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Complex oxide heterostructures provide access to emergent functional and structural phases which are not present in the bulk constituent materials. In this Rapid Communication, we focus on La0.67Sr0.33CoO3 (LSCO)/Gd heterostructures due to the high oxygen ion conductivity, as well as the coupled magnetic and electronic properties of LSCO, which are strongly dependent on the oxygen stoichiometry. This combination of properties enables the ionic control of the functional properties of LSCO thin films through the presence of oxygen getter layers such as Gd. We utilize X-ray nanodiffraction to directly image the nanoscale morphology of LSCO thin films as they are progressively transformed from the equilibrium perovskite phase to the metastable brownmillerite (BM) phase with increasing Gd thickness. Our studies show the coexistence of perovskite and BM phases with a critical oxygen vacancy concentration threshold which leads to the formation of extended BM filaments. In addition to lateral phase separation, we observed phase separation within the film thickness possibly due to pinning of the perovskite and BM phases by the substrate/LSCO and LSCO/Gd interface, respectively. Our studies provide a nanoscale survey of the phase separation in the cobaltites and shed light on the formation of the metastable BM phase.

Hybrid spin–mechanical systems provide a platform for integrating quantum registers and transducers. Efficient creation and control of such systems require a comprehensive understanding of the individual spin and mechanical components as well as their mutual interactions. Point defects in silicon carbide (SiC) offer long-lived, optically addressable spin registers in a wafer-scale material with low acoustic losses, making them natural candidates for integration with high-quality-factor mechanical resonators. Here, we show Gaussian focusing of a surface acoustic wave in SiC, characterized using a stroboscopic X-ray diffraction imaging technique, which delivers direct, strain amplitude information at nanoscale spatial resolution. Using ab initio calculations, we provide a more complete picture of spin–strain coupling for various defects in SiC with C 3v symmetry. This reveals the importance of shear strain for future device engineering and enhanced spin–mechanical coupling. We demonstrate all-optical detection of acoustic paramagnetic resonance without microwave magnetic fields, relevant for sensing applications. Finally, we show mechanically driven Autler–Townes splittings and magnetically forbidden Rabi oscillations. These results offer a basis for full strain control of three-level spin systems.

Endocrine therapies (ET) with cyclin-dependent kinase 4/6 (CDK4/6) inhibition are the standard treatment for estrogen receptor-α-positive (ER+) breast cancer, however drug resistance is common. In this study, proteogenomic analyses of patient-derived xenografts (PDXs) from patients with 22 ER+ breast cancer demonstrated that protein kinase, membrane-associated tyrosine/threonine one (PKMYT1), a WEE1 homolog, is estradiol (E2) regulated in E2-dependent PDXs and constitutively expressed when growth is E2-independent. In clinical samples, high PKMYT1 mRNA levels associated with resistance to both ET and CDK4/6 inhibition. The PKMYT1 inhibitor lunresertib (RP-6306) with gemcitabine selectively and synergistically reduced the viability of ET and palbociclib-resistant ER+ breast cancer cells without functional p53. In vitro the combination increased DNA damage and apoptosis. In palbociclib-resistant, TP53 mutant PDX-derived organoids and PDXs, RP-6306 with low-dose gemcitabine induced greater tumor volume reduction compared to treatment with either single agent. Our study demonstrates the clinical potential of RP-6306 in combination with gemcitabine for ET and CDK4/6 inhibitor resistant TP53 mutant ER+ breast cancer., (©2024 The Authors; Published by the American Association for Cancer Research.)

Sixteen patient-derived xenografts (PDXs) were analyzed using a mass spectrometry (MS)-based kinase inhibitor pull-down assay (KIPA), leading to the observation that death-associated protein kinase 3 (DAPK3) is significantly and specifically overexpressed in the triple-negative breast cancer (TNBC) models. Validation studies confirmed enrichment of DAPK3 protein, in both TNBC cell lines and tumors, independent of mRNA levels. Genomic knockout of DAPK3 in TNBC cell lines inhibited in vitro migration and invasion, along with down-regulation of an epithelial-mesenchymal transition (EMT) signature, which was confirmed in vivo. The kinase and leucine-zipper domains within DAPK3 were shown by a mutational analysis to be essential for functionality. Notably, DAPK3 was found to inhibit the levels of desmoplakin (DSP), a crucial component of the desmosome complex, thereby explaining the observed migration and invasion effects. Further exploration with immunoprecipitation-mass spectrometry (IP-MS) identified that leucine-zipper protein 1 (LUZP1) is a preferential binding partner of DAPK3. LUZP1 engages in a leucine-zipper domain-mediated interaction that protects DAPK3 from proteasomal degradation. Thus, the DAPK3/LUZP1 heterodimer emerges as a newly discovered regulator of EMT/desmosome components that promote TNBC cell migration., (© The Author(s) 2024. Published by Oxford University Press on behalf of National Academy of Sciences.)

Adaptive networks can sense and adjust to dynamic environments to optimize their performance. Understanding their nanoscale responses to external stimuli is essential for applications in nanodevices and neuromorphic computing. However, it is challenging to image such responses on the nanoscale with crystallographic sensitivity. Here, the evolution of nanodomain networks in (PbTiO 3 ) n /(SrTiO 3 ) n superlattices (SLs) is directly visualized in real space as the system adapts to ultrafast repetitive optical excitations that emulate controlled neural inputs. The adaptive response allows the system to explore a wealth of metastable states that are previously inaccessible. Their reconfiguration and competition are quantitatively measured by scanning x-ray nanodiffraction as a function of the number of applied pulses, in which crystallographic characteristics are quantitatively assessed by assorted diffraction patterns using unsupervised machine-learning methods. The corresponding domain boundaries and their connectivity are drastically altered by light, holding promise for light-programable nanocircuits in analogy to neuroplasticity. Phase-field simulations elucidate that the reconfiguration of the domain networks is a result of the interplay between photocarriers and transient lattice temperature. The demonstrated optical control scheme and the uncovered nanoscopic insights open opportunities for the remote control of adaptive nanoscale domain networks., (© 2024 The Author(s). Advanced Materials published by Wiley‐VCH GmbH.)

Mott metal-insulator transitions possess electronic, magnetic, and structural degrees of freedom promising next-generation energy-efficient electronics. A previously unknown, hierarchically ordered, and anisotropic supercrystal state is reported and its intrinsic formation characterized in-situ during a Mott transition in a Ca 2 RuO 4 thin film. Machine learning-assisted X-ray nanodiffraction together with cryogenic electron microscopy reveal multi-scale periodic domain formation at and below the film transition temperature (T Film  ≈ 200-250 K) and a separate anisotropic spatial structure at and above T Film . Local resistivity measurements imply an intrinsic coupling of the supercrystal orientation to the material's anisotropic conductivity. These findings add a new degree of complexity to the physical understanding of Mott transitions, opening opportunities for designing materials with tunable electronic properties., (© 2024 Wiley‐VCH GmbH.)

