TomoJ: tomography software for three-dimensional reconstruction in transmission electron microscopy

Skin hepcidin initiates psoriasiform skin inflammation via Fe-driven hyperproliferation and neutrophil recruitment

Psoriasis is a multifactorial, chronic inflammatory skin disease with unresolved questions on its primary events. Iron overload has been described in the epidermis of psoriasis patients, but its relevance remains unknown. We found that the key iron regulatory hormone hepcidin was highly expressed in the epidermis of psoriasis patients, especially the pustular variants resistant to treatments. In a murine model of acute skin inflammation, keratinocyte-derived hepcidin was required for iron retention in keratinocytes, leading to hyperproliferation of the epidermal layer and neutrophil recruitment, two main features of psoriatic skin lesions. Keratinocytes overexpressing hepcidin were sufficient to elicit these psoriasiform features in a transgenic mouse model. Furthermore, transcriptome analysis of these keratinocytes revealed canonical pathways found in human psoriasis, pointing to a causal role for hepcidin in the pathogenesis of the disease. Altogether, our data suggest that hepcidin could be an actionable target for skin psoriasis treatment, in addition to current therapeutics, or targeted as maintenance therapy during remission to prevent recurrence.

Colossal Core/Shell CdSe/CdS Quantum Dot Emitters

Single-photon sources are essential for advancing quantum technologies with scalable integration being a crucial requirement. To date, deterministic positioning of single-photon sources in large-scale photonic structures remains a challenge. In this context, colloidal quantum dots (QDs), particularly core/shell configurations, are attractive due to their solution processability. However, traditional QDs are typically small, about 3 to 6 nm, which restricts their deterministic placement and utility in large-scale photonic devices, particularly within optical cavities. The largest existing core/shell QDs are a family of giant CdSe/CdS QDs, with total diameters ranging from about 20 to 50 nm. Pushing beyond this size limit, we introduce a synthesis strategy for colossal CdSe/CdS QDs, with sizes ranging from 30 to 100 nm, using a stepwise high-temperature continuous injection method. Electron microscopy reveals a consistent hexagonal diamond morphology composed of 12 semipolar {101̅1} facets and one polar (0001) facet. We also identify conditions where shell growth is disrupted, leading to defects, islands, and mechanical instability, which suggest synthetic requirements for growing crystalline particles beyond 100 nm. The stepwise growth of thick CdS shells on CdSe cores enables the synthesis of emissive QDs with long photoluminescence lifetimes of a few microseconds and suppressed blinking at room temperature. Notably, QDs with 80 and 100 CdS monolayers exhibit high single-photon emission purity with second-order photon correlation g(2)(0) values below 0.2.

Controlling the Formation of Polyhedral Block Copolymer Nanoparticles: Insights from Process Variables and Dynamic Modeling

This study delves into the formation of nanoscale polyhedral block copolymer particles (PBCPs) exhibiting cubic, octahedral, and variant geometries. These structures represent a pioneering class that has never been fabricated previously. PBCP features distinct variations in curvature on the outer surface, aligning with the edges and corners of polyhedral shapes. This characteristic sharply contrasts with previous block copolymers (BCPs), which displayed a smooth spherical surface. The emergence of these cornered morphologies presents an intriguing and counterintuitive phenomenon and is linked to process parameters, such as evaporation rates and initial concentration, while keeping other variables constant. Using a system of coupled Cahn-Hillard (CCH) equations, we uncover the mechanisms driving polyhedral particle formation, emphasizing the importance of controlling relaxation parameters for shape variable u and microphase separation v. This unconventional approach, differing from traditional steepest descent method, allows for precise control and diverse polyhedral particle generation. Accelerating the shape variable u proves crucial for expediting precipitation and aligns with experimental observations. Employing the above theoretical model, we achieve shape predictions for particles and the microphase separation within them, which overcomes the limitations of ab initio computations. Additionally, a numerical stability analysis discerns the transient nature versus local minimizer characteristics. Overall, our findings contribute to understanding the complex interplay between process variables and the morphology of polyhedral BCP nanoparticles.

The application and development of electron microscopy for three-dimensional reconstruction in life science: a review

Imaging technologies have played a pivotal role in advancing biological research by enabling visualization of biological structures and processes. While traditional electron microscopy (EM) produces two-dimensional images, emerging techniques now allow high-resolution three-dimensional (3D) characterization of specimens in situ, meeting growing needs in molecular and cellular biology. Combining transmission electron microscopy (TEM) with serial sectioning inaugurated 3D imaging, attracting biologists seeking to explore cell ultrastructure and driving advancement of 3D EM reconstruction. By comprehensively and precisely rendering internal structure and distribution, 3D TEM reconstruction provides unparalleled ultrastructural insights into cells and molecules, holding tremendous value for elucidating structure-function relationships and broadly propelling structural biology. Here, we first introduce the principle of 3D reconstruction of cells and tissues by classical approaches in TEM and then discuss modern technologies utilizing TEM and on new SEM-based as well as cryo-electron microscope (cryo-EM) techniques. 3D reconstruction techniques from serial sections, electron tomography (ET), and the recent single-particle analysis (SPA) are examined; the focused ion beam scanning electron microscopy (FIB-SEM), the serial block-face scanning electron microscopy (SBF-SEM), and automatic tape-collecting lathe ultramicrotome (ATUM-SEM) for 3D reconstruction of large volumes are discussed. Finally, we review the challenges and development prospects of these technologies in life science. It aims to provide an informative reference for biological researchers.

Understanding the Effect of Curvature on the Magnetization Reversal of Three-Dimensional Nanohelices

Comprehending the interaction between geometry and magnetism in three-dimensional (3D) nanostructures is important to understand the fundamental physics of domain wall (DW) formation and pinning. Here, we use focused-electron-beam-induced deposition to fabricate magnetic nanohelices with increasing helical curvature with height. Using electron tomography and Lorentz transmission electron microscopy, we reconstruct the 3D structure and magnetization of the nanohelices. The surface curvature, helical curvature, and torsion of the nanohelices are then quantified from the tomographic reconstructions. Furthermore, by using the experimental 3D reconstructions as inputs for micromagnetic simulations, we can reveal the influence of surface and helical curvature on the magnetic reversal mechanism. Hence, we can directly correlate the magnetic behavior of a 3D nanohelix to its experimental structure. These results demonstrate how the control of geometry in nanohelices can be utilized in the stabilization of DWs and control of the response of the nanostructure to applied magnetic fields.

