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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
NASA NTRS2004

THz Instrumentation for the Herschel Space Observatory's Heterodyne Instrument for Far Infrared

The Heterodyne Instrument for Far Infrared (HIFI) on ESA's Herschel Space Observatory utilizes a variety of novel RF components in its five SIS receiver channels covering 480-1250 GHz and two HEB receiver channels covering 1410-1910 GHz. The local oscillator unit will be passively cooled while the focal plane unit is cooled by superfluid helium and cold helium vapors. HIFI employs W-band GaAs amplifiers, InP HEMT low noise IF amplifiers, fixed tuned broadband planar diode multipliers, high power W-bapd Isolators, and novel material systems in the SIS mixers. The National Aeronautics and Space Administration through the Jet Propulsion Laboratory is managing the development of the highest frequency (1119-1250 GHz) SIS mixers, the local oscillators oscillators for the three highest frequency receivers as well as W-band power amplifiers, high power W-band isolators, varactor diode devices for all high frequency multipliers and InP HEMT components for all the receiver channels intermediate frequency amplifiers. The NASA developed components represent a significant advancement in the available performance. This paper presents an update of the performance and the current state of development.

local oscillators↗
NASA NTRS2010

High Power Local Oscillator Sources for 1-2 THz

Recent results from the Heterodyne Instrument for Far-Infrared (HIFI) on the Herschel Space Telescope have confirmed the usefulness of high resolution spectroscopic data for a better understanding of our Universe. This paper will explore the current status of tunable local oscillator sources beyond HIFI and provide demonstration of how power combining of GaAs Schottky diodes can be used to increase both power and upper operating frequency for heterodyne receivers. Availability of power levels greater than 1 watt in the W-band now makes it possible to design a 1900 GHz source with more than 100 microwatts of expected output power.

Schottky diodes↗
DOE OSTI2021

Four chromosome scale genomes and a pan-genome annotation to accelerate pecan tree breeding

Genome-enabled biotechnologies have the potential to accelerate breeding efforts in long-lived perennial crop species. Despite the transformative potential of molecular tools in pecan and other outcrossing tree species, highly heterozygous genomes, significant presence–absence gene content variation, and histories of interspecific hybridization have constrained breeding efforts. To overcome these challenges, here, we present diploid genome assemblies and annotations of four outbred pecan genotypes, including a PacBio HiFi chromosome-scale assembly of both haplotypes of the ‘Pawnee’ cultivar. Comparative analysis and pan-genome integration reveal substantial and likely adaptive interspecific genomic introgressions, including an over-retained haplotype introgressed from bitternut hickory into pecan breeding pedigrees. Further, by leveraging our pan-genome presence–absence and functional annotation database among genomes and within the two outbred haplotypes of the ‘Lakota’ genome, we identify candidate genes for pest and pathogen resistance. Combined, these analyses and resources highlight significant progress towards functional and quantitative genomics in highly diverse and outbred crops.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

A chromosome-level genome assembly of the varied leaved jewelflower, Streptanthus diversifolius, reveals a recent whole genome duplication

Abstract The Streptanthoid complex, a clade of primarily Streptanthus and Caulanthus species in the Thelypodieae (Brassicaceae) is an emerging model system for ecological and evolutionary studies. This complex spans the full range of the California Floristic Province including desert, foothill, and mountain environments. The ability of these related species to radiate into dramatically different environments makes them a desirable study subject for exploring how plant species expand their ranges and adapt to new environments over time. Ecological and evolutionary studies for this complex have revealed fascinating variation in serpentine soil adaptation, defense compounds, germination, flowering, and life history strategies. Until now a lack of publicly available genome assemblies has hindered the ability to relate these phenotypic observations to their underlying genetic and molecular mechanisms. To help remedy this situation, we present here a chromosome-level genome assembly and annotation of Streptanthus diversifolius, a member of the Streptanthoid Complex, developed using Illumina, Hi-C, and HiFi sequencing technologies. Construction of this assembly also provides further evidence to support the previously reported recent whole genome duplication unique to the Thelypodieae. This whole genome duplication may have provided individuals in the Streptanthoid Complex the genetic arsenal to rapidly radiate throughout the California Floristic Province and to occupy commonly inhospitable environments including serpentine soils.

