Genome editing demonstrates that the -5 kb Nanog enhancer regulates Nanog expression by modulating RNAPII initiation and/or recruitment.

Transcriptional enhancers have been defined by their ability to operate independent of distance and orientation in plasmid-based reporter assays of gene expression. At present, histone marks are used to identify and define enhancers but do not consider the endogenous role of an enhancer in the context of native chromatin. We employed a combination of genomic editing, single cell analyses, and sequencing approaches to investigate a Nanog-associated cis-regulatory element, which has been reported by others to be either an alternative promoter or a super-enhancer. We first demonstrate both distance and orientation independence in native chromatin, eliminating the issues raised with plasmid-based approaches. We next demonstrate that the dominant super-enhancer modulates Nanog globally and operates by recruiting and/or initiating RNA Polymerase II. Our studies have important implications to how transcriptional enhancers are defined and how they regulate gene expression.

Cyclin-dependent kinase 1 (CDK1) and CDK2 have opposing roles in regulating interactions of splicing factor 3B1 with chromatin.

Splicing factor 3B1 (SF3B1) is a core splicing protein that stabilizes the interaction between the U2 snRNA and the branch point in the mRNA target during splicing. SF3B1 is heavily phosphorylated at its N terminus and a substrate of cyclin-dependent kinases (CDKs). Although SF3B1 phosphorylation coincides with splicing catalysis, the functional significance of SF3B1 phosphorylation is largely undefined. Here, we show that SF3B1 phosphorylation follows a dynamic pattern during cell cycle progression that depends on CDK activity. SF3B1 is known to interact with chromatin, and we found that SF3B1 maximally interacts with nucleosomes during G1/S and that this interaction requires CDK2 activity. In contrast, SF3B1 disassociates from nucleosomes at G2/M, coinciding with a peak in CDK1-mediated SF3B1 phosphorylation. Thus, CDK1 and CDK2 appear to have opposing roles in regulating SF3B1-nucleosome interactions. Importantly, these interactions were modified by the presence and phosphorylation status of linker histone H1, particularly the H1.4 isoform. Performing genome-wide analysis of SF3B1-chromatin binding in synchronized cells, we observed that SF3B1 preferentially bound exons. Differences in SF3B1 chromatin binding to specific sites, however, did not correlate with changes in RNA splicing, suggesting that the SF3B1-nucleosome interaction does not determine cell cycle-dependent changes to mRNA splicing. Our results define a cell cycle stage-specific interaction between SF3B1 and nucleosomes that is mediated by histone H1 and depends on SF3B1 phosphorylation. Importantly, this interaction does not seem to be related to SF3B1's splicing function and, rather, points toward its potential role as a chromatin modifier.

Deletion of Tet proteins results in quantitative disparities during ESC differentiation partially attributable to alterations in gene expression.

BACKGROUND: The Tet protein family (Tet1, Tet2, and Tet3) regulate DNA methylation through conversion of 5-methylcytosine to 5-hydroxymethylcytosine which can ultimately result in DNA demethylation and play a critical role during early mammalian development and pluripotency. While multiple groups have generated knockouts combining loss of different Tet proteins in murine embryonic stem cells (ESCs), differences in genetic background and approaches has made it difficult to directly compare results and discern the direct mechanism by which Tet proteins regulate the transcriptome. To address this concern, we utilized genomic editing in an isogenic pluripotent background which permitted a quantitative, flow-cytometry based measurement of pluripotency in combination with genome-wide assessment of gene expression and DNA methylation changes. Our ultimate goal was to generate a resource of large-scale datasets to permit hypothesis-generating experiments. RESULTS: We demonstrate a quantitative disparity in the differentiation ability among Tet protein deletions, with Tet2 single knockout exhibiting the most severe defect, while loss of Tet1 alone or combinations of Tet genes showed a quantitatively intermediate phenotype. Using a combination of transcriptomic and epigenomic approaches we demonstrate an increase in DNA hypermethylation and a divergence of transcriptional profiles in pluripotency among Tet deletions, with loss of Tet2 having the most profound effect in undifferentiated ESCs. CONCLUSIONS: We conclude that loss of Tet2 has the most dramatic effect both on the phenotype of ESCs and the transcriptome compared to other genotypes. While loss of Tet proteins increased DNA hypermethylation, especially in gene promoters, these changes in DNA methylation did not correlate with gene expression changes. Thus, while loss of different Tet proteins alters DNA methylation, this change does not appear to be directly responsible for transcriptome changes. Thus, loss of Tet proteins likely regulates the transcriptome epigenetically both through altering 5mC but also through additional mechanisms. Nonetheless, the transcriptome changes in pluripotent Tet2-/- ESCs compared to wild-type implies that the disparities in differentiation can be partially attributed to baseline alterations in gene expression.

