Search NASA⌕ Search

SEARCH · Search NASA

Results for “sequence features”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression

Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species’ divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species’ pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Numerical weather prediction in low latitudes

Based on the results of a number of numerical prediction experiments, the differential heating between land and ocean is an important and critical factor for investigation of phenomenon such as the onset of monsoons over the Indian subcontinent. The pre-onset period during the month of May shows a rather persistent flow field in the monsoon region. At low levels the circulation exhibits anticyclonic excursions over the Arabian Sea, flowing essentially parallel to the west coast of India from the north. Over the Indian subcontinent the major feature is a shallow heat low over northern India. As the heat sources commence a rapid northwestward movement toward the southern edge of the Tibetan Plateau, an interesting configuration of the large-scale divergent circulation occurs. A favorable configuration for a rapid exchange of energy from the divergent to the rotational kinetic energy develops. Strong low level monsoonal circulations evolve, attendant with that the onset of monsoon rains occurs. In order to test this observational sequence, a series of short-range numerical prediction experiments were initiated to define the initial heat sources.

Krishnamurti, T. N.↗
DOE OSTI2021

Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator

Gene activator proteins comprise distinct DNA-binding and transcriptional activation domains (ADs). Because few ADs have been described, we tested domains tiling all yeast transcription factors for activation in vivo and identified 150 ADs. By mRNA display, we showed that 73% of ADs bound the Med15 subunit of Mediator, and that binding strength was correlated with activation. AD-Mediator interaction in vitro was unaffected by a large excess of free activator protein, pointing to a dynamic mechanism of interaction. Structural modeling showed that ADs interact with Med15 without shape complementarity (‘fuzzy’ binding). ADs shared no sequence motifs, but mutagenesis revealed biochemical and structural constraints. Finally, a neural network trained on AD sequences accurately predicted ADs in human proteins and in other yeast proteins, including chromosomal proteins and chromatin remodeling complexes. These findings solve the longstanding enigma of AD structure and function and provide a rationale for their role in biology.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Effects of rigidity on the selectivity of protein kinase inhibitors

Established strategies for discovering selective kinase inhibitors are target-centric as they often target certain structural or reactive features in the target kinase. In the absence of such prominent features, there is a lack of general methods for discovering selective inhibitors. As such, here we describe a new strategy that exploits conformational flexibility of kinases for achieving selective kinase inhibition. Through ring closure, we designed and synthesized a panel of isoquinoline-containing compounds as rigidified analogs of an amidophenyl-containing parent compound. These analogs potently inhibit kinases including Abl and BRAF but have diminished inhibition against some other kinases compared to the parent compound. Sequence analysis reveals that many of the kinases that are potently inhibited by the isoquonoline-containing compounds contain a long insertion within their catalytic domains. A crystal structure of one rigid compound bound to BRAF confirmed its binding mode. Our findings highlight the potential of a novel strategy of rigidification for improving the selectivity of kinase inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Behavior of an air-cooled thermosiphon during a non-air gas ingress event

Here, this study investigates the transient response of an air-cooled thermosiphon subjected to a sudden non-air gas ingress event. Results presented are from experimental testing conducted on a large-scale thermal hydraulic facility that examines heat removal performance of the Reactor Cavity Cooling System (RCCS) concept, a passive safety system for advanced nuclear reactors. Relying on buoyancy driven natural circulation flow, these systems feature a series of riser standpipes and coupled chimney network that provide a pathway for heat rejection to the atmosphere. In this work, the facility was modified to allow a transition of the draft intake from normal ambient air, to draft intake from an open-top volume containing high purity argon. Testing began by establishing normal operation and allowing the facility to reach steady-state thermal hydraulic flow conditions with natural air draft. The transitioned sequence was then initiated which simultaneously changed the inlet boundary from open air to a pathway from the quiescent argon volume. This event caused 1,200 cu-feet of the heavy gas, twice the internal volume of total facility flow path, to be drawn into the inlet plenum and ingress into the heated riser standpipes. With the upper chimney network still containing residual air, there was insufficient density difference to maintain buoyancy driven natural circulation. After a period of only 90 s past the ingress event, the facility experienced complete flow stagnation before entering an extended period of severely degraded system flow. Due to the cessation of bulk fluid movement and subsequent failure of its heat removal function, fluid and structural temperatures began to rise sharply. Re-circulation patterns developed within the multiple parallel riser standpipes, where hot gas near the outlets was observed to travel downward and re-enter the inlet of adjacent channels. After approximately 18-minutes, fluid temperatures and their associated density difference rose to a level sufficient to allow reestablishment of buoyancy driven system flow, and ultimately, recovery of facility operation to normal behavior.

