Inadequate DNA Damage Repair Promotes Mammary Transdifferentiation, Leading to BRCA1 Breast Cancer.

Loss of BRCA1 p220 function often results in basal-like breast cancer (BLBC), but the underlying disease mechanism is largely opaque. In mammary epithelial cells (MECs), BRCA1 interacts with multiple proteins, including NUMB and HES1, to form complexes that participate in interstrand crosslink (ICL) DNA repair and MEC differentiation control. Unrepaired ICL damage results in aberrant transdifferentiation to a mesenchymal state of cultured, human basal-like MECs and to a basal/mesenchymal state in primary mouse luminal MECs. Loss of BRCA1, NUMB, or HES1 or chemically induced ICL damage in primary murine luminal MECs results in persistent DNA damage that triggers luminal to basal/mesenchymal transdifferentiation. In vivo single-cell analysis revealed a time-dependent evolution from normal luminal MECs to luminal progenitor-like tumor cells with basal/mesenchymal transdifferentiation during murine BRCA1 BLBC development. Growing DNA damage accompanied this malignant transformation.

DNA Demethylation Dynamics in the Human Prenatal Germline.

Global DNA demethylation in humans is a fundamental process that occurs in pre-implantation embryos and reversion to naive ground state pluripotent stem cells (PSCs). However, the extent of DNA methylation reprogramming in human germline cells is unknown. Here, we performed whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq) of human prenatal germline cells from 53 to 137 days of development. We discovered that the transcriptome and methylome of human germline is distinct from both human PSCs and the inner cell mass (ICM) of human blastocysts. Using this resource to monitor the outcome of global DNA demethylation with reversion of primed PSCs to the naive ground state, we uncovered hotspots of ultralow methylation at transposons that are protected from demethylation in the germline and ICM. Taken together, the human germline serves as a valuable in vivo tool for monitoring the epigenome of cells that have emerged from a global DNA demethylation event.

Ig Superfamily Ligand and Receptor Pairs Expressed in Synaptic Partners in Drosophila.

Information processing relies on precise patterns of synapses between neurons. The cellular recognition mechanisms regulating this specificity are poorly understood. In the medulla of the Drosophila visual system, different neurons form synaptic connections in different layers. Here, we sought to identify candidate cell recognition molecules underlying this specificity. Using RNA sequencing (RNA-seq), we show that neurons with different synaptic specificities express unique combinations of mRNAs encoding hundreds of cell surface and secreted proteins. Using RNA-seq and protein tagging, we demonstrate that 21 paralogs of the Dpr family, a subclass of immunoglobulin (Ig)-domain containing proteins, are expressed in unique combinations in homologous neurons with different layer-specific synaptic connections. Dpr interacting proteins (DIPs), comprising nine paralogs of another subclass of Ig-containing proteins, are expressed in a complementary layer-specific fashion in a subset of synaptic partners. We propose that pairs of Dpr/DIP paralogs contribute to layer-specific patterns of synaptic connectivity.

Probabilistic splicing of Dscam1 establishes identity at the level of single neurons.

The Drosophila Dscam1 gene encodes a vast number of cell recognition molecules through alternative splicing. These exhibit isoform-specific homophilic binding and regulate self-avoidance, the tendency of neurites from the same cell to repel one another. Genetic experiments indicate that different cells must express different isoforms. How this is achieved is unknown, as expression of alternative exons in vivo has not been shown. Here, we modified the endogenous Dscam1 locus to generate splicing reporters for all variants of exon 4. We demonstrate that splicing does not occur in a cell-type-specific fashion, that cells sharing the same anatomical location in different individuals express different exon 4 variants, and that the splicing pattern in a given neuron can change over time. We conclude that splicing is probabilistic. This is compatible with a widespread role in neural circuit assembly through self-avoidance and is incompatible with models in which specific isoforms of Dscam1 mediate homophilic recognition between processes of different cells.

Revealing the Interaction of Charge Carrier-Phonon Coupling by Quantification of Electronic Properties at the SrTiO3/TiO2 Heterointerface.