High-Resolution Electron Diffraction of Hydrated Protein Crystals at Room Temperature

Structural characterization is crucial to understanding protein function. Compared with X-ray diffraction methods, electron crystallography can be performed on nanometer-sized crystals and can provide additional information from the resulting Coulomb potential map. Whereas electron crystallography has successfully resolved three-dimensional structures of vitrified protein crystals, its widespread use as a structural biology tool has been limited. One main reason is the fragility of such crystals. Protein crystals can be easily damaged by mechanical stress, change in temperature, or buffer conditions as well as by electron irradiation. This work demonstrates a methodology to preserve these nanocrystals in their natural environment at room temperature for electron diffraction experiments as an alternative to existing cryogenic techniques. Lysozyme crystals in their crystallization solution are hermetically sealed via graphene-coated grids, and their radiation damage is minimized by employing a low-dose data collection strategy in combination with a hybrid-pixel direct electron detector. Diffraction patterns with reflections of up to 3 Å are obtained and successfully indexed using a template-matching algorithm. These results demonstrate the feasibility of in situ protein electron diffraction. The method described will also be applicable to structural studies of hydrated nanocrystals important in many research and technological developments.

Evaluation of Electron Tomography Capabilities for Shale Imaging

Despite the advantageous resolution of electron tomography (ET), reconstruction of three-dimensional (3D) images from multiple two-dimensional (2D) projections presents several challenges, including small signal-to-noise ratios, and a limited projection range. This study evaluates the capabilities of ET for thin sections of shale, a complex nanoporous medium. A numerical phantom with 1.24 nm pixel size is constructed based on the tomographic reconstruction of a Barnett shale. A dataset of 2D projection images is numerically generated from the 3D phantom and studied over a range of conditions. First, common reconstruction techniques are used to reconstruct the shale structure. The reconstruction uncertainty is quantified by comparing overall values of storage and transport metrics, as well as the misclassification of pore voxels compared to the phantom. We then select the most robust reconstruction technique and we vary the acquisition conditions to quantify the effect of artifacts. We find a strong agreement for large pores over the different acquisition workflows, while a wider variability exists for nanometer-scale features. The limited projection range and reconstruction are identified as the main experimental bottlenecks, thereby suggesting that sample thinning, advanced holders, and advanced reconstruction algorithms offer opportunities for improvement.

Revealing the 3D Structure of Block Copolymers with Electron Microscopy: Current Status and Future Directions

Block copolymers (BCPs) are considered model systems for understanding and utilizing self-assembly in soft matter. Their tunable nanometric structure and composition enable comprehensive studies of self-assembly processes as well as make them relevant materials in diverse applications. A key step in developing and controlling BCP nanostructures is a full understanding of their three-dimensional (3D) structure and how this structure is affected by the BCP chemistry, confinement, boundary conditions, and the self-assembly evolution and dynamics. Electron microscopy (EM) is a leading method in BCP 3D characterization owing to its high resolution in imaging nanosized structures. Here we discuss the two main 3D EM methods: namely, transmission EM tomography and slice and view scanning EM tomography. We present each method's principles, examine their strengths and weaknesses, and discuss ways researchers have devised to overcome some of the challenges in BCP 3D characterization with EM- from specimen preparation to imaging radiation-sensitive materials. Importantly, we review current and new cutting-edge EM methods such as direct electron detectors, energy dispersive X-ray spectroscopy of soft matter, high temporal rate imaging, and single-particle analysis that have great potential for expanding the BCP understanding through EM in the future.

WRAP: A wavelet-regularised reconstruction algorithm for magnetic vector electron tomography

Magnetic vector electron tomography (VET) is a promising technique that enables better understanding of micro- and nano-magnetic phenomena through the reconstruction of 3D magnetic fields at high spatial resolution. Here we introduce WRAP (Wavelet Regularised A Program), a reconstruction algorithm for magnetic VET that directly reconstructs the magnetic vector potential A using a compressed sensing framework which regularises for sparsity in the wavelet domain. We demonstrate that using WRAP leads to a significant increase in the fidelity of the 3D reconstruction and is especially robust when dealing with very limited data; using datasets simulated with realistic noise, we compare WRAP to a conventional reconstruction algorithm and find an improvement of ca. 60% when averaged over several performance metrics. Moreover, we further validate WRAP's performance on experimental electron holography data, revealing the detailed magnetism of vortex states in a CuCo nanowire. We believe WRAP represents a major step forward in the development of magnetic VET as a tool for probing magnetism at the nanoscale.

Ultrastructural features mirror metabolic derangement in human endothelial cells exposed to high glucose

High glucose-induced endothelial dysfunction is the early event that initiates diabetes-induced vascular disease. Here we employed Cryo Soft X-ray Tomography to obtain three-dimensional maps of high D-glucose-treated endothelial cells and their controls at nanometric spatial resolution. We then correlated ultrastructural differences with metabolic rewiring. While the total mitochondrial mass does not change, high D-glucose promotes mitochondrial fragmentation, as confirmed by the modulation of fission-fusion markers, and dysfunction, as demonstrated by the drop of membrane potential, the decreased oxygen consumption and the increased production of reactive oxygen species. The 3D ultrastructural analysis also indicates the accumulation of lipid droplets in cells cultured in high D-glucose. Indeed, because of the decrease of fatty acid β-oxidation induced by high D-glucose concentration, triglycerides are esterified into fatty acids and then stored into lipid droplets. We propose that the increase of lipid droplets represents an adaptive mechanism to cope with the overload of glucose and associated oxidative stress and metabolic dysregulation.

Cones and spirals: Multi-axis acquisition for scalar and vector electron tomography

Electron tomography (ET) has become an important tool for understanding the 3D nature of nanomaterials, with recent developments enabling not only scalar reconstructions of electron density, but also vector reconstructions of magnetic fields. However, whilst new signals have been incorporated into the ET toolkit, the acquisition schemes have largely kept to conventional single-axis tilt series for scalar ET, and dual-axis schemes for magnetic vector ET. In this work, we explore the potential of using multi-axis tilt schemes including conical and spiral tilt schemes to improve reconstruction fidelity in scalar and magnetic vector ET. Through a combination of systematic simulations and a proof-of-concept experiment, we show that spiral and conical tilt schemes have the potential to produce substantially improved reconstructions, laying the foundations of a new approach to electron tomography acquisition and reconstruction.