42 ENGINEERING↗
DOE OSTI2023

The structure of the high-affinity nickel-binding site in the Ni,Zn-HypA•UreE2 complex

Abstract The maturation pathway for the nickel-dependent enzyme urease utilizes the protein UreE as a metallochaperone to supply Ni(II) ions. In Helicobacter pylori urease maturation also requires HypA and HypB, accessory proteins that are commonly associated with hydrogenase maturation. Herein we report on the characterization of a protein complex formed between HypA and the UreE2 dimer. Nuclear magnetic resonance (NMR) coupled with molecular modelling show that the protein complex apo, Zn-HypA•UreE2, forms between the rigorously conserved Met-His-Glu (MHE motif) Ni-binding N-terminal sequence of HypA and the two conserved His102A and His102B located at the dimer interface of UreE2. This complex forms in the absence of Ni(II) and is supported by extensive protein contacts that include the use of the C-terminal sequences of UreE2 to form additional strands of β-sheet with the Ni-binding domain of HypA. The Ni-binding properties of apo, Zn-HypA•UreE2 and the component proteins were investigated by isothermal titration calorimetry using a global fitting strategy that included all of the relevant equilibria, and show that the Ni,Zn-HypA•UreE2 complex contains a single Ni(II)-binding site with a sub-nanomolar KD. The structural features of this novel Ni(II) site were elucidated using proteins produced with specifically deuterated amino acids, protein point mutations, and the analyses of X-ray absorption spectroscopy, hyperfine shifted NMR features, as well as molecular modeling coupled with quantum-mechanical calculations. The results show that the complex contains a six-coordinate, high-spin Ni(II) site with ligands provided by both component proteins.

Zambelli, Barbara (ORCID:0000000238760051)↗
DOE OSTI2018

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

The Human Phenotype Ontology (HPO)––a standardized vocabulary of phenotypic abnormalities associated with 7000+ diseases––is used by thousands of researchers, clinicians, informaticians and electronic health record systems around the world. Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease. The HPO’s interoperability with other ontologies has enabled it to be used to improve diagnostic accuracy by incorporating model organism data. It also plays a key role in the popular Exomiser tool, which identifies potential disease-causing variants from whole-exome or whole-genome sequencing data. Since the HPO was first introduced in 2008, its users have become both more numerous and more diverse. To meet these emerging needs, the project has added new content, language translations, mappings and computational tooling, as well as integrations with external community data. The HPO continues to collaborate with clinical adopters to improve specific areas of the ontology and extend standardized disease descriptions. The newly redesigned HPO website (www.human-phenotypeontology.org) simplifies browsing terms and exploring clinical features, diseases, and human genes.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1993

Compact Robotic Vehicle

Radio-controlled microrover features light weight and agility. Miniature robotic vehicle, called Go-For, implements new fork-wheeled mobility concept to traverse extremely rough terrain. Weighs 4 kg and is 0.4 m long, climbs over obstacles as large as 60 percent of its length. Mobility concept applied to much larger vehicles. Demonstrates such applications as exploration of planetary surfaces, military surveillance, and assessing hazardous situations. Video camera on vehicle sends images to control station, where human supervisor chooses sequence of paths to traverse to reach locations of interest. For planetary exploration, spectrometer and seisometer on vehicle sends scientific data to control station, and onboard tools collect soil and rock samples. Terrestrial version equipped similarly to take samples in chemically and/or biologically contaminated areas.