Oxide heterointerfaces with high carrier density can interact strongly with the lattice phonons, generating considerable plasmon-phonon coupling and thereby perturbing the fascinating optical and electronic properties, such as two-dimensional electron gas, ferromagnetism, and superconductivity. Here we use infrared-spectroscopic nanoimaging based on scattering-type scanning near-field optical microscopy (s-SNOM) to quantify the interaction of electron-phonon coupling and the spatial distribution of local charge carriers at the SrTiO3/TiO2 interface. We found an increased high-frequency dielectric constant (ε∞ = 7.1-9.0) and charge carrier density (n = 6.5 × 1019 to 1.5 × 1020 cm-3) near the heterointerface. Moreover, quantitative information between the charge carrier density and extension thickness across the heterointerface has been extracted by monochromatic near-field imaging. A direct evaluation of the relationship between the thickness and the interaction of charge carrier-phonon coupling of the heterointerface would provide valuable information for the development of oxide-based electronic devices.

Exciton-exciton annihilation in thin indium selenide layers.

The photocarrier recombination in van der Waals layers may determine the device performance based on these materials. Here, we investigated the photocarrier dynamics in a multilayer indium selenide nanofilm using transient absorption spectroscopy. The sub-bandgap transient absorption feature was attributed to the indirect intraband absorption of the photocarriers, which was then exploited as a probe to monitor the photocarrier dynamics. With increasing pump intensities, the photocarrier decay was accelerated because of the rising contribution from a bimolecular recombination channel that was then assigned to exciton-exciton annihilation. The rate constant of the exciton-exciton annihilation was given as (1.8 ± 0.1) × 10-15 cm2 ps-1 from a global fitting of the photocarrier decay kinetics for different pump intensities. Our finding suggests that, in contrast with their monolayer counterpart, the exciton-exciton annihilation is rather inefficient in multilayers due to their weaker Coulomb interaction. Hence, compared with monolayers, the lifetime of photocarriers in multilayers would not be significantly reduced under high-intensity pump conditions, and the apparent photocarrier lifetime could be further improved just by suppressing the monomolecular recombination channels such as trapping.

Facilitating the Deprotonation of OH to O through Fe4+ -Induced States in Perovskite LaNiO3 Enables a Fast Oxygen Evolution Reaction.

Aliovalent doping is widely adopted to tune the electronic structure of transition-metal oxides for design of low-cost, active electrocatalysts. Here, using single-crystalline thin films as model electrocatalysts, the structure-activity relationship of Fe states doping in perovskite LaNiO3 for oxygen evolution reaction (OER) is studied. Fe4+ state is found to be crucial for enhancing the OER activity of LaNiO3 , dramatically increasing the activity by six times, while Fe3+ has negligible effect. Spectroscopic studies and DFT calculations indicate Fe4+ states enhance the degree of Ni/Fe 3d and O 2p hybridization, and meanwhile produce down-shift of the unoccupied density of states towards lower energies. Such electronic features reduce the energy barrier for interfacial electron transfer for water oxidization by 0.2 eV. Further theoretical calculations and H/D isotope experiments reveal the electronic states associated with Fe4+ -O2- -Ni3+ configuration accelerate the deprotonation of *OH to *O (rate-determining step), and thus facilitate fast OER kinetics.

Hot-carrier transfer at photocatalytic silicon/platinum interfaces.

Interfacial charge transfer from silicon to heterogeneous catalysts plays a key role in silicon-based photoelectrochemical systems. In general, prior to interfacial charge transfer, carriers that are generated by photons with energies above the bandgap dissipate the excess kinetic energy via hot-carrier cooling, and such energy loss limits the maximum power conversion efficiency. The excess energy of hot-carriers, however, could be utilized through hot-carrier transfer from silicon to the catalysts, but such hot-carrier extraction has not yet been demonstrated. Here, we exploit transient reflection spectroscopy to interrogate charge transfer at the interface between silicon and platinum. Quantitative modeling of the surface carrier kinetics indicates that the velocity of charge transfer from silicon to platinum exceeds 2.6 × 107 cm s-1, corresponding to an average carrier temperature of extracted carriers of ∼600 K, two times higher than the lattice temperature. The charge transfer velocity can be controllably reduced by inserting silica spacing layers between silicon and platinum.