Shedding Light on Osteosarcoma Cell Differentiation: Impact on Biomineralization and Mitochondria Morphology

Osteosarcoma (OS) is the most common primary malignant bone tumor and its etiology has recently been associated with osteogenic differentiation dysfunctions. OS cells keep a capacity for uncontrolled proliferation showing a phenotype similar to undifferentiated osteoprogenitors with abnormal biomineralization. Within this context, both conventional and X-ray synchrotron-based techniques have been exploited to deeply characterize the genesis and evolution of mineral depositions in a human OS cell line (SaOS-2) exposed to an osteogenic cocktail for 4 and 10 days. A partial restoration of the physiological biomineralization, culminating with the formation of hydroxyapatite, was observed at 10 days after treatment together with a mitochondria-driven mechanism for calcium transportation within the cell. Interestingly, during differentiation, mitochondria showed a change in morphology from elongated to rounded, indicating a metabolic reprogramming of OS cells possibly linked to an increase in glycolysis contribution to energy metabolism. These findings add a dowel to the genesis of OS giving new insights on the development of therapeutic strategies able to restore the physiological mineralization in OS cells.

A druggable copper-signalling pathway that drives inflammation

Inflammation is a complex physiological process triggered in response to harmful stimuli1. It involves cells of the immune system capable of clearing sources of injury and damaged tissues. Excessive inflammation can occur as a result of infection and is a hallmark of several diseases2-4. The molecular bases underlying inflammatory responses are not fully understood. Here we show that the cell surface glycoprotein CD44, which marks the acquisition of distinct cell phenotypes in the context of development, immunity and cancer progression, mediates the uptake of metals including copper. We identify a pool of chemically reactive copper(II) in mitochondria of inflammatory macrophages that catalyses NAD(H) redox cycling by activating hydrogen peroxide. Maintenance of NAD+ enables metabolic and epigenetic programming towards the inflammatory state. Targeting mitochondrial copper(II) with supformin (LCC-12), a rationally designed dimer of metformin, induces a reduction of the NAD(H) pool, leading to metabolic and epigenetic states that oppose macrophage activation. LCC-12 interferes with cell plasticity in other settings and reduces inflammation in mouse models of bacterial and viral infections. Our work highlights the central role of copper as a regulator of cell plasticity and unveils a therapeutic strategy based on metabolic reprogramming and the control of epigenetic cell states.

Clinical transfer of AGuIX®-based radiation treatments for locally advanced cervical cancer: MR quantification and in vitro insights in the NANOCOL clinical trial framework

Clinical trials incorporating metallic nanoparticles (NPs) have recently begun. Radiotherapy planning does not take into account NPs concentrations observed in the patients' target volumes. In the framework of the NANOCOL clinical trial including patients treated for locally advanced cervical cancers, this study proposes a complete method to evaluate the radiation-induced biological effects of NPs. For this, calibration phantom was developed and MRI sequences with variable flip angles were acquired. This process allowed the quantification of NPs in the tumor of 4 patients, which was compared to the results of mass spectrometry obtained from 3 patient biopsies. The concentration of the NPs was reproduced in 3D cell models. Based on clonogenic assays, the radio-enhancement effects were quantified for radiotherapy and brachytherapy, and the impact in terms of local control was evaluated. T₁ signal change in GTVs revealed NPs accumulation ~12.4 μmol/L, in agreement with mass spectrometry. Radio-enhancement effects of about 15 % at 2 Gy were found for both modalities, with a positive impact on local tumor control. Even if further follow-up of patients in this and subsequent clinical trials will be necessary to assess the reliability of this proof of concept, this study opens the way to the integration of a dose modulation factor to better take into account the impact of NPs in radiotherapy treatment.

Automatic Differentiation for Inverse Problems in X-ray Imaging and Microscopy

Computational techniques allow breaking the limits of traditional imaging methods, such as time restrictions, resolution, and optics flaws. While simple computational methods can be enough for highly controlled microscope setups or just for previews, an increased level of complexity is instead required for advanced setups, acquisition modalities or where uncertainty is high; the need for complex computational methods clashes with rapid design and execution. In all these cases, Automatic Differentiation, one of the subtopics of Artificial Intelligence, may offer a functional solution, but only if a GPU implementation is available. In this paper, we show how a framework built to solve just one optimisation problem can be employed for many different X-ray imaging inverse problems.

Structural diversity in three-dimensional self-assembly of nanoplatelets by spherical confinement

Nanoplatelets offer many possibilities to construct advanced materials due to new properties associated with their (semi)two-dimensional shapes. However, precise control of both positional and orientational order of the nanoplatelets in three dimensions, which is required to achieve emerging and collective properties, is challenging to realize. Here, we combine experiments, advanced electron tomography and computer simulations to explore the structure of supraparticles self-assembled from nanoplatelets in slowly drying emulsion droplets. We demonstrate that the rich phase behaviour of nanoplatelets, and its sensitivity to subtle changes in shape and interaction potential can be used to guide the self-assembly into a wide range of different structures, offering precise control over both orientation and position order of the nanoplatelets. Our research is expected to shed light on the design of hierarchically structured metamaterials with distinct shape- and orientation- dependent properties.

Grid batch-dependent tuning of glow discharge parameters

Sample preparation on cryo-EM grids can give various results, from very thin ice and homogeneous particle distribution (ideal case) to unwanted behavior such as particles around the “holes” or complexes that do not entirely correspond to the one in solution (real life). We recently run into such a case and finally found out that variations in the 3D reconstructions were systematically correlated with the grid batches that were used. We report the use of several techniques to investigate the grids' characteristics, namely TEM, SEM, Auger spectroscopy and Infrared Interferometry. This allowed us to diagnose the origin of grid preparation problems and to adjust glow discharge parameters. The methods used for each approach are described and the results obtained on a common specific case are reported.

ClusterAlign: A fiducial tracking and tilt series alignment tool for thick sample tomography

Thick specimens, as encountered in cryo-scanning transmission electron tomography, offer special challenges to conventional reconstruction workflows. The visibility of features, including gold nanoparticles introduced as fiducial markers, varies strongly through the tilt series. As a result, tedious manual refinement may be required in order to produce a successful alignment. Information from highly tilted views must often be excluded to the detriment of axial resolution in the reconstruction. We introduce here an approach to tilt series alignment based on identification of fiducial particle clusters that transform coherently in rotation, essentially those that lie at similar depth. Clusters are identified by comparison of tilted views with a single untilted reference, rather than with adjacent tilts. The software, called ClusterAlign, proves robust to poor signal to noise ratio and varying visibility of the individual fiducials and is successful in carrying the alignment to the ends of the tilt series where other methods tend to fail. ClusterAlign may be used to generate a list of tracked fiducials, to align a tilt series, or to perform a complete 3D reconstruction. Tools to evaluate alignment error by projection matching are included. Execution involves no manual intervention, and adherence to standard file formats facilitates an interface with other software, particularly IMOD/etomo, tomo3d, and tomoalign.