The inorganic perovskite CsPbI 3 shows promising photophysical properties for a range of potential optoelectronic applications but is metastable at room temperature. To address this, Br can be alloyed into the X-site to create compositions such as CsPbI 2 Br that are stable at room temperature but have bandgaps >1.9 eV - severely limiting solar applications. Herein, in an effort to achieve phase stable films with bandgaps <1.85 eV, we investigate alloying chlorine into iodine-rich triple-halide CsPb(I 0.8 Br 0.2- x Cl x ) 3 with 0 < x < 0.1. We show that partial substitution of iodine with bromine and chlorine provides a path to maintain broadband terrestrial absorption while improving upon the perovskite phase stability due to chlorine's smaller size and larger ionization potential than bromine. At moderate Cl loading up to ≈5%, X-ray diffraction reveals an increasingly smaller orthorhombic unit cell, suggesting chlorine incorporation into the lattice. Most notably, this Cl incorporation is accompanied by a significant enhancement over Cl-free controls in the duration of black-phase stability of up to 7× at elevated temperatures. Additionally, we observe up to 5× increased steady state photoluminescence intensity (PL), along with a small blue-shift. In contrast, at high loading (≈10%), Cl accumulates in a second phase that is visible at grain boundaries via synchrotron fluorescence microscopy and negatively impacts the perovskite phase stability. Thus, replacing small fractions of bromine for chlorine in the iodine-rich inorganic perovskite lattice results in distinct improvement thermal stability and optoelectronic quality while minimally impacting the bandgap., Competing Interests: There are no conflicts to declare., (This journal is © The Royal Society of Chemistry.)

Understanding the microscopic origin of the superior electromechanical response in relaxor ferroelectrics requires knowledge not only of the atomic-scale formation of polar nanodomains (PNDs) but also the rules governing the arrangements and stimulated response of PNDs over longer distances. Using x-ray coherent nanodiffraction, we show the staggered self-assembly of PNDs into unidirectional mesostructures that we refer to as polar laminates in the relaxor ferroelectric 0.68PbMg 1/3 Nb 2/3 O 3 -0.32PbTiO 3 (PMN-0.32PT). We reveal the highly heterogeneous electric-field-driven responses of intra- and interlaminate PNDs and establish their correlation with the local strain and the nature of the PND walls. Our observations highlight the critical role of hierarchical lattice organizations on macroscopic material properties and provide guiding principles for the understanding and design of relaxors and a wide range of quantum and functional materials.

Transitioning from polycrystalline to single-crystalline nickel-rich cathodes has garnered considerable attention in both academia and industry, driven by advantages of high tap density and enhanced mechanical properties. However, cathodes with high nickel content (>70%) suffer from substantial capacity degradation, which poses a challenge to their commercial viability. Leveraging multiscale spatial resolution diffraction and imaging techniques, we observe that lattice rotations occur universally in single-crystalline cathodes and play a pivotal role in the structure degradation. These lattice rotations prove unrecoverable and govern the accumulation of adverse lattice distortions over repeated cycles, contributing to structural and mechanical degradation and fast capacity fade. These findings bridge the previous knowledge gap that exists in the mechanistic link between fast performance failure and atomic-scale structure degradation.

Protein kinases are frequently dysregulated and/or mutated in cancer and represent essential targets for therapy. Accurate quantification is essential. For breast cancer treatment, the identification and quantification of the protein kinase ERBB2 is critical for therapeutic decisions. While immunohistochemistry (IHC) is the current clinical diagnostic approach, it is only semiquantitative. Mass spectrometry-based proteomics offers quantitative assays that, unlike IHC, can be used to accurately evaluate hundreds of kinases simultaneously. The enrichment of less abundant kinase targets for quantification, along with depletion of interfering proteins, improves sensitivity and thus promotes more effective downstream analyses. Multiple kinase inhibitors were therefore deployed as a capture matrix for kinase inhibitor pulldown (KiP) assays designed to profile the human protein kinome as broadly as possible. Optimized assays were initially evaluated in 16 patient derived xenograft models (PDX) where KiP identified multiple differentially expressed and biologically relevant kinases. From these analyses, an optimized single-shot parallel reaction monitoring (PRM) method was developed to improve quantitative fidelity. The PRM KiP approach was then reapplied to low quantities of proteins typical of yields from core needle biopsies of human cancers. The initial prototype targeting 100 kinases recapitulated intrinsic subtyping of PDX models obtained from comprehensive proteomic and transcriptomic profiling. Luminal and HER2 enriched OCT-frozen patient biopsies subsequently analyzed through KiP-PRM also clustered by subtype. Finally, stable isotope labeled peptide standards were developed to define a prototype clinical method. Data are available via ProteomeXchange with identifiers PXD044655 and PXD046169., (© 2024. The Author(s).)

Coherent imaging techniques provide an unparalleled multi-scale view of materials across scientific and technological fields, from structural materials to quantum devices, from integrated circuits to biological cells. Driven by the construction of brighter sources and high-rate detectors, coherent imaging methods like ptychography are poised to revolutionize nanoscale materials characterization. However, these advancements are accompanied by significant increase in data and compute needs, which precludes real-time imaging, feedback and decision-making capabilities with conventional approaches. Here, we demonstrate a workflow that leverages artificial intelligence at the edge and high-performance computing to enable real-time inversion on X-ray ptychography data streamed directly from a detector at up to 2 kHz. The proposed AI-enabled workflow eliminates the oversampling constraints, allowing low-dose imaging using orders of magnitude less data than required by traditional methods., (© 2023. UChicago Argonne, LLC, Operator of Argonne National Laboratory.)

Domain switching is crucial for achieving desired functions in ferroic materials that are used in various applications. Fast control of domains at sub-nanosecond timescales remains a challenge despite its potential for high-speed operation in random-access memories, photonic, and nanoelectronic devices. Here, ultrafast laser excitation is shown to transiently melt and reconfigure ferroelectric stripe domains in multiferroic bismuth ferrite on a timescale faster than 100 picoseconds. This dynamic behavior is visualized by picosecond- and nanometer-resolved X-ray diffraction and time-resolved X-ray diffuse scattering. The disordering of stripe domains is attributed to the screening of depolarization fields by photogenerated carriers resulting in the formation of charged domain walls, as supported by phase-field simulations. Furthermore, the recovery of disordered domains exhibits subdiffusive growth on nanosecond timescales, with a non-equilibrium domain velocity reaching up to 10 m s -1 . These findings present a new approach to image and manipulate ferroelectric domains on sub-nanosecond timescales, which can be further extended into other complex photoferroic systems to modulate their electronic, optical, and magnetic properties beyond gigahertz frequencies. This approach could pave the way for high-speed ferroelectric data storage and computing, and, more broadly, defines new approaches for visualizing the non-equilibrium dynamics of heterogeneous and disordered materials., (© 2023 UChicago Argonne, LLC, Operator of Argonne National Laboratory and The Authors. Advanced Materials published by Wiley-VCH GmbH.)