Strain-Tunable Quantum Integrated Photonics.

Semiconductor quantum dots are crucial parts of the photonic quantum technology toolbox because they show excellent single-photon emission properties in addition to their potential as solid-state qubits. Recently, there has been an increasing effort to deterministically integrate single semiconductor quantum dots into complex photonic circuits. Despite rapid progress in the field, it remains challenging to manipulate the optical properties of waveguide-integrated quantum emitters in a deterministic, reversible, and nonintrusive manner. Here we demonstrate a new class of hybrid quantum photonic circuits combining III-V semiconductors, silicon nitride, and piezoelectric crystals. Using a combination of bottom-up, top-down, and nanomanipulation techniques, we realize strain tuning of a selected, waveguide-integrated, quantum emitter and a planar integrated optical resonator. Our findings are an important step toward realizing reconfigurable quantum-integrated photonics, with full control over the quantum sources and the photonic circuit.

Deterministic Integration of Single Photon Sources in Silicon Based Photonic Circuits.

A major step toward fully integrated quantum optics is the deterministic incorporation of high quality single photon sources in on-chip optical circuits. We show a novel hybrid approach in which preselected III-V single quantum dots in nanowires are transferred and integrated in silicon based photonic circuits. The quantum emitters maintain their high optical quality after integration as verified by measuring a low multiphoton probability of 0.07 ± 0.07 and emission line width as narrow as 3.45 ± 0.48 GHz. Our approach allows for optimum alignment of the quantum dot light emission to the fundamental waveguide mode resulting in very high coupling efficiencies. We estimate a coupling efficiency of 24.3 ± 1.7% from the studied single-photon source to the photonic channel and further show by finite-difference time-domain simulations that for an optimized choice of material and design the efficiency can exceed 90%.

High-Yield Growth and Characterization of ⟨100⟩ InP p-n Diode Nanowires.

Semiconductor nanowires are nanoscale structures holding promise in many fields such as optoelectronics, quantum computing, and thermoelectrics. Nanowires are usually grown vertically on (111)-oriented substrates, while (100) is the standard in semiconductor technology. The ability to grow and to control impurity doping of ⟨100⟩ nanowires is crucial for integration. Here, we discuss doping of single-crystalline ⟨100⟩ nanowires, and the structural and optoelectronic properties of p-n junctions based on ⟨100⟩ InP nanowires. We describe a novel approach to achieve low resistance electrical contacts to nanowires via a gradual interface based on p-doped InAsP. As a first demonstration in optoelectronic devices, we realize a single nanowire light emitting diode in a ⟨100⟩-oriented InP nanowire p-n junction. To obtain high vertical yield, which is necessary for future applications, we investigate the effect of the introduction of dopants on the nanowire growth.

Nanowire waveguides launching single photons in a Gaussian mode for ideal fiber coupling.

Quantum communication as well as integrated photonic circuits require single photons propagating in a well-defined Gaussian mode. However, tailoring the emission mode to a Gaussian remains an unsolved challenge for solid-state quantum emitters due to their random positioning in the host material or photonic structure. Here, we overcome these limitations by embedding a semiconductor quantum dot in a tapered nanowire waveguide. Owing to the deterministic positioning of the emitter in the waveguide, we demonstrate a Gaussian emission profile in the far field. Hence, we further couple the emission into a single-mode optical fiber with a record efficiency of 93%, thereby addressing a major hurdle for practical implementation of single photon sources in emerging photonic technologies.

A novel role for IQGAP1 protein in cell motility through cell retraction.

IQGAP1 has emerged as a key component in the regulation of cytoskeleton dynamics during cell migration, maintenance of adherens junctions, microbial pathogenesis and intracellular trafficking. IQGAP1 is known to localize to the protruding edge of lamellipodia in a variety of cell types and interact with regulators of actin dynamics. Here, we provide evidence suggesting a novel role of IQGAP1 in cell motility through cell edge retraction. In some of the cell lines examined, IQGAP1 was markedly separated from WAVE localization suggesting IQGAP1 may localize to retracting edges. B16F10 mouse melanoma cells exhibited the most restricted separation in which the appearance of GFP-IQGAP1 correlated with cell edge retraction velocity and the disappearance of mCherry-Arp3. These results demonstrate that in some cell types IQGAP1 may function to promote cell retraction not lamellipodium edge protrusion. In addition, we examined co-localization of IQGAP1 with adhesion site markers, myosin IIA, calmodulin and IQGAP2. In areas rich in IQGAP1 there was decreased immunofluorescence staining of vinculin, paxillin and phosphorylated-tyrosine indicating adhesion site disassembly. Interestingly, calmodulin, but not myosin IIA or IQGAP2, co-localized with IQGAP1 in areas of cell retraction. Overall these results suggest a new role of IQGAP1, distinct form IQGAP2, in cell migration through up regulation of contractility and downregulation of adhesion sites potentially through calmodulin interaction.

