Microbial exposure during early human development primes fetal immune cells.

The human fetal immune system begins to develop early during gestation; however, factors responsible for fetal immune-priming remain elusive. We explored potential exposure to microbial agents in utero and their contribution toward activation of memory T cells in fetal tissues. We profiled microbes across fetal organs using 16S rRNA gene sequencing and detected low but consistent microbial signal in fetal gut, skin, placenta, and lungs in the 2nd trimester of gestation. We identified several live bacterial strains including Staphylococcus and Lactobacillus in fetal tissues, which induced in vitro activation of memory T cells in fetal mesenteric lymph node, supporting the role of microbial exposure in fetal immune-priming. Finally, using SEM and RNA-ISH, we visualized discrete localization of bacteria-like structures and eubacterial-RNA within 14th weeks fetal gut lumen. These findings indicate selective presence of live microbes in fetal organs during the 2nd trimester of gestation and have broader implications toward the establishment of immune competency and priming before birth.

An Integrated Genome-wide CRISPRa Approach to Functionalize lncRNAs in Drug Resistance.

Resistance to chemotherapy plays a significant role in cancer mortality. To identify genetic units affecting sensitivity to cytarabine, the mainstay of treatment for acute myeloid leukemia (AML), we developed a comprehensive and integrated genome-wide platform based on a dual protein-coding and non-coding integrated CRISPRa screening (DICaS). Putative resistance genes were initially identified using pharmacogenetic data from 760 human pan-cancer cell lines. Subsequently, genome scale functional characterization of both coding and long non-coding RNA (lncRNA) genes by CRISPR activation was performed. For lncRNA functional assessment, we developed a CRISPR activation of lncRNA (CaLR) strategy, targeting 14,701 lncRNA genes. Computational and functional analysis identified novel cell-cycle, survival/apoptosis, and cancer signaling genes. Furthermore, transcriptional activation of the GAS6-AS2 lncRNA, identified in our analysis, leads to hyperactivation of the GAS6/TAM pathway, a resistance mechanism in multiple cancers including AML. Thus, DICaS represents a novel and powerful approach to identify integrated coding and non-coding pathways of therapeutic relevance.

The ergodicity question when imaging DNA conformation using liquid cell electron microscopy.

Assessing the ergodicity of graphene liquid cell electron microscope measurements, we report that loop states of circular DNA interconvert reversibly and that loop numbers follow the Boltzmann distribution expected for this molecule in bulk solution, provided that the electron dose is low (80-keV electron energy and electron dose rate 1-20 e- Å-2 s-1). This imaging technique appears to act as a "slow motion" camera that reveals equilibrated distributions by imaging the time average of a few molecules without the need to image a spatial ensemble.

Unraveling sources of emission heterogeneity in Silicon Vacancy color centers with cryo-cathodoluminescence microscopy.

Diamond color centers have proven to be versatile quantum emitters and exquisite sensors of stress, temperature, electric and magnetic fields, and biochemical processes. Among color centers, the silicon-vacancy (SiV[Formula: see text]) defect exhibits high brightness, minimal phonon coupling, narrow optical linewidths, and high degrees of photon indistinguishability. Yet the creation of reliable and scalable SiV[Formula: see text]-based color centers has been hampered by heterogeneous emission, theorized to originate from surface imperfections, crystal lattice strain, defect symmetry, or other lattice impurities. Here, we advance high-resolution cryo-electron microscopy combined with cathodoluminescence spectroscopy and 4D scanning transmission electron microscopy (STEM) to elucidate the structural sources of heterogeneity in SiV[Formula: see text] emission from nanodiamond with sub-nanometer-scale resolution. Our diamond nanoparticles are grown directly on TEM membranes from molecular-level seedings, representing the natural formation conditions of color centers in diamond. We show that individual subcrystallites within a single nanodiamond exhibit distinct zero-phonon line (ZPL) energies and differences in brightness that can vary by 0.1 meV in energy and over 70% in brightness. These changes are correlated with the atomic-scale lattice structure. We find that ZPL blue-shifts result from tensile strain, while ZPL red shifts are due to compressive strain. We also find that distinct crystallites host distinct densities of SiV[Formula: see text] emitters and that grain boundaries impact SiV[Formula: see text] emission significantly. Finally, we interrogate nanodiamonds as small as 40 nm in diameter and show that these diamonds exhibit no spatial change to their ZPL energy. Our work provides a foundation for atomic-scale structure-emission correlation, e.g., of single atomic defects in a range of quantum and two-dimensional materials.

