Genomic Patterns of De Novo Mutation in Simplex Autism.

To further our understanding of the genetic etiology of autism, we generated and analyzed genome sequence data from 516 idiopathic autism families (2,064 individuals). This resource includes >59 million single-nucleotide variants (SNVs) and 9,212 private copy number variants (CNVs), of which 133,992 and 88 are de novo mutations (DNMs), respectively. We estimate a mutation rate of ∼1.5 × 10-8 SNVs per site per generation with a significantly higher mutation rate in repetitive DNA. Comparing probands and unaffected siblings, we observe several DNM trends. Probands carry more gene-disruptive CNVs and SNVs, resulting in severe missense mutations and mapping to predicted fetal brain promoters and embryonic stem cell enhancers. These differences become more pronounced for autism genes (p = 1.8 × 10-3, OR = 2.2). Patients are more likely to carry multiple coding and noncoding DNMs in different genes, which are enriched for expression in striatal neurons (p = 3 × 10-3), suggesting a path forward for genetically characterizing more complex cases of autism.

Interlayer Coupling Controlled Ordering and Phases in Polar Vortex Superlattices.

The recent discovery of polar topological structures has opened the door for exciting physics and emergent properties. There is, however, little methodology to engineer stability and ordering in these systems, properties of interest for engineering emergent functionalities. Notably, when the surface area is extended to arbitrary thicknesses, the topological polar texture becomes unstable. Here we show that this instability of the phase is due to electrical coupling between successive layers. We demonstrate that this electrical coupling is indicative of an effective screening length in the dielectric, similar to the conductor-ferroelectric interface. Controlling the electrostatics of the superlattice interfaces, the system can be tuned between a pure topological vortex state and a mixed classical-topological phase. This coupling also enables engineering coherency among the vortices, not only tuning the bulk phase diagram but also enabling the emergence of a 3D lattice of polar textures.

Non-volatile electric-field control of inversion symmetry.

Competition between ground states at phase boundaries can lead to significant changes in properties under stimuli, particularly when these ground states have different crystal symmetries. A key challenge is to stabilize and control the coexistence of symmetry-distinct phases. Using BiFeO3 layers confined between layers of dielectric TbScO3 as a model system, we stabilize the mixed-phase coexistence of centrosymmetric and non-centrosymmetric BiFeO3 phases at room temperature with antipolar, insulating and polar semiconducting behaviour, respectively. Application of orthogonal in-plane electric (polar) fields results in reversible non-volatile interconversion between the two phases, hence removing and introducing centrosymmetry. Counterintuitively, we find that an electric field 'erases' polarization, resulting from the anisotropy in octahedral tilts introduced by the interweaving TbScO3 layers. Consequently, this interconversion between centrosymmetric and non-centrosymmetric phases generates changes in the non-linear optical response of over three orders of magnitude, resistivity of over five orders of magnitude and control of microscopic polar order. Our work establishes a platform for cross-functional devices that take advantage of changes in optical, electrical and ferroic responses, and demonstrates octahedral tilts as an important order parameter in materials interface design.

Near-Field Coupling with a Nanoimprinted Probe for Dark Exciton Nanoimaging in Monolayer WSe2.

Tip-enhanced photoluminescence (TRPL) is a powerful technique for spatially and spectrally probing local optical properties of 2-dimensional (2D) materials that are modulated by the local heterogeneities, revealing inaccessible dark states due to bright state overlap in conventional far-field microscopy at room temperature. While scattering-type near-field probes have shown the potential to selectively enhance and reveal dark exciton emission, their technical complexity and sensitivity can pose challenges under certain experimental conditions. Here, we present a highly reproducible and easy-to-fabricate near-field probe based on nanoimprint lithography and fiber-optic excitation and collection. The novel near-field measurement configuration provides an ∼3 orders of magnitude out-of-plane Purcell enhancement, diffraction-limited excitation spot, and subdiffraction hyperspectral imaging resolution (below 50 nm) of dark exciton emission. The effectiveness of this high spatial XD mapping technique was then demonstrated through reproducible hyperspectral mapping of oxidized sites and bubble areas.

Transferable nano-patterned ALD membrane.