The goal of precision oncology is to translate the molecular features of cancer into predictive and prognostic tests that can be used to individualize treatment leading to improved outcomes and decreased toxicity. Success for this strategy in breast cancer is exemplified by efficacy of trastuzumab in tumors overexpressing ERBB2 and endocrine therapy for tumors that are estrogen receptor positive. However, other effective treatments, including chemotherapy, immune checkpoint inhibitors, and CDK4/6 inhibitors are not associated with strong predictive biomarkers. Proteomics promises another tier of information that, when added to genomic and transcriptomic features (proteogenomics), may create new opportunities to improve both treatment precision and therapeutic hypotheses. Here, we review both mass spectrometry-based and antibody-dependent proteomics as complementary approaches. We highlight how these methods have contributed toward a more complete understanding of breast cancer and describe the potential to guide diagnosis and treatment more accurately., (Copyright © 2023 Cold Spring Harbor Laboratory Press; all rights reserved.)

Transcriptionally active ESR1 fusions (ESR1-TAF) are a potent cause of breast cancer endocrine therapy (ET) resistance. ESR1-TAFs are not directly druggable because the C-terminal estrogen/anti-estrogen-binding domain is replaced with translocated in-frame partner gene sequences that confer constitutive transactivation. To discover alternative treatments, a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) was deployed to identify druggable kinases that are upregulated by diverse ESR1-TAFs. Subsequent explorations of drug sensitivity validated RET kinase as a common therapeutic vulnerability despite remarkable ESR1-TAF C-terminal sequence and structural diversity. Organoids and xenografts from a pan-ET-resistant patient-derived xenograft model that harbors the ESR1-e6>YAP1 TAF were concordantly inhibited by the selective RET inhibitor pralsetinib to a similar extent as the CDK4/6 inhibitor palbociclib. Together, these findings provide preclinical rationale for clinical evaluation of RET inhibition for the treatment of ESR1-TAF-driven ET-resistant breast cancer., Significance: Kinome analysis of ESR1 translocated and mutated breast tumors using drug bead-based mass spectrometry followed by drug-sensitivity studies nominates RET as a therapeutic target. See related commentary by Wu and Subbiah, p. 3159., (©2023 The Authors; Published by the American Association for Cancer Research.)

Triple-negative breast cancer (TNBC) constitutes 10%-15% of all breast tumors. The current standard of care is multiagent chemotherapy, which is effective in only a subset of patients. The original objective of this study was to deploy a mass spectrometry (MS)-based kinase inhibitor pulldown assay (KIPA) to identify kinases elevated in non-pCR (pathologic complete response) cases for therapeutic targeting. Frozen optimal cutting temperature compound-embedded core needle biopsies were obtained from 43 patients with TNBC before docetaxel- and carboplatin-based neoadjuvant chemotherapy. KIPA was applied to the native tumor lysates that were extracted from samples with high tumor content. Seven percent of all identified proteins were kinases, and none were significantly associated with lack of pCR. However, among a large population of "off-target" purine-binding proteins (PBP) identified, seven were enriched in pCR-associated samples ( P < 0.01). In orthogonal mRNA-based TNBC datasets, this seven-gene "PBP signature" was associated with chemotherapy sensitivity and favorable clinical outcomes. Functional annotation demonstrated IFN gamma response, nuclear import of DNA repair proteins, and cell death associations. Comparisons with standard tandem mass tagged-based discovery proteomics performed on the same samples demonstrated that KIPA-nominated pCR biomarkers were unique to the platform. KIPA is a novel biomarker discovery tool with unexpected utility for the identification of PBPs related to cytotoxic drug response. The PBP signature has the potential to contribute to clinical trials designed to either escalate or de-escalate therapy based on pCR probability., Significance: The identification of pretreatment predictive biomarkers for pCR in response to neoadjuvant chemotherapy would advance precision treatment for TNBC. To complement standard proteogenomic discovery profiling, a KIPA was deployed and unexpectedly identified a seven-member non-kinase PBP pCR-associated signature. Individual members served diverse pathways including IFN gamma response, nuclear import of DNA repair proteins, and cell death., (© 2023 The Authors; Published by the American Association for Cancer Research.)

NF1 is a key tumor suppressor that represses both RAS and estrogen receptor-α (ER) signaling in breast cancer. Blocking both pathways by fulvestrant (F), a selective ER degrader, together with binimetinib (B), a MEK inhibitor, promotes tumor regression in NF1-depleted ER + models. We aimed to establish approaches to determine how NF1 protein levels impact B+F treatment response to improve our ability to identify B+F sensitive tumors. We examined a panel of ER + patient-derived xenograft (PDX) models by DNA and mRNA sequencing and found that more than half of these models carried an NF1 shallow deletion and generally have low mRNA levels. Consistent with RAS and ER activation, RET and MEK levels in NF1-depleted tumors were elevated when profiled by mass spectrometry (MS) after kinase inhibitor bead pulldown. MS showed that NF1 can also directly and selectively bind to palbociclib-conjugated beads, aiding quantification. An IHC assay was also established to measure NF1, but the MS-based approach was more quantitative. Combined IHC and MS analysis defined a threshold of NF1 protein loss in ER + breast PDX, below which tumors regressed upon treatment with B+F. These results suggest that we now have a MS-verified NF1 IHC assay that can be used for patient selection as a complement to somatic genomic analysis., Significance: A major challenge for targeting the consequence of tumor suppressor disruption is the accurate assessment of protein functional inactivation. NF1 can repress both RAS and ER signaling, and a ComboMATCH trial is underway to treat the patients with binimetinib and fulvestrant. Herein we report a MS-verified NF1 IHC assay that can determine a threshold for NF1 loss to predict treatment response. These approaches may be used to identify and expand the eligible patient population., (© 2023 The Authors; Published by the American Association for Cancer Research.)

Local crystallographic features negatively affect quantum spin defects by changing the local electrostatic environment, often resulting in degraded or varied qubit optical and coherence properties. Few tools exist that enable the deterministic synthesis and study of such intricate systems on the nano-scale, making defect-to-defect strain environment quantification difficult. In this paper, we highlight state-of-the-art capabilities from the U.S. Department of Energy's Nanoscale Science Research Centers that directly address these shortcomings. Specifically, we demonstrate how complementary capabilities of nano-implantation and nano-diffraction can be used to demonstrate the quantum relevant, spatially deterministic creation of neutral divacancy centers in 4H silicon carbide, while investigating and characterizing these systems on the≤25nmscale with strain sensitivities on the order of1×10-6,relevant to defect formation dynamics. This work lays the foundation for ongoing studies into the dynamics and deterministic formation of low strain homogeneous quantum relevant spin defects in the solid state., (Creative Commons Attribution license.)