Understanding the mechanisms of anisotropic dissolution in metal oxides by applying radiolysis simulations to liquid-phase TEM.

Iron-based redox-active minerals are ubiquitous in soils, sediments, and aquatic systems. Their dissolution is of great importance for microbial impacts on carbon cycling and the biogeochemistry of the lithosphere and hydrosphere. Despite its widespread significance and extensive prior study, the atomic-to-nanoscale mechanisms of dissolution remain poorly understood, particularly the interplay between acidic and reductive processes. Here, we use in situ liquid-phase-transmission electron microscopy (LP-TEM) and simulations of radiolysis to probe and control acidic versus reductive dissolution of akaganeite (ß-FeOOH) nanorods. Informed by crystal structure and surface chemistry, the balance between acidic dissolution at rod tips and reductive dissolution at rod sides was systematically varied using pH buffers, background chloride anions, and electron beam dose. We find that buffers, such as bis-tris, effectively inhibited dissolution by consuming radiolytic acidic and reducing species such as superoxides and aqueous electrons. In contrast, chloride anions simultaneously suppressed dissolution at rod tips by stabilizing structural elements while promoting dissolution at rod sides through surface complexation. Dissolution behaviors were systematically varied by shifting the balance between acidic and reductive attacks. The findings show LP-TEM combined with simulations of radiolysis effects can provide a unique and versatile platform for quantitatively investigating dissolution mechanisms, with implications for understanding metal cycling in natural environments and the development of tailored nanomaterials.

Structure determination by cryoEM at 100 keV.

Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.

Resolving exit strategies of mycobacteria in Dictyostelium discoideum by combining high-pressure freezing with 3D-correlative light and electron microscopy.

The infection course of Mycobacterium tuberculosis is highly dynamic and comprises sequential stages that require damaging and crossing of several membranes to enable the translocation of the bacteria into the cytosol or their escape from the host. Many important breakthroughs such as the restriction of mycobacteria by the autophagy pathway and the recruitment of sophisticated host repair machineries to the Mycobacterium-containing vacuole have been gained in the Dictyostelium discoideum/M. marinum system. Despite the availability of well-established light and advanced electron microscopy techniques in this system, a correlative approach integrating both methods with near-native ultrastructural preservation is currently lacking. This is most likely due to the low ability of D. discoideum to adhere to surfaces, which results in cell loss even after fixation. To address this problem, we improved the adhesion of cells and developed a straightforward and convenient workflow for 3D-correlative light and electron microscopy. This approach includes high-pressure freezing, which is an excellent technique for preserving membranes. Thus, our method allows to monitor the ultrastructural aspects of vacuole escape which is of central importance for the survival and dissemination of bacterial pathogens.

Formation and function of a highly specialised type of organelle in cardiac valve cells.

Within a cell, vesicles play a crucial role in the transport of membrane material and proteins to a given target membrane, and thus regulate a variety of cellular functions. Vesicular transport occurs by means of, among others, endocytosis, where cargoes are taken up by the cell and are processed further upon vesicular trafficking, i.e. transported back to the plasma membrane via recycling endosomes or the degraded by fusion of the vesicles with lysosomes. During evolution, a variety of vesicles with individual functions arose, with some of them building up highly specialised subcellular compartments. In this study, we have analysed the biosynthesis of a new vesicular compartment present in the valve cells of Drosophila melanogaster. We show that the compartment is formed by invaginations of the plasma membrane and grows via re-routing of the recycling endosomal pathway. This is achieved by inactivation of other membrane-consuming pathways and a plasma membrane-like molecular signature of the compartment in these highly specialised heart cells.