We demonstrate fabrication of nano-patterned thin ALD (Atomic layer deposition) membrane (suspended/transferable) by using a bi-layer resist process where the bottom layer resist acts as a sacrificial layer. This method enables an all dry deterministic transfer of nano-patterned ALD membrane on desired substrate, allowing assembly of multitude of hetero-structures and functionalities that are not yet accessible. Unlike conventional ways of achieving patterned alumina membrane reported in literature our technique requires significantly less fabrication steps and paves the way for novel ALD membrane-based technology.

Non-local dielectric effects in nanoscience.

The physical properties of charges and excitations in nanoscale materials are influenced both by the dielectric properties of the material itself and the surrounding environment. This non-local dielectric effect was first discussed in the context of molecules in solvents over a century ago. In this perspective, we discuss non-local dielectric effects in zero-dimensional, one-dimensional, and two-dimensional nanoscale systems.

Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility.

Genetic differences that specify unique aspects of human evolution have typically been identified by comparative analyses between the genomes of humans and closely related primates, including more recently the genomes of archaic hominins. Not all regions of the genome, however, are equally amenable to such study. Recurrent copy number variation (CNV) at chromosome 16p11.2 accounts for approximately 1% of cases of autism and is mediated by a complex set of segmental duplications, many of which arose recently during human evolution. Here we reconstruct the evolutionary history of the locus and identify bolA family member 2 (BOLA2) as a gene duplicated exclusively in Homo sapiens. We estimate that a 95-kilobase-pair segment containing BOLA2 duplicated across the critical region approximately 282 thousand years ago (ka), one of the latest among a series of genomic changes that dramatically restructured the locus during hominid evolution. All humans examined carried one or more copies of the duplication, which nearly fixed early in the human lineage--a pattern unlikely to have arisen so rapidly in the absence of selection (P < 0.0097). We show that the duplication of BOLA2 led to a novel, human-specific in-frame fusion transcript and that BOLA2 copy number correlates with both RNA expression (r = 0.36) and protein level (r = 0.65), with the greatest expression difference between human and chimpanzee in experimentally derived stem cells. Analyses of 152 patients carrying a chromosome 16p11. rearrangement show that more than 96% of breakpoints occur within the H. sapiens-specific duplication. In summary, the duplicative transposition of BOLA2 at the root of the H. sapiens lineage about 282 ka simultaneously increased copy number of a gene associated with iron homeostasis and predisposed our species to recurrent rearrangements associated with disease.

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA.

We performed whole-genome sequencing (WGS) of 208 genomes from 53 families affected by simplex autism. For the majority of these families, no copy-number variant (CNV) or candidate de novo gene-disruptive single-nucleotide variant (SNV) had been detected by microarray or whole-exome sequencing (WES). We integrated multiple CNV and SNV analyses and extensive experimental validation to identify additional candidate mutations in eight families. We report that compared to control individuals, probands showed a significant (p = 0.03) enrichment of de novo and private disruptive mutations within fetal CNS DNase I hypersensitive sites (i.e., putative regulatory regions). This effect was only observed within 50 kb of genes that have been previously associated with autism risk, including genes where dosage sensitivity has already been established by recurrent disruptive de novo protein-coding mutations (ARID1B, SCN2A, NR3C2, PRKCA, and DSCAM). In addition, we provide evidence of gene-disruptive CNVs (in DISC1, WNT7A, RBFOX1, and MBD5), as well as smaller de novo CNVs and exon-specific SNVs missed by exome sequencing in neurodevelopmental genes (e.g., CANX, SAE1, and PIK3CA). Our results suggest that the detection of smaller, often multiple CNVs affecting putative regulatory elements might help explain additional risk of simplex autism.

Interchromosomal core duplicons drive both evolutionary instability and disease susceptibility of the Chromosome 8p23.1 region.

Recurrent rearrangements of Chromosome 8p23.1 are associated with congenital heart defects and developmental delay. The complexity of this region has led to inconsistencies in the current reference assembly, confounding studies of genetic variation. Using comparative sequence-based approaches, we generated a high-quality 6.3-Mbp alternate reference assembly of an inverted Chromosome 8p23.1 haplotype. Comparison with nonhuman primates reveals a 746-kbp duplicative transposition and two separate inversion events that arose in the last million years of human evolution. The breakpoints associated with these rearrangements map to an ape-specific interchromosomal core duplicon that clusters at sites of evolutionary inversion (P = 7.8 × 10-5). Refinement of microdeletion breakpoints identifies a subgroup of patients that map to the same interchromosomal core involved in the evolutionary formation of the duplication blocks. Our results define a higher-order genomic instability element that has shaped the structure of specific chromosomes during primate evolution contributing to rearrangements associated with inversion and disease.