Quantitative Evaluation of Supported Catalysts Key Properties from Electron Tomography Studies: Assessing Accuracy Using Material-Realistic 3D-Models

Electron Tomography (ET) reconstructions can be analysed, via segmentation techniques, to obtain quantitative, 3D-information about individual nanoparticles in supported catalysts. This includes values of parameters out of reach for any other technique, like their volume and surface, which are required to determine the dispersion of the supported particle system or the specific surface area of the support; two figures that play a major role in the performance of this type of catalysts.

However, both the experimental conditions during the acquisition of the tilt series and the limited fidelity of the reconstruction and segmentation algorithms, restrict the quality of the ET results and introduce an undefined amount of error both in the qualitative features of the reconstructions and in all the quantitative parameters measured from them.

Here, a method based on the use of well-defined 3D geometrical models (phantoms), with morphological features closely resembling those observed in experimental images of an Au/CeO2 catalyst, has been devised to provide a precise estimation of the accuracy of the reconstructions. Using this approach, the influence of noise and the number of projections on the errors of reconstructions obtained using a Total Variation Minimization in 3D (TVM-3D) algorithm have been determined. Likewise, the benefits of using smart denoising techniques based on Undecimated Wavelet Transforms (UWT) have been also evaluated.

The results clearly reveal a large impact of usual noise levels on both the quality of the reconstructions and nanometrological measurement errors. Quantitative clues about the key role of UWT to largely compensate them are also provided.

3D multiscale analysis of the hierarchical porosity in Coscinodiscus sp. diatoms using a combination of tomographic techniques

A full 3D analysis of the hierarchical porosity in Coscinodiscus sp. diatom structures was carried out by using a multiscale approach that combines three advanced volumetric imaging techniques with resolutions and fields of view covering all the porous characteristics of such complex architectures: electron tomography, "slice and view" approach that uses a dual-beam microscope (FIB-SEM), and array tomography consisting of serial imaging of ultrathin specimen sections. This multiscale approach allowed the whole porosity network to be quantified and provided an unprecedented structural insight into these natural nanostructured materials with internal organization ranging from micrometer to nanometer. The analysed species is made of several nested layers with different pore sizes, shapes and connectivities and characterized by the presence of interconnected pores structured in various ways. The first evidence of the presence of a nanometric porosity made of ellipsoidal pores in the siliceous diatom frustules is also provided.

Thermal Evolution of C-Fe-Bi Nanocomposite System: From Nanoparticle Formation to Heterogeneous Graphitization Stage

Carbon xerogel nanocomposites with integrated Bi and Fe particles (C–Bi–Fe) represent an interesting model of carbon nanostructures decorated with multifunctional nanoparticles (NPs) with applicability for electrochemical sensors and catalysts. The present study addresses the fundamental aspects of the catalyzed growth of nano-graphites in C–Bi–Fe systems, relevant in charge transport and thermo-chemical processes. The thermal evolution of a C–Bi–Fe xerogel is investigated using different pyrolysis treatments. At lower temperatures (~750°C), hybrid bismuth iron oxide (BFO) NPs are frequently observed, while graphitization manifests under more specific conditions such as higher temperatures (~1,050°C) and reduction yields. An in situ heating TEM experiment reveals graphitization activity between 800 and 900°C. NP motion is directly correlated with textural changes of the carbon support due to the catalyzed growth of graphitic nanoshells and nanofibers as confirmed by HR-TEM and electron tomography (ET) for the graphitized sample. An exponential growth model for the catalyst dynamics enables the approximation of activation energies as 0.68 and 0.29–0.34 eV during reduction and graphitization stages. The results suggest some similarities with the tip growth mechanism, while oxygen interference and the limited catalyst–feed gas interactions are considered as the main constraints to enhanced growth.

Correlative 3D cryo X-ray imaging reveals intracellular location and effect of designed antifibrotic protein-nanomaterial hybrids

Revealing the intracellular location of novel therapeutic agents is paramount for the understanding of their effect at the cell ultrastructure level. Here, we apply a novel correlative cryo 3D imaging approach to determine the intracellular fate of a designed protein–nanomaterial hybrid with antifibrotic properties that shows great promise in mitigating myocardial fibrosis. Cryo 3D structured illumination microscopy (cryo-3D-SIM) pinpoints the location and cryo soft X-ray tomography (cryo-SXT) reveals the ultrastructural environment and subcellular localization of this nanomaterial with spatial correlation accuracy down to 70 nm in whole cells. This novel high resolution 3D cryo correlative approach unambiguously locates the nanomaterial after overnight treatment within multivesicular bodies which have been associated with endosomal trafficking events by confocal microscopy. Moreover, this approach allows assessing the cellular response towards the treatment by evaluating the morphological changes induced. This is especially relevant for the future usage of nanoformulations in clinical practices. This correlative super-resolution and X-ray imaging strategy joins high specificity, by the use of fluorescence, with high spatial resolution at 30 nm (half pitch) provided by cryo-SXT in whole cells, without the need of staining or fixation, and can be of particular benefit to locate specific molecules in the native cellular environment in bio-nanomedicine.

A novel 3D cryo correlative approach locates designed therapeutic protein–nanomaterial hybrids in whole cells with high specificity and resolution. Detection of treatment-induced morphological changes, crucial for pre-clinical studies, are revealed.

Transmission Electron Microscopy Tilt-Series Data from In-Situ Chondrocyte Primary Cilia

The primary cilium has recently become the focus of intensive investigations into understanding the physical structure and processes of eukaryotic cells. This paper describes two tilt-series image datasets, acquired by transmission electron microscopy, of in situ chick-embryo sternal-cartilage primary cilia. These data have been released under an open-access licence, and are well suited to tomographic reconstruction and modelling of the cilium.

Quantifying nanotherapeutic penetration using a hydrogel-based microsystem as a new 3D in vitro platform

The huge gap between 2D in vitro assays used for drug screening and the in vivo 3D physiological environment hampered reliable predictions for the route and accumulation of nanotherapeutics in vivo. For such nanotherapeutics, multi-cellular tumour spheroids (MCTS) are emerging as a good alternative in vitro model. However, the classical approaches to produce MCTS suffer from low yield, slow process, difficulties in MCTS manipulation and compatibility with high-magnification fluorescence optical microscopy. On the other hand, spheroid-on-chip set-ups developed so far require a practical knowledge of microfluidics difficult to transfer to a cell biology laboratory. We present here a simple yet highly flexible 3D model microsystem consisting of agarose-based microwells. Fully compatible with the multi-well plate format conventionally used in cell biology, our simple process enables the formation of hundreds of reproducible spheroids in a single pipetting. Immunostaining and fluorescence imaging including live high-resolution optical microscopy can be performed in situ, with no manipulation of spheroids. As a proof of principle of the relevance of such an in vitro platform for nanotherapeutic evaluation, this study investigates the kinetics and localisation of nanoparticles within colorectal cancer MCTS cells (HCT-116). The nanoparticles chosen are sub-5 nm ultrasmall nanoparticles made of polysiloxane and gadolinium chelates that can be visualized in MRI (AGuIX®, currently implicated in clinical trials as effective radiosensitizers for radiotherapy) and confocal microscopy after addition of Cy5.5. We show that the amount of AGuIX® nanoparticles within cells is largely different in 2D and 3D. Using our flexible agarose-based microsystems, we are able to resolve spatially and temporally the penetration and distribution of AGuIX® nanoparticles within MCTS. The nanoparticles are first found in both extracellular and intracellular space of MCTS. While the extracellular part is washed away after a few days, we evidenced intracellular localisation of AGuIX®, mainly within the lysosomal compartment, but also occasionally within mitochondria. Hence, our agarose-based microsystem appears as a promising 3D in vitro user-friendly platform for investigation of nanotherapeutic transport, ahead of in vivo studies.

