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At least 685 records · Page 38

RNAseq-based transcriptome assembly of Clostridium acetobutylicum for functional genome annotation and discovery

Accurate genome annotations are essential in modern biology and biotechnology, yet they are still largely based on genome sequencing and comparative analyses. We show that the Clostridium acetobutylicum genome annotation can be markedly improved by integrating bioinformatic predictions with RNA sequencing (RNAseq) data. Samples were acquired under butanol, butyrate, and unstressed treatments across various growth conditions. Analysis of an initial assembly revealed errors due to background signals and limitations of assembly algorithms. Hurdles for RNAseq transcriptome mapping include optimizing library complexity and sequencing depth, yet most studies report low sequencing depth and ignore the effect of ribosomal RNA abundance. An integrative analysis was developed to combine motif predictions, single-nucleotide resolution sequencing depth, and library complexity to resolve difficulties in assembly curation. This minimized false positive error and determined gene boundaries, in some cases, to the exact base-pair of prior studies. This will be the first strand-specific transcriptome assembly in a Clostridium organism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Development of intelligent control module for the J-TEXT electron cyclotron emission imaging system

An Electron Cyclotron Emission Imaging (ECEI) system has been developed on the J-TEXT tokamak and employed for the multi-dimensional electron temperature fluctuation imaging measurement in 2019 campaign. The intelligent control module has been developed and been used to flexibly setup the 256-channel ECEI system configurations for different plasma scenarios. The adjustments of key parameters are merged in this module including size and position of the geometric observation window, and the dynamic range of the signal and image resolution. The user-friendly interface is also developed for the tokamak operator to set the ECEI system focusing on physics interested region. Furthermore, this module is installed close to the diagnostic system around the J-TEXT tokamak, which can be remotely controlled by authorized operators in the control room. It significantly improves ECEI flexibility and stability, and also keeps the operation technician away from the harsh radiation environment.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Convection-permitting hindcasting of diurnal variation of Mei-yu rainfall over East China with a global variable-resolution model

Two sets of 48-hr hindcast experiments for Mei-yu season using non-hydrostatic global variable-resolution model (MPAS-Atmosphere) with regional refinement at 4km resolution (V4km) and uniform 60km resolution (U60km) are first-time conducted to attempt at simulating the Mei-yu rainfall in 2015 over East China. The analysis focuses on the seasonal average of diurnal variation of precipitation amount (PA), intensity (PI), and frequency (PF). Both simulations reasonably reproduce the spatial distribution of PA. V4km is more skillful in simulating the spatial distributions and magnitudes of PF and PI. The diurnal cycle of Mei-yu rainfall shows a major early morning peak and a minor afternoon peak, contributed by precipitation during two sub-periods with distinct synoptic circulations. With strong Mei-yu in the first sub-period, the diurnal variation of PA is controlled by nocturnal southwesterly jet. V4km overestimates the morning peak mainly due to its bias in simulating boundary layer inertial oscillation. Although differences in PA between the simulations are small, U60km overestimates PF and underestimates PI. With weak Mei-yu in the second sub-period, the diurnal variation of PA is controlled by both synoptic circulation and local convection. At both resolutions, deviations in the large-scale circulation modulated by a few typhoons lead to positive biases in the morning peak of PA. After removing the typhoon impacts, V4km captures the observed diurnal cycle of PA well, while U60km significantly underestimates PA and PI particularly in the afternoon. Future studies focusing on advancing modeling of southwesterly jet and typhoons may further improve convection permitting simulation of Mei-yu rainfall.

Xu, Mingyue↗

cAMP binding to closed pacemaker ion channels is non-cooperative

Electrical activity in the brain and heart depends on rhythmic generation of action potentials by pacemaker ion channels (HCN) whose activity is regulated by cAMP binding. Previous work has uncovered evidence for both positive and negative cooperativity in cAMP binding, but such bulk measurements suffer from limited parameter resolution. Efforts to eliminate this ambiguity using single-molecule techniques have been hampered by the inability to directly monitor binding of individual ligand molecules to membrane receptors at physiological concentrations. Here we overcome these challenges using nanophotonic zero-mode waveguides4 to directly resolve binding dynamics of individual ligands to multimeric HCN1 and HCN2 ion channels. We show that cAMP binds independently to all four subunits when the pore is closed, despite a subsequent conformational isomerization to a flip state at each site. The different dynamics in binding and isomerization are likely to underlie physiologically distinct responses of each isoform to cAMP and provide direct validation of the ligand-induced flip-state model. Furthermore, this approach for observing stepwise binding in multimeric proteins at physiologically relevant concentrations can directly probe binding allostery at single-molecule resolution in other intact membrane proteins and receptors.