Wilcox, Brian H.↗
NASA NTRS1994

Aging jets from low-mass stars

An extended faint optical jet is associated with the compact emission region plus faint star known as HH 55. HH 55 is located in the Lupus 2 cloud 2 min SW of the well studied T Tauri star RU Lupi. The HH 55 jet extends 55 sec N and 35 sec S in PA 160 deg. The HH 55 star is an emission line star of spectral type M3.5. Its image in the emission lines of H-alpha and (S II) is slightly elongated by 2 sec - 3 sec to the S but in continuum light is symmetrical and pointlike ((full width at half maximum) (FWHM) = 1.7 sec). The star and jet have several features in common with the star and jet known as Sz 102 = Th 28 in the nearby Lupus 3 cloud. We suggest that these objects are representative of the late evolutionary stage of the HH jet-outflow phenomenon and point out that such objects may be quite common although difficult to detect. With L(sub bol) approximately = 0.005 solar luminosity, and log T(sub e) approximately = 3.5, the HH 55 star is close to the main sequence and evolutionary tracks suggest an age of 3 x 10(exp 7) yr.

Graham, J. A.↗
NASA NTRS2012

Photospheric Magnetic Evolution in the WHI Active Regions

Sequences of line-of-sight (LOS) magnetograms recorded by the Michelson Doppler Imager are used to quantitatively characterize photospheric magnetic structure and evolution in three active regions that rotated across the Sun s disk during the Whole Heliosphere Interval (WHI), in an attempt to relate the photospheric magnetic properties of these active regions to flares and coronal mass ejections (CMEs). Several approaches are used in our analysis, on scales ranging from whole active regions, to magnetic features, to supergranular scales, and, finally, to individual pixels. We calculated several parameterizations of magnetic structure and evolution that have previously been associated with flare and CME activity, including total unsigned magnetic flux, magnetic flux near polarity-inversion lines, amount of canceled flux, the "proxy Poynting flux," and helicity flux. To catalog flare events, we used flare lists derived from both GOES and RHESSI observations. By most such measures, AR 10988 should have been the most flare- and CME-productive active region, and AR 10989 the least. Observations, however, were not consistent with this expectation: ARs 10988 and 10989 produced similar numbers of flares, and AR 10989 also produced a few CMEs. These results highlight present limitations of statistics-based flare and CME forecasting tools that rely upon line-of-sight photospheric magnetic data alone.

Welsch, B. T.↗
DOE OSTI2018

Analysis of T cell receptor repertoire in monozygotic twins concordant and discordant for chronic hepatitis B infection

Highlights: • TCR Repertoire features from twin pairs show heritable bias. • TCR repertoires show antigen biases in chronic viral infection patients. • TCR repertoires show a high level of concordance among HBeAg-positive HBV twins. • Shared clonotypes in identical cured twins show therapeutic potential. Due to their identical inheritance and shared surroundings, identical twins have been the recommended group for studying the susceptibility and prognosis of diseases. Here, CD8{sup +} T cell receptor beta (TCRβ) chains were analyzed by high-throughput sequencing in three pairs of healthy identical twins and chronic hepatitis B patients. The data showed a high level of similarity in the TCR repertoire of each pair in terms of average TCR Vβ segment expression and frequency of the complementary determining region 3 (CDR3) pattern and skewed or oligoclonal clonotypes. Notably, the level of similarity in TCR Vβ expression between the twins appeared to be independent of the consistency or inconsistency of chronic HBV infection, although the detailed CDR3 pattern and frequency were related to disease prognosis. There were more immunodominant clonotypes in patients with HBV antigen seroconversion, which showed an increased abundance. These immunodominant clonotypes may be used as favorable prognostic biomarkers and potential targets for immunotherapy. Thus, delineating the CD8{sup +} T cell repertoire of identical twins with concordant chronic viral infections provides a promising means to screen protective TCR genes for immunotherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Description and Genome Characterization of Three Novel Fungal Strains Isolated from Mars 2020 Mission-Associated Spacecraft Assembly Facility Surfaces—Recommendations for Two New Genera and One Species