Genetics & Heredity↗
DOE OSTI2025

A haplotype-resolved reference genome for Eucalyptus grandis

Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70-90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E. grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.

Lötter, Anneri↗
DOE OSTI2026

Chromosome-scale Genome Assembly of the Most Abundant Ectomycorrhizal Fungus Cenococcum Geophilum Reveals Massive TE Expansion and RIP Defense Mechanism

Transposable elements (TEs) play crucial roles in genome evolution and ecological adaptation in fungi, yet their dynamics in ectomycorrhizal species remain poorly understood. Cenococcum geophilum, the most widespread ectomycorrhizal fungus in boreal and temperate forests with its large, repeat-rich genome, represents an ideal system to investigate TE-mediated adaptation to the physical environment and symbiotic lifestyle. However, previous studies have been limited by fragmented genome assemblies that prevented the resolution of repeat-rich regions. We assembled a telomere-to-telomere reference genome of C. geophilum strain 1.58 using PacBio HiFi and Hi-C datasets, resulting in a 178.54 Mbp genome with seven contiguous chromosomes. We identified 14,145 genes and over 78% of the genome consists of transposable elements (TEs). Of these, 94% are affected by repeat-induced point mutations (RIP), a genome defense mechanism that acts during the sexual reproduction phase, indicating cryptic or ancient sexual reproduction in this putatively asexual fungus. Long terminal repeat retrotransposons, LINEs, and DNA transposons dominate, with three TE families (Ty3, Ty1, and Tad1) contributing over 60% of the genome size, indicating recent transposition bursts. Screening of 15 additional C. geophilum strains revealed recent and lineage-specific TE expansions, implying that several TEs escaped the RIP machinery and retained potential activity. Supporting TE activity in the context of symbiosis, we found 56 TEs differentially transcribed between ectomycorrhizal and free-living mycelium tissues. An even higher number (n = 66) of TEs were differentially expressed between stress resistance morphology (i.e. sclerotia) and free-living mycelium. This supports that TEs are differentially regulated as a response to symbiotic and stress-related conditions. Our results demonstrate that the C. geophilum genome expansion was driven by a few lineage-specific TE families in recent history, with high RIP activity attesting to sexual reproduction. We also provide insights how TEs could respond to lifestyle transitions and traits associated with desiccation resistance.

Cenococcum geophilum↗
DOE OSTI2024

Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements

Asgard archaea are of great interest as the progenitors of Eukaryotes, but little is known about the mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs that replicate in Atabeyarchaeia, a wetland Asgard archaea lineage represented by two complete genomes. We used soil depth–resolved population metagenomic data sets to track 18 MGEs for which genome structures were defined and precise chromosome integration sites could be identified for confident host linkage. Additionally, we identified a complete 20.67 kbp circular plasmid and two family-level groups of viruses linked to Atabeyarchaeia, via CRISPR spacer targeting. Closely related 40 kbp viruses possess a hypervariable genomic region encoding combinations of specific genes for small cysteine-rich proteins structurally similar to restriction-homing endonucleases. One 10.9 kbp integrative conjugative element (ICE) integrates genomically into theAtabeyarchaeum deiterrae-1chromosome and has a 2.5 kbp circularizable element integrated within it. The 10.9 kbp ICE encodes an expressed Type IIG restriction-modification system with a sequence specificity matching an active methylation motif identified by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing. Restriction-modification of Atabeyarchaeia differs from that of another coexisting Asgard archaea, Freyarchaeia, which has few identified MGEs but possesses diverse defense mechanisms, including DISARM and Hachiman, not found in Atabeyarchaeia. Overall, defense systems and methylation mechanisms of Asgard archaea likely modulate their interactions with MGEs, and integration/excision and copy number variation of MGEs in turn enable host genetic versatility.