Spemann organizer transcriptome induction by early beta-catenin, Wnt, Nodal, and Siamois signals in Xenopus laevis.

The earliest event in Xenopus development is the dorsal accumulation of nuclear ß-catenin under the influence of cytoplasmic determinants displaced by fertilization. In this study, a genome-wide approach was used to examine transcription of the 43,673 genes annotated in the Xenopus laevis genome under a variety of conditions that inhibit or promote formation of the Spemann organizer signaling center. Loss of function of ß-catenin with antisense morpholinos reproducibly reduced the expression of 247 mRNAs at gastrula stage. Interestingly, only 123 ß-catenin targets were enriched on the dorsal side and defined an early dorsal ß-catenin gene signature. These genes included several previously unrecognized Spemann organizer components. Surprisingly, only 3 of these 123 genes overlapped with the late Wnt signature recently defined by two other groups using inhibition by Dkk1 mRNA or Wnt8 morpholinos, which indicates that the effects of ß-catenin/Wnt signaling in early development are exquisitely regulated by stage-dependent mechanisms. We analyzed transcriptome responses to a number of treatments in a total of 46 RNA-seq libraries. These treatments included, in addition to ß-catenin depletion, regenerating dorsal and ventral half-embryos, lithium chloride treatment, and the overexpression of Wnt8, Siamois, and Cerberus mRNAs. Only some of the early dorsal ß-catenin signature genes were activated at blastula whereas others required the induction of endomesoderm, as indicated by their inhibition by Cerberus overexpression. These comprehensive data provide a rich resource for analyzing how the dorsal and ventral regions of the embryo communicate with each other in a self-organizing vertebrate model embryo.

Activation of Notch1 synergizes with multiple pathways in promoting castration-resistant prostate cancer.

Metastatic castration-resistant prostate cancer (CRPC) is the primary cause of prostate cancer-specific mortality. Defining new mechanisms that can predict recurrence and drive lethal CRPC is critical. Here, we demonstrate that localized high-risk prostate cancer and metastatic CRPC, but not benign prostate tissues or low/intermediate-risk prostate cancer, express high levels of nuclear Notch homolog 1, translocation-associated (Notch1) receptor intracellular domain. Chronic activation of Notch1 synergizes with multiple oncogenic pathways altered in early disease to promote the development of prostate adenocarcinoma. These tumors display features of epithelial-to-mesenchymal transition, a cellular state associated with increased tumor aggressiveness. Consistent with its activation in clinical CRPC, tumors driven by Notch1 intracellular domain in combination with multiple pathways altered in prostate cancer are metastatic and resistant to androgen deprivation. Our study provides functional evidence that the Notch1 signaling axis synergizes with alternative pathways in promoting metastatic CRPC and may represent a new therapeutic target for advanced prostate cancer.

Genome-wide analysis of dorsal and ventral transcriptomes of the Xenopus laevis gastrula.

