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At least 721 records · Page 40

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DOE OSTI2024

Gut enterotype-dependent modulation of gut microbiota and their metabolism in response to xanthohumol supplementation in healthy adults

Xanthohumol (XN), a polyphenol found in the hop plant (Humulus lupulus), has antioxidant, anti-inflammatory, prebiotic, and anti-hyperlipidemic activity. Preclinical evidence suggests the gut microbiome is essential in mediating these bioactivities; however, relatively little is known about XN’s impact on human gut microbiota in vivo. We conducted a randomized, triple-blinded, placebo-controlled clinical trial (ClinicalTrials.gov NCT03735420) to determine safety and tolerability of XN in healthy adults. Thirty healthy participants were randomized to 24 mg/day XN or placebo for 8 weeks. As secondary outcomes, quantification of bacterial metabolites and 16S rRNA gene sequencing were utilized to explore the relationships between XN supplementation, gut microbiota, and biomarkers of gut health. Although XN did not significantly change gut microbiota composition, it did re-shape individual taxa in an enterotype-dependent manner. High levels of inter-individual variation in metabolic profiles and bioavailability of XN metabolites were observed. Moreover, reductions in microbiota-derived bile acid metabolism were observed, which were enterotype-dependent. These results suggest interactions between XN and gut microbiota in healthy adults are highly inter-individualized and potentially indicate that XN elicits effects on gut health in an enterotype-dependent manner.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments

Coastal waters such as those found in the Baltic Sea already suffer from anthropogenic related problems including increased algal blooming and hypoxia while ongoing and future climate change will likely worsen these effects. Microbial communities in sediments play a crucial role in the marine energy- and nutrient cycling, and how they are affected by climate change and shape the environment in the future is of great interest. The aims of this study were to investigate potential effects of prolonged warming on microbial community composition and nutrient cycling including sulfate reduction in surface (∼0.5 cm) to deeper sediments (∼ 24 cm). To investigate this, 16S rRNA gene amplicon sequencing was performed, and sulfate concentrations were measured and compared between sediments in a heated bay (which has been used as a cooling water outlet from a nearby nuclear power plant for approximately 50 years) and a nearby but unaffected control bay. The results showed variation in overall microbial diversity according to sediment depth and higher sulfate flux in the heated bay compared to the control bay. A difference in vertical community structure reflected increased relative abundances of sulfur oxidizing- and sulfate reducing bacteria along with a higher proportion of archaea, such as Bathyarchaeota, in the heated compared to the control bay. This was particularly evident closer to the sediment surface, indicating a compression of geochemical zones in the heated bay. These results corroborate findings in previous studies and additionally point to an amplified effect of prolonged warming deeper in the sediment, which could result in elevated concentrations of toxic compounds and greenhouse gases closer to the sediment surface.

16S rRNA gene amplicon↗

DOE OSTI2017

Hyperspectral Image Classification Using Graph Clustering Methods

Hyperspectral imagery is a challenging modality due to the dimension of the pixels which can range from hundreds to over a thousand frequencies depending on the sensor. Most methods in the literature reduce the dimension of the data using a method such as principal component analysis, however this procedure can lose information. More recently methods have been developed to address classification of large datasets in high dimensions. This paper presents two classes of graph-based classification methods for hyperspectral imagery. Using the full dimensionality of the data, we consider a similarity graph based on pairwise comparisons of pixels. The graph is segmented using a pseudospectral algorithm for graph clustering that requires information about the eigenfunctions of the graph Laplacian but does not require computation of the full graph. We develop a parallel version of the Nyström extension method to randomly sample the graph to construct a low rank approximation of the graph Laplacian. With at most a few hundred eigenfunctions, we can implement the clustering method designed to solve a variational problem for a graph-cut-based semi-supervised or unsupervised classification problem. We implement OpenMP directive-based parallelism in our algorithms and show performance improvement and strong, almost ideal, scaling behavior. The method can handle very large datasets including a video sequence with over a million pixels, and the problem of segmenting a data set into a pre-determined number of classes.

47 OTHER INSTRUMENTATION↗

NASA NTRS1971

Relationship between siderophilic-element content and oxidation state of ordinary chondrites.