Biochemistry & Molecular Biology↗
DOE OSTI2023

The first two chromosome‐scale genome assemblies of American hazelnut enable comparative genomic analysis of the genus Corylus

Summary The native, perennial shrub American hazelnut ( Corylus americana ) is cultivated in the Midwestern United States for its significant ecological benefits, as well as its high‐value nut crop. Implementation of modern breeding methods and quantitative genetic analyses of C. americana requires high‐quality reference genomes, a resource that is currently lacking. We therefore developed the first chromosome‐scale assemblies for this species using the accessions ‘Rush’ and ‘Winkler’. Genomes were assembled using HiFi PacBio reads and Arima Hi‐C data, and Oxford Nanopore reads and a high‐density genetic map were used to perform error correction. N50 scores are 31.9 Mb and 35.3 Mb, with 90.2% and 97.1% of the total genome assembled into the 11 pseudomolecules, for ‘Rush’ and ‘Winkler’, respectively. Gene prediction was performed using custom RNAseq libraries and protein homology data. ‘Rush’ has a BUSCO score of 99.0 for its assembly and 99.0 for its annotation, while ‘Winkler’ had corresponding scores of 96.9 and 96.5, indicating high‐quality assemblies. These two independent assemblies enable unbiased assessment of structural variation within C. americana , as well as patterns of syntenic relationships across the Corylus genus. Furthermore, we identified high‐density SNP marker sets from genotyping‐by‐sequencing data using 1343 C. americana , C. avellana and C. americana × C. avellana hybrids, in order to assess population structure in natural and breeding populations. Finally, the transcriptomes of these assemblies, as well as several other recently published Corylus genomes, were utilized to perform phylogenetic analysis of sporophytic self‐incompatibility (SSI) in hazelnut, providing evidence of unique molecular pathways governing self‐incompatibility in Corylus .

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Assembly, comparative analysis, and utilization of a single haplotype reference genome for soybean

Cultivar Williams 82 has served as the reference genome for the soybean research community since 2008, but is known to have areas of genomic heterogeneity among different sub-lines. This work provides an updated assembly (version Wm82.a6) derived from a specific sub-line known as Wm82-ISU-01 (seeds available under USDA accession PI 704477). The genome was assembled using Pacific BioSciences HiFi reads and integrated into chromosomes using HiC. The 20 soybean chromosomes assembled into a genome of 1.01Gb, consisting of 36 contigs. The genome annotation identified 48 387 gene models, named in accordance with previous assembly versions Wm82.a2 and Wm82.a4. Comparisons of Wm82.a6 with other near-gapless assemblies of Williams 82 reveal large regions of genomic heterogeneity, including regions of differential introgression from the cultivar Kingwa within approximately 30 Mb and 25 Mb segments on chromosomes 03 and 07, respectively. Additionally, our analysis revealed a previously unknown large (> 20 Mb) heterogeneous region in the pericentromeric region of chromosome 12, where Wm82.a6 matches the ‘Williams’ haplotype while the other two near-gapless assemblies do not match the haplotype of either parent of Williams 82. In addition to the Wm82.a6 assembly, we also assembled the genome of ‘Fiskeby III,’ a rich resource for abiotic stress resistance genes. A genome comparison of Wm82.a6 with Fiskeby III revealed the nucleotide and structural polymorphisms between the two genomes within a QTL region for iron deficiency chlorosis resistance. The Wm82.a6 and Fiskeby III genomes described here will enhance comparative and functional genomics capacities and applications in the soybean community.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)

Quercus variabilis (Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources from Q. variabilis are still lacking. Here, we present a high-quality Q. variabilis genome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We used ab initio , RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed that Q. variabilis was more closely related to Q. suber than to Q. lobata or Q. robur. We found no evidence for species-specific whole genome duplications in Quercus after the species had diverged. This study provides the first genome assembly and the first gene annotation data for Q. variabilis. These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.