Insights into the intraparticle morphology of dendritic mesoporous silica nanoparticles from electron tomographic reconstructions

HYPOTHESIS

Although many synthetic pathways allow to fine-tune the morphology of dendritic mesoporous silica nanoparticles (DMSNs), the control of their particle size and mesopore diameter remains a challenge. Our study focuses on either increasing the mean particle size or adjusting the pore size distribution, changing only one parameter (particle or pore size) at a time. The dependence of key morphological features (porosity; pore shape and pore dimensions) on radial distance from the particle center has been investigated in detail.

EXPERIMENTS

Three-dimensional reconstructions of the particles obtained by scanning transmission electron microscopy (STEM) tomography were adapted as geometrical models for the quantification of intraparticle morphologies by radial porosity and chord length distribution analyses. Structural properties of the different synthesized DMSNs have been complementary characterized using TEM, SEM, nitrogen physisorption, and dynamic light scattering.

FINDINGS

The successful independent tuning of particle and pore sizes of the DMSNs could be confirmed by conventional analysis methods. Unique morphological features, which influence the uptake and release of guest molecules in biomedical applications, were uncovered from analyzing the STEM tomography-based reconstructions. It includes the quantification of structural hierarchy, identification of intrawall openings and pores, as well as the distinction of pore shapes (conical vs. cylindrical).

Insight into the Formation and Stability of Solid Electrolyte Interphase for Nanostructured Silicon-Based Anode Electrodes Used in Li-Ion Batteries

Silicon-based anode fabrication with nanoscale structuration improves the energy density and life cycle of Li-ion batteries. As-synthesized silicon (Si) nanowires (NWs) or nanoparticles (NPs) directly on the current collector represent a credible alternative to conventional graphite anodes. However, the operating potentials of these electrodes are below the electrochemical stability window of all electrolytes used in commercial Li-ion systems. During the first charging phase of the cell, partial decomposition of the electrolyte takes place, which leads to the formation of a layer at the surface of the electrode, called solid electrolyte interphase (SEI). A stable and continuous SEI layer formation is a critical factor to achieve reliable lifetime stability of the battery. Once formed, the SEI acts as a passivation layer that minimizes further degradation of the electrolyte during cycling, while allowing lithium-ion diffusion with their subsequent insertion into the active material and ensuring reversible operation of the electrode. However, one of the major issues requiring deeper investigation is the assessment of the morphological extension of the SEI layer into the active material, which is one of the main parameters affecting the anode performances. In the present study, we use electron tomography with a low electron dose to retrieve three-dimensional information on the SEI layer formation and its stability around SiNWs and SiNPs. The possible mechanisms of SEI evolution could be inferred from the interpretation and analysis of the reconstructed volumes. Significant volume variations in the SiNW and an inhomogeneous distribution of the SEI layer around the NWs are observed during cycling and provide insights into the potential mechanism leading to the generally reported SiNW anode capacity fading. By contrast, analysis of the reconstructed SiNPs' volume for a sample undergoing one lithiation-delithiation cycle shows that the SEI remains homogeneously distributed around the NPs that retain their spherical morphology and points to the potential benefit of such nanoscale Si anode materials to improve their cycling lifetime.

Tomographic Study of Mesopore Formation in Ceria Nanorods

Porosity in functional oxide nanorods is a recently discovered new type of microstructure, which is not yet fully understood and still under evaluation for its impact on applications in catalysis and gas/ion storage. Here we explore the shape and distribution of pores in ceria in three dimensions using a modified algorithm of geometric tomography as a reliable tool for reconstructing defective and strained nanoobjects. The pores are confirmed as "negative-particle" or "inverse-particle" cuboctahedral shapes located exclusively beneath the flat surface of the rods separated via a sub-5 nm thin ceria wall from the outside. New findings also comprise elongated "negative-rod" defects, seen as embryonic nanotubes, and pores in cube-shaped ceria. Furthermore, we report near-sintering secondary heat treatment of nanorods and cubes, confirming persistence of pores beyond external surface rounding. We support our experiments with molecular modeling and predict that the growth history of voids is via diffusion and aggregation of atomic point defects. In addition, we use density functional theory to show that the relative stability of pore (shape) increases in the order "cuboidal" < "hexagonal-prismatic" < "octahedral". The results indicate that by engineering voids into nanorods, via a high-temperature postsynthetic heat treatment, a potential future alternative route of tuning catalytic activities might become possible.

Calcite as a Precursor of Hydroxyapatite in the Early Biomineralization of Differentiating Human Bone-Marrow Mesenchymal Stem Cells

Biomineralization is the process by which living organisms generate organized mineral crystals. In human cells, this phenomenon culminates with the formation of hydroxyapatite, which is a naturally occurring mineral form of calcium apatite. The mechanism that explains the genesis within the cell and the propagation of the mineral in the extracellular matrix still remains largely unexplained, and its characterization is highly controversial, especially in humans. In fact, up to now, biomineralization core knowledge has been provided by investigations on the advanced phases of this process. In this study, we characterize the contents of calcium depositions in human bone mesenchymal stem cells exposed to an osteogenic cocktail for 4 and 10 days using synchrotron-based cryo-soft-X-ray tomography and cryo-XANES microscopy. The reported results suggest crystalline calcite as a precursor of hydroxyapatite depositions within the cells in the biomineralization process. In particular, both calcite and hydroxyapatite were detected within the cell during the early phase of osteogenic differentiation. This striking finding may redefine most of the biomineralization models published so far, taking into account that they have been formulated using murine samples while studies in human cell lines are still scarce.

