4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids.

New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue-scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice light-sheet imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70 × 60 × 40 µm xyz) at 5.7 s/frame. We developed an open-source data analysis package termed pyLattice to process the resulting large (∼60 Gb) movie data sets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from ∼35 cells at a time, resulting in ∼4000 processed tracks per movie. On the basis of their localization in the organoid, we classified CME tracks into apical, lateral, and basal events and found that CME dynamics is similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative high temporal and spatial resolution analysis of subcellular events within tissues

Impact of Anion Vacancies on the Local and Electronic Structures of Iron-Based Oxyfluoride Electrodes

The properties of crystalline solids can be significantly modified by deliberately introducing point defects. Understanding these effects, however, requires understanding the changes in geometry and electronic structure of the host material. Here we report the effect of forming anion vacancies, via dehydroxylation, in a hexagonal-tungsten-bronze–structured iron oxyfluoride, which has potential use as a lithium-ion battery cathode. Our combined pairdistribution function and density-functional–theory analysis indicates that oxygen vacancy formation is accompanied by a spontaneous rearrangement of fluorine anions and vacancies, producing dual pyramidal (FeF4)–O–(FeF4) structural units containing five-fold–coordinated Fe atoms. The addition of lattice oxygen introduces new electronic states above the top of the valence band, with a corresponding reduction in the optical band gap from 4.05 eV to 2.05 eV. This band gap reduction relative to the FeF3 parent material is correlated with a significant improvement in lithium insertion capability relative to defect-free compound

Exploiting Cationic Vacancies for Increased Energy Densities in Dual-Ion Batteries

© 2019 Elsevier B.V. Dual-ion Li–Mg batteries offer a potential route to cells that combine desirable properties of both single-ion species. To maximize the energy density of a dual-ion battery, we propose a strategy for achieving simultaneous intercalation of both ionic species, by chemically modifying the intercalation host material to produce a second, complementary, class of insertion sites. We show that donor-doping of anatase TiO2 to form large numbers of cationic vacancies allows the complementary insertion of Li+ and Mg2+ in a dual-ion cell with a net increase in cell energy density, due to a combination of an increased reversible capacity, an increased operating voltage, and a reduced polarization. By tuning the lithium concentration in the electrolyte, we achieve full utilization of the Ti4+/Ti3+ redox couple with excellent cyclability and rate capability. We conclude that native interstitial sites preferentially accommodate Li+ ions, while Mg2+ ions occupy single-vacancy sites. We also predict a narrow range of electrochemical conditions where adjacent vacancy pairs preferentially accommodate one ion of each species, i.e., a [LiTi ​+ ​MgTi] configuration. These results demonstrate the implementation of additional host sites such as cationic sites as an effective approach to increase the energy density in dual-ion batteries

Correlated Anion Disorder in Heteroanionic Cubic TiOF 2

Resolving anion configurations in heteroanionic materials is crucial for understanding and controlling their properties. For anion-disordered oxyfluorides, conventional Bragg diffraction cannot fully resolve the anionic structure, necessitating alternative structure determination methods. We have investigated the anionic structure of anion-disordered cubic (ReO3-type) TiOF2 using X-ray pair distribution function (PDF), 19F MAS NMR analysis, density functional theory (DFT), cluster expansion modeling, and genetic-algorithm structure prediction. Our computational data predict short-range anion ordering in TiOF2, characterized by predominant cis-[O2F4] titanium coordination, resulting in correlated anion disorder at longer ranges. To validate our predictions, we generated partially disordered supercells using genetic-algorithm structure prediction and computed simulated X-ray PDF data and 19F MAS NMR spectra, which we compared directly to experimental data. To construct our simulated 19F NMR spectra, we derived new transformation functions for mapping calculated magnetic shieldings to predicted magnetic chemical shifts in titanium (oxy)­fluorides, obtained by fitting DFT-calculated magnetic shieldings to previously published experimental chemical shift data for TiF4. We find good agreement between our simulated and experimental data, which supports our computationally predicted structural model and demonstrates the effectiveness of complementary experimental and computational techniques in resolving anionic structure in anion-disordered oxyfluorides. From additional DFT calculations, we predict that increasing anion disorder makes lithium intercalation more favorable by, on average, up to 2 eV, highlighting the significant effect of variations in short-range order on the intercalation properties of anion-disordered materials