Han, Biao↗
NASA NTRS1990

Deep Fabry-Perot imaging of NGC 6240: Kinematic evidence for merging galaxies

The authors have observed the superluminous, infrared galaxy NGC 6240 (z = 0.025) at H alpha with the Hawaii Imaging Fabry-Perot Interferometer (HIFI - Bland and Tully 1989). During the past decade, observational evidence from all wavebands indicates that the unusual appearance of NGC 6240 has resulted from a collision between two gas-rich systems, a view which is supported by our spectrophotometric data. However, the origin of the enormous infrared luminosity (4 times 10(exp 11) solar luminosity) detected by the Infrared Astronomy Satellite (IRAS) remains highly controversial, where opinions differ on the relative roles of large-scale shocks, massive star formation or a buried 'active' nucleus. These mechanisms are discussed in the light of the author's Fabry-Perot observations.

Hawthorn, J. Bland↗
NASA NTRS1994

The nuclear superbubble of NGC 3079

We have used the Hawaii Imaging Fabry-Perot Interferometer (HIFI) at the CFH 3.6 m telescope to map H-alpha + (N II) lambda-lambda 6548, 6583 emission-line profiles across the entire edge-on, nearby SBc galaxy NGC 3079, with resolution 70 km/s and subarcsecond sampling. Blue and red long-slit spectra were obtained with the Double Spectrograph on the Palomar 5 meter telescope to provide additional emission-line diagnostics. A spectacular, line emitting bubble of diameter 13 sec (approximately 1.1 kpc) is observed immediately east of the nucleus. Its unusual gaseous excitation (e.g., (N II) lambda(6583)/H-alpha greater than 1) suggests that shocks are important. Extremely violent gas motions that range over 2000 km/s are detected across the bubble and diametrically opposite on the west side of the nucleus. Nonrotational motions are also found in the inner galaxy disk. The superbubble of NGC 3079 is the most powerful example known of a wind-blown bubble, and an excellent laboratory to study wind dynamics. The dimensions and energies of the bubble imply that is likely to be in the blowout phase and partially ruptured. The predicted rate of kinetic energy output from the central starburst appears sufficient to power most of this outflow. It is possible that a central active galactic nucleus also contributes to the outflow.

Veilleux, S.↗
NASA NTRS1995

The interstellar disk-halo connection in the spiral galaxy NGC 3079

We discuss the morphology and excitation of ionized gas in the nearby Sc galaxy NGC 3079. The almost edge-on orientation is ideal for studying the vertical structure of the gaseous disk, and especially the diffuse ionized medium (DIM) found between the bright H II regions. We used the Hawaii Imaging Fabry-Perot Interferometer (HIFI) to map 150,000 H-alpha + (N II) lambda lambda 6548, 6583 emission-line profiles across the entire disk, with resolution 70 km/s at subarcsecond steps, down to a flux level of approximately 10(exp -17) ergs/s/sq cm (EM approximately equal to 4 cm(exp -6) pc). The DIM contributes approximately 30% of the total disk H-alpha emission within a radius of 10 kpc. The DIM has broader emission lines and larger (N II) H-alpha flux ratios than the adjacent H II regions. Within a radius of 5 kpc, we find that the X-shaped filaments reported in previous studies emerge from the inner (R approximately equal to 1.5 kpc) disk, and rise more than 4 kpc above the disk plane. The morphology, kinematics, and excitation of the filaments suggest that they form a biconic interface between the undisturbed disk gas, and gas entrained in the wide-angle outflow. The DIM beyond 5 kpc radius is more vertically extended than the thick ionized disk detected in our Galaxy and in a few nearby edge-on systems. After correcting for dust, the vertical profile of this DIM has an exponential scale height of about 1.1 kpc, similar to that of the H I disk. The (N II) lambda 6538/H-alpha flux ratio of the DIM increases monotonically with vertical height, reaching unity for absolute value of z greater than or approximately equal to 2.5 kpc. The flux required to keep the DIM ionized at R = 8 kpc is similar to that near the solar circle of our Galaxy. Highly dilute radiation from O stars in the galactic plane probably maintains the DIM. The total mass of the DIM is of order 10(exp 8) - 10(exp 9) solar mass, representing less than 1% of the total dynamical mass of NGC 3079. Mechanical energy from intense star formation in the disk probably lifts the DIM above the disk. The several bubbles and filaments within 1 kpc of the disk plane is direct evidence for gas flow between the disk and halo.

