Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography.

Bacterial spores owe their incredible resistance capacities to molecular structures that protect the cell content from external aggressions. Among the determinants of resistance are the quaternary structure of the chromosome and an extracellular shell made of proteinaceous layers (the coat), the assembly of which remains poorly understood. Here, in situ cryo-electron tomography on lamellae generated by cryo-focused ion beam micromachining provides insights into the ultrastructural organization of Bacillus subtilis sporangia. The reconstructed tomograms reveal that early during sporulation, the chromosome in the forespore adopts a toroidal structure harboring 5.5-nm thick fibers. At the same stage, coat proteins at the surface of the forespore form a stack of amorphous or structured layers with distinct electron density, dimensions and organization. By analyzing mutant strains using cryo-electron tomography and transmission electron microscopy on resin sections, we distinguish seven nascent coat regions with different molecular properties, and propose a model for the contribution of coat morphogenetic proteins.

Adaptive traits of cysts of the snow alga Sanguina nivaloides unveiled by 3D subcellular imaging.

Sanguina nivaloides is the main alga forming red snowfields in high mountains and Polar Regions. It is non-cultivable. Analysis of environmental samples by X-ray tomography, focused-ion-beam scanning-electron-microscopy, physicochemical and physiological characterization reveal adaptive traits accounting for algal capacity to reside in snow. Cysts populate liquid water at the periphery of ice, are photosynthetically active, can survive for months, and are sensitive to freezing. They harbor a wrinkled plasma membrane expanding the interface with environment. Ionomic analysis supports a cell efflux of K+, and assimilation of phosphorus. Glycerolipidomic analysis confirms a phosphate limitation. The chloroplast contains thylakoids oriented in all directions, fixes carbon in a central pyrenoid and produces starch in peripheral protuberances. Analysis of cells kept in the dark shows that starch is a short-term carbon storage. The biogenesis of cytosolic droplets shows that they are loaded with triacylglycerol and carotenoids for long-term carbon storage and protection against oxidative stress.

3D-reconstructions of zygospores in Zygnema vaginatum (Charophyta) reveal details of cell wall formation, suggesting adaptations to extreme habitats.

The streptophyte green algal class Zygnematophyceae is the immediate sister lineage to land plants. Their special form of sexual reproduction via conjugation might have played a key role during terrestrialization. Thus, studying Zygnematophyceae and conjugation is crucial for understanding the conquest of land. Moreover, sexual reproduction features are important for species determination. We present a phylogenetic analysis of a field-sampled Zygnema strain and analyze its conjugation process and zygospore morphology, both at the micro- and nanoscale, including 3D-reconstructions of the zygospore architecture. Vegetative filament size (26.18 ± 1.07 µm) and reproductive features allowed morphological determination of Zygnema vaginatum, which was combined with molecular analyses based on rbcL sequencing. Transmission electron microscopy (TEM) depicted a thin cell wall in young zygospores, while mature cells exhibited a tripartite wall, including a massive and sculptured mesospore. During development, cytological reorganizations were visualized by focused ion beam scanning electron microscopy (FIB-SEM). Pyrenoids were reorganized, and the gyroid cubic central thylakoid membranes, as well as the surrounding starch granules, degraded (starch granule volume: 3.58 ± 2.35 µm3 in young cells; 0.68 ± 0.74 µm3 at an intermediate stage of zygospore maturation). Additionally, lipid droplets (LDs) changed drastically in shape and abundance during zygospore maturation (LD/cell volume: 11.77% in young cells; 8.79% in intermediate cells, 19.45% in old cells). In summary, we provide the first TEM images and 3D-reconstructions of Zygnema zygospores, giving insights into the physiological processes involved in their maturation. These observations help to understand mechanisms that facilitated the transition from water to land in Zygnematophyceae.

(De)Lithiation and Strain Mechanism in Crystalline Ge Nanoparticles.