Proteomic analysis and in vivo visualization of extracellular vesicles from mouse oviducts during pre-implantation embryo development.

Pre-implantation embryonic development occurs in the oviduct during the first few days of pregnancy. The presence of oviductal extracellular vesicles (oEVs, also called oviductosomes) is crucial for pre-implantation embryonic development in vivo as oEVs often contain molecular transmitters such as proteins. Therefore, evaluating oEV cargo during early pregnancy could provide insights into factors required for proper early embryonic development that are missing in the current in vitro embryo culture setting. In this study, we isolated oEVs from the oviductal fluid at estrus and different stages of early embryonic development. The 2306-3066 proteins in oEVs identified at the different time points revealed 58-60 common EV markers identified in exosome databases. Oviductal extracellular vesicle proteins from pregnant samples significantly differed from those in non-pregnant samples. In addition, superovulation changes the protein contents in oEVs compared to natural ovulation at estrus. Importantly, we have identified that embryo-protectant proteins such as high-mobility protein group B1 and serine (or cysteine) peptidase inhibitor were only enriched in the presence of embryos. We also visualized the physical interaction of EVs and the zona pellucida of 4- to 8-cell stage embryos using transmission electron microscopy as well as in vivo live imaging of epithelial cell-derived GFP-tagged CD9 mouse model. All protein data in this study are readily available to the scientific community in a searchable format at https://genes.winuthayanon.com/winuthayanon/oviduct_ev_proteins/. In conclusion, we identified oEVs proteins that could be tested to determine whether they can improve embryonic developmental outcomes in vivo and in vitro setting.

Revealing synergetic structural activation of a CuAu surface during water-gas shift reaction.

Bimetallic alloy catalysts show strong structural and compositional dependence on their activity, selectivity, and stability. Often referred to as the "synergetic effect" of two metal elements in the alloys, their detailed dynamic information, structurally and chemically, of catalyst surface under reaction conditions remains largely elusive. Here, using aberration-corrected environmental transmission electron microscopy, we visualize the atomic-scale synergetic surface activation of CuAu under a water­gas shift reaction condition. The unique "periodic" structural activation largely determines the dominating reaction pathway, which is related to a possible "carboxyl" reaction route corroborated by density functional theory­based calculation and ab initio molecular dynamics simulation. These results demonstrate how the alloy surface is activated and catalyzes the chemical reaction, which provides insights into catalyst design with atom precision.

Real-space determination of the isolated magnetic skyrmion deformation under electric current flow.

The manipulation and control of electron spins, the fundamental building blocks of magnetic domains and spin textures, are at the core of spintronics. Of particular interest is the effect of the electric current on topological magnetic skyrmions, such as the current-induced deformation of isolated skyrmions. The deformation has consequences ranging from perturbed dynamics to modified packing configurations. In this study, we measured the current-driven real-space deformation of isolated, pinned skyrmions within Co10Zn10 at room temperature. We observed that the skyrmions are surprisingly soft, readily deforming during electric current application into an elliptical shape with a well-defined deformation axis (semimajor axis). We found that this axis rotates unidirectionally toward the current direction irrespective of electric current polarity and that the elliptical deformation reverses back upon current termination. We quantified the average distortion δ, which increased by ∼90% during the largest applied current density |j| = 8.46 ×109 A/m2 when compared with the skyrmion's intrinsic shape ([Formula: see text]). Additionally, we demonstrated an approximately 120% average skyrmion core size expansion during current application, highlighting the skyrmions' inherent topological protection. This evaluation of in situ electric current-induced skyrmion deformation paints a clearer picture of spin-polarized electron-skyrmion interactions and may prove essential in designing spintronic devices.