Comprehensive Characterization of a Mesoporous Cerium Oxide Nanomaterial with High Surface Area and High Thermal Stability

In the present study, the pore space of a mesoporous cerium oxide material is investigated, which forms by the self-assembly of primary particles into a spherical secondary structure possessing a disordered mesopore space. The material under study exhibits quite stable mesoporosity upon aging at high temperatures (800 °C) and is, thus, of potential interest in high-temperature catalysis. Here, different characterization techniques were applied to elucidate the structural evolution taking place between heat treatment at 400 °C and aging at 800 °C, i.e., in a water-containing atmosphere, which is usually detrimental to nanoscaled porosity. The changes in the mesoporosity were monitored by advanced physisorption experiments, including hysteresis scanning, and electron tomography analysis coupled with a 3D reconstruction of the mesopore space. These methods indicate that the 3D spatial arrangement of the primary particles during the synthesis under hydrothermal conditions via thermal hydrolysis is related to the thermal stability of the hierarchical mesopore structure. The assembly of the primary CeO₂ particles (∼4 nm in size) results in an interparticulate space constituting an open 3D mesopore network, as revealed by skeleton analysis of tomography data, being in conformity with hysteresis scanning. At elevated temperatures (800 °C), sinter processes occur resulting in the growth of the primary particles, but the 3D mesopore network and the spherical secondary structure are preserved.

Structural and chemical characterization of MoO2/MoS2 triple-hybrid materials using electron microscopy in up to three dimensions

This work presents the synthesis of MoO₂/MoS₂ core/shell nanoparticles within a carbon nanotube network and their detailed electron microscopy investigation in up to three dimensions. The triple-hybrid core/shell material was prepared by atomic layer deposition of molybdenum oxide onto carbon nanotube networks, followed by annealing in a sulfur-containing gas atmosphere. High-resolution transmission electron microscopy together with electron diffraction, supported by chemical analysis via energy dispersive X-ray and electron energy loss spectroscopy, gave proof of a MoO₂ core covered by few layers of a MoS₂ shell within an entangled network of carbon nanotubes. To gain further insights into this complex material, the analysis was completed with 3D electron tomography. By using Z-contrast imaging, distinct reconstruction of core and shell material was possible, enabling the analysis of the 3D structure of the material. These investigations showed imperfections in the nanoparticles which can impact material performance, i.e. for faradaic charge storage or electrocatalysis.

Niemann Pick C2 protein enables cholesterol transfer from endo-lysosomes to the plasma membrane for efflux by shedding of extracellular vesicles

The Niemann-Pick C2 protein (NPC2) is a sterol transfer protein in the lumen of late endosomes and lysosomes (LE/LYSs). Absence of functional NPC2 leads to endo-lysosomal buildup of cholesterol and other lipids. How NPC2's known capacity to transport cholesterol between model membranes is linked to its function in living cells is not known. Using quantitative live-cell imaging combined with modeling of the efflux kinetics, we show that NPC2-deficient human fibroblasts can export the cholesterol analog dehydroergosterol (DHE) from LE/LYSs. Internalized NPC2 accelerated sterol efflux extensively, accompanied by reallocation of LE/LYSs containing fluorescent NPC2 and DHE to the cell periphery. Using quantitative fluorescence loss in photobleaching of TopFluor-cholesterol (TF-Chol), we estimate a residence time for a rapidly exchanging sterol pool in LE/LYSs localized in close proximity to the plasma membrane (PM), of less than one min and observed non-vesicular sterol exchange between LE/LYSs and the PM. Excess sterol was released from the PM by shedding of cholesterol-rich vesicles. The ultrastructure of such vesicles was analyzed by combined fluorescence and cryo soft X-ray tomography (SXT), revealing that they can contain lysosomal cargo and intraluminal vesicles. Treating cells with apoprotein A1 and with nuclear receptor liver X-receptor (LXR) agonists to upregulate expression of ABC transporters enhanced cholesterol efflux from the PM, at least partly by accelerating vesicle release. We conclude that NPC2 inside LE/LYSs facilitates non-vesicular sterol exchange with the PM for subsequent sterol efflux to acceptor proteins and for shedding of sterol-rich vesicles from the cell surface.

Porosity and Structure of Hierarchically Porous Ni/Al2O3 Catalysts for CO2 Methanation

CO2 methanation is often performed on Ni/Al2O3 catalysts, which can suffer from mass transport limitations and, therefore, decreased efficiency. Here we show the application of a hierarchically porous Ni/Al2O3 catalyst for methanation of CO2. The material has a well-defined and connected meso- and macropore structure with a total porosity of 78%. The pore structure was thoroughly studied with conventional methods, i.e., N2 sorption, Hg porosimetry, and He pycnometry, and advanced imaging techniques, i.e., electron tomography and ptychographic X-ray computed tomography. Tomography can quantify the pore system in a manner that is not possible using conventional porosimetry. Macrokinetic simulations were performed based on the measures obtained by porosity analysis. These show the potential benefit of enhanced mass-transfer properties of the hierarchical pore system compared to a pure mesoporous catalyst at industrially relevant conditions. Besides the investigation of the pore system, the catalyst was studied by Rietveld refinement, diffuse reflectance ultraviolet-visible (DRUV/vis) spectroscopy, and H2-temperature programmed reduction (TPR), showing a high reduction temperature required for activation due to structural incorporation of Ni into the transition alumina. The reduced hierarchically porous Ni/Al2O3 catalyst is highly active in CO2 methanation, showing comparable conversion and selectivity for CH4 to an industrial reference catalyst.

Cellular pathways of calcium transport and concentration toward mineral formation in sea urchin larvae

Sea urchin larvae have an endoskeleton consisting of two calcitic spicules. The primary mesenchyme cells (PMCs) are the cells that are responsible for spicule formation. PMCs endocytose sea water from the larval internal body cavity into a network of vacuoles and vesicles, where calcium ions are concentrated until they precipitate in the form of amorphous calcium carbonate (ACC). The mineral is subsequently transferred to the syncytium, where the spicule forms. Using cryo-soft X-ray microscopy we imaged intracellular calcium-containing particles in the PMCs and acquired Ca-L2,3 X-ray absorption near-edge spectra of these Ca-rich particles. Using the prepeak/main peak (L2'/ L2) intensity ratio, which reflects the atomic order in the first Ca coordination shell, we determined the state of the calcium ions in each particle. The concentration of Ca in each of the particles was also determined by the integrated area in the main Ca absorption peak. We observed about 700 Ca-rich particles with order parameters, L2'/ L2, ranging from solution to hydrated and anhydrous ACC, and with concentrations ranging between 1 and 15 M. We conclude that in each cell the calcium ions exist in a continuum of states. This implies that most, but not all, water is expelled from the particles. This cellular process of calcium concentration may represent a widespread pathway in mineralizing organisms.

