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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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At least 919 records · Page 51
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

A lack of useful small molecule tools has precluded thorough interrogation of the biological function of SMYD2, a lysine methyltransferase with known tumor-suppressor substrates. Systematic exploration of the structure–activity relationships of a previously known benzoxazinone compound led to the synthesis of A-893, a potent and selective SMYD2 inhibitor (IC 50 : 2.8 nM). A cocrystal structure reveals the origin of enhanced potency, and effective suppression of p53K370 methylation is observed in a lung carcinoma (A549) cell line.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Structure and Biophysics for a Six Letter DNA Alphabet that Includes Imidazo[1,2- a ]-1,3,5-triazine-2(8 H )-4(3 H )-dione (X) and 2,4-Diaminopyrimidine (K)

A goal of synthetic biology is to develop new nucleobases that retain the desirable properties of natural nucleobases at the same time as expanding the genetic alphabet. The nonstandard Watson–Crick pair between imidazo[1,2- a ]-1,3,5-triazine-2(8 H )-4(3 H )-dione ( X ) and 2,4-diaminopyrimidine ( K ) does exactly this, pairing via complementary arrangements of hydrogen bonding in these two nucleobases, which do not complement any natural nucleobase. In this paper, we report the crystal structure of a duplex DNA oligonucleotide in B-form including two consecutive X : K pairs in GATC XK DNA determined as a host–guest complex at 1.