Veilleux, Sylvain↗
NASA NTRS2000

Spectroscopic Capabilities and Possibilities of the Far Infrared and Submillimeter Telescope Mission

The Far Infrared and Submillimeter Telescope (FIRST) mission is the fourth European Space Agency corner stone mission. FIRST will be an observatory with a passively cooled (80 Kelvin) 3.5 meter class telescope and three cryogenic instruments covering the 670 to 80 mm spectral region. The mission is slated for a 4.5 year operational lifetime in an L2 orbit. It will share an Arian 5 launch with PLANCK in early 2007. The three payload instruments include the Spectral and Photometric Imaging Receiver (SPIRE), which is a bolometer array with Martin-Puplett FTS for 200-670 microns, the Photoconductor Array Camera and Spectrometer (PACS), which is a photoconductor array with a grating spectrometer for 80-210 microns and the Heterodyne Instrument for FIRST (HIFI), which is a series of seven heterodyne receivers covering 480-1250 GHz and portions of 1410-1910 GHz and 2400-2700 GHz. FIRST will make many detailed spectral surveys of a wide variety of objects previously obscured by the atmosphere and in regions of the spectrum seldom used for astronomical observations, With all of the spectroscopic capability on FIRST a great deal of laboratory spectroscopic support will be needed for accurate interpretation of the spectral data.

Pearson, J. C.↗
NASA NTRS2002

THz frequency multiplier chains base on planar Schottky diodes

The Herschel Space Observatory (HSO), an ESA cornerstone mission with NASA contribution, will enable a comprehensive study of the galactic as well as the extra galactic universe. At the heart of this exploration are ultra sensitive coherent detectors that can allow for high-resolution spectroscopy. Successful operation of these receivers is predicated on providing a sufficiently powerful local oscillator (LO) source. Historically, a versatile space qualified LO source for frequencies beyond 500 GHz has been difficult if not impossible. This paper will focus on the effort under way to develop, build, characterize and qualify a LO chain to 1200 GHz (Band 5 on HSO) that is based on planar GaAs diodes mounted in waveguide circuits. State-of-the-art performance has been obtained from a three-stage ( x2 x 2 x 3 ) multiplier chain that can provide a peak output power of 120 uW (1178 GHz) at room temperature and a peak output power of 190 uW at 1183 GHz when cooled to 113 K. Implementation of this LO source for the Heterodyne Instrument for Far Infrared (HIFI) on HSO will be discussed in detail.

oscillator spectroscopy↗
NASA NTRS2004

Tunable All-Solid-State Local Oscillators to 1900 GHz

We present a status report of an ongoing effort to develop robust tunable all-solid-state sources up to 1900 GHz for the Heterodyne Instrument for the Far Infrared (HIFI) on the Herschel Space Observatory. GaAs based multi-chip power amplifier modules at W-band are used to drive cascaded chains of multipliers. We have demonstrated performance from chains comprised of four doublers up to 1600 GHz as well as from a x2x3x3 chain to 1900 GHz. Measured peak output power of 23 (micro)W at 1782 GHz and 2.6 (micro)W at 1900 GHz has been achieved when the multipliers are cooled to 120K. The 1900 GHz tripler was pumped with a four anode tripler that produces a peak of 4 mW at 630 GHz when cooled to 120 K. We believe that these sources can now be used to pump hot electron bolometer (HEB) heterodyne mixers.ter (HEB) heterodyne mixers.

local oscillator↗