Rigid Band Shifts in Two-Dimensional Semiconductors through External Dielectric Screening.

We investigate the effects of external dielectric screening on the electronic dispersion and the band gap in the atomically thin, quasi-two-dimensional (2D) semiconductor WS_{2} using angle-resolved photoemission and optical spectroscopies, along with first-principles calculations. We find the main effect of increased external dielectric screening to be a reduction of the quasiparticle band gap, with rigid shifts to the bands themselves. Specifically, the band gap of monolayer WS_{2} is decreased by about 140 meV on a graphite substrate as compared to a hexagonal boron nitride substrate, while the electronic dispersion of WS_{2} remains unchanged within our experimental precision of 17 meV. These essentially rigid shifts of the valence and conduction bands result from the special spatial structure of the changes in the Coulomb potential induced by the dielectric environment of the monolayer.

Enhancement of Exciton-Phonon Scattering from Monolayer to Bilayer WS2.

Layered transition metal dichalcogenides exhibit the emergence of a direct bandgap at the monolayer limit along with pronounced excitonic effects. In these materials, interaction with phonons is the dominant mechanism that limits the exciton coherence lifetime. Exciton-phonon interaction also facilitates energy and momentum relaxation, and influences exciton diffusion under most experimental conditions. However, the fundamental changes in the exciton-phonon interaction are not well understood as the material undergoes the transition from a direct to an indirect bandgap semiconductor. Here, we address this question through optical spectroscopy and microscopic theory. In the experiment, we study room-temperature statistics of the exciton line width for a large number of mono- and bilayer WS2 samples. We observe a systematic increase in the room-temperature line width of the bilayer compared to the monolayer of 50 meV, corresponding to an additional scattering rate of ∼0.1 fs-1. We further address both phonon emission and absorption processes by examining the temperature dependence of the width of the exciton resonances. Using a theoretical approach based on many-body formalism, we are able to explain the experimental results and establish a microscopic framework for exciton-phonon interactions that can be applied to naturally occurring and artificially prepared multilayer structures.

Dynamic Optical Tuning of Interlayer Interactions in the Transition Metal Dichalcogenides.

Modulation of weak interlayer interactions between quasi-two-dimensional atomic planes in the transition metal dichalcogenides (TMDCs) provides avenues for tuning their functional properties. Here we show that above-gap optical excitation in the TMDCs leads to an unexpected large-amplitude, ultrafast compressive force between the two-dimensional layers, as probed by in situ measurements of the atomic layer spacing at femtosecond time resolution. We show that this compressive response arises from a dynamic modulation of the interlayer van der Waals interaction and that this represents the dominant light-induced stress at low excitation densities. A simple analytic model predicts the magnitude and carrier density dependence of the measured strains. This work establishes a new method for dynamic, nonequilibrium tuning of correlation-driven dispersive interactions and of the optomechanical functionality of TMDC quasi-two-dimensional materials.

Divergent target recognition by coexpressed 5'-isomiRs of miR-142-3p and selective viral mimicry.

Sequence heterogeneity at the ends of mature microRNAs (miRNAs) is well documented, but its effects on miRNA function are largely unexplored. Here we studied the impact of miRNA 5'-heterogeneity, which affects the seed region critical for target recognition. Using the example of miR-142-3p, an emerging regulator of the hematopoietic lineage in vertebrates, we show that naturally coexpressed 5'-variants (5'-isomiRs) can recognize largely distinct sets of binding sites. Despite this, both miR-142-3p isomiRs regulate exclusive and shared targets involved in actin dynamics. Thus, 5'-heterogeneity can substantially broaden and enhance regulation of one pathway. Other 5'-isomiRs, in contrast, recognize largely overlapping sets of binding sites. This is exemplified by two herpesviral 5'-isomiRs that selectively mimic one of the miR-142-3p 5'-isomiRs. We hypothesize that other cellular and viral 5'-isomiRs can similarly be grouped into those with divergent or convergent target repertoires, based on 5'-sequence features. Taken together, our results provide a detailed characterization of target recognition by miR-142-3p and its 5'-isomiR-specific viral mimic. We furthermore demonstrate that miRNA 5'-end variation leads to differential targeting and can thus broaden the target range of miRNAs.