Germanium is a promising active material for high energy density anodes in Li-ion batteries thanks to its good Li-ion conduction and mechanical properties. However, a deep understanding of the (de)lithiation mechanism of Ge requires advanced characterizations to correlate structural and chemical evolution during charge and discharge. Here we report a combined operando X-ray diffraction (XRD) and ex situ 7Li solid-state NMR investigation performed on crystalline germanium nanoparticles (c-Ge Nps) based anodes during partial and complete cycling at C/10 versus Li metal. High-resolution XRD data, acquired along three successive partial cycles, revealed the formation process of crystalline core-amorphous shell particles and their associated strain behavior, demonstrating the reversibility of the c-Ge lattice strain, unlike what is observed in the crystalline silicon nanoparticles. Moreover, the crystalline and amorphous lithiated phases formed during a complete lithiation cycle are identified. Amorphous Li7Ge3 and Li7Ge2 are formed successively, followed by the appearance of crystalline Li15Ge4 (c-Li15Ge4) at the end of lithiation. These results highlight the enhanced mechanical properties of germanium compared to silicon, which can mitigate pulverization and increase structural stability, in the perspective for developing high-performance anodes.

A biological nanofoam: The wall of coniferous bisaccate pollen.

The outer layer of the pollen grain, the exine, plays a key role in the survival of terrestrial plant life. However, the exine structure in different groups of plants remains enigmatic. Here, modern and fossil coniferous bisaccate pollen were examined to investigate the detailed three-dimensional structure and properties of the pollen wall. X-ray nanotomography and volume electron microscopy are used to provide high-resolution imagery, revealing a solid nanofoam structure. Atomic force microscopy measurements were used to compare the pollen wall with other natural and synthetic foams and to demonstrate that the mechanical properties of the wall in this type of pollen are retained for millions of years in fossil specimens. The microscopic structure of this robust biological material has potential applications in materials sciences and also contributes to our understanding of the evolutionary success of conifers and other plants over geological time.

Correlative transmission electron microscopy and high-resolution hard X-ray fluorescence microscopy of cell sections to measure trace element concentrations at the organelle level.

Metals are essential for life and their concentration and distribution in organisms are tightly regulated. Indeed, in their free form, most transition metal ions are toxic. Therefore, an excess of physiologic metal ions or the uptake of non-physiologic metal ions can be highly detrimental to the organism. It is thus fundamental to understand metal distribution under physiological, pathological or environmental conditions, for instance in metal-related pathologies or upon environmental exposure to metals. Elemental imaging techniques can serve this purpose, by allowing the visualization and the quantification of metal species in tissues down to the level of cell organelles. Synchrotron radiation-based X-ray fluorescence (SR-XRF) microscopy is one of the most sensitive techniques to date, and great progress was made to reach nanoscale spatial resolution. Here we propose a correlative method to couple SR-XRF to electron microscopy (EM), with the possibility to quantify selected elemental contents in a specific organelle of interest with 50 × 50 nm2 raster scan resolution. We performed EM and SR-XRF on the same section of hepatocytes exposed to silver nanoparticles, in order to identify mitochondria through EM and visualize Ag co-localized with these organelles through SR-XRF. We demonstrate the accumulation of silver in mitochondria, which can reach a 10-fold higher silver concentration compared to the surrounding cytosol. The sample preparation and experimental setup can be adapted to other scientific questions, making the correlative use of SR-XRF and EM suitable to address a large panel of biological questions related to metal homeostasis.

Morphological bases of phytoplankton energy management and physiological responses unveiled by 3D subcellular imaging.

Eukaryotic phytoplankton have a small global biomass but play major roles in primary production and climate. Despite improved understanding of phytoplankton diversity and evolution, we largely ignore the cellular bases of their environmental plasticity. By comparative 3D morphometric analysis across seven distant phytoplankton taxa, we observe constant volume occupancy by the main organelles and preserved volumetric ratios between plastids and mitochondria. We hypothesise that phytoplankton subcellular topology is modulated by energy-management constraints. Consistent with this, shifting the diatom Phaeodactylum from low to high light enhances photosynthesis and respiration, increases cell-volume occupancy by mitochondria and the plastid CO2-fixing pyrenoid, and boosts plastid-mitochondria contacts. Changes in organelle architectures and interactions also accompany Nannochloropsis acclimation to different trophic lifestyles, along with respiratory and photosynthetic responses. By revealing evolutionarily-conserved topologies of energy-managing organelles, and their role in phytoplankton acclimation, this work deciphers phytoplankton responses at subcellular scales.