59 BASIC BIOLOGICAL SCIENCES↗

A flexible neutron spectrometer concept with a new ultra-high field steady-state vertical-bore magnet

The proposed facility explores materials under ultra-high magnetic fields. By combining the power of high fields to tune materials and of neutron scattering to probe the resulting changes down to the atomic scale, this facility will enable transformative progress in the study of quantum materials and is named for the “TITAN” subset of Greek gods to reflect this transformation. TITAN will offer DC magnetic fields up to at least 20 T. Exploiting the record brightness and bandwidth of the Second Target Station at the Spallation Neutron Source, TITAN will probe atomic-scale responses through high efficiency neutron spectroscopy up to 80 meV energy transfer, high resolution diffraction, and small angle neutron scattering. Focusing neutron optics will maximize flux on accurately positioned samples, while radial collimation and optimized shielding and detection strategies will minimize backgrounds.

47 OTHER INSTRUMENTATION↗

Infrared atlas charts of the eclipsed moon.

The objective of this atlas is to present the thermal response of the lunar surface observed during an eclipse of the moon with accurate position data. The observations were made at a wavelength of 11 microns with an angular resolution of 10 sec, equivalent to 17 km at the disk center. Over a thousand thermally anomalous regions (hot spots) were detected. They cool more slowly than their environs and remain warmer than their environs during the umbral phase. In addition to these very localized hot spots, some of the maria show thermal enhancements during the eclipse. Fourty four charts make up this atlas which are identical in coverage and projection to the Lunar Atlas Charts (LAC) series. The charts are in the form of digital images of a normalized temperature difference which is particularly useful for studying regions of small thermal enhancements. Each increase of intensity corresponds to a 4 K temperature increase.

Shorthill, R. W.↗

High resolution spectral measurement of the HNO3 11.3-micron band using tunable diode lasers

High resolution spectra in the region of the 2-nu9 band of nitric acid have been obtained for selected portions of the HNO3 spectrum using tunable diode laser techniques. Continuous spectra are presented from 891.25/cm to 898.77/cm, with a spectral resolution less than or equal to 0.001/cm (30 MHz). Absolute line intensities and line positions are presented. Absolute wavelength calibration was obtained by frequency mixing the diode laser with a C(13)O2(16) isotope laser. Self and foreign gas (N2) broadening coefficients were iteratively calculated from the experimental data and were determined.

Brockman, P.↗

X-ray studies of quasars with the Einstein Observatory

Results of an investigation of the X-ray properties of quasars conducted using the Einstein Observatory (HEAO 2) are reported. The positions, fluxes and luminosities of 35 known quasars were observed by the Einstein high-resolution imaging detector and the imaging proportional counter. Assuming optical redshifts as valid distance indicators, 0.5-4.5 keV X-ray luminosities ranging from 10 to the 43rd to 10 to the 47 ergs/sec are obtained, with evidence of very little cold gas absorption. Flux variability on a time scale of less than 10,000 sec is observed for the quasar OX 169, which implies a mass between 8 x 10 to the 5th and 2 x 10 to the 8th solar masses for the black hole assumed to be responsible for the emission. Preliminary results of the quasar survey also indicate that quasars contribute significantly to the diffuse X-ray background.

Tananbaum, H.↗

Specification of a NAVSTAR Global Positioning System (GPS) receiver for a differential GPS ground system

One step towards the successful completion of a functional ground unit for the Differential Global Positioning System (DGPS) will be in choosing a currently available GPS receiver that will accurately measure the propagation times of the satellite signals and have the capability to be electrically interfaced with and controlled by a Digital Equipment Corporation (DEC) PDP-11/34A computer. The minimum requirements and characteristics of a NAVSTAR Global Positioning System (GPS) receiver are described. The specific technical specifications addressed include data accuracies and resolutions, receiver interface/external control, enclosure dimensions and mounting requirements, receiver operation, and environmental specifications.