The Investigation of Neuromimetic Dynamics in Ferroelectrics via In Situ TEM.

The core task of neuromorphic devices is to effectively simulate the behavior of neurons and synapses. Based on the functionality of ferroelectric domains with the advantages of low power consumption and high-speed response, great progress has been made in realizing neuromimetic behaviors such as ferroelectric synaptic devices. However, the correlation between the ferroelectric domain dynamics and neuromimetic behavior remains unclear. Here, we reveal the correlation between domain/domain wall dynamics and neuromimetic behaviors from a microscopic perspective in real-time by using high temporal and spatial resolution in situ transmission electron microscopy. Furthermore, we propose utilizing ferroelectric microstructures for the simultaneous simulation of neuronal and synaptic plasticity, which is expected to improve the integration and performance of ferroelectric neuromorphic devices. We believe that this work to study neuromimetic behavior from the perspective of domain dynamics is instructive for the development of ferroelectric neuromorphic devices.

Understanding the Growth of Electrodeposited PtNi Nanoparticle Films Using Correlated In Situ Liquid Cell Transmission Electron Microscopy and Synchrotron Radiation.

Electrodeposition is a versatile method for synthesizing nanostructured films, but controlling the morphology of films containing two or more elements requires a detailed understanding of the deposition process. We used liquid cell transmission electron microscopy to follow the electrodeposition of PtNi nanoparticle films on a carbon electrode during cyclic voltammetry. These in situ observations show that the film thickness increases with each cycle, and by the fourth cycle, branched and porous structures could be deposited. Synchrotron studies using in situ transmission X-ray microscopy further revealed that Ni was deposited in the oxide phase. Ex situ studies of bulk electrodeposited PtNi nanoparticle films indicated the number of cycles and the scanning rate were the most influential parameters, resulting in a different thickness, a different homogeneity, a different nanoparticle size, and a different surface structure, while the precursor concentration did not have a significant influence. By varying the potential range, we were able to obtain films with different elemental compositions.

Unveiling Corrosion Pathways of Sn Nanocrystals through High-Resolution Liquid Cell Electron Microscopy.

Unveiling materials' corrosion pathways is significant for understanding the corrosion mechanisms and designing corrosion-resistant materials. Here, we investigate the corrosion behavior of Sn@Ni3Sn4 and Sn nanocrystals in an aqueous solution in real time by using high-resolution liquid cell transmission electron microscopy. Our direct observation reveals an unprecedented level of detail on the corrosion of Sn metal with/without a coating of Ni3Sn4 at the nanometric and atomic levels. The Sn@Ni3Sn4 nanocrystals exhibit "pitting corrosion", which is initiated at the defect sites in the Ni3Sn4 protective layer. The early stage isotropic etching transforms into facet-dependent etching, resulting in a cavity terminated with low-index facets. The Sn nanocrystals under fast etching kinetics show uniform corrosion, and smooth surfaces are obtained. Sn nanocrystals show "creeping-like" etching behavior and rough surfaces. This study provides critical insights into the impacts of coating, defects, and ion diffusion on corrosion kinetics and the resulting morphologies.

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.

Structural Complexities in Sodium Ion Conductive Antiperovskite Revealed by Cryogenic Transmission Electron Microscopy.

We use low-dose cryogenic transmission electron microscopy (cryo-TEM) to investigate the atomic-scale structure of antiperovskite Na2NH2BH4 crystals by preserving the room-temperature cubic phase and carefully monitoring the electron dose. Via quantitative analysis of electron beam damage using selected area electron diffraction, we find cryogenic imaging provides 6-fold improvement in beam stability for this solid electrolyte. Cryo-TEM images obtained from flat crystals revealed the presence of a new, long-range-ordered supercell with a cubic phase. The supercell exhibits doubled unit cell dimensions of 9.4 Å × 9.4 Å as compared to the cubic lattice structure revealed by X-ray crystallography of 4.7 Å × 4.7 Å. The comparison between the experimental image and simulated potential map indicates the origin of the supercell is a vacancy ordering of sodium atoms. This work demonstrates the potential of using cryo-TEM imaging to study the atomic-scale structure of air- and electron-beam-sensitive antiperovskite-type solid electrolytes.