Biological Applications of Short Wavelength Microscopy Based on Compact, Laser-Produced Gas-Puff Plasma Source

Over the last decades, remarkable efforts have been made to improve the resolution in photon-based microscopes. The employment of compact sources based on table-top laser-produced soft X-ray (SXR) in the “water window” spectral range (λ = 2.3–4.4 nm) and extreme ultraviolet (EUV) plasma allowed to overcome the limitations imposed by large facilities, such as synchrotrons and X-ray free electron lasers (XFEL), because of their high complexity, costs, and limited user access. A laser-plasma double stream gas-puff target source represents a powerful tool for microscopy operating in transmission mode, significantly improving the spatial resolution into the nanometric scale, comparing to the traditional visible light (optical) microscopes. Such an approach allows generating the plasma efficiently, without debris, providing a high flux of EUV and SXR photons. In this review, we present the development and optimization of desktop imaging systems: a EUV and an SXR full field microscope, allowing to achieve a sub-50 nm spatial resolution with short exposure time and an SXR contact microscope, capable to resolve internal structures in a thin layer of sensitive photoresist. Details about the source, as well as imaging results for biological applications, will be presented and discussed.

Determination of Microtubule Lattice Parameters from Cryo-electron Microscope Images Using TubuleJ

The α-β tubulin heterodimer undergoes subtle conformational changes during microtubule assembly. These can be modulated by external factors, whose effects on microtubule structure can be characterized on 2D views obtained by cryo-electron microscopy. Analysis of microtubule images is facilitated if they are straight enough to interpret and filter their image Fourier transform, which provide useful information concerning the arrangement of tubulin molecules inside the microtubule lattice. Here, we describe the use of the TubuleJ software to straighten microtubules and determine their lattice parameters. Basic 3D reconstructions can be performed to evaluate the relevance of these parameters. This approach can be used to analyze the effects of nucleotide analogues, drugs or MAPs on microtubule structure, or to select microtubule images prior to high-resolution 3D reconstructions.

Spatial Nano-Morphology of the Prolamellar Body in Etiolated Arabidopsis thaliana Plants With Disturbed Pigment and Polyprenol Composition

The prolamellar body (PLB) is a periodic bicontinuous membrane structure based on tubular tetrahedral units. PLBs are present in plant etioplasts and, upon illumination, directly transform into the lamellar thylakoid networks within chloroplasts. Efficient tubular-lamellar rearrangement and later formation of the photosynthetically active thylakoid membranes are crucial steps in the development of plant autotrophy. PLB membranes are mainly composed of galactolipids, carotenoids, and protochlorophyllide (Pchlide), the chlorophyll precursor, bound in a complex with NADPH and Pchlide oxidoreductase. Although the PLB structure has been studied for over 50 years, the direct role of particular membrane components in the formation of the PLB paracrystalline network remains elusive. Moreover, despite the numerous literature data regarding the PLB geometry, their reliable comparative analysis is complicated due to variable experimental conditions. Therefore, we performed comprehensive ultrastructural and low-temperature fluorescence analysis of wild type Arabidopsis thaliana (Arabidopsis) seedlings grown in different conditions typical for studies on etiolated seedlings. We established that the addition of sucrose to the growing media significantly affected the size and compactness of the PLB. The etiolation period was also an important factor influencing the PLB structural parameters and the ratio of free to complex-bound Pchlide. Thus, a reliable PLB structural and spectral analysis requires particular attention to the applied experimental conditions. We investigated the influence of the pigment and polyprenol components of the etioplast membranes on the formation of the PLB spatial structure. The PLB 3D structure in several Arabidopsis mutants (ccr1-1, lut5-1, szl1-1npq1-2, aba1-6, pif1, cpt7) with disturbed levels of particular pigments and polyprenols using electron tomography technique was studied. We found that the PLB nano-morphology was mainly affected in the pif1 and aba1-6 mutants. An increased level of Pchlide (pif1) resulted in the substantial shift of the structural balance between outer and inner PLB water channels and overall PLB compactness compared to wild type plants. The decrease in the relative content of β-branch xanthophylls in aba1-6 plants was manifested by local disturbances in the paracrystalline structure of the PLB network. Therefore, proper levels of particular etioplast pigments are essential for the formation of stable and regular PLB structure.

Morphology-transport relationships for SBA-15 and KIT-6 ordered mesoporous silicas

Quantitative morphology-transport relationships are derived for ordered mesoporous silicas through direct numerical simulation of hindered diffusion in realistic geometrical models of the pore space obtained from physical reconstruction by electron tomography. We monitor accessible porosity and effective diffusion coefficients resulting from steric and hydrodynamic interactions between passive tracers and the pore space confinement as a function of λ = d_tracer/d_meso (ratio of tracer diameter to mean mesopore diameter) in SBA-15 (d_meso = 9.1 nm) and KIT-6 (d_meso = 10.5 nm) silica samples. For λ = 0, the pointlike tracers reproduce the true diffusive tortuosities. For 0 ≤λ < 0.5, the derived hindrance factor quantifies the extent to which diffusion of finite-size tracers through the materials is hindered compared with free diffusion in the bulk liquid. The hindrance factor connects the transport properties of the ordered silicas to their mesopore space morphologies and enables quantitative comparison with random mesoporous silicas. Key feature of the ordered silicas is a narrow, symmetric mesopore size distribution (∼10% relative standard deviation), which engenders a sharper decline of the accessible-porosity window with increasing λ than observed for random silicas with their wide, asymmetric mesopore size distributions. As support structures, ordered mesoporous silicas should offer benefits for applications where spatial confinement effects and molecular size-selectivity are of prime importance. On the other hand, random mesoporous silicas enable higher diffusivities for λ > 0.3, because the larger pores carry most of the diffusive flux and keep pathways open when smaller pores have closed off.

Cells Undergo Major Changes in the Quantity of Cytoplasmic Organelles after Uptake of Gold Nanoparticles with Biologically Relevant Surface Coatings

Here, we use cryo soft X-ray tomography (cryo-SXT), which delivers 3D ultrastructural volumes of intact cells without chemical fixation or staining, to gain insight about nanoparticle uptake for nanomedicine. We initially used dendritic polyglycerol sulfate (dPGS) with potential diagnostic and therapeutic applications in inflammation. Although dPGS-coated gold nanoparticle (dPGS-AuNP) uptake followed a conventional endocytic/degradative pathway in human lung epithelial cell lines (A549), with cryo-SXT, we detected ∼5% of dPGS-AuNPs in the cytoplasm, a level undetectable by confocal light microscopy. We also observed ∼5% of dPGS-AuNPs in a rarely identified subcellular site, namely, lipid droplets, which are important for cellular energy metabolism. Finally, we also found substantial changes in the quantity of cytoplasmic organelles upon dPGS-AuNP uptake over the 1-6 h incubation period; the number of small vesicles and mitochondria significantly increased, and the number of multivesicular bodies and the number and volume of lipid droplets significantly decreased. Although nearly all organelle numbers at 6 h were still significantly different from controls, most appeared to be returning to normal levels. To test for generality, we also examined cells after uptake of gold nanoparticles coated with a different agent, polyethylenimine (PEI), used for nucleic acid delivery. PEI nanoparticles did not enter lipid droplets, but they induced similar, albeit less pronounced, changes in the quantity of cytoplasmic organelles. We confirmed these changes in organelle quantities for both nanoparticle coatings by confocal fluorescence microscopy. We suggest this cytoplasmic remodeling could reflect a more common cellular response to coated gold nanoparticle uptake.

