On the Use of High-Frequency Surface Wave Oceanographic Research Radars as Bistatic Single-Frequency Oblique Ionospheric Sounders

We demonstrate that bistatic reception of high-frequency oceanographic radars can be used as single-frequency oblique ionospheric sounders. We develop methods that are agnostic of the software-defined radio system to estimate the group range from the bistatic observations. The group range observations are used to estimate the virtual height and equivalent vertical frequency at the midpoint of the oblique propagation path. Uncertainty estimates of the virtual height and equivalent vertical frequency are presented. We apply this analysis to observations collected from two experiments run at two locations in different years, but utilizing similar software-defined radio data collection systems. In the first experiment, 10 d of data were collected in March 2016 at a site located in Maryland, USA, while the second experiment collected 20 d of data in October 2020 at a site located in South Carolina, USA. In both experiments, three Coastal Oceanographic Dynamics and Applications Radars (CODARs) located along the Virginia and North Carolina coast of the US were bistatically observed at 4.53718 MHz. The virtual height and equivalent virtual frequency were estimated in both experiments and compared with contemporaneous observations from a vertical incident digisonde-ionosonde at Wallops Island, VA, USA. We find good agreement between the oblique CODAR-derived and WP937 digisonde virtual heights. Variations in the virtual height from the CODAR observations and the digisonde are found to be nearly in phase with each other. We conclude from this investigation that observations of oceanographic radar can be used as single-frequency oblique incidence sounders. We discuss applications with respect to investigations of traveling ionospheric disturbances, studies of day-to-day ionospheric variability, and using these observations in data assimilation

Genetic dissection of maturity using RFLPs.

Several genetic regions having major effects on maturity have been identified using RFLP analysis. One such region on chromosomes 8 is important across several diverse genotypes and ccounts for up to 50% of the variation for maturity in a cross involving an inbred line (N28) and a 20-backcross generation derivative (N28E). In addition to the chromsome 8 QTL for maturity, we have evidence using the backcross-derived line approach for regions controlling maturity on chromosomes 1, 2, 3, 5, 7, and 9. Chromosome 5 appears to be especially important in both magnitude of effect and across several genetic hackground. Maturity as measured by days to pollen shed or silking may be controlled by additive or nearly dominant gene action depending on the chromosome region. The marker-trait linkages were consistent across environnments based on A662 X B73 F3 per se and testcross evaluations from three locations in one year. UMC12 (chromosome 8) and UMC54 (chromosome 5) also marked important regions for maturity in these materials

Current Closure in the Auroral Ionosphere: Results from the Auroral Current and Electrodynamics Structure Rocket Mission

The Auroral Current and Electrodynamics Structure (ACES) mission consisted of two sounding rockets launched nearly simultaneously from Poker Flat Research Range, AK on January 29, 2009 into a dynamic multiple-arc aurora. The ACES rocket mission was designed to observe electrodynamic and plasma parameters above and within the current closure region of the auroral ionosphere. Two well instrumented payloads were flown along very similar magnetic field footprints, at different altitudes, with small temporal separation between both payloads. The higher altitude payload (apogee 360 km), obtained in-situ measurements of electrodynamic and plasma parameters above the current closure region to determine the input signature. The low altitude payload (apogee 130 km), made similar observations within the current closure region. Results are presented comparing observations of the electric fields, magnetic components, and the differential electron energy flux at magnetic footpoints common to both payloads. In situ data is compared to the ground based all-sky imager data, which presents the evolution of the auroral event as the payloads traversed through magnetically similar regions. Current measurements derived from the magnetometers on the high altitude payload observed upward and downward field-aligned currents. The effect of collisions with the neutral atmosphere is investigated to determine if it is a significant mechanism to explain discrepancies in the low energy electron flux. The high altitude payload also observed time-dispersed arrivals in the electron flux and perturbations in the electric and magnetic field components, which are indicative of Alfven waves

Impacts of acoustic and gravity waves on the ionosphere

The impact of regional-scale neutral atmospheric waves has been demonstrated to have profound effects on the ionosphere, but the circumstances under which they generate ionospheric disturbances and seed plasma instabilities are not well understood. Neutral atmospheric waves vary from infrasonic waves of <20 Hz to gravity waves with periods on the order of 10 min, for simplicity, hereafter they are combined under the common term Acoustic and Gravity Waves (AGWs). There are other longer period waves like planetary waves from the lower and middle atmosphere, whose effects are important globally, but they are not considered here. The most ubiquitous and frequently observed impact of AGWs on the ionosphere are Traveling Ionospheric Disturbances (TIDs), but AGWs also affect the global ionosphere/thermosphere circulation and can trigger ionospheric instabilities (e.g., Perkins, Equatorial Spread F). The purpose of this white paper is to outline additional studies and observations that are required in the coming decade to improve our understanding of the impact of AGWs on the ionosphere