RNA sequencing has allowed high-throughput screening of differential gene expression in many tissues and organisms. Xenopus laevis is a classical embryological and cell-free extract model system, but its genomic sequence had been lacking due to difficulties arising from allotetraploidy. There is currently much excitement surrounding the release of the completed X. laevis genome (version 9.1) by the Joint Genome Institute (JGI), which provides a platform for genome-wide studies. Here we present a deep RNA-seq dataset of transcripts expressed in dorsal and ventral lips of the early Xenopus gastrula embryo using the new genomic information, which was further annotated by blast searches against the human proteome. Overall, our findings confirm previous results from differential screenings using other methods that uncovered classical dorsal genes such as Chordin, Noggin and Cerberus, as well as ventral genes such as Sizzled, Ventx, Wnt8 and Bambi. Complete transcriptome-wide tables of mRNAs suitable for data mining are presented, which include many novel dorsal- and ventral-specific genes. RNA-seq was very quantitative and reproducible, and allowed us to define dorsal and ventral signatures useful for gene set expression analyses (GSEA). As an example of a new gene, we present here data on an organizer-specific secreted protein tyrosine kinase known as Pkdcc (protein kinase domain containing, cytoplasmic) or Vlk (vertebrate lonesome kinase). Overexpression experiments indicate that Pkdcc can act as a negative regulator of Wnt/ ß-catenin signaling independently of its kinase activity. We conclude that RNA-Seq in combination with the X. laevis complete genome now available provides a powerful tool for unraveling cell-cell signaling pathways during embryonic induction.

A Single-Step Hydrothermal Route to 3D Hierarchical Cu2 O/CuO/rGO Nanosheets as High-Performance Anode of Lithium-Ion Batteries.

As anodes of Li-ion batteries, copper oxides (CuO) have a high theoretical specific capacity (674 mA h g-1 ) but own poor cyclic stability owing to the large volume expansion and low conductivity in charges/discharges. Incorporating reduced graphene oxide (rGO) into CuO anodes with conventional methods fails to build robust interaction between rGO and CuO to efficiently improve the overall anode performance. Here, Cu2 O/CuO/reduced graphene oxides (Cu2 O/CuO/rGO) with a 3D hierarchical nanostructure are synthesized with a facile, single-step hydrothermal method. The Cu2 O/CuO/rGO anode exhibits remarkable cyclic and high-rate performances, and particularly the anode with 25 wt% rGO owns the best performance among all samples, delivering a record capacity of 550 mA h g-1 at 0.5 C after 100 cycles. The pronounced performances are attributed to the highly efficient charge transfer in CuO nanosheets encapsulated in rGO network and the mitigated volume expansion of the anode owing to its robust 3D hierarchical nanostructure.

Coordination-dependent surface strain and rational construction of robust structures.

A surface relaxation model is established to study the elastic properties of nanoscale structures. This model predicts coordination-dependent strain at the surface and thickness-dependent stiffness of a material. Several atomic layers at the surface endure a significant strain gradient, which is dominated by the intrinsic properties of the material. The stiffness of low-dimensional materials is enhanced by surface relaxation effect. Surface effects on strong structures, including honeycomb structure and octet-truss structure with a high stiffness-to-weight ratio, are discussed. For these structures assembled with nanobeams, the Young's modulus decreases with decreasing size of the struts. The coupling between Young's modulus and relative density can be scaled down by engineering tensile strain on the struts.

Size- and dimensionality-dependent optical, magnetic and magneto-optical properties of binary europium-based nanocrystals: EuX (X = O, S, Se, Te).

Europium chalcogenides (EuX, X = O, S, Se, Te), a class of prototypical Heisenberg magnetic semiconductors, exhibit intriguing properties in optics, magnetism, and magneto-optics at the nanoscale, and have broad application potential in optical/magnetic sensors, spintronics, optical isolators, etc. EuX nanocrystals (NCs) exhibit enhanced properties, such as high saturation magnetization, a strong magneto-optic effect (Faraday rotation), and high magneto resistance, which are all unanimously dependent on the NC's size, shape, and surface information. In this report, we give an overview of the fundamental properties of bulk EuX, and illustrate the quantum confinement effects on the optical, magnetic and magneto-optical properties of EuX nanostructures. We then focus on doping and self-assembly-two efficient methods that enhance magnetic properties by manipulating magnetic coupling in EuX nanostructures. In particular, we look towards future research on Eu(2+) NCs, which along with the overview provides an up-to-date platform for evaluating the fundamental properties and application potential of Eu-based semiconductors.

FamAnn: an automated variant annotation pipeline to facilitate target discovery for family-based sequencing studies.