Macroscopic tunneling probe of Moiré spin textures in twisted CrI3.

Various noncollinear spin textures and magnetic phases have been predicted in twisted two-dimensional CrI3 due to competing ferromagnetic (FM) and antiferromagnetic (AFM) interlayer exchange from moiré stacking-with potential spintronic applications even when the underlying material possesses a negligible Dzyaloshinskii-Moriya or dipole-dipole interaction. Recent measurements have shown evidence of coexisting FM and AFM layer order in small-twist-angle CrI3 bilayers and double bilayers. Yet, the nature of the magnetic textures remains unresolved and possibilities for their manipulation and electrical readout are unexplored. Here, we use tunneling magnetoresistance to investigate the collective spin states of twisted double-bilayer CrI3 under both out-of-plane and in-plane magnetic fields together with detailed micromagnetic simulations of domain dynamics based on magnetic circular dichroism. Our results capture hysteretic and anisotropic field evolutions of the magnetic states and we further uncover two distinct non-volatile spin textures (out-of-plane and in-plane domains) at ≈1° twist angle, with a different global tunneling resistance that can be switched by magnetic field.

Ultraclean emission from InAsP quantum dots in defect-free wurtzite InP nanowires.

We report on the ultraclean emission from single quantum dots embedded in pure wurtzite nanowires. Using a two-step growth process combining selective-area and vapor-liquid-solid epitaxy, we grow defect-free wurtzite InP nanowires with embedded InAsP quantum dots, which are clad to diameters sufficient for waveguiding at λ ~ 950 nm. The absence of nearby traps, at both the nanowire surface and along its length in the vicinity of the quantum dot, manifests in excitonic transitions of high spectral purity. Narrow emission line widths (30 µeV) and very-pure single photon emission with a probability of multiphoton emission below 1% are achieved, both of which were not possible in previous work where stacking fault densities were significantly higher.

Electric field induced removal of the biexciton binding energy in a single quantum dot.

We control the electrostatic environment of a single InAsP quantum dot in an InP nanowire with two contacts and two lateral gates positioned to an individual nanowire. We empty the quantum dot of excess charges and apply an electric field across its radial dimension. A large tuning range for the biexciton binding energy of 3 meV is obtained in a lateral electric field. At finite lateral electric field the exciton and biexciton emission overlap within their optical line width resulting in an enhancement of the observed photoluminescence intensity. The electric field dependence of the exciton and biexciton is compared to theoretical predictions and found to be in good qualitative agreement. This result is promising toward generating entangled photon pairs on demand without the requirement to remove the anisotropic exchange splitting from asymmetric quantum dots.

Semiconductor nanowire metamaterial for broadband near-unity absorption.

The realization of a semiconductor near-unity absorber in the infrared will provide new capabilities to transform applications in sensing, health, imaging, and quantum information science, especially where portability is required. Typically, commercially available portable single-photon detectors in the infrared are made from bulk semiconductors and have efficiencies well below unity. Here, we design a novel semiconductor nanowire metamaterial, and show that by carefully arranging an InGaAs nanowire array and by controlling their shape, we demonstrate near-unity absorption efficiency at room temperature. We experimentally show an average measured efficiency of 93% (simulated average efficiency of 97%) over an unprecedented wavelength range from 900 to 1500 nm. We further show that the near-unity absorption results from the collective response of the nanowire metamaterial, originating from both coupling into leaky resonant waveguide and transverse modes. These coupling mechanisms cause light to be absorbed directly from the top and indirectly as light scatters from one nanowire to neighbouring ones. This work leads to the possible development of a new generation of quantum detectors with unprecedented broadband near-unity absorption in the infrared, while operating near room temperature for a wider range of applications.

Single electron charging in optically active nanowire quantum dots.

We report optical experiments of a charge tunable, single nanowire quantum dot subject to an electric field tuned by two independent voltages. First, we control tunneling events through an applied electric field along the nanowire growth direction. Second, we modify the chemical potential in the nanowire with a back-gate. We combine these two field-effects to isolate a single electron and independently tune the tunnel coupling of the quantum dot with the contacts. Such charge control is a first requirement for opto-electrical single electron spin experiments on a nanowire quantum dot.