Impacts of acoustic and gravity waves on the ionosphere

The impact of regional-scale neutral atmospheric waves has been demonstrated to have profound effects on the ionosphere, but the circumstances under which they generate ionospheric disturbances and seed plasma instabilities are not well understood. Neutral atmospheric waves vary from infrasonic waves of <20 Hz to gravity waves with periods on the order of 10 min, for simplicity, hereafter they are combined under the common term Acoustic and Gravity Waves (AGWs). There are other longer period waves like planetary waves from the lower and middle atmosphere, whose effects are important globally, but they are not considered here. The most ubiquitous and frequently observed impact of AGWs on the ionosphere are Traveling Ionospheric Disturbances (TIDs), but AGWs also affect the global ionosphere/thermosphere circulation and can trigger ionospheric instabilities (e.g., Perkins, Equatorial Spread F). The purpose of this white paper is to outline additional studies and observations that are required in the coming decade to improve our understanding of the impact of AGWs on the ionosphere

Chromosome-level genome assembly of a regenerable maize inbred line A188.

BACKGROUND The maize inbred line A188 is an attractive model for elucidation of gene function and improvement due to its high embryogenic capacity and many contrasting traits to the first maize reference genome, B73, and other elite lines. The lack of a genome assembly of A188 limits its use as a model for functional studies. RESULTS Here, we present a chromosome-level genome assembly of A188 using long reads and optical maps. Comparison of A188 with B73 using both whole-genome alignments and read depths from sequencing reads identify approximately 1.1 Gb of syntenic sequences as well as extensive structural variation, including a 1.8-Mb duplication containing the Gametophyte factor1 locus for unilateral cross-incompatibility, and six inversions of 0.7 Mb or greater. Increased copy number of carotenoid cleavage dioxygenase 1 (ccd1) in A188 is associated with elevated expression during seed development. High ccd1 expression in seeds together with low expression of yellow endosperm 1 (y1) reduces carotenoid accumulation, accounting for the white seed phenotype of A188. Furthermore, transcriptome and epigenome analyses reveal enhanced expression of defense pathways and altered DNA methylation patterns of the embryonic callus. CONCLUSIONS The A188 genome assembly provides a high-resolution sequence for a complex genome species and a foundational resource for analyses of genome variation and gene function in maize. The genome, in comparison to B73, contains extensive intra-species structural variations and other genetic differences. Expression and network analyses identify discrete profiles for embryonic callus and other tissues

Characterization of autonomous Dart1 transposons belonging to the hAT superfamily in rice

An endogenous 0.6-kb rice DNA transposon, nDart1-0, was found as an active nonautonomous element in a mutable virescent line, pyl-v, displaying leaf variegations. Here, we demonstrated that the active autonomous element aDart in pyl-v corresponds to Dart1-27 on chromosome 6 in Nipponbare, which carries no active aDart elements, and that aDart and Dart1-27 are identical in their sequences and chromosomal locations, indicating that Dart1-27 is epigenetically silenced in Nipponbare. The identification of aDart in pyl-v was first performed by map-based cloning and by detection of the accumulated transposase transcripts. Subsequently, various transposition activities of the cloned Dart1-27 element from Nipponbare were demonstrated in Arabidopsis. Dart1-27 in Arabidopsis was able to excise nDart1-0 and Dart1-27 from cloned sites, generating footprints, and to integrate into new sites, generating 8-bp target site duplications. In addition to Dart1-27, Nipponbare contains 37 putative autonomous Dart1 elements because their putative transposase genes carry no apparent nonsense or frameshift mutations. Of these, at least four elements were shown to become active aDart elements in transgenic Arabidopsis plants, even though considerable sequence divergence arose among their transposases. Thus, these four Dart1 elements and Dart1-27 in Nipponbare must be potential autonomous elements silenced epigenetically. The regulatory and evolutionary implications of the autonomous Dart1 elements and the development of an efficient transposon-tagging system in rice are discussed

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis