely carrying optical signals from one point to another. These elements could contribute to the integrated circuit functionality if they were modulated either by variations of the core optical properties, or by using tunable claddings. In this work, the use of liquid crystals as electro-optically active claddings for driving integrated waveguides has been explored.

Rapid detection of pathogens using lyotropic liquid crystals.

Lyotropic liquid crystals play an important role in many biological environments, such as micelles, liposomes, and phospholipid bilayers of cell membranes. In this work, we explore the performance of lyotropic liquid crystals as biosensors for macromolecules, proteins and whole microorganisms in hydrophilic media, i.e.

Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.

Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of ~ 7.

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).

Dynamic multilevel spiral phase plate generator.

The design and characterisation of a reconfigurable multi-level spiral phase plate is shown. The device is based on a pie-shape liquid-crystal structure with 24 slices driven by custom electronics that allow independent excitation control of each electrode. The electrooptical cell was manufactured using maskless laser ablation lithography and has shown an unprecedented high fill factor.

Evaluation of replicas manufactured in a 3D-printed nanoimprint unit.

Nanoimprint lithography has become a useful tool to prepare elements containing nanoscale features at quite reasonable cost, especially if the fabrication elements are created in the own laboratory. We have designed and fabricated a whole nanoimprint manufacturing system and analyzed the resulting surfaces using ad hoc packages developed on an open-software AFM image analysis suite. To complete the work, a number of polymers have been thoroughly studied in order to select the best material for this implementation.

All-organic switching polarizer based on polymer waveguides and liquid crystals.

This paper reports on the design, fabrication and characterization of an all-organic photonic integrated circuit working as a switching polarizer for visible light (630nm), combining organic waveguides and liquid crystals that can be electrically driven. The device was made in commercially available epoxy by laser direct writing lithography. A device with a 2dB loss and a 20dB extinction ratio for both polarizations, was simulated; the manufactured devices proved the working principle of the design.

Blind estimation of DED camera gain in Electron Microscopy.

The introduction of Direct Electron Detector (DED) videos in the Electron Microscope field has boosted Single Particle Analysis to a point in which it is currently considered to be a key technique in Structural Biology. In this article we introduce an approach to estimate the DED camera gain at each pixel from the movies themselves. This gain is needed to have the set of recorded frames into a coherent gray level range, homogeneous over the whole image.

A 3D-printed device for polymer nanoimprint lithography.

Nanoimprint lithography (NIL) is an imprinting technique which has experienced an increasing popularity due to its versatility in fabrication processes. Commercial NIL machines are readily available achieving high quality results; however, these machines involve a relatively high investment. Hence, small laboratories often choose to perform NIL copies in a more rudimentary and cheaper way.

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.

A Survey of the Use of Iterative Reconstruction Algorithms in Electron Microscopy.

One of the key steps in Electron Microscopy is the tomographic reconstruction of a three-dimensional (3D) map of the specimen being studied from a set of two-dimensional (2D) projections acquired at the microscope. This tomographic reconstruction may be performed with different reconstruction algorithms that can be grouped into several large families: direct Fourier inversion methods, back-projection methods, Radon methods, or iterative algorithms. In this review, we focus on the latter family of algorithms, explaining the mathematical rationale behind the different algorithms in this family as they have been introduced in the field of Electron Microscopy.

XTEND: Extending the depth of field in cryo soft X-ray tomography.

We have developed a new data collection method and processing framework in full field cryo soft X-ray tomography to computationally extend the depth of field (DOF) of a Fresnel zone plate lens. Structural features of 3D-reconstructed eukaryotic cells that are affected by DOF artifacts in standard reconstruction are now recovered. This approach, based on focal series projections, is easily applicable with closed expressions to select specific data acquisition parameters.

Liquid crystal spherical microlens array with high fill factor and optical power.

A novel liquid crystal spherical microlens array with high optical power and almost 100% of fill-factor is proposed and experimentally demonstrated. The combination of a specific structure and electrical waveforms applied to the electrodes generates an array of spherical microlenses with square aperture. The manufacturing process is simple (patterned electrodes) and the microlenses are reconfigurable by low voltage signals (the electrodes are in contact with the LC layer).

Morphology of SiO films as a key factor in alignment of liquid crystals with negative dielectric anisotropy.

Control of liquid crystal (LC) orientation using a proper SiO alignment layer is essential for the optimization of vertically aligned nematic (VAN) displays. With this aim, we studied the optical anisotropy of thin SiO films by generalized ellipsometry as a function of deposition angle. The columnar SiO structure orientation measured by a noninvasive ellipsometry technique is reported for the first time, and its morphology influence on the LC alignment is demonstrated for large deposition angles.