Evaluation of pasting and gelling properties of commercial flours under high heating temperatures using Rapid Visco Analyzer 4800.

In this study, pasting and gelling behaviors of flours were investigated at heating temperatures of 95-140 °C. Overall, both peak and breakdown viscosities of the flours were positively correlated with starch contents (p < 0.01) but inversely correlated with protein (p < 0.01) and fiber contents (p < 0.05) at 95-140 °C. When the heating temperature increased, pasting temperatures and peak viscosities of most waxy and normal flours largely remained the same, but their holding strengths and final viscosities gradually decreased. However, pulse and high-amylose maize flours required a holding temperature above 95 °C to achieve the highest peak and final viscosities. Normal maize and pulse flours formed hard gels after cooking at 120 °C, and high-amylose maize flour developed the firmest gel after cooking at 140 °C. Chemical compositions, particle sizes, and thermal properties of the studied flours influenced their pasting and gelling properties to certain levels under the different heating temperatures.

DOT1L inhibitors block abnormal self-renewal induced by cohesin loss.

Acute myeloid leukemia (AML) is a high-risk malignancy characterized by a diverse spectrum of somatic genetic alterations. The mechanisms by which these mutations contribute to leukemia development and how this informs the use of targeted therapies is critical to improving outcomes for patients. Importantly, how to target loss-of-function mutations has been a critical challenge in precision medicine. Heterozygous inactivating mutations in cohesin complex genes contribute to AML in adults by increasing the self-renewal capacity of hematopoietic stem and progenitor cells (HSPCs) by altering PRC2 targeting to induce HOXA9 expression, a key self-renewal transcription factor. Here we sought to delineate the epigenetic mechanism underpinning the enhanced self-renewal conferred by cohesin-haploinsufficiency. First, given the substantial difference in the mutational spectrum between pediatric and adult AML patients, we first sought to identify if HOXA9 was also elevated in children. Next, using primary HSPCs as a model we demonstrate that abnormal self-renewal due to cohesin loss is blocked by DOT1L inhibition. In cohesin-depleted cells, DOT1L inhibition is associated with H3K79me2 depletion and a concomitant increase in H3K27me3. Importantly, we find that there are cohesin-dependent gene expression changes that promote a leukemic profile, including HoxA overexpression, that are preferentially reversed by DOT1L inhibition. Our data further characterize how cohesin mutations contribute to AML development, identifying DOT1L as a potential therapeutic target for adult and pediatric AML patients harboring cohesin mutations.

Measurement and simulation of polarization transients in dispersion compensation modules.

We examine both theoretically and experimentally rapid polarization transients generated by mechanical impacts on dispersion compensation modules (DCMs). In our experiments, the transient response of the output polarization to sudden mechanical impacts is found to remain constant among successive measurements. That is, the Stokes vector traces the same path over the Poincaré sphere provided that the interval of time between measurements is less than the time associated with the slow thermal drift of the fiber birefringence profile. Experimentally we can measure angular velocities (AVs) of the Stokes vector over the Poincaré sphere exceeding 100 krad∕s. We demonstrate theoretically with a simple model for the excitation that the patterns of the AV observed in experiments can be reproduced through simulation and that the amplitude of the AV increases with the volume of the fiber affected by the impact. Our model is sufficiently simple to be employed in system simulations.

Tapered InP nanowire arrays for efficient broadband high-speed single-photon detection.

Superconducting nanowire single-photon detectors with peak efficiencies above 90% and unrivalled timing jitter (<30 ps) have emerged as a potent technology for quantum information and sensing applications. However, their high cost and cryogenic operation limit their widespread applicability. Here, we present an approach using tapered InP nanowire p-n junction arrays for high-efficiency, broadband and high-speed photodetection without the need for cryogenic cooling. The truncated conical nanowire shape enables a broadband, linear photoresponse in the ultraviolet to near-infrared range (~500 nm bandwidth) with external quantum efficiencies exceeding 85%. The devices exhibit a high gain beyond 105, such that a single photon per pulse can be distinguished from the dark noise, while simultaneously showing a fast pulse rise time (<1 ns) and excellent timing jitter (<20 ps). Such detectors open up new possibilities for applications in remote sensing, dose monitoring for cancer treatment, three-dimensional imaging and quantum communication.

Mirc11 Disrupts Inflammatory but Not Cytotoxic Responses of NK Cells.