A Reversible Phase Transition for Sodium Insertion in Anatase TiO₂

Anatase TiO2 is a potential negative electrode for sodium-ion batteries. Thesodium storage mechanism is, however, still under debate, yet its comprehension is required to optimize the electrochemical properties. To clarify the sodium storage mechanism occurring in anatase, we have used both electrochemical and chemical routes from which we obtained similar trends. During the first discharge, an irreversible plateau region is observed which corresponds to the insertion of Na+ within the interstitial sites of anatase and is accompanied by a drastic loss of the long-range order as revealed by X-ray diffraction, high resolution of high angle annular dark-field scanning transmission electron microscope (HAADF-STEM), and pair distribution function (PDF) analysis. Further structural analysis of the total scattering data indicates that the sodiated phase displays a layered-like rhombohedral R3m structure built from the stacking of Ti and Na slabs. Because of the initial 3D network of anatase, the reduced phase shows strong disorder due to cationic intermixing between the Ti and Na slabs and the refined chemical formula is (Na0.43Ti0.57)3a□0.22Na0.39Ti0.39)3bO2, where □ refers to vacancy. The presence of high valence Ti ions in the Na layers induces a contraction of the c-parameter as compared to the ordered phase. Upon desodiation, the structure further amorphized and the local structure probed by PDF is shown to be similar to the anatase TiO2, suggesting that the 3D network is recovered. The reversible sodium insertion/deinsertion is thus attributed to the rhombohedral active phase formed during the first discharge, and an oxidized phase featuring the local structure of anatase. Due to the amorphous nature of the two phases, the potential-composition curves are characterized by a sloping curve. Finally, a comparison between the intercalation of lithium and sodium into anatase TiO2 performed by DFT calculations confirmed that, for the sodiated phase, the rhombohedral structure is more stable than the tetragonal phase observed during the lithiation of nanoparticles

Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences

Correlating data from different microscopy techniques holds the potential to discover new facets of signaling events in cellular biology. Here we report for the first time a hardware set-up capable of achieving simultaneous co-localized imaging of spatially correlated far-field super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted by the Abbe diffraction limit. We detail system integration and demonstrate system performance using sub-resolution fluorescent beads and applied to a test sample consisting of human bone osteosarcoma epithelial cells, with plasma membrane transporter 1 (MCT1) tagged with an enhanced green fluorescent protein (EGFP) at the N-terminal.Ana I. Gomez Varela wishes to acknowledge support from the Xunta de Galicia, Conselleria de Cultura, Educacion e Ordenacion Universitaria e da Conselleria de Economia, Emprego e Industria (Programa de axudas de apoio a etapa de formacion posdoutoral 2017). Adelaide Miranda and Pieter De Beule acknowledge financial support from Norte's Regional Operational Programme 2014-2020-Norte2020 (NORTE-01-0145-FEDER-000019). Sandra Paiva and Rosana Alves thank Fulbright Commission Portugal and Luso-American Development Foundation (FLAD) for their financial support to perform research work at UC Berkeley, California, USA. We thank the U.S. Embassy in Portugal for supporting David Drubin's visit to Portugal. We thank Ann Fisher of the UC Berkeley Cell Culture Facility for help with cell culture. We thank Dr. Kartoosh Heydari of the Cancer Research Lab Flow Cytometry Core Facility of UC Berkeley. Rosana Alves and Claudia Barata-Antunes are recipients of PhD fellowships from the Portuguese Foundation for Science and Technology (PD/BD/113813/2015 and PD/BD/135208/2017, respectively). The authors want to thank Nikon and Izasa Scientific for their support to the experiment by providing a N SIM-E microscope set-up on loan. We also gratefully acknowledge Dr. Kees van der Oord from Nikon Instruments Europe B.V. for his assistance with the SIM microscope as well as Paulo Madureira and Carlos Pitaes from IZASA Portugal and Jordi Recasens from IZASA Spain for their assistance with the integration of the SIM and AFM microscopes. Finally, we want to thank Benjamin Holmes for fruitful discussions and relentless support

Impact of Solution Chemistry on Growth and Structural Features of Mo-Substituted Spinel Iron Oxides