The concentrations of Ni and Ir have been determined by neutron activation in a suite of ordinary chondrites for which accurate ferromagnesian-mineral compositional data were available. Although hiatus between the individual groups exist, the trends within the groups are in keeping with the hypothesis that the ordinary chondrites form a continuous fractionation sequence. A significant negative correlation is observed between the abundance of Ni or Ir and the Fe content of the ferromagnesian minerals in the H and L groups, and for Ir in the LL group, as expected if the metal-silicate fractionation and the variation in oxidation states were produced by the same or related processes. The Ir/Ni ratio decreases by a factor of 1.2 between the H and LL groups. This fractionation must have occurred at an early stage in the condensation phase of the solar nebula.

Mueller, O.↗

NASA NTRS1975

Dust injection into the Martian atmosphere

The sequence of events culminating in a global Martian dust storm is reviewed in the light of current theories on dust storm generation. Based upon experimental results, a mechanism for the initiation of global dust storms on Mars is proposed. According to this mechanism, the diurnal variation of surface temperature results in desorption of adsorbed CO2, which under certain conditions can inject large amounts of fine (1-10 microns) dust into the atmosphere.

Johnson, D. W.↗

NASA NTRS1980

Predictions of mineral assemblages in planetary interiors

It is shown that mineral compatibilities in the model system CaO-MgO-Al2O3-SiO2 can be applied to deduce the mineral assemblages expected in planetary interiors and their variation with depth. In general, the available estimates of bulk composition of the terrestrial planets suggest that the terrestrial planets can be divided into two groups based on their predicted mineral assemblages. The terrestrial, Venusian, and lunar bulk compositions are expected to display the following sequence of mineral assemblages with increasing pressure: plagioclase lherzolite, spinel lherzolite, and garnet lherzolite. The sequences expected in Martian and Mercurian are different: spinel-plagioclase wehrlite, spinel lherzolite, and spinel-garnet wehrlite. These assemblages have a major influence on the compositions of liquids produced by melting of these planetary interiors, on the solidus temperatures, and thus on the nature of planetary differentiation and the types of magmas extruded at planetary surfaces.

Stolper, E.↗

NASA NTRS1987

Radio emissions from Uranus

The hardware of the Planetary Radio Astronomy Experiment aboard Voyager 2 and the results of the measurements of radio emissions from Uranus are described. Strong 40-kHz to 850-kHz radio emissions were detected after closest approach on the day-side of Uranus. The time variations of these emissions were periodic, with a period of 17.24 h closely matching that of Uranus's rotation and evidently being controlled by the strength and shape of its magnetic field. The instrument also recorded possible Uranian electrostatic discharges, vertex early arcs occurring in sequences of more than a dozen events with approximately 10-min period, and very intense isolated bursts lasting tens of minutes.

Warwick, J. W.↗

NASA NTRS1991

Nucleic acid probes in diagnostic medicine

The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

Oberry, Phillip A.↗

NASA NTRS1994

Variable extinction in HD 45677 and the evolution of dust grains in pre-main-sequence disks

Changes in the UV extinction and IR emission were sought in the Herbig Ae/Be star candidate HD 45677 (= FS CMa) by comparing UV, optical, and IR observations made approximately 10 yr apart. HD 45677 varied significantly, becoming more than 50% brighter in the UV and optical than it was a decade ago. A comparison of the observations between epochs indicates that if the variations are due to changes in dust obscuration, the dust acts as a gray absorber into the near-IR and must be depleted in grains smaller than 1 micron. This is similar to the results obtained on the circumstellar disks of stars like Vega and Beta Pic, and suggests that radiation pressure may be responsible for the small-grain depletion. In addition, the total IR flux seems to have declined, indicating a decrease in the total mass of the dust envelope that contributes to the IR emission in this part of the spectrum. Due to the anomalous nature of the extinction, the use of normal extinction curves to deredden the spectral energy distributions of stars with circumstellar dust may lead to significant errors and should be used with great caution.