National Aeronautics and Space Administration’s (NASA) spacecraft assembly facilities are monitored for the presence of any bacteria or fungi that might conceivably survive a transfer to an extraterrestrial environment. Fungi present a broad and diverse range of phenotypic and functional traits to adapt to extreme conditions, hence the detection of fungi and subsequent eradication of them are needed to prevent forward contamination for future NASA missions. During the construction and assembly for the Mars 2020 mission, three fungal strains with unique morphological and phylogenetic properties were isolated from spacecraft assembly facilities. The reconstruction of phylogenetic trees based on several gene loci (ITS, LSU, SSU, RPB, TUB, TEF1) using multi-locus sequence typing (MLST) and whole genome sequencing (WGS) analyses supported the hypothesis that these were novel species. Here we report the genus or species-level classification of these three novel strains via a polyphasic approach using phylogenetic analysis, colony and cell morphology, and comparative analysis of WGS. The strain FJI-L9-BK-P1 isolated from the Jet Propulsion Laboratory Spacecraft Assembly Facility (JPL-SAF) exhibited a putative phylogenetic relationship with the strain Aaosphaeria arxii CBS175.79 but showed distinct morphology and microscopic features. Another JPL-SAF strain, FJII-L3-CM-DR1, was phylogenetically distinct from members of the family Trichomeriaceae and exhibited morphologically different features from the genera Lithohypha and Strelitziana. The strain FKI-L1-BK-DR1 isolated from the Kennedy Space Center facility was identified as a member of Dothideomycetes incertae sedis and is closely related to the family Kirschsteiniotheliaceae according to a phylogenetic analysis. The polyphasic taxonomic approach supported the recommendation for establishing two novel genera and one novel species. The names Aaosphaeria pasadenensis (FJI-L9-BK-P1 = NRRL 64424 = DSM 114621), Pasadenomyces melaninifex (FJII-L3-CM-DR1 = NRRL 64433 = DSM 114623), and Floridaphiala radiotolerans (FKI-L1-BK-DR1 = NRRL 64434 = DSM 114624) are proposed as type species. Furthermore, resistance to ultraviolet-C and presence of specific biosynthetic gene cluster(s) coding for metabolically active compounds are unique to these strains.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

EP 250108a/SN 2025kg: Observations of the Most Nearby Broad-line Type Ic Supernova Following an Einstein Probe Fast X-Ray Transient

With a small sample of fast X-ray transients (FXTs) with multiwavelength counterparts discovered to date, their progenitors and connections to γ-ray bursts (GRBs) and supernovae (SNe) remain ambiguous. Here, we present photometric and spectroscopic observations of SN 2025kg, the SN counterpart to the FXT EP 250108a. At z = 0.17641, this is the closest known SN discovered following an Einstein Probe (EP) FXT. We show that SN 2025kg’s optical spectra reveal the hallmark features of a broad-lined Type Ic SN. Its light-curve evolution and expansion velocities are comparable to those of GRB-SNe, including SN 1998bw, and two past FXT-SNe. We present JWST/NIRSpec spectroscopy taken around SN 2025kg’s maximum light, and find weak absorption due to He I 1.0830 μm and 2.0581 μm and a broad, unidentified emission feature at ∼4–4.5 μm. Further, we observe broadened Hα in optical data at 42.5 days that is not detected at other epochs, indicating interaction with H-rich material. From its light curve, we derive a 56 Ni mass of 0.2–0.6 M ⊙ . Together with our companion Letter, our broadband data are consistent with a trapped or low-energy (≲10 51 erg) jet-driven explosion from a collapsar with a zero-age main-sequence mass of 15–30 M ⊙ . Finally, we show that the sample of EP FXT-SNe supports past estimates that low-luminosity jets seen through FXTs are more common than successful (GRB) jets, and that similar FXT-like signatures are likely present in at least a few percent of the brightest Type Ic-BL SNe.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1982

On the role of successive downstream development in East Asian polar air outbreaks

Common features were drawn from 16 events of wintertime migration of cold Siberian air moving southeastward across the east Asia coast, accompanied by strong northerly winds. Criteria for including an event as an instance of a typical synoptic scale occurrence comprised a surface pressure gradient over Korea exceeding 2.5 mb/100 km, and a drop in the daily mean temperature of over 5 C in one day. The events were required to have at least a 10 day separation. A sequence of events was discerned, including the formation of troughs and ridges over the western north Atlantic 6-7 days before an event, their development and decay downstream from one another across the Eurasian continent, and then an outbreak of polar weather. The troughs and ridges displayed maximum amplitude in the same places in the majority of cases studied, with the center moving along a curved trajectory of the 300 mb flow at nearly 30 deg longitudinally every day.

