Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes

Shielded covalent (SC) probes combine programmable base pairing, molecular conformation change, and activatable covalent crosslinking to achieve selective and durable capture of nucleic acid targets, including efficient discrimination of SNPs. Capture yields appear consistent with the thermodynamics of probe/target hybridization, allowing rational probe design. We will demonstrate RNA pull-down using surface-immobilized SC probes, exploiting covalent target capture to remove unwanted material using stringent washes, and then reversing the crosslinks to recover the targets. RNA pull-downs using SC probes will provide a powerful framework for exploring the in vivo binding partners of RNAs

A Search for AGN sources of the IceCube Diffuse Neutrino Flux

The origin of the diffuse astrophysical neutrino flux measured by the IceCube Observatory remains largely unknown. Although NGC 1068 and TXS 0506+056 have been identified as potential neutrino sources, the diffuse flux of neutrinos must have additional sources that have not yet been identified. Here we investigate potential correlations between IceCube's neutrino events and the Fermi and MOJAVE source catalogs, using the publicly-available IceCube data set. We perform three separate spatially-dependent, energy-dependent, and time-dependent searches, and find no statistically significant sources outside of NGC 1068. We find that no more than 13% of IceCube's neutrino flux originates from blazars over the whole sky. Then, using an energy-dependent likelihood analysis, the limit on neutrinos originating from blazars reduces to 9% in the Northern hemisphere. Finally, we set limits on individual sources from the MOJAVE radio catalog after finding no statistically significant time-flaring sources.Comment: 18 pages, 7 figure

Development Toward a Ground-Based Interferometric Phased Array for Radio Detection of High Energy Neutrinos

The in-ice radio interferometric phased array technique for detection of high energy neutrinos looks for Askaryan emission from neutrinos interacting in large volumes of glacial ice, and is being developed as a way to achieve a low energy threshold and a large effective volume at high energies. The technique is based on coherently summing the impulsive Askaryan signal from multiple antennas, which increases the signal-to-noise ratio for weak signals. We report here on measurements and a simulation of thermal noise correlations between nearby antennas, beamforming of impulsive signals, and a measurement of the expected improvement in trigger efficiency through the phased array technique. We also discuss the noise environment observed with an analog phased array at Summit Station, Greenland, a possible site for an interferometric phased array for radio detection of high energy neutrinos.Comment: 13 Pages, 14 Figure

Measurements and Modeling of Near-Surface Radio Propagation in Glacial Ice and Implications for Neutrino Experiments

We present measurements of radio transmission in the $\sim$100 MHz range through a $\sim100$ m deep region below the surface of the ice at Summit Station, Greenland, called the firn. In the firn, the index of refraction changes due to the transition from snow at the surface to glacial ice below, affecting the propagation of radio signals in that region. We compare our observations to a finite-difference time-domain (FDTD) electromagnetic wave simulation, which supports the existence of three classes of propagation: a bulk propagation ray-bending mode that leads to so-called "shadowed" regions for certain geometries of transmission, a surface-wave mode induced by the ice/air interface, and an arbitrary-depth horizontal propagation mode that requires perturbations from a smooth density gradient. In the non-shadowed region, our measurements are consistent with the bulk propagation ray-bending mode both in timing and in amplitude. We also observe signals in the shadowed region, in conflict with a bulk-propagation-only ray-bending model, but consistent with FDTD simulations using a variety of firn models for Summit Station. The amplitude and timing of our measurements in all geometries are consistent with the predictions from FDTD simulations. In the shadowed region, the amplitude of the observed signals is consistent with a best-fit coupling fraction value of $2.4$% (0.06% in power) or less to a surface or horizontal propagation mode from the bulk propagation mode. The relative amplitude of observable signals in the two regions is important for experiments that aim to detect radio emission from astrophysical high-energy neutrinos interacting in glacial ice, which rely on a radio propagation model to inform simulations and perform event reconstruction.Comment: 14 pages, 13 figures, version accepted to PR

Accelerator measurements of magnetically-induced radio emission from particle cascades with applications to cosmic-ray air showers

For fifty years, cosmic-ray air showers have been detected by their radio emission. We present the first laboratory measurements that validate electrodynamics simulations used in air shower modeling. An experiment at SLAC provides a beam test of radio-frequency (RF) radiation from charged particle cascades in the presence of a magnetic field, a model system of a cosmic-ray air shower. This experiment provides a suite of controlled laboratory measurements to compare to particle-level simulations of RF emission, which are relied upon in ultra-high-energy cosmic-ray air shower detection. We compare simulations to data for intensity, linearity with magnetic field, angular distribution, polarization, and spectral content. In particular, we confirm modern predictions that the magnetically induced emission in a dielectric forms a cone that peaks at the Cherenkov angle and show that the simulations reproduce the data within systematic uncertainties.Comment: 5 pages, 7 figure