Sitko, Michael L.↗

DOE OSTI2019

Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences

Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. We report the structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

Despite the important roles of soil microbes, especially the most diverse rare taxa in maintaining community diversity and multifunctionality, how different climate regimes alter the stability and functions of the rare microbial biosphere remains unknown. We reciprocally transplanted field soils across a latitudinal gradient to simulate climate change and sampled the soils annually after harvesting the maize over the following 6 years (from 2005 to 2011). By sequencing microbial 16S ribosomal RNA gene amplicons, we found that changing climate regimes significantly altered the composition and dynamics of soil microbial communities. A continuous succession of the rare and abundant communities was observed. Rare microbial communities were more stable under changing climatic regimes, with lower variations in temporal dynamics, and higher stability and constancy of diversity. More nitrogen cycling genes were detected in the rare members than in the abundant members, including amoA, napA, nifH, nirK, nirS, norB and nrfA. Random forest analysis and receiver operating characteristics analysis showed that rare taxa may act as potential contributors to maize yield under changing climatics. The study indicates that the taxonomically and functionally diverse rare biosphere has the potential to increase functional redundancy and enhance the ability of soil communities to counteract environmental disturbances. With ongoing global climate change, exploring the succession process and functional changes of rare taxa may be important in elucidating the ecosystem stability and multifunctionality that are mediated by microbial communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Genome-wide scans of selection highlight the impact of biotic and abiotic constraints in natural populations of the model grass Brachypodium distachyon

Grasses are essential plants for ecosystem functioning. Quantifying the selective pressures that act on natural variation in grass species is therefore essential regarding biodiversity maintenance. Here, in this study, we investigate the selection pressures that act on two distinct populations of the grass model Brachypodium distachyon without prior knowledge about the traits under selection. We took advantage of whole-genome sequencing data produced for 44 natural accessions of B. distachyon and used complementary genome-wide selection scans (GWSS) methods to detect genomic regions under balancing and positive selection. We show that selection is shaping genetic diversity at multiple temporal and spatial scales in this species, and affects different genomic regions across the two populations. Gene ontology annotation of candidate genes reveals that pathogens may constitute important factors of positive and balancing selection in B. distachyon. We eventually cross-validated our results with quantitative trait locus data available for leaf-rust resistance in this species and demonstrate that, when paired with classical trait mapping, GWSS can help pinpointing candidate genes for further molecular validation. Thanks to a near base-perfect reference genome and the large collection of freely available natural accessions collected across its natural range, B. distachyon appears as a prime system for studies in ecology, population genomics and evolutionary biology.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Compilation and utilization of a sorghum transcriptome compendium for gene regulatory network analysis and crop trait engineering

Sorghum bicolor (Sorghum) is a drought and heat tolerant C4 grass crop used to produce grain, forage, biofuels, and other bioproducts. Genetic improvement of sorghum hybrid crops is aided by a large and diverse germplasm, sorghum's diploid inbreeding genetics, and a relatively small genome that has facilitated genomic research. Over the past 20 years, the sorghum research community characterized the cytogenetic and recombinant landscapes of sorghum's 10 chromosomes, sequenced and annotated the sorghum genome, and used that information to identify genes/alleles that modulate flowering time, plant height, seed shattering, and other important traits. More recently, >1000 RNA-seq transcriptome profiles were collected from 15 sorghum genotypes to help understand the genetic basis of variation in growth and development of sorghum stems, tillers, roots, and leaves, and the regulation of biosynthetic pathways that produce epicuticular wax, dhurrin, and RFOs, compounds that contribute to sorghum's resilience. Transcriptome studies were designed to identify differentially expressed genes that are co-expressed during development or in response to a treatment to enable construction of gene regulatory networks. Co-expression and network analysis identified transcription factors and their cognate binding sites in target gene promoters and signaling pathways that modulate gene regulatory networks providing gene editing targets for further trait optimization. RNA-seq data from >20 experiments targeting sorghum organs, tissues, cell types, developmental stages, and responses to environmental conditions (i.e., diel, day-length, shading, water-deficit, temperature) has been compiled in a sorghum transcriptome compendium. The goal of this resource paper is to describe compendium content, accessibility, and a compendium data analysis pipeline and to illustrate the types of information that can be derived from the compendium with a focus on the elucidation of gene regulatory networks useful for guiding the improvement of sorghum traits through gene editing.

RNA-seq↗

DOE OSTI2017

The kinetics of pre-mRNA splicing in the Drosophila genome and the influence of gene architecture

Production of most eukaryotic mRNAs requires splicing of introns from pre-mRNA. The splicing reaction requires definition of splice sites, which are initially recognized in either intron-spanning (‘intron definition’) or exon-spanning (‘exon definition’) pairs. To understand how exon and intron length and splice site recognition mode impact splicing, we measured splicing rates genome-wide in Drosophila, using metabolic labeling/RNA sequencing and new mathematical models to estimate rates. We found that the modal intron length range of 60–70 nt represents a local maximum of splicing rates, but that much longer exon-defined introns are spliced even faster and more accurately. We observed unexpectedly low variation in splicing rates across introns in the same gene, suggesting the presence of gene-level influences, and we identified multiple gene level variables associated with splicing rate. Together our data suggest that developmental and stress response genes may have preferentially evolved exon definition in order to enhance the rate or accuracy of splicing.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1972

High resolution spectroscopy of the disk chromosphere. II - Time sequence observations of Ca II H and K emissions.