Unveiling the multiscale morphology of chemically stabilized proton exchange membranes for fuel cells by means of Fourier and real space studies.

We recently presented the elaboration and functional properties of a new generation of hybrid membranes for PEMFC applications showing promising performances and durability. The strategy was to form, inside a commercial sPEEK membrane, via in situ sol-gel (SG) synthesis, a reactive SG phase able to reduce oxidative species generated during FC operation. In order to understand structure-properties interplay, we use a combination of direct space (AFM/3D FIB-SEM) and reciprocal space (SANS/WAXS) techniques to cover dimensional scales ranging from a hundred to few nanometers. AFM modulus images showed the SG phase distributed into spherical domains whose size increases with the SG uptake (ca. 100-200 nm range). Using contrast variation SANS, we observed that the sPEEK nanostructure is mostly unaffected by the insertion of the SG phase which presents a fractal-like multiscale structure. Additionally, the size of both the particles (aggregates/primary) is much too large to be sequestered in the ionic pathways of sPEEK. These findings indicate that the SG-NPs mainly grow within the amorphous interbundle domains. Noticeable rightward shift and widening of the ionomer peak are observed with the SG content, suggesting ion channel compression and greater heterogeneity of the ionic domain size. The SG phase develops in the interbundle regions with a limited impact on the water uptake but leading to a discontinuity of ionic conductivity. This Fourier and real spaces study clarifies the structure of the hybrid membranes and brings into the question the ideal distribution/localization of the SG phase to optimize the membrane's stabilization.

Evaluation of the Dermal Toxicity of InZnP Quantum Dots Before and After Accelerated Weathering: Toward a Safer-By-Design Strategy.

Quantum dots (QDs) are colloidal fluorescent semiconductor nanocrystals with exceptional optical properties. Their widespread use, particularly in light-emitting diodes (LEDs), displays, and photovoltaics, is questioning their potential toxicity. The most widely used QDs are CdSe and CdTe QDs, but due to the toxicity of cadmium (Cd), their use in electrical and electronic equipment is now restricted in the European Union through the Restriction of hazardous substances in electrical and electronic equipment (RoHS) directive. This has prompted the development of safer alternatives to Cd-based QDs; among them, InP QDs are the most promising ones. We recently developed RoHS-compliant QDs with an alloyed core composed of InZnP coated with a Zn(Se,S) gradient shell, which was further coated with an additional ZnS shell to protect the QDs from oxidative surface degradation. In this study, the toxicity of single-shelled InZnP/Zn(Se,S) core/gradient shell and of double-shelled InZnP/Zn(Se,S)/ZnS core/shell/shell QDs was evaluated both in their pristine form and after aging in a climatic chamber, mimicking a realistic environmental weathering. We show that both pristine and aged QDs, whatever their composition, accumulate in the cytoplasm of human primary keratinocytes where they form agglomerates at the vicinity of the nucleus. Pristine QDs do not show overt toxicity to cells, while aged QDs show cytotoxicity and genotoxicity and significantly modulate the mRNA expression of proteins involved in zinc homeostasis, cell redox response, and inflammation. While the three aged QDs show similar toxicity, the toxicity of pristine gradient-shell QD is higher than that of pristine double-shell QD, confirming that adding a second shell is a promising safer-by-design strategy. Taken together, these results suggest that end-of-life degradation products from InP-based QDs are detrimental to skin cells in case of accidental exposure and that the mechanisms driving this effect are oxidative stress, inflammation, and disturbance of cell metal homeostasis, particularly Zn homeostasis. Further efforts to promote safer-by-design formulations of QDs, for instance by reducing the In and Zn content and/or implementing a more robust outer shell, are therefore warranted.