Halide perovskites doped with magnetic impurities (such as the transition metals Mn 2+ , Co 2+ , Ni 2+ ) are being explored for a wide range of applications beyond photovoltaics, such as spintronic devices, stable light-emitting diodes, single-photon emitters, and magneto-optical devices. However, despite several recent studies, there is no consensus on whether the doped magnetic ions will predominantly replace the octahedral B-site metal via substitution or reside at interstitial defect sites. Here, by performing correlated nanoscale X-ray microscopy, spatially and temporally resolved photoluminescence measurements, and magnetic force microscopy on the inorganic 2D perovskite Cs 2 PbI 2 Cl 2 , we show that doping Mn 2+ into the structure results in a lattice expansion. The observed lattice expansion contrasts with the predicted contraction expected to arise from the B-site metal substitution, thus implying that Mn 2+ does not replace the Pb 2+ sites. Photoluminescence and electron paramagnetic resonance measurements confirm the presence of Mn 2+ in the lattice, while correlated nano-XRD and X-ray fluorescence track the local strain and chemical composition. Density functional theory calculations predict that Mn 2+ atoms reside at the interstitial sites between two octahedra in the triangle formed by one Cl - and two I - atoms, which results in a locally expanded structure. These measurements show the fate of the transition metal dopants, the local structure, and optical emission when they are doped at dilute concentrations into a wide band gap semiconductor.

Mechanical integrity issues such as particle cracking are considered one of the leading causes of structural deterioration and limited long-term cycle stability for Ni-rich cathode materials of Li-ion batteries. Indeed, the detrimental effects generated from the crack formation are not yet entirely addressed. Here, applying physicochemical and electrochemical ex situ and in situ characterizations, the effect of Co and Mn on the mechanical properties of the Ni-rich material are thoroughly investigated. As a result, we successfully mitigate the particle cracking issue in Ni-rich cathodes via rational concentration gradient design without sacrificing the electrode capacity. Our result reveals that the Co-enriched surface design in Ni-rich particles benefits from its low stiffness, which can effectively suppress the formation of particle cracking. Meanwhile, the Mn-enriched core limits internal expansion and improve structural integrity. The concentration gradient design also promotes morphological stability and cycling performances in Li metal coin cell configuration., (© 2021. This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.)

Histone variants contribute to the complexity of the chromatin landscape and play an integral role in defining DNA domains and regulating gene expression. The histone H3 variant H3.3 is incorporated into genic elements independent of DNA replication by its chaperone HIRA. Here we demonstrate that Hira is required for the self-renewal of adult hematopoietic stem cells (HSCs) and to restrain erythroid differentiation. Deletion of Hira led to rapid depletion of HSCs while differentiated hematopoietic cells remained largely unaffected. Depletion of HSCs after Hira deletion was accompanied by increased expression of bivalent and erythroid genes, which was exacerbated upon cell division and paralleled increased erythroid differentiation. Assessing H3.3 occupancy identified a subset of polycomb-repressed chromatin in HSCs that depends on HIRA to maintain the inaccessible, H3.3-occupied state for gene repression. HIRA-dependent H3.3 incorporation thus defines distinct repressive chromatin that represses erythroid differentiation of HSCs., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Histones are the primary protein component of chromatin and are involved in virtually all DNA-templated processes. Histones are abundantly post-translationally modified by a variety of chromatin-modifying machinery. These post-translational modifications (PTMs) are recognized by a range of "reader" proteins, which recruit additional proteins to specific locations on chromatin and impart precise and powerful effects on gene regulation. Each PTM typically exerts a positive or negative effect on transcription, and recent studies have shown that histone PTMs function in a combinatorial histone code: that is, histone PTMs function in combination to exert precise DNA-templated regulation. Thus, there is a need to identify and understand proteoforms, or unambiguously defined single protein molecules with all combinations of modifications. Top-down proteomics is currently the only viable approach for identifying and quantitating histone proteoforms, and mass spectrometry instruments have become sufficiently powerful to perform these quantitative analyses in a robust and high-throughput fashion. These recent innovations have enabled new experimental directions in chromatin research but have also introduced temporal and other constraints. This has led us to develop the protocols described here, which increase throughput, reduce sample requirements, and maintain robust quantitation. Although originally designed for high-throughput quantitative top-down proteomics, the protocols described here are useful for a wide range of chromatin biology applications. Starting with small amounts of cells or tissue, we describe two basic protocols for exceptionally rapid and efficient nuclei isolation, acid extraction of histones, and high-performance liquid chromatography fractionation of histones into histone families. We additionally describe the quantitative top-down proteomic analysis of histone H4 proteoforms. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Nuclei isolation and acid extraction of histones from mammalian cells in culture/tissues Basic Protocol 2: HPLC fractionation of histones and histone H4 HPLC-MS/MS Support Protocol: Preparation of intact H3 histone tails by Glu-C digestion., (© 2021 Wiley Periodicals LLC.)

Despite the established roles of the epigenetic factor UHRF1 in oncogenesis, no UHRF1-targeting therapeutics have been reported to date. In this study, we use fragment-based ligand discovery to identify novel scaffolds for targeting the isolated UHRF1 tandem Tudor domain (TTD), which recognizes the heterochromatin-associated histone mark H3K9me3 and supports intramolecular contacts with other regions of UHRF1. Using both binding-based and function-based screens of a ~ 2300-fragment library in parallel, we identified 2,4-lutidine as a hit for follow-up NMR and X-ray crystallography studies. Unlike previous reported ligands, 2,4-lutidine binds to two binding pockets that are in close proximity on TTD and so has the potential to be evolved into more potent inhibitors using a fragment-linking strategy. Our study provides a useful starting point for developing potent chemical probes against UHRF1.

Control of the metal-insulator phase transition is vital for emerging neuromorphic and memristive technologies. The ability to alter the electrically driven transition between volatile and non-volatile states is particularly important for quantum-materials-based emulation of neurons and synapses. The major challenge of this implementation is to understand and control the nanoscale mechanisms behind these two fundamental switching modalities. Here, in situ X-ray nanoimaging is used to follow the evolution of the nanostructure and disorder in the archetypal Mott insulator VO 2 during an electrically driven transition. Our findings demonstrate selective and reversible stabilization of either the insulating or metallic phases achieved by manipulating the defect concentration. This mechanism enables us to alter the local switching response between volatile and persistent regimes and demonstrates a new possibility for nanoscale control of the resistive switching in Mott materials., (© 2020 Wiley-VCH GmbH.)

Fiber proteins are commonly found in eukaryotic and prokaryotic viruses, where they play important roles in mediating viral attachment and host cell entry. They typically form trimeric structures and are incorporated into virions via noncovalent interactions. Orsay virus, a small RNA virus which specifically infects the laboratory model nematode Caenorhabditis elegans , encodes a fibrous protein δ that can be expressed as a free protein and as a capsid protein-δ (CP-δ) fusion protein. Free δ has previously been demonstrated to facilitate viral exit following intracellular expression; however, the biological significance and prevalence of CP-δ remained relatively unknown. Here, we demonstrate that Orsay CP-δ is covalently incorporated into infectious particles, the first example of any attached viral fibers known to date. The crystal structure of δ(1-101) (a deletion mutant containing the first 101 amino acid [aa] residues of δ) reveals a pentameric, 145-Å long fiber with an N-terminal coiled coil followed by multiple β-bracelet repeats. Electron micrographs of infectious virions depict particle-associated CP-δ fibers with dimensions similar to free δ. The δ proteins from two other nematode viruses, Le Blanc and Santeuil, which both specifically infect Caenorhabditis briggsae , were also found to form fibrous molecules. Recombinant Le Blanc δ was able to block Orsay virus infection in worm culture and vice versa, suggesting these two viruses likely compete for the same cell receptor(s). Thus, we propose that while CP-δ likely mediates host cell attachment for all three nematode viruses, additional downstream factor(s) ultimately determine the host specificity and range of each virus. IMPORTANCE Viruses often have extended fibers to mediate host cell recognition and entry, serving as promising targets for antiviral drug development. Unlike other known viral fibers, the δ proteins from the three recently discovered nematode viruses are incorporated into infectious particles as protruding fibers covalently linked to the capsid. Crystal structures of δ revealed novel pentameric folding repeats, which we term β-bracelets, in the intermediate shaft region. Based on sequence analysis, the β-bracelet motif of δ is conserved in all three nematode viruses and could account for ∼60% of the total length of the fiber. Our study indicated that δ plays important roles in cell attachment for this group of nematode viruses. In addition, the tightly knitted β-bracelet fold, which presumably allows δ to survive harsh environments in the worm gut, could be applicable to bioengineering applications given its potentially high stability., (Copyright © 2020 Guo et al.)

The Consortium for Top-Down Proteomics (www.topdownproteomics.org) launched the present study to assess the current state of top-down mass spectrometry (TD MS) and middle-down mass spectrometry (MD MS) for characterizing monoclonal antibody (mAb) primary structures, including their modifications. To meet the needs of the rapidly growing therapeutic antibody market, it is important to develop analytical strategies to characterize the heterogeneity of a therapeutic product's primary structure accurately and reproducibly. The major objective of the present study is to determine whether current TD/MD MS technologies and protocols can add value to the more commonly employed bottom-up (BU) approaches with regard to confirming protein integrity, sequencing variable domains, avoiding artifacts, and revealing modifications and their locations. We also aim to gather information on the common TD/MD MS methods and practices in the field. A panel of three mAbs was selected and centrally provided to 20 laboratories worldwide for the analysis: Sigma mAb standard (SiLuLite), NIST mAb standard, and the therapeutic mAb Herceptin (trastuzumab). Various MS instrument platforms and ion dissociation techniques were employed. The present study confirms that TD/MD MS tools are available in laboratories worldwide and provide complementary information to the BU approach that can be crucial for comprehensive mAb characterization. The current limitations, as well as possible solutions to overcome them, are also outlined. A primary limitation revealed by the results of the present study is that the expert knowledge in both experiment and data analysis is indispensable to practice TD/MD MS.

Most characterized protein methylation events encompass arginine and lysine N -methylation, and only a few cases of protein methionine thiomethylation have been reported. Newly discovered oncohistone mutations include lysine-to-methionine substitutions at positions 27 and 36 of histone H3.3. In these instances, the methionine substitution localizes to the active-site pocket of the corresponding histone lysine methyltransferase, thereby inhibiting the respective transmethylation activity. SET domain-containing 3 (SETD3) is a protein ( i.e. actin) histidine methyltransferase. Here, we generated an actin variant in which the histidine target of SETD3 was substituted with methionine. As for previously characterized histone SET domain proteins, the methionine substitution substantially (76-fold) increased binding affinity for SETD3 and inhibited SETD3 activity on histidine. Unexpectedly, SETD3 was active on the substituted methionine, generating S -methylmethionine in the context of actin peptide. The ternary structure of SETD3 in complex with the methionine-containing actin peptide at 1.9 Å resolution revealed that the hydrophobic thioether side chain is packed by the aromatic rings of Tyr 312 and Trp 273 , as well as the hydrocarbon side chain of Ile 310 Our results suggest that placing methionine properly in the active site-within close proximity to and in line with the incoming methyl group of SAM-would allow some SET domain proteins to selectively methylate methionine in proteins., Competing Interests: Conflict of interest—The authors declare no competing interests with the contents of this article., (© 2020 Dai et al.)

Trees are used by animals, humans and machines to classify information and make decisions. Natural tree structures displayed by synapses of the brain involves potentiation and depression capable of branching and is essential for survival and learning. Demonstration of such features in synthetic matter is challenging due to the need to host a complex energy landscape capable of learning, memory and electrical interrogation. We report experimental realization of tree-like conductance states at room temperature in strongly correlated perovskite nickelates by modulating proton distribution under high speed electric pulses. This demonstration represents physical realization of ultrametric trees, a concept from number theory applied to the study of spin glasses in physics that inspired early neural network theory dating almost forty years ago. We apply the tree-like memory features in spiking neural networks to demonstrate high fidelity object recognition, and in future can open new directions for neuromorphic computing and artificial intelligence.

Ferroelectric domain walls in single-crystal complex oxide thin films are found to be orders of magnitude slower when the interfacial bonds with the heteroepitaxial substrate are broken to create a freestanding film. This drastic change in domain wall kinetics does not originate from the alteration of epitaxial strain; rather, it is correlated with the structural ripples at mesoscopic length scale and associated flexoelectric effects induced in the freestanding films. In contrast, the effects of the bond-breaking on the local static ferroelectric properties of both top and bottom layers of the freestanding films, such as domain wall width and spontaneous polarization, are modest and governed by the change in epitaxy-induced compressive strain., (© 2019 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Defect-based quantum systems in wide bandgap semiconductors are strong candidates for scalable quantum-information technologies. However, these systems are often complicated by charge-state instabilities and interference by phonons, which can diminish spin-initialization fidelities and limit room-temperature operation. Here, we identify a pathway around these drawbacks by showing that an engineered quantum well can stabilize the charge state of a qubit. Using density-functional theory and experimental synchrotron X-ray diffraction studies, we construct a model for previously unattributed point defect centers in silicon carbide as a near-stacking fault axial divacancy and show how this model explains these defects' robustness against photoionization and room temperature stability. These results provide a materials-based solution to the optical instability of color centers in semiconductors, paving the way for the development of robust single-photon sources and spin qubits.