Mccall, D. L.↗

White-light movies of the solar photosphere from the SOUP instrument on Spacelab

Initial results are presented on solar granulation, pores and sunspots from the white-light films obtained by the Solar Optical Universal Polarimeter (SOUP) instrument in Spacelab 2. Several hours of movies were taken at various disk and limb positions in quiet and active regions. The images are diffraction-limited at 0.5 arcsec resolution and are, of course, free of atmospheric seeing and distortion. Properties of the granulation in magnetic and nonmagnetic regions are compared and are found to differ significantly in size, rate of intensity variation, and lifetime. In quiet sun, on the order of fifty-percent of the area has at least one 'exploding granule' occurring in it during a 25-min period. Local correlation tracking has detected several types of transverse flows, including systematic outflow from the penumbral boundary of a spot, motion of penumbral filaments, and cellular flow patterns of supergranular and mesogranular size. Feature tracking has shown that, in the quiet sun, the average granule fragment has a velocity of about one kilometer/second.

Title, A. M.↗

Recycling isotachophoresis - A novel approach to preparative protein fractionation

The concept of automated recycling isotachophoresis (RITP) as a purification methodology is discussed, in addition to a description of the apparatus. In the present automated RITP, the computer system follows the achievement of steady state using arrays of universal and specific sensors, monitors the position of the front edge of the zone structure, activates the counterflow if the leading boundary passes a specified position along the separation axis, or changes the applied current, accordingly. The system demonstrates high resolution, in addition to higher processing rates than are possible in zone electrophoresis or isoelectric focusing.

Sloan, Jeffrey E.↗

H2 and H I emission line imaging of the ring nebula (NGC 6720)

Infrared emission-line images of the v = 1-0 S(1) transition of molecular hydrogen and Br-gamma recombination line of atomic hydrogen which cover the entire extent of NGC 6720, the Ring nebula. The maps presented here are the highest angular resolution images of these transitions yet produced for this object and have very low relative positional uncertainty. As a result, the spatial stratification of the ionized and shocked molecular zones within the nebula is clearly resolved. These data, and data from the Infrared Astronomical Satellite, are used to determine the H2, H I, and dust mass within the nebula. Energy sources for the dust heating, formation and destruction of the H2, and overall evolution of the nebula are also discussed.

Greenhouse, Matthew A.↗

Aerosols and polar stratospheric clouds measurements during the EASOE campaign

Preliminary results of observations performed using two different lidar systems during the EASOE (European Arctic Stratospheric Ozone Experiment), which has taken place in the winter of 1991-1992 in the northern hemisphere lattitude regions, are presented. The first system is a ground based multiwavelength lidar intended to perform measurements of the ozone vertical distribution in the 5 km to 40 km altitude range. It was located in Sodankyla (67 degrees N, 27 degrees E) as part of the ELSA experiment. The objectives of the ELSA cooperative project is to study the relation between polar stratospheric cloud events and ozone depletion with high vertical resolution and temporal continuity, and the evolution of the ozone distribution in relation to the position of the polar vortex. The second system is an airborne backscatter lidar (Leandre) which allows for the study of the 3-D structure and the optical properties of polar stratospheric clouds. The Leandre instrument is a dual-polarization lidar system, emitting at 532 nm, which allows for the determination of the type of clouds observed, according to the usual classification of polar stratospheric clouds. More than 60 hours of flight were performed in Dec. 1991, and Jan. and Feb. 1992 in Kiruna, Sweden. The operation of the Leandre instrument has led to the observation of the short scale variability of the Pinatubo volcanic cloud in the high latitude regions and to several episodes of polar stratospheric clouds. Preliminary analysis of the data is presented.

Haner, D.↗

Development of a calibration workstation for SIR-C

The paper describes the status of a comprehensive synthetic aperture radar (SAR) software package developed specifically to aid the calibration of a multifrequency and multipolarization radar like the Shuttle Imaging Radar, SIR-C. The primary data types processed are engineering telemetry, point targets (corner reflectors and polarimetric active radar calibrators), distributed targets (clutter), tone-generators, and ground receivers. The parameters derived to aid the calibration of the production processor include measurements of relative radiometric channel to channel imbalance, absolute calibration constants, antenna pattern corrections, noise levels, polarimetric cross-talk, and geometric offsets. The software reports standard performance measurements such as resolution, peak and integrated sidelobes, radiometric response accuracy, and geometrical distortions such as scale errors, position bias and standard deviation, and image skew. Furthermore, the inclusion of software to allow updates of the shuttle-state vector (position and velocity) is considered.