A Scalable Silicon Nanowires-Grown-On-Graphite Composite for High-Energy Lithium Batteries.

Silicon (Si) is the most promising anode candidate for the next generation of lithium-ion batteries but difficult to cycle due to its poor electronic conductivity and large volume change during cycling. Nanostructured Si-based materials allow high loading and cycling stability but remain a challenge for process and engineering. We prepare a Si nanowires-grown-on-graphite one-pot composite (Gt-SiNW) via a simple and scalable route. The uniform distribution of SiNW and the graphite flakes alignment prevent electrode pulverization and accommodate volume expansion during cycling, resulting in very low electrode swelling. Our designed nanoarchitecture delivers outstanding electrochemical performance with a capacity retention of 87% after 250 cycles at 2C rate with an industrial electrode density of 1.6 g cm-3. Full cells with NMC-622 cathode display a capacity retention of 70% over 300 cycles. This work provides insights into the fruitful engineering of active composites at the nano- and microscales to design efficient Si-rich anodes.

Safer-by-design biocides made of tri-thiol bridged silver nanoparticle assemblies.

Silver nanoparticles (AgNPs) are efficient biocides increasingly used in consumer products and medical devices. Their activity is due to their capacity to release bioavailable Ag(i) ions making them long-lasting biocides but AgNPs themselves are usually easily released from the product. Besides, AgNPs are highly sensitive to various chemical environments that triggers their transformation, decreasing their activity. Altogether, widespread use of AgNPs leads to bacterial resistance and safety concerns for humans and the environment. There is thus a crucial need for improvement. Herein, a proof of concept for a novel biocide based on AgNP assemblies bridged together by a tri-thiol bioinspired ligand is presented. The final nanomaterial is stable and less sensitive to chemical environments with AgNPs completely covered by organic molecules tightly bound via their thiol functions. Therefore, these AgNP assemblies can be considered as safer-by-design and innovative biocides, since they deliver a sufficient amount of Ag(i) for biocidal activity with no release of AgNPs, which are insensitive to transformations in the nanomaterial.

Nano-Architectured Composite Anode Enabling Long-Term Cycling Stability for High-Capacity Lithium-Ion Batteries.

Failure mechanisms associated with silicon-based anodes are limiting the implementation of high-capacity lithium-ion batteries. Understanding the aging mechanism that deteriorates the anode performance and introducing novel-architectured composites offer new possibilities for improving the functionality of the electrodes. Here, the characterization of nano-architectured composite anode composed of active amorphous silicon domains (a-Si, 20 nm) and crystalline iron disilicide (c-FeSi2 , 5-15 nm) alloyed particles dispersed in a graphite matrix is reported. This unique hierarchical architecture yields long-term mechanical, structural, and cycling stability. Using advanced electron microscopy techniques, the nanoscale morphology and chemical evolution of the active particles upon lithiation/delithiation are investigated. Due to the volumetric variations of Si during lithiation/delithiation, the morphology of the a-Si/c-FeSi2 alloy evolves from a core-shell to a tree-branch type structure, wherein the continuous network of the active a-Si remains intact yielding capacity retention of 70% after 700 cycles. The root cause of electrode polarization, initial capacity fading, and electrode swelling is discussed and has profound implications for the development of stable lithium-ion batteries.

Correlative investigation of Mg doping in GaN layers grown at different temperatures by atom probe tomography and off-axis electron holography.

Correlation between off-axis electron holography and atom probe tomography (APT) provides morphological, chemical and electrical information about Mg doping (p-type) in gallium nitride (GaN) layers that have been grown at different temperatures at a nanometric scale. APT allows access to the three-dimensional distribution of atoms and their chemical nature. In particular, this technique allows visualisation of the Mg-rich clusters observed in p-doped GaN layers grown by metal-organic chemical vapour deposition. As the layer growth temperature increases, the cluster density decreases but their size indicted by the number of atoms increases. Moreover, APT reveals that threading dislocations are decorated with Mg atoms. Off-axis electron holography provides complementary information about the electrical activity of the Mg doping. As only a small fraction of dopant atoms are ionised at room temperature, this fraction is increased by annealing the specimen to 400 °C in situ in a transmission electron microscope (TEM). A strong reduction of the dopant electrical activity is observed for increases in the layer growth temperature. The correlation of APT with TEM-based techniques was shown to be a unique approach in order to investigate how the growth temperature affects both the chemical distribution and electrical activity of Mg dopant atoms.