Proteins physiologically exist as "proteoforms" that arise from one gene and acquire additional function by post-translational modifications (PTM). When multiple PTMs coexist on single protein molecules, top-down proteomics becomes the only feasible method of characterization; however, most top-down methods have limited quantitative capacity and insufficient throughput to truly address proteoform biology. Here we demonstrate that top-down proteomics can be quantitative, reproducible, sensitive, and high throughput. The proteoforms of histone H4 are well studied both as a challenging proteoform identification problem and due to their essential role in the regulation of all eukaryotic DNA-templated processes. Much of histone H4's function is obfuscated from prevailing methods due to combinatorial mechanisms. Starting from cells or tissues, after an optimized protein purification process, the H4 proteoforms are physically separated by on-line C3 chromatography, narrowly isolated in MS1 and sequenced with ETD fragmentation. We achieve more than 30 replicates from a single 35-mm tissue culture dish by loading 55 ng of H4 on column. Parallelization and automation yield a sustained throughput of 12 replicates per day. We achieve reproducible quantitation (average biological Pearson correlations of 0.89) of hundreds of proteoforms (about 200-300) over almost six orders of magnitude and an estimated LLoQ of 0.001% abundance. We demonstrate the capacity of the method to precisely measure well-established changes with sodium butyrate treatment of SUM159 cells. We show that the data produced by a quantitative top-down method can be amenable to parametric statistical comparisons and is capable of delineating relevant biological changes at the full proteoform level.

Histone post-translational modifications (PTMs) have been intensively investigated due to their essential function in eukaryotic genome regulation. Histone modifications have been effectively studied using modified bottom-up proteomics approaches; however, the methods often do not capture single-molecule combinations of PTMs (proteoforms) that mediate known and expected biochemical mechanisms. Both middle-down mass spectrometry (MS) and top-down MS quantitation of H4 proteoforms present viable access to this important information. Histone H4 middle-down has previously avoided GluC digestion due to complex digestion products and interferences; however, the common AspN digestion cleaves at amino acid 23, disconnecting K31ac from other PTMs. Here, we demonstrate the effective use of GluC-based middle-down quantitation and compare it to top-down-based quantitation of proteoforms. Despite potential interferences in the m/z space, the proteoforms arising from all three GluC products (E52, E53, and E63) and intact H4 are chromatographically resolved and successfully analyzed in a single LC-MS analysis. Quantitative results and associated analytical metrics are compared between the different analytes of a single sample digested to different extents to reveal general concordance as well as the relative biases and complementarity of each approach. There is moderate proteoform discordance between digestion products (e.g., E52 and E53); however, each digestion product exhibits high concordance, regardless of digestion time. Under the conditions used, the GluC products are better chromatographically resolved yet show greater variance than the top-down quantitation that are more extensively sampled for MS2. GluC-based middle-down of H4 is thus viable. Both top-down and middle-down approaches have comparable quantitation capacity and are complementary.

Control of local lattice perturbations near optically-active defects in semiconductors is a key step to harnessing the potential of solid-state qubits for quantum information science and nanoscale sensing. We report the development of a stroboscopic scanning X-ray diffraction microscopy approach for real-space imaging of dynamic strain used in correlation with microscopic photoluminescence measurements. We demonstrate this technique in 4H-SiC, which hosts long-lifetime room temperature vacancy spin defects. Using nano-focused X-ray photon pulses synchronized to a surface acoustic wave launcher, we achieve an effective time resolution of ~100 ps at a 25 nm spatial resolution to map micro-radian dynamic lattice curvatures. The acoustically induced lattice distortions near an engineered scattering structure are correlated with enhanced photoluminescence responses of optically-active SiC quantum defects driven by local piezoelectric effects. These results demonstrate a unique route for directly imaging local strain in nanomechanical structures and quantifying dynamic structure-function relationships in materials under realistic operating conditions.

While the properties of wurtzite GaAs have been extensively studied during the past decade, little is known about the influence of the crystal polytype on ternary (In,Ga)As quantum well structures. We address this question with a unique combination of correlated, spatially resolved measurement techniques on core-shell nanowires that contain extended segments of both the zincblende and wurtzite polytypes. Cathodoluminescence hyperspectral imaging reveals a blue-shift of the quantum well emission energy by 75 ± 15 meV in the wurtzite polytype segment. Nanoprobe X-ray diffraction and atom probe tomography enable k · p calculations for the specific sample geometry to reveal two comparable contributions to this shift. First, there is a 30% drop in In mole fraction going from the zincblende to the wurtzite segment. Second, the quantum well is under compressive strain, which has a much stronger impact on the hole ground state in the wurtzite than in the zincblende segment. Our results highlight the role of the crystal structure in tuning the emission of (In,Ga)As quantum wells and pave the way to exploit the possibilities of three-dimensional band gap engineering in core-shell nanowire heterostructures. At the same time, we have demonstrated an advanced characterization toolkit for the investigation of semiconductor nanostructures.

The factors limiting the performance of alternative polycrystalline solar cells as compared with their single-crystal counterparts are not fully understood, but are thought to originate from structural and chemical heterogeneities at various length scales. Here, it is demonstrated that multimodal focused nanobeam X-ray microscopy can be used to reveal multiple aspects of the problem in a single measurement by mapping chemical makeup, lattice structure and charge collection efficiency simultaneously in a working solar cell. This approach was applied to micrometre-sized individual grains in a Cu(In,Ga)Se 2 polycrystalline film packaged in a working device. It was found that, near grain boundaries, collection efficiency is increased, and that in these regions the lattice parameter of the material is expanded. These observations are discussed in terms of possible physical models and future experiments., (open access.)

Advanced fibers revolutionized structural materials in the second half of the 20th century. However, all high-strength fibers developed to date are brittle. Recently, pioneering simultaneous ultrahigh strength and toughness were discovered in fine (<250 nm) individual electrospun polymer nanofibers (NFs). This highly desirable combination of properties was attributed to high macromolecular chain alignment coupled with low crystallinity. Quantitative analysis of the degree of preferred chain orientation will be crucial for control of NF mechanical properties. However, quantification of supramolecular nanoarchitecture in NFs with low crystallinity in the ultrafine diameter range is highly challenging. Here, we discuss the applicability of traditional as well as emerging methods for quantification of polymer chain orientation in nanoscale one-dimensional samples. Advantages and limitations of different techniques are critically evaluated on experimental examples. It is shown that straightforward application of some of the techniques to sub-wavelength-diameter NFs can lead to severe quantitative and even qualitative artifacts. Sources of such size-related artifacts, stemming from instrumental, materials, and geometric phenomena at the nanoscale, are analyzed on the example of polarized Raman method but are relevant to other spectroscopic techniques. A proposed modified, artifact-free method is demonstrated. Outstanding issues and their proposed solutions are discussed. The results provide guidance for accurate nanofiber characterization to improve fundamental understanding and accelerate development of nanofibers and related nanostructured materials produced by electrospinning or other methods. We expect that the discussion in this review will also be useful to studies of many biological systems that exhibit nanofilamentary architectures and combinations of high strength and toughness.