Oriented Assembly of Lead Halide Perovskite Nanocrystals.

Cesium lead halide nanostructures have highly tunable optical and optoelectronic properties. Establishing precise control in forming perovskite single-crystal nanostructures is key to unlocking the full potential of these materials. However, studying the growth kinetics of colloidal cesium lead halides is challenging due to their sensitivity to light, electron beam, and environmental factors like humidity. In this study, in situ observations of CsPbBr3-particle dynamics were made possible through extremely low dose liquid cell transmission electron microscopy, showing that oriented attachment is the dominant pathway for the growth of single-crystal CsPbBr3 architectures from primary nanocubes. In addition, oriented assembly and fusion of ligand-stabilized cubic CsPbBr3 nanocrystals are promoted by electron beam irradiation or introduction of polar additives that both induce partial desorption of the original ligands and polarize the nanocube surfaces. These findings advance our understanding of cesium lead halide growth mechanisms, aiding the controlled synthesis of other perovskite nanostructures.

Structural Reversibility of Nanoscaled Sn Anodes.

Alloying-type anode materials provide high capacity for lithium-ion batteries; however, they suffer pulverization problems resulting from the volume change during cycling. Realizing the cycling reversibility of these anodes is therefore critical for sustaining their electrochemical performance. Here, we investigate the structural reversibility of Sn NPs during cycling at atomic-level resolution utilizing in situ high-resolution TEM. We observed a surprisingly near-perfect structural reversibility after a complete cycle. A three-step phase transition happens during lithiation, accompanied by the generation of a significant number of defects, grain boundaries, and up to 202% volume expansion. In subsequent delithiation, the volume, morphology, and crystallinity of the Sn NPs were restored to their initial state. Theoretical calculations show that compressive stress drives the removal of vacancies generated within the NPs during delithiation, therefore maintaining their intact morphology. This work demonstrates that removing vacancies during cycling can efficiently improve the structural reversibility of high-capacity anode materials.

Abnormal Silicon Etching Behaviors in Nanometer-Sized Channels.

Modern semiconductor fabrication is challenged by difficulties in overcoming physical and chemical constraints. A major challenge is the wet etching of dummy gate silicon, which involves the removal of materials inside confined spaces of a few nanometers. These chemical processes are significantly different in the nanoscale and bulk. Previously, electrical double-layer formation, bubble entrapment, poor wettability, and insoluble intermediate precipitation have been proposed. However, the exact suppression mechanisms remain unclear due to the lack of direct observation methods. Herein, we investigate limiting factors for the etching kinetics of silicon with tetramethylammonium hydroxide at the nanoscale by using liquid-phase transmission electron microscopy, three-dimensional electron tomography, and first-principles calculations. We reveal suppressed chemical reactions, unstripping phenomena, and stochastic etching behaviors that have never been observed on a macroscopic scale. We expect that solutions can be suggested from this comprehensive insight into the scale-dependent limiting factors of fabrication.

Measuring Electrical Resistivity at the Nanoscale in Phase-Change Materials.

Electrical resistivity is the key parameter in the active regions of many current nanoscale devices, from memristors to resistive random-access memory and phase-change memories. The local resistivity of the materials is engineered on the nanoscale to fit the performance requirements. Phase-change memories, for example, rely on materials whose electrical resistance increases dramatically with a change from a crystalline to an amorphous phase. Electrical characterization methods have been developed to measure the response of individual devices, but they cannot map the local resistance across the active area. Here, we propose a method based on operando electron holography to determine the local resistance within working devices. Upon switching the device, we show that electrical resistance is inhomogeneous on the scale of only a few nanometers.