High-Precision Scanning Water Vapor Radiometers for Cosmic Microwave Background Site Characterization and Comparison

The compelling science case for the observation of B-mode polarization in the cosmic microwave background (CMB) is driving the CMB community to expand the observed sky fraction, either by extending survey sizes or by deploying receivers to potential new northern sites. For ground-based CMB instruments, poorly-mixed atmospheric water vapor constitutes the primary source of short-term sky noise. This results in short-timescale brightness fluctuations, which must be rejected by some form of modulation. To maximize the sensitivity of ground-based CMB observations, it is useful to understand the effects of atmospheric water vapor over timescales and angular scales relevant for CMB polarization measurements. To this end, we have undertaken a campaign to perform a coordinated characterization of current and potential future observing sites using scanning 183 GHz water vapor radiometers (WVRs). So far, we have deployed two identical WVR units; one at the South Pole, Antarctica, and the other at Summit Station, Greenland. The former site has a long heritage of ground-based CMB observations and is the current location of the Bicep/Keck Array telescopes as well as the South Pole Telescope. The latter site, though less well characterized, is under consideration as a northern-hemisphere location for future CMB receivers. Data collection from this campaign began in January 2016 at South Pole and July 2016 at Summit Station. Data analysis is ongoing to reduce the data to a single spatial and temporal statistic that can be used for one-to-one site comparison.Comment: Published in Proc. SPIE. Presented at SPIE Astronomical Telescopes and Instrumentation Conference 10708: Millimeter, Submillimeter, and Far-Infrared Detectors and Instrumentation for Astronomy XI, June 2018. 10 pages, 11 figure

Selective Nucleic Acid Capture with Shielded Covalent Probes

Nucleic acid probes are used for diverse applications in vitro, in situ, and in vivo. In any setting, their power is limited by imperfect selectivity (binding of undesired targets) and incomplete affinity (binding is reversible, and not all desired targets bound). These difficulties are fundamental, stemming from reliance on base pairing to provide both selectivity and affinity. Shielded covalent (SC) probes eliminate the longstanding trade-off between selectivity and durable target capture, achieving selectivity via programmable base pairing and molecular conformation change, and durable target capture via activatable covalent cross-linking. In pure and mixed samples, SC probes covalently capture complementary DNA or RNA oligo targets and reject two-nucleotide mismatched targets with near-quantitative yields at room temperature, achieving discrimination ratios of 2–3 orders of magnitude. Semiquantitative studies with full-length mRNA targets demonstrate selective covalent capture comparable to that for RNA oligo targets. Single-nucleotide DNA or RNA mismatches, including nearly isoenergetic RNA wobble pairs, can be efficiently rejected with discrimination ratios of 1–2 orders of magnitude. Covalent capture yields appear consistent with the thermodynamics of probe/target hybridization, facilitating rational probe design. If desired, cross-links can be reversed to release the target after capture. In contrast to existing probe chemistries, SC probes achieve the high sequence selectivity of a structured probe, yet durably retain their targets even under denaturing conditions. This previously incompatible combination of properties suggests diverse applications based on selective and stable binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent washes in vitro or in situ, or by enzymes in vivo)

Dynamic nuclear polarization at 9 T using a novel 250 GHz gyrotron microwave source

In this communication, we report enhancements of nuclear spin polarization by dynamic nuclear polarization (DNP) in static and spinning solids at a magnetic field strength of 9 T (250 GHz for g = 2 electrons, 380 MHz for [superscript 1]H). In these experiments, [superscript 1]H enhancements of up to 170 ± 50 have been observed in 1-[superscript 13]C-glycine dispersed in a 60:40 glycerol/water matrix at temperatures of 20 K; in addition, we have observed significant enhancements in [superscript 15]N spectra of unoriented pf1-bacteriophage. Finally, enhancements of ~17 have been obtained in two-dimensional [superscript 13]C–[superscript 13]C chemical shift correlation spectra of the amino acid U–[superscript 13]C, [superscript 15]N-proline during magic angle spinning (MAS), demonstrating the stability of the DNP experiment for sustained acquisition and for quantitative experiments incorporating dipolar recoupling. In all cases, we have exploited the thermal mixing DNP mechanism with the nitroxide radical 4-amino-TEMPO as the paramagnetic dopant. These are the highest frequency DNP experiments performed to date and indicate that significant signal enhancements can be realized using the thermal mixing mechanism even at elevated magnetic fields. In large measure, this is due to the high microwave power output of the 250 GHz gyrotron oscillator used in these experiments.Natural Sciences and Engineering Research Council of Canada (Postgraduate Scholarship Fellowship)National Institutes of Health (U.S.) (Grant GM-35382)National Institutes of Health (U.S.) (Grant GM-55327)National Institutes of Health (U.S.) (Grant RR-00995