The role of the alkali metal cations in halide perovskite solar cells is not well understood. Using synchrotron-based nano-x-ray fluorescence and complementary measurements, we found that the halide distribution becomes homogenized upon addition of cesium iodide, either alone or with rubidium iodide, for substoichiometric, stoichiometric, and overstoichiometric preparations, where the lead halide is varied with respect to organic halide precursors. Halide homogenization coincides with long-lived charge carrier decays, spatially homogeneous carrier dynamics (as visualized by ultrafast microscopy), and improved photovoltaic device performance. We found that rubidium and potassium phase-segregate in highly concentrated clusters. Alkali metals are beneficial at low concentrations, where they homogenize the halide distribution, but at higher concentrations, they form recombination-active second-phase clusters., (Copyright © 2019 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.)

Background: The dynamics of histone post-translational modifications (PTMs) are sparsely described, especially in their true physiological context of proteoforms (single histone molecules harboring combinations of PTMs)., Methods: Here we time-resolve the response of cells to SUV4-20 methyltransferase inhibition and unbiasedly quantitate the dynamic response of histone H4 PTMs and proteoforms., Results: Contrary to the prevailing dogma, cells exhibit an immediate-early response with changes to histone proteoforms. Cells also recover to basal-like conditions upon removal of epigenetic inhibitors rapidly. Inhibition of SUV4-20 results in decreased H4{K20me2}; however, no effects on H4{K20me3} are observed, implying that another enzyme mediates H4K20me3. Most surprisingly, SUV4-20 inhibition results in an increase in histone H4 acetylation attributable to proteoforms containing K20me2. This led us to hypothesize that hyperacetylated proteoforms protect K20me2 from demethylation as an evolved compensatory mechanism. This concept is supported by subsequent results that pretreatment with an HDACi substantially diminishes the effects of SUV4-20 inhibition in prone cells and is further confirmed by HATi-facilitating SUV4-20 inhibition to decrease discrete H4{K20me2} in resistant cells., Conclusions: The chromatin response of cells to sudden perturbations is significantly faster, nuanced and complex than previously described. The persistent nature of chromatin regulation may be achieved by a network of dynamic equilibria with compensatory mechanisms that operate at the proteoform level.

Post-translational modifications (PTMs) of histones are important epigenetic regulatory mechanisms that are often dysregulated in cancer. We employ middle-down proteomics to investigate the PTMs and proteoforms of histone H4 during cell cycle progression. We use pH gradient weak cation exchange-hydrophilic interaction liquid chromatography (WCX-HILIC) for on-line liquid chromatography-mass spectrometry analysis to separate and analyze the proteoforms of histone H4. This procedure provides enhanced separation of proteoforms, including positional isomers, and simplifies downstream data analysis. We use ultrahigh mass accuracy and resolution Fourier transform-ion cyclotron resonance (FT-ICR) mass spectrometer to unambiguously distinguish between acetylation and tri-methylation (∆m = 0.036 Da). In total, we identify and quantify 233 proteoforms of histone H4 in two breast cancer cell lines. We observe significant increases in S1 phosphorylation during mitosis, implicating an important role in mitotic chromatin condensation. A decrease of K20 unmodified proteoforms is observed as the cell cycle progresses, corresponding to an increase of K20 mono- and di-methylation. Acetylation at K5, K8, K12, and K16 declines as cells traverse from S phase to mitosis, suggesting cell cycle-dependence and an important role during chromatin replication and condensation. These new insights into the epigenetics of the cell cycle may provide new diagnostic and prognostic biomarkers., (© 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Quantum devices formed in high-electron-mobility semiconductor heterostructures provide a route through which quantum mechanical effects can be exploited on length scales accessible to lithography and integrated electronics. The electrostatic definition of quantum dots in semiconductor heterostructure devices intrinsically involves the lithographic fabrication of intricate patterns of metallic electrodes. The formation of metal/semiconductor interfaces, growth processes associated with polycrystalline metallic layers, and differential thermal expansion produce elastic distortion in the active areas of quantum devices. Understanding and controlling these distortions present a significant challenge in quantum device development. We report synchrotron X-ray nanodiffraction measurements combined with dynamical X-ray diffraction modeling that reveal lattice tilts with a depth-averaged value up to 0.04° and strain on the order of 10 -4 in the two-dimensional electron gas (2DEG) in a GaAs/AlGaAs heterostructure. Elastic distortions in GaAs/AlGaAs heterostructures modify the potential energy landscape in the 2DEG due to the generation of a deformation potential and an electric field through the piezoelectric effect. The stress induced by metal electrodes directly impacts the ability to control the positions of the potential minima where quantum dots form and the coupling between neighboring quantum dots.

The ferroelectric domain pattern within lithographically defined PbTiO 3 /SrTiO 3 ferroelectric/dielectric heteroepitaxial superlattice nanostructures is strongly influenced by the edges of the structures. Synchrotron X-ray nanobeam diffraction reveals that the spontaneously formed 180° ferroelectric stripe domains exhibited by such superlattices adopt a configuration in rectangular nanostructures in which domain walls are aligned with long patterned edges. The angular distribution of X-ray diffuse scattering intensity from nanodomains indicates that domains are aligned within an angular range of approximately 20° with respect to the edges. Computational studies based on a time-dependent Landau-Ginzburg-Devonshire model show that the preferred direction of the alignment results from lowering of the bulk and electrostrictive contributions to the free energy of the system due to the release of the lateral mechanical constraint. This unexpected alignment appears to be intrinsic and not a result of distortions or defects caused by the patterning process. Our work demonstrates how nanostructuring and patterning of heteroepitaxial superlattices allow for pathways to create and control ferroelectric structures that may appear counterintuitive.

III-As nanowires are candidates for near-infrared light emitters and detectors that can be directly integrated onto silicon. However, nanoscale to microscale variations in structure, composition, and strain within a given nanowire, as well as variations between nanowires, pose challenges to correlating microstructure with device performance. In this work, we utilize coherent nanofocused X-rays to characterize stacking defects and strain in a single InGaAs nanowire supported on Si. By reconstructing diffraction patterns from the 21̅1̅0 Bragg peak, we show that the lattice orientation varies along the length of the wire, while the strain field along the cross-section is largely unaffected, leaving the band structure unperturbed. Diffraction patterns from the 011̅0 Bragg peak are reproducibly reconstructed to create three-dimensional images of stacking defects and associated lattice strains, revealing sharp planar boundaries between different crystal phases of wurtzite (WZ) structure that contribute to charge carrier scattering. Phase retrieval is made possible by developing multiangle Bragg projection ptychography (maBPP) to accommodate coherent nanodiffraction patterns measured at arbitrary overlapping positions at multiple angles about a Bragg peak, eliminating the need for scan registration at different angles. The penetrating nature of X-ray radiation, together with the relaxed constraints of maBPP, will enable the in operando imaging of nanowire devices.