Madsen, S. N.↗

Airborne gravimetry, altimetry, and GPS navigation errors

Proper interpretation of airborne gravimetry and altimetry requires good knowledge of aircraft trajectory. Recent advances in precise navigation with differential GPS have made it possible to measure gravity from the air with accuracies of a few milligals, and to obtain altimeter profiles of terrain or sea surface correct to one decimeter. These developments are opening otherwise inaccessible regions to detailed geophysical mapping. Navigation with GPS presents some problems that grow worse with increasing distance from a fixed receiver: the effect of errors in tropospheric refraction correction, GPS ephemerides, and the coordinates of the fixed receivers. Ionospheric refraction and orbit error complicate ambiguity resolution. Optimal navigation should treat all error sources as unknowns, together with the instantaneous vehicle position. To do so, fast and reliable numerical techniques are needed: efficient and stable Kalman filter-smoother algorithms, together with data compression and, sometimes, the use of simplified dynamics.

Colombo, Oscar L.↗

Large area mapping of soil moisture using the ESTAR passive microwave radiometer

Investigations designed to study land surface hydrologic-atmospheric interactions, showing the potential of L band passive microwave radiometry for measuring surface soil moisture over large areas, are discussed. Satisfying the data needs of these investigations requires the ability to map large areas rapidly. With aircraft systems this means a need for more beam positions over a wider swath on each flightline. For satellite systems the essential problem is resolution. Both of these needs are currently being addressed through the development and verification of Electronically Scanned Thinned Array Radiometer (ESTAR) technology. The ESTAR L band radiometer was evaluated for soil moisture mapping applications in two studies. The first was conducted over the semiarid rangeland Walnut Gulch watershed located in south eastern Arizona (U.S.). The second was performed in the subhumid Little Washita watershed in south west Oklahoma (U.S.). Both tests showed that the ESTAR is capable of providing soil moisture with the same level of accuracy as existing systems.

Jackson, T. J.↗

The First Detection of [O IV] from an Ultraluminous X-ray Source with Spitzer: Evidence of High Unbeamed Luminosity in Holmberg II ULX

We present the first Spitzer Infrared Spectrograph (IRS) observations of the [O IV] 25.89 micron emission line detected from the ultraluminous X-ray source (ULX) in Holmberg II. This line is a well established signature of high excitation, usually associated with AGN. Its detection suggests that the ULX has a strong impact on the surrounding gas. A Spitzer high resolution spectral map shows that the [O IV] is coincident with the X-ray position of the Holmberg II ULX. We find that the luminosity and the morphology of the line emission is consistent with photoionization by the soft X-ray and far ultraviolet (FUV) radiation from the accretion disk of the binary system and inconsistent with narrow beaming. We show that the emission nebula is radiation bounded both in the line of sight direction and to the west, and probably matter bounded to the east. Evidence for a massive black hole (BH) in this ULX is mounting. Detailed photoionization models favor an intermediate mass black hole of at least 85 Solar Mass as the ionization source for the [OIV] emission. We find that the spectral type of the companion star strongly affects the expected strength of the [O IV] emission. This finding could explain the origin of [O IV] in some starburst galaxies containing black hole binaries.

Berghea, C. T.↗

The First Detection of [O IV] from an Ultraluminous X-ray Source with Spitzer. I. Observational Results for Holmberg II ULX

We presen the first Spitzer Infrared Spectrograph (IRS) observations of the [O IV] 25.89 um emission line detected from the ultraluminous X-ray source (ULX) in Holmberg II. This line is a well established signature of high excitation usually associated with AGN. Its detection suggests that the ULX has a strong impact on the surrounding gas. A Spitzer high resolution spectral map shows that the [O IV] is coincident with the X-ray position of the ULX. The ratios of the [O IV] to lower ionization lines are similar to those observed in AGN, suggesting that a strong UV and X-ray source is responsible for the, photoionization. The best XMM-Newton data is used to model the X-ray band which is then extrapolated into the UV. We perform infrared and ultraviolet photometry, and use its previously published optical and radio data to construct the full SED for the ULX and its companion. The preferred model to describe the SED includes an accretion disk which dominates the soft X-rays but contributes little at UV and optical wavelengths. The optical counterpart is consistent with a B supergiant as previously suggested in other studies. The bolometric luminosity of the ULX suggests the presence of an intermediate-mass black hole with mass >85 M for sub-Eddington accretion or, alternatively, a stellar-mass black hole that is accreting at super-Eddington rates. In a follow-up second paper we perform detailed photoionization modeling of the infrared lines in order to constrain the bolometric luminosity of the ULX.

Berghea, C. T.↗