Natural killer (NK) cells generate proinflammatory cytokines that are required to contain infections and tumor growth. However, the posttranscriptional mechanisms that regulate NK cell functions are not fully understood. Here, we define the role of the microRNA cluster known as Mirc11 (which includes miRNA-23a, miRNA-24a, and miRNA-27a) in NK cell-mediated proinflammatory responses. Absence of Mirc11 did not alter the development or the antitumor cytotoxicity of NK cells. However, loss of Mirc11 reduced generation of proinflammatory factors in vitro and interferon-γ-dependent clearance of Listeria monocytogenes or B16F10 melanoma in vivo by NK cells. These functional changes resulted from Mirc11 silencing ubiquitin modifiers A20, Cbl-b, and Itch, allowing TRAF6-dependent activation of NF-κB and AP-1. Lack of Mirc11 caused increased translation of A20, Cbl-b, and Itch proteins, resulting in deubiquitylation of scaffolding K63 and addition of degradative K48 moieties on TRAF6. Collectively, our results describe a function of Mirc11 that regulates generation of proinflammatory cytokines from effector lymphocytes.

Intrinsic Response Towards Physiologic Stiffness is Cell-Type Dependent.

In the continuous search for better tissue engineering scaffolds it has become increasingly clear that the substrate properties dramatically affect cell responses. Here we compared cells from a physiologically stiff tissue, melanoma, to cells isolated from a physiologically soft tissue, brain. We measured the cell line responses to laminin immobilized onto glass or polyacrylamide hydrogels tuned to have a Young's modulus ranging from 1 to 390 kPa. Single cells were analyzed for spreading area, shape, total actin content, actin-based morphological features and modification of immobilized laminin. Both cell types exhibited stiffness- and laminin concentration-dependent responses on polyacrylamide and glass. Melanoma cells exhibited very little spreading and were rounded on soft (1, 5, and 15 kPa) hydrogels while cells on stiff (40, 100, and 390 kPa) hydrogels were spread and had a polarized cell shape with large lamellipodia. On rigid glass surfaces, spreading and actin-based morphological features were not observed until laminin concentration was much higher. Similarly, increased microglia cell spreading and presence of actin-based structures were observed on stiff hydrogels. However, responses on rigid glass surfaces were much different. Microglia cells had large spreading areas and elongated shapes on glass compared to hydrogels even when immobilized laminin density was consistent on all gels. While cell spreading and shape varied with Young's modulus of the hydrogel, the concentration of f-actin was constant. A decrease in laminin immunofluorescence was associated with melanoma and microglia cell spreading on glass with high coating concentration of laminin, indicating modification of immobilized laminin triggered by supraphysiologic stiffness and high ligand density. These results suggest that some cell lines are more sensitive to mechanical properties matching their native tissue environment while other cell lines may require stiffness and extracellular ligand density well above physiologic tissue before saturation in cell spreading, elongation and cytoskeletal re-organization are reached.

Ras GAP-related and C-terminal domain-dependent localization and tumorigenic activities of IQGAP1 in melanoma cells.

IQGAP1 interacts with a number of binding partners through a calponin homology domain (CHD), a WW motif, IQ repeats, a Ras GAP-related domain (GRD), and a conserved C-terminal (CT) domain. Among various biological and cellular functions, IQGAP1 is known to play a role in actin cytoskeleton dynamics during membrane ruffling and lamellipodium protrusion. In addition, phosphorylation near the CT domain is thought to control IQGAP1 activity through regulation of intramolecular interaction. In a previous study, we discovered that IQGAP1 preferentially localizes to retracting areas in B16F10 mouse melanoma cells, not areas of membrane ruffling and lamellipodium protrusion. Nothing is known of the domains needed for retraction localization and very little is known of IQGAP1 function in the actin cytoskeleton of melanoma cells. Thus, we examined localization of IQGAP1 mutants to retracting areas, and characterized knock down phenotypes on tissue culture plastic and physiologic-stiffness hydrogels. Localization of IQGAP1 mutants (S1441E/S1443D, S1441A/S1443A, ΔCHD, ΔGRD or ΔCT) to retracting and protruding cell edges were measured. In retracting areas there was a decrease in S1441A/S1443A, ΔGRD and ΔCT localization, a minor decrease in ΔCHD localization, and normal localization of the S1441E/S1443D mutant. In areas of cell protrusion just behind the lamellipodium leading edge, we surprisingly observed both ΔGRD and ΔCT localization, and increased number of microtubules. IQGAP1 knock down caused loss of cell polarity on laminin-coated glass, decreased proliferation on tissue culture polystyrene, and abnormal spheroid growth on laminin-coated hydrogels. We propose that the GRD and CT domains regulate IQGAP1 localization to retracting actin networks to promote a tumorigenic role in melanoma cells.