Applications and Challenges of Machine Learning to Enable Realistic Cellular Simulations

In this perspective, we examine three key aspects of an end-to-end pipeline for realistic cellular simulations: reconstruction and segmentation of cellular structures; generation of cellular structures; and mesh generation, simulation, and data analysis. We highlight some of the relevant prior work in these distinct but overlapping areas, with a particular emphasis on current use of machine learning technologies, as well as on future opportunities.

Synthesis of mesoporous ceria using metal- and halogen-free ordered mesoporous carbon as a hard template

Ordered mesoporous cerias were synthesised by employing metal- and halogen-free ordered mesoporous carbons (OMCs) as the hard templates in a 'nanocasting' procedure. TEM, small angle (SA) and wide angle (WA) XRD, and N₂ physisorption analyses were used to characterise the templates, intermediates and ceria products and electron tomography (STEM-HAADF) was used to explore the 3D morphology of the ceria nanostructures grown within the carbon templates. This allowed the relationships between the structures of the OMC templates and the products to be considered in detail as two parameters were varied. These were: the method of impregnation of the ceria precursor; and the temperature of calcination of the OMC template. Of the four impregnation methods tested, the solid-liquid method was found to be the most successful. This gave a high quality product with the highest yield of uniform mesopores, and crystalline nanorods of ceria arrayed in clear long-range order, as viewed by TEM and determined in SA and WAXRD. The specific surface area and pore volume exhibited by this sample were 111 m² g^-1 and 0.39 cm³ g^-1, respectively. 3D electron tomography reconstructions revealed the presence of a network of ordered, nanoscale, rod-like structures interlinked in a complex fashion. The effect of calcination temperature of the template on uptake of the ceria precursor during impregnation was studied by calcining OMCs at temperatures from 350 to 800 °C and using these as hard templates for the nanocasting of ceria. Of these, the carbon template calcined at 400 °C gave the highest quality product.

Colloidal plasmonic nanostar antennas with wide range resonance tunability

Gold nanostars display exceptional field enhancement properties and tunable resonant modes that can be leveraged to create effective imaging tags, phototherapeutic agents, and hot electron-based photocatalytic platforms. Despite having emerged as the cornerstone among plasmonic nanoparticles with respect to resonant strength and tunability, some well-known limitations have hampered their technological implementation. Herein we tackle these recognized intrinsic weaknesses, which stem from the complex, and thus computationally untreatable morphology and the limited sample monodispersity, by proposing a novel 6-spike nanostar, which we have computationally studied and synthetically realized, as the epitome of 3D plasmonic nanoantenna with wide range plasmonic tunability. Our concerted computational and experimental effort shows that these nanostars combine the unique advantages of nanostructures fabricated from the top-down and those synthesized from the bottom-up, showcasing a unique plasmonic response that remains largely unaltered on going from the single particle to the ensemble. Furthermore, they display multiple, well-separated, narrow resonances, the most intense of which extends in space much farther than that observed before for any plasmonic mode localized around a colloidal nanostructure. Importantly, the unique close correlation between morphology and plasmonic response leads the resonant modes of these particles to be tunable between 600 and 2000 nm, a unique feature that could find relevance in cutting edge technological applications.

Electroactive Area from Porous Oxide Films Loaded with Silver Nanoparticles: Electrochemical and Electron Tomography Observations

Electrochemical studies of nanomaterial-based electrodes have been widely developed for catalyst and energy-harvesting applications. The evolution of these electrodes over time and their efficiency have been extensively studied and analyzed in order to optimize their performance. However, the electrochemical responses of electrodes are rarely studied in terms of the position of the active species within these electrodes. In this paper, we highlight that the spatial location of silver nanoparticles (NPs) embedded inside semiconductive porous films, TiO₂ or Fe₂O₃, is crucial for the electrochemical response. In fact, by using cycling voltammetry and electron tomography experiments, we show the existence of an "electroactive area", corresponding to a reduced thickness of the sample in close vicinity to a fluorine-doped tin oxide substrate where most of the electrochemical responses originate. Our results demonstrate that, for a film thickness of several hundred nanometers, only less than 30 nm close to the substrate responds electrochemically. However, cyclic voltammetry empties the electroactive area of silver NPs. Therefore, application of chronoamperometry coupled to irradiation allowed regeneration of this area thanks to an increased diffusion of silver species. In this paper, we also show the significant diffusion of silver species within the film during electrochemical experiments, a phenomenon even increased by irradiation. These results are therefore an important step that shows the importance of the localization of active species within a porous film and help in understanding and increasing the durability of nanomaterial-based electrodes.

Galactolipid deficiency disturbs spatial arrangement of the thylakoid network in Arabidopsis thaliana plants

The chloroplast thylakoid network is a dynamic structure which, through possible rearrangements, plays a crucial role in regulation of photosynthesis. Although the importance of the main components of the thylakoid membrane matrix, galactolipids, in the formation of the network of internal plastid membrane was found before, the structural role of monogalactosyldiacylglycerol (MGDG) and digalactosylidacylglycerol (DGDG) is still largely unknown. We elucidated detailed structural modifications of the thylakoid membrane system in Arabidopsis thaliana MGDG- and DGDG-deficient mutants. An altered MGDG/DGDG ratio was structurally reflected by formation of smaller grana, local changes in grana stacking repeat distance, and significant changes in the spatial organization of the thylakoid network compared with wild-type plants. The decrease of the MGDG level impaired the formation of the typical helical grana structure and resulted in a 'helical-dichotomic' arrangement. DGDG deficiency did not affect spatial grana organization but changed the shape of the thylakoid membrane network in situ from lens like into a flattened shape. Such structural disturbances were accompanied by altered composition of carotenoid and chlorophyll-protein complexes, which eventually led to the decreased photosynthetic efficiency of MGDG- and DGDG-deficient plants.