Energy Transfer from Quantum Dots to Graphene and MoS2: The Role of Absorption and Screening in Two-Dimensional Materials.

We report efficient nonradiative energy transfer (NRET) from core-shell, semiconducting quantum dots to adjacent two-dimensional sheets of graphene and MoS2 of single- and few-layer thickness. We observe quenching of the photoluminescence (PL) from individual quantum dots and enhanced PL decay rates in time-resolved PL, corresponding to energy transfer rates of 1-10 ns(-1). Our measurements reveal contrasting trends in the NRET rate from the quantum dot to the van der Waals material as a function of thickness. The rate increases significantly with increasing layer thickness of graphene, but decreases with increasing thickness of MoS2 layers. A classical electromagnetic theory accounts for both the trends and absolute rates observed for the NRET. The countervailing trends arise from the competition between screening and absorption of the electric field of the quantum dot dipole inside the acceptor layers. We extend our analysis to predict the type of NRET behavior for the near-field coupling of a chromophore to a range of semiconducting and metallic thin film materials.

MicroRNA-mediated transformation by the Kaposi's sarcoma-associated herpesvirus Kaposin locus.

UNLABELLED: The human oncogenic Kaposi's sarcoma-associated herpesvirus (KSHV) expresses a set of ∼20 viral microRNAs (miRNAs). miR-K10a stands out among these miRNAs because its entire stem-loop precursor overlaps the coding sequence for the Kaposin (Kap) A/C proteins. The ectopic expression of KapA has been reported to lead to transformation of rodent fibroblasts. However, these experiments inadvertently also introduced miR-K10a, which raises the question whether the transforming activity of the locus could in fact be due to miR-K10a expression. To answer this question, we have uncoupled miR-K10a and KapA expression. Our experiments revealed that miR-K10a alone transformed cells with an efficiency similar to that when it was coexpressed with KapA. Maintenance of the transformed phenotype was conditional upon continued miR-K10a but not KapA protein expression, consistent with its dependence on miRNA-mediated changes in gene expression. Importantly, miR-K10a taps into an evolutionarily conserved network of miR-142-3p targets, several of which are expressed in 3T3 cells and are also known inhibitors of cellular transformation. In summary, our studies of miR-K10a serve as an example of an unsuspected function of an mRNA whose precursor is embedded within a coding transcript. In addition, our identification of conserved miR-K10a targets that limit transformation will point the way to a better understanding of the role of this miRNA in KSHV-associated tumors. IMPORTANCE: Kaposi's sarcoma-associated herpesvirus (KSHV) is a human tumor virus. The viral Kaposin locus has known oncogenic potential, which has previously been attributed to the encoded KapA protein. Here we show that the virally encoded miR-K10a miRNA, whose precursor overlaps the KapA-coding region, may account for the oncogenic properties of this locus. Our data suggest that miR-K10a mimics the cellular miRNA miR-142-3p and thereby represses several known inhibitors of oncogenic transformation. Our work demonstrates that functional properties attributed to a coding region may in fact be carried out by an embedded noncoding element and sheds light on the functions of viral miR-K10a.

Probing the Dynamics of the Metallic-to-Semiconducting Structural Phase Transformation in MoS2 Crystals.

We have investigated the phase transformation of bulk MoS2 crystals from the metastable metallic 1T/1T' phase to the thermodynamically stable semiconducting 2H phase. The metastable 1T/1T' material was prepared by Li intercalation and deintercalation. The thermally driven kinetics of the phase transformation were studied with in situ Raman and optical reflection spectroscopies and yield an activation energy of 400 ± 60 meV (38 ± 6 kJ/mol). We calculate the expected minimum energy pathways for these transformations using DFT methods. The experimental activation energy corresponds approximately to the theoretical barrier for a single formula unit, suggesting that nucleation of the phase transformation is quite local. We also report that femtosecond laser writing converts 1T/1T' to 2H in a single laser pass. The mechanisms for the phase transformation are discussed.