In materials where two or more ordering degrees of freedom are closely matched in their free energies, coupling between them, or multiferroic behavior can occur. These phenomena can produce a very rich phase behavior, as well as emergent phases that offer useful properties and opportunities to reveal novel phenomena in phase transitions. The ordered alloy FeRh undergoes an antiferromagnetic to ferromagnetic phase transition at ~375 K, which illustrates the interplay between structural and magnetic order mediated by a delicate energy balance between two configurations. We have examined this transition using a combination of high-resolution x-ray structural and magnetic imaging and comprehensive x-ray magnetic circular dichroism spectroscopy. We find that the transition proceeds via a defect-driven domain nucleation and growth mechanism, with significant return point memory in both the structural and magnetic domain configurations. The domains show evidence of inhibited growth after nucleation, resulting in a quasi-2 nd order temperature behavior.

Histone posttranslational modifications (PTMs) help regulate DNA templated processes; however, relatively little work has unbiasedly explored the single-molecule combinations of histone PTMs, their dynamics on short timescales, or how these preexisting histone PTMs modulate further histone modifying enzyme activity. We use quantitative top down proteomics to unbiasedly measure histone H4 proteoforms (single-molecule combinations of PTMs) upon butyrate treatment. Our results show that histone proteoforms change in cells within 10 minutes of application of sodium butyrate. Cells recover from treatment within 30 minutes after removal of butyrate. Surprisingly, K20me2 containing proteoforms are the near-exclusive substrate of histone acetyltransferases upon butyrate treatment. Single-molecule hierarchies of progressive PTMs mostly dictate the addition and removal of histone PTMs (K16ac > K12ac ≥ K8ac > K5ac, and the reverse on recovery). This reveals the underlying single-molecule mechanism that explains the previously reported but indistinct and unexplained patterns of H4 acetylation. Thus, preexisting histone PTMs strongly modulate histone modifying enzyme activity and this suggests that proteoform constrained reaction pathways are crucial mechanisms that enable the long-term stability of the cellular epigenetic state.

Redox-driven phase transformations in solids determine the performance of lithium-ion batteries, crucial in the technological transition from fossil fuels. Couplings between chemistry and strain define reversibility and fatigue of an electrode. The accurate definition of all phases in the transformation, their energetics, and nanoscale location within a particle produces fundamental understanding of these couplings needed to design materials with ultimate performance. Here we demonstrate that scanning X-ray diffraction microscopy (SXDM) extends our ability to image battery processes in single particles. In LiFePO 4 crystals equilibrated after delithiation, SXDM revealed the existence of domains of miscibility between LiFePO 4 and Li 0.6 FePO 4 . These solid solutions are conventionally thought to be metastable, and were previously undetected by spectromicroscopy. The observation provides experimental verification of predictions that the LiFePO 4 -FePO 4 phase diagram can be altered by coherency strain under certain interfacial orientations. It enriches our understanding of the interaction between diffusion, chemistry, and mechanics in solid state transformations.

Urine as a true non-invasive sampling source holds great potential for biomarker discovery. While approximately 2000 proteins can be detected by mass spectrometry in urine from healthy people, the amount of these proteins vary considerably. A systematic evaluation of a large number of samples is needed to determine the range of the variations. Current biomarker studies often measure limited number of urine samples in the discovery phase, which makes it difficult to determine whether proteins differentially expressed between control and disease groups represent actual difference, or are just physiological variations among the individuals, leads to failures in the validation phase with the increased sample numbers. Here, we report a streamlined workflow with capacity of measuring 8 urine proteomes per day at the coverage of >1500 proteins. With this workflow, we evaluated variations in 497 urine proteomes from 167 healthy donors, establishing reference intervals (RIs) that covered urine protein variations. We demonstrated that RIs could be used to monitor physiological changes by detecting transient outlier proteins. Furthermore, we provided a RIs-based algorithm for biomarker discovery and validation to screen for diseases such as cancer. This study provided a proof-of-principle workflow for the use of urine proteome for health monitoring and disease screening., (Copyright © 2017. Published by Elsevier B.V.)

Despite the wide use of Caenorhabditis elegans as a model organism, the first virus naturally infecting this organism was not discovered until six years ago. The Orsay virus and its related nematode viruses have a positive-sense RNA genome, encoding three proteins: CP, RdRP, and a novel δ protein that shares no homology with any other proteins. δ can be expressed either as a free δ or a CP-δ fusion protein by ribosomal frameshift, but the structure and function of both δ and CP-δ remain unknown. Using a combination of electron microscopy, X-ray crystallography, computational and biophysical analyses, here we show that the Orsay δ protein forms a ~420-Å long, pentameric fiber with an N-terminal α-helical bundle, a β-stranded filament in the middle, and a C-terminal head domain. The pentameric nature of the δ fiber has been independently confirmed by both mass spectrometry and analytical ultracentrifugation. Recombinant Orsay capsid containing CP-δ shows protruding long fibers with globular heads at the distal end. Mutant viruses with disrupted CP-δ fibers were generated by organism-based reverse genetics. These viruses were found to be either non-viable or with poor infectivity according to phenotypic and qRT-PCR analyses. Furthermore, addition of purified δ proteins to worm culture greatly reduced Orsay infectivity in a sequence-specific manner. Based on the structure resemblance between the Orsay CP-δ fiber and the fibers from reovirus and adenovirus, we propose that CP-δ functions as a cell attachment protein to mediate Orsay entry into worm intestine cells.

Coherent X-ray microscopy by phase retrieval of Bragg diffraction intensities enables lattice distortions within a crystal to be imaged at nanometre-scale spatial resolutions in three dimensions. While this capability can be used to resolve structure-property relationships at the nanoscale under working conditions, strict data measurement requirements can limit the application of current approaches. Here, we introduce an efficient method of imaging three-dimensional (3D) nanoscale lattice behaviour and strain fields in crystalline materials with a methodology that we call 3D Bragg projection ptychography (3DBPP). This method enables 3D image reconstruction of a crystal volume from a series of two-dimensional X-ray Bragg coherent intensity diffraction patterns measured at a single incident beam angle. Structural information about the sample is encoded along two reciprocal-space directions normal to the Bragg diffracted exit beam, and along the third dimension in real space by the scanning beam. We present our approach with an analytical derivation, a numerical demonstration, and an experimental reconstruction of lattice distortions in a component of a nanoelectronic prototype device.