FamAnn is an automated variant annotation pipeline designed for facilitating target discovery for family-based sequencing studies. It can apply a different inheritance pattern or a de novo mutations discovery model to each family and select single nucleotide variants and small insertions and deletions segregating in each family or shared by multiple families. It also provides a variety of variant annotations and retains and annotates all transcripts hit by a single variant. Excel-compatible outputs including all annotated variants segregating in each family or shared by multiple families will be provided for users to prioritize variants based on their customized thresholds. A list of genes that harbor the segregating variants will be provided as well for possible pathway/network analyses. FamAnn uses the de facto community standard Variant Call Format as the input format and can be applied to whole exome, genome or targeted resequencing data. AVAILABILITY: https://sites.google.com/site/famannotation/home CONTACT: jianchaoyao@gmail.com, kelvinzhang@mednet.ucla.edu, mccombie@cshl.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Association between type 2 inflammatory diseases and neurodevelopmental disorders in low-birth-weight children and adolescents.

Background: Evidence of the association of certain neurodevelopmental disorder with specific type 2 inflammatory (T2) disease has been found. However, the association of various neurodevelopmental disorders with T2 diseases as a whole remains unclear in low-birth-weight (LBW) infants. Objective: To evaluate the association of type 2 inflammatory (T2) diseases with intellectual disability (ID), autism spectrum disorder (ASD), attention deficit hyperactivity disorder (ADHD), and learning disability (LD) in LBW children and adolescents. Methods: The study sample was derived from 2005 to 2018 National Health Interview Survey sample child files. LBW children and adolescents aged 3-17 were included. History of T2 diseases (including asthma and atopic dermatitis) and four neurodevelopmental disorders were reported by adults in families. The relationship between T2 diseases and the risk of four neurodevelopmental disorders was investigated through multiple-weighted logistic regression. Age, sex, race/ethnicity, region, highest education in family and ratio of family income to the poverty threshold were adjusted as covariates for model estimation. Subgroup analyses were conducted by age stratification (3-11 and 12-17 years), sex (male and female), and race (white and non-white). Results: 11,260 LBW children aged 3-17 years [mean age (SE), 9.73 (0.05) years] were included, in which 3,191 children had T2 diseases. History of T2 diseases was associated with an increased risk of neurodevelopmental disorders, with an OR of 1.35 (95% CI, 0.99-1.84) for ID, 1.47 (95% CI, 1.05-2.05) for ASD, 1.81 (95% CI, 1.51-2.16) for ADHD, and 1.74 (95% CI, 1.49-2.04) for LD following the adjustment of all the covariates. The correlations between T2 disorders and each of the four neurodevelopmental disorders were significantly different by sex and race (all P for interaction < 0.001), and no differences were found in age stratification (all P for interaction > 0.05). Conclusion: In a nationally representative sample of children, we found a significant association of T2 diseases with ASD, ADHD, and LD, even after adjusting for demographic baseline. We also found that the association of T2 disease with neurodevelopmental disorders differed between sex and race. Further investigation is needed to evaluate causal relationships and elucidate their potential mechanisms.

Ferromagnetic Insulating Ground-State Resolved in Mixed Protons and Oxygen Vacancies-Doped La0.67Sr0.33CoO3 Thin Films via Ionic Liquid Gating.

The realization of ferromagnetic insulating ground state is a critical prerequisite for spintronic applications. By applying electric field-controlled ionic liquid gating (ILG) to stoichiometry La0.67Sr0.33CoO3 thin films, the doping of protons (H+) has been achieved for the first time. Furthermore, a hitherto-unreported ferromagnetic insulating phase with a remarkably high Tc up to 180 K has been observed which can be attributed to the doping of H+ and the formation of oxygen vacancies (VO). The chemical formula of the dual-ion migrated film has been identified as La2/3Sr1/3CoO8/3H2/3 based on combined Co L23-edge absorption spectra and configuration interaction cluster calculations, from which we are able to explain the ferromagnetic ground state in terms of the distinct magnetic moment contributions from Co ions with octahedral (Oh) and tetrahedral (Td) symmetries following antiparallel spin alignments. Further density functional theory calculations have been performed to verify the functionality of H+ as the transfer ion and the origin of the novel ferromagnetic insulating ground state. Our results provide a fundamental understanding of the ILG regulation mechanism and shed light on the manipulating of more functionalities in other correlated compounds through dual-ion manipulation.