Two independent sets of high resolution time series spectra of the Ca II H and K emission obtained at the Solar Tower and at the Big Dome of the Sacramento Peak Observatory on September 11th, 1971 are reported. The evolutionary behavior of the emission first reported by Wilson and Evans is confirmed, but the detail of the evolution is found to be more complex. In one case, a doubly peaked feature showing some K3 emission evolves into a single K2 (red) peak with no K3 emission. Coincidentally, a neighboring doubly peaked feature evolves to a very strong blue peak. In an entirely independent sequence a doubly peaked feature evolves into a single red peak. The K2 emission then fades completely although the continuum threads are still strong. Finally a strong K2 blue peak appears. It is concluded that the observed evolution of the K2 emission is due to temporal variations in the physical conditions which give rise to them.

Wilson, P. R.↗

NASA NTRSDate not supplied

Demand-Capacity Balancing Algorithms for Urban Air Mobility Operations

This paper proposes new Demand/Capacity Balancing (DCB) algorithms that resolve imbalances at enroute waypoints, such as crossing, merging, and UAM corridor entry or exit waypoints, in addition to vertiports; we refer to this algorithm as DCB-Waypoint, still using pre-departure delay as the sole resolution mechanism. Like DCB-Vertiport, DCB-Waypoint takes one flight at a time and resolves imbalances one waypoint at a time, starting from the origin vertiport followed by the sequence of constrained waypoints and, finally, the destination vertiport. The next advancement assigns airborne delays, in addition to pre-departure delays at vertiports. This algorithm, called DCB-Airborne-Delays, uses information on flight speeds to ensure that the assigned delays are feasible, meaning that variations in flight speeds are within feasible aircraft speed ranges. The proposed algorithms are being implemented in a new fast-time simulation tool developed especially for simulating UAM operations. The full paper will provide additional details of the new DCB algorithms that have been developed, as well as the results from simulations using these algorithms. Finally, the DCB algorithms will be compared against one another to obtain insights and recommendations for the future development of more advanced DCB algorithms.

urban air mobility, demand-capacity balancing↗

NASA NTRSDate not supplied

Demand-Capacity Balancing Algorithms for Urban Air Mobility Operations

urban air mobility↗

NASA NTRS2024

TIC 290061484: A Triply Eclipsing Triple System With the Shortest Known Outer Period of 24.5 Days

We have discovered a triply eclipsing triple star system, TIC 290061484, with the shortest known outer period, $P_{\rm out}$, of only 24.5 days. This `eclipses' the previous record set by $\lambda$ Tauri at 33.02 days which held for 68 years \citep{1956ApJ...124..507E}. The inner binary, with an orbital period of $P_{\rm in}=1.8$ days, produces primary and secondary eclipses, and exhibits prominent eclipse timing variations with the same periodicity as the outer orbit. The tertiary star eclipses, and is eclipsed by, the inner binary with pronounced asymmetric profiles. The inclinations of both orbits evolve on observable timescales such that the third-body eclipses exhibit dramatic depth variations in TESS data. A photodynamical model provides a complete solution for all orbital and physical parameters of the triple system, showing that the three stars have masses of \MAa M$_\odot$, \MAb M$_\odot$, and \MB M$_\odot$, radii near those corresponding to the main sequence, and $T_{\rm eff}$ in the range of 21,000 K - 23,700 K. Remarkably, the model shows that the triple is in fact a subsystem of a hierarchical 2+1+1 quadruple with a distant fourth star. The outermost star has a period of $\sim3,200$ days and a mass comparable to the stars in the inner triple. In $\sim20$ Myr, all three components of the triple subsystem will merge, undergo a type II supernova explosion, and leave a single remnant neutron star. At the time of writing, TIC 290061484 is the most compact triple system, and one of the tighter known compact triples (i.e., $P_{\rm out}/P_{\rm in} = 13.7$).

V B Kostov↗