Multi-scale quantification and modeling of aged nanostructured silicon-based composite anodes.

Advanced anode material designs utilizing dual phase alloy systems like Si/FeSi2 nano-composites show great potential to decrease the capacity degrading and improve the cycling capability for Lithium (Li)-ion batteries. Here, we present a multi-scale characterization approach to understand the (de-)lithiation and irreversible volumetric changes of the amorphous silicon (a-Si)/crystalline iron-silicide (c-FeSi2) nanoscale phase and its evolution due to cycling, as well as their impact on the proximate pore network. Scattering and 2D/3D imaging techniques are applied to probe the anode structural ageing from nm to µm length scales, after up to 300 charge-discharge cycles, and combined with modeling using the collected image data as an input. We obtain a quantified insight into the inhomogeneous lithiation of the active material induced by the morphology changes due to cycling. The electrochemical performance of Li-ion batteries does not only depend on the active material used, but also on the architecture of its proximity.

Canalicular domain structure and function in matrix-free hepatic spheroids.

Liver is pivotal in organism metabolism. This organ is receiving nutriments from the portal vein and then storing, metabolizing, distributing in the circulation or excreting excess and xenobiotics in bile. Liver architecture and hepatocyte polarization are crucial to achieve these functions. To study these mechanisms in details, relevant cell culture systems are required, which is not the case with standard 2D cell culture. Besides, primary hepatocytes rapidly de-differenciate making them inefficient in forming physiological system. Herein, we used an hepatoma-derived cell line to produce matrix-free hepatic spheroids and developed an integrated structural cell biology methodology by combining light sheet fluorescence microscopy and 3D electron microscopy to study their function and structure. Within these spheroids, hepatocytes polarize and organize to form bile canaliculi active for both organics and inorganics excretion. Besides, live imaging revealed the high dynamic of actin networks in basal membranes compared to their high stability in the apical pole that constitutes bile canaliculi. Finally, the first structure of active bile canaliculi was solved at nm resolution and showed the very high density of microvilli coming from all cells constituting the canaliculus. Therefore, this study is the first comprehensive and in-depth functional and structural study of bile canaliculi in a physiological-relevant context.

Multiscale Multiphase Lithiation and Delithiation Mechanisms in a Composite Electrode Unraveled by Simultaneous Operando Small-Angle and Wide-Angle X-Ray Scattering.

The (de)lithiation process and resulting atomic and nanoscale morphological changes of an a-Si/c-FeSi2/graphite composite negative electrode are investigated within a Li-ion full cell at several current rates (C-rates) and after prolonged cycling by simultaneous operando synchrotron wide-angle and small-angle X-ray scattering (WAXS and SAXS). WAXS allows the probing of the local crystalline structure. In particular, the observation of the graphite (de)lithiation process, revealed by the LixC6 Bragg reflections, enables access to the respective capacities of both graphite and active silicon. Simultaneously and independently, information on the silicon state of (de)lithiation and nanoscale morphology (1 to 60 nm) is obtained through SAXS. During lithiation, the SAXS intensity in the region corresponding to characteristic distances within the a-Si/c-FeSi2 domains increases. The combination of the SAXS/WAXS measurements over the course of several charge/discharge cycles, in pristine and aged electrodes, provides a complete picture of the C-rate-dependent sequential (de)lithiation mechanism of the a-Si/c-FeSi2/graphite anode. Our results indicate that, within the composite electrode, the active silicon volume does not increase linearly with lithium insertion and point toward the important role of the electrode morphology to accommodate the nanoscale silicon expansion, an effect that remains beneficial after cell aging and most probably explains the excellent performance of the composite material.