Educational Attainment and Later-Life Cognitive Function in High- and Middle-Income Countries: Evidence From the Harmonized Cognitive Assessment Protocol.

OBJECTIVES: Identifying social policies that can promote cognitive health is crucial for reducing the global burden of dementia. We evaluated the importance of educational attainment for later-life cognitive function in various social and geographic settings. METHODS: Using harmonized data for individuals aged ≥65 years from the United States Health and Retirement Study (HRS) and its international partner studies in England, Mexico, China, and India, and each study's respective Harmonized Cognitive Assessment Protocol (HCAP), we conducted a cross-national comparative study to examine the role of educational attainment in later-life cognitive function across countries (n = 14,980, 2016-2019). We used multivariable-adjusted regression to estimate associations between educational attainment and harmonized global cognitive function scores. RESULTS: In Mexico, China, and India, the general cognitive function scores on average are approximately one standard deviation of the HRS-HCAP cognitive function score distribution lower compared to the United States and England, paralleling patterns of educational attainment across countries. In all countries, higher educational attainment was associated with progressively higher later-life cognitive function scores. Population-level differences in educational attainment explained about 50%-90% of the observed differences in cognitive function scores across countries. DISCUSSION: The relationship between education and later-life cognitive function across social and geographic contexts underscores the crucial role of education to promote cognitive health and reduce dementia risk. Continual improvement of educational attainment in low- and middle-income settings may yield a significant pay-off in later-life cognitive health.

Dynamic restructuring of nickel sulfides for electrocatalytic hydrogen evolution reaction.

Transition metal chalcogenides have been identified as low-cost and efficient electrocatalysts to promote the hydrogen evolution reaction in alkaline media. However, the identification of active sites and the underlying catalytic mechanism remain elusive. In this work, we employ operando X-ray absorption spectroscopy and near-ambient pressure X-ray photoelectron spectroscopy to elucidate that NiS undergoes an in-situ phase transition to an intimately mixed phase of Ni3S2 and NiO, generating highly active synergistic dual sites at the Ni3S2/NiO interface. The interfacial Ni is the active site for water dissociation and OH* adsorption while the interfacial S acts as the active site for H* adsorption and H2 evolution. Accordingly, the in-situ formation of Ni3S2/NiO interfaces enables NiS electrocatalysts to achieve an overpotential of only 95 ± 8 mV at a current density of 10 mA cm-2. Our work highlighted that the chemistry of transition metal chalcogenides is highly dynamic, and a careful control of the working conditions may lead to the in-situ formation of catalytic species that boost their catalytic performance.

Generating active metal/oxide reverse interfaces through coordinated migration of single atoms.

Identification of active sites in catalytic materials is important and helps establish approaches to the precise design of catalysts for achieving high reactivity. Generally, active sites of conventional heterogeneous catalysts can be single atom, nanoparticle or a metal/oxide interface. Herein, we report that metal/oxide reverse interfaces can also be active sites which are created from the coordinated migration of metal and oxide atoms. As an example, a Pd1/CeO2 single-atom catalyst prepared via atom trapping, which is otherwise inactive at 30 °C, is able to completely oxidize formaldehyde after steam treatment. The enhanced reactivity is due to the formation of a Ce2O3-Pd nanoparticle domain interface, which is generated by the migration of both Ce and Pd atoms on the atom-trapped Pd1/CeO2 catalyst during steam treatment. We show that the generation of metal oxide-metal interfaces can be achieved in other heterogeneous catalysts due to the coordinated mobility of metal and oxide atoms, demonstrating the formation of a new active interface when using metal single-atom material as catalyst precursor.