The effect of crystallizing solution chemistry on the chemistry of subsequently as-grown materials was investigated for Mo-substituted iron oxides prepared by thermally activated co-precipitation. In the presence of Mo ions, we find that varying the oxidation state of the iron precursor from Fe(II) to Fe(III) causes a progressive loss of atomic long-range order with the stabilization of 2-4 nm particles for the sample prepared with Fe(III). The oxidation state of the Fe precursor also affects the distribution of Fe and Mo cations within the spinel structure. Increasing the Fe precursor oxidation state gives decreased Fe-ion occupation and increased Mo-ion occupation of tetrahedral sites, as revealed by the extended X-ray absorption fine structure. The stabilization of Mo within tetrahedral sites appears to be unexpected, considering the octahedral preferred coordination number of Mo(VI). The analysis of the atomic structure of the sample prepared with Fe(III) indicates a local ordering of vacancies and that the occupation of tetrahedral sites by Mo induces a contraction of the interatomic distances within the polyhedra as compared to Fe atoms. Moreover, the occupancy of Mo into the thermodynamic site preference of a Mo dopant in Fe2O3 assessed by density functional theory calculations points to a stronger preference for Mo substitution at octahedral sites. Hence, we suggest that the synthetized compound is thermodynamically metastable, that is, kinetically trapped. Such a state is suggested to be a consequence of the tetrahedral site occupation by Mo ions. The population of these sites, known to be reactive sites enabling particle growth, is concomitant with the stabilization of very small particles. We confirmed our hypothesis by using a blank experiment without Mo ions, further supporting the impact of tetrahedral Mo ions on the growth of iron oxide nanoparticles. Our findings provide new insights into the relationships between the Fe-chemistry of the crystallizing solution and the structural features of the as-grown Mo-substituted Fe-oxide materials. </p

Impact of Solution Chemistry on Growth and Structural Features of Mo-Substituted Spinel Iron Oxides

International audienceThe effect of crystallizing solution chemistry on the chemistry of subsequently as-grown materials was investigated for Mo-substituted iron oxides prepared by thermally activated co-precipitation. In the presence of Mo ions, we find that varying the oxidation state of the iron precursor from Fe(II) to Fe(III) causes a progressive loss of atomic long-range order with the stabilization of 2–4 nm particles for the sample prepared with Fe(III). The oxidation state of the Fe precursor also affects the distribution of Fe and Mo cations within the spinel structure. Increasing the Fe precursor oxidation state gives decreased Fe-ion occupation and increased Mo-ion occupation of tetrahedral sites, as revealed by the extended X-ray absorption fine structure. The stabilization of Mo within tetrahedral sites appears to be unexpected, considering the octahedral preferred coordination number of Mo(VI). The analysis of the atomic structure of the sample prepared with Fe(III) indicates a local ordering of vacancies and that the occupation of tetrahedral sites by Mo induces a contraction of the interatomic distances within the polyhedra as compared to Fe atoms. Moreover, the occupancy of Mo into the thermodynamic site preference of a Mo dopant in Fe2O3 assessed by density functional theory calculations points to a stronger preference for Mo substitution at octahedral sites. Hence, we suggest that the synthetized compound is thermodynamically metastable, that is, kinetically trapped. Such a state is suggested to be a consequence of the tetrahedral site occupation by Mo ions. The population of these sites, known to be reactive sites enabling particle growth, is concomitant with the stabilization of very small particles. We confirmed our hypothesis by using a blank experiment without Mo ions, further supporting the impact of tetrahedral Mo ions on the growth of iron oxide nanoparticles. Our findings provide new insights into the relationships between the Fe-chemistry of the crystallizing solution and the structural features of the as-grown Mo-substituted Fe-oxide materials

Atomic Insights into Aluminium-Ion Insertion in Defective Anatase for Batteries

International audienceAluminium batteries constitute a safe and sustainable high‐energy‐density electrochemical energy‐storage solution. Viable Al‐ion batteries require suitable electrode materials that can readily intercalate high‐charge Al3+ ions. Here, we investigate the Al3+ intercalation chemistry of anatase TiO2 and how chemical modifications influence the accommodation of Al3+ ions. We use fluoride‐ and hydroxide‐doping to generate high concentrations of titanium vacancies. The coexistence of these hetero‐anions and titanium vacancies leads to a complex insertion mechanism, attributed to three distinct types of host sites: native interstitial sites, single vacancy sites, and paired vacancy sites. We demonstrate that Al3+ induces a strong local distortion within the modified TiO2 structure, which affects the insertion properties of the neighbouring host sites. Overall, specific structural features induced by the intercalation of highly polarising Al3+ ions should be considered when designing new electrode materials for polyvalent batteries