Algal Remodeling in a Ubiquitous Planktonic Photosymbiosis.

Photosymbiosis between single-celled hosts and microalgae is common in oceanic plankton, especially in oligotrophic surface waters. However, the functioning of this ecologically important cell-cell interaction and the subcellular mechanisms allowing the host to accommodate and benefit from its microalgae remain enigmatic. Here, using a combination of quantitative single-cell structural and chemical imaging techniques (FIB-SEM, nanoSIMS, Synchrotron X-ray fluorescence), we show that the structural organization, physiology, and trophic status of the algal symbionts (the haptophyte Phaeocystis) significantly change within their acantharian hosts compared to their free-living phase in culture. In symbiosis, algal cell division is blocked, photosynthesis is enhanced, and cell volume is increased by up to 10-fold with a higher number of plastids (from 2 to up to 30) and thylakoid membranes. The multiplication of plastids can lead to a 38-fold increase of the total plastid volume in a cell. Subcellular mapping of nutrients (nitrogen and phosphorous) and their stoichiometric ratios shows that symbiotic algae are impoverished in phosphorous and suggests a higher investment in energy-acquisition machinery rather than in growth. Nanoscale imaging also showed that the host supplies a substantial amount of trace metals (e.g., iron and cobalt), which are stored in algal vacuoles at high concentrations (up to 660 ppm). Sulfur mapping reveals a high concentration in algal vacuoles that may be a source of antioxidant molecules. Overall, this study unveils an unprecedented morphological and metabolic transformation of microalgae following their integration into a host, and it suggests that this widespread symbiosis is a farming strategy wherein the host engulfs and exploits microalgae.

Imaging Plastids in 2D and 3D: Confocal and Electron Microscopy.

Internal chloroplast structures present complex and various characteristics, which are still largely undetermined due to insufficient imaging investigation. Information on chloroplast morphology has traditionally been collected using light microscopy (LM), confocal laser scanning microscopy (CLSM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM) techniques. However, recent technological progresses in the field of microscopy have made it possible to visualize the internal structure of chloroplast in far greater detail and in 3D. Here we recapitulate protocols to visualize chloroplasts from Arabidopsis leaves and Phaeodactylum tricornutum cells with confocal and transmission electron microscopy together with a new technique using a focused ion beam-scanning electron microscope (FIB-SEM) allowing for 3D imaging.

Dopant radial inhomogeneity in Mg-doped GaN nanowires.

Using atom probe tomography, it is demonstrated that Mg doping of GaN nanowires grown by Molecular Beam Epitaxy results in a marked radial inhomogeneity, namely a higher Mg content in the periphery of the nanowires. This spatial inhomogeneity is attributed to a preferential incorporation of Mg through the m-plane sidewalls of nanowires and is related to the formation of a Mg-rich surface which is stabilized by hydrogen. This is further supported by Raman spectroscopy experiments which give evidence of Mg-H complexes in the doped nanowires. A Mg doping mechanism such as this, specific to nanowires, may lead to higher levels of Mg doping than in layers, boosting the potential interest of nanowires for light emitting diode applications.

Plastid thylakoid architecture optimizes photosynthesis in diatoms.

Photosynthesis is a unique process that allows independent colonization of the land by plants and of the oceans by phytoplankton. Although the photosynthesis process is well understood in plants, we are still unlocking the mechanisms evolved by phytoplankton to achieve extremely efficient photosynthesis. Here, we combine biochemical, structural and in vivo physiological studies to unravel the structure of the plastid in diatoms, prominent marine eukaryotes. Biochemical and immunolocalization analyses reveal segregation of photosynthetic complexes in the loosely stacked thylakoid membranes typical of diatoms. Separation of photosystems within subdomains minimizes their physical contacts, as required for improved light utilization. Chloroplast 3D reconstruction and in vivo spectroscopy show that these subdomains are interconnected, ensuring fast equilibration of electron carriers for efficient optimum photosynthesis. Thus, diatoms and plants have converged towards a similar functional distribution of the photosystems although via different thylakoid architectures, which likely evolved independently in the land and the ocean.