Jung, C. H.↗
NASA NTRS1986

Networking ground-based images of Comet Halley during the Giotto encounter

During the period immediately before and after the European, Russian, and Japanese spacecraft encounters with Comet Halley in early March 1986, sequences of ground-based electronic images of the comet, obtained at Table Mountain Observatory (TMO), CA, were transmitted via the Space Physics Analysis Network (SPAN) to the European Space Operations Centre (ESOC), and to University College London (UCL). During the 48-h period when the European Space Agency spacecraft Giotto was within the extended coma of Comet Halley, the ground-based images revealed that the comet displayed several spectacular near-nuclear and large-scale features. The TMO images provided a format for the interpretation of the unique in situ results obtained during the closest of the five spacecraft encounters with Comet Halley.

Rees, David↗
NASA NTRS1992

Geologic evolution of the east rim of the Hellas basin, Mars

The east rim of the Hellas basin, one of the largest obvious impact features on Mars, is studied. The distribution of geologic materials in the region is documented, and their modes of origin are constrained based on their geomorphologic characteristics. Superposition relationship and crater size-frequency distributions allow the relative ages of the geologic units to be determined and provide information regarding the timing and extent of the geologic processes emplacing and modifying the surface materials. Systematic analysis of the degradation of the Hellas basin is used to illustrate the sequence of events and interplay of geologic processes which control the evolution of many regions on Mars.

Crown, David A.↗
NASA NTRS1993

Well-resolved observations by ISEE 2 of ion dispersion in the magnetospheric cusp

During a prolonged period of southward IMF on October 30, 1978, the ISEE 2 spacecraft observed an unusually prolonged and distinct region of ion energy-time dispersion in the dayside dawn magnetosphere. Observed plasma features included the (1) presence of magnetosheath electrons and initial absence of magnetosheath ions and (2) subsequent arrival and energy-time dispersion of magnetosheath ions as the spacecraft transited outbound from 6.03 to 7.66 Earth radii. We use ISEE 2 ion measurements to illustrate these dispersive time-of-flight effects and to support our interpretation of a location in the north magnetospheric cusp. Ion energy dispersion persists for about 35 min and includes well-resolved sequences of magnetosheath and magnetospheric ion distributions. We focus primarily on observations and time-of-flight analysis of ions from the magnetosheath, which are observed simultaneously entering and exiting the cusp at different energies. We discuss the observational support and shortcomings of various ion injection locations and durations and conclude that quasi-steady merging at the dayside magnetopause, with ion dispersion caused by spacecraft motion away from the last closed field line, is the most likely scenario.

Phillips, J. L.↗
NASA NTRS2004

Impact Constraints on the Age and Origin of the Crustal Dichotomy on Mars

MOLA data have revealed a large population of 'Quasi-Circular Depressions' (QCDs) with little or no visible expression in image data. These likely buried impact basins have important implications for the age of the lowland crust, how that compares with original highland crust, and when and how the crustal dichotomy may have formed. The buried lowlands are of Early Noachian age, likely slightly younger than the buried highlands but older than the exposed (visible) highland surface. A depopulation of large visible basins at diameters 800 to 1300 km suggests some global scale event early in martian history, maybe related to the formation of the lowlands and/or the development of Tharsis. A suggested early disappearance of the global magnetic field can be placed within a temporal sequence of formation of the very largest impact basins. The global field appears to have disappeared at about the time the lowlands formed. It seems likely the topographic crustal dichotomy was produced very early in martian history by processes which operated very quickly. This and the preservation of large relic impact basins in the northern hemisphere, which themselves can account for the lowland topography, suggest that large impacts played the major role in the origin Mars fundamental crustal feature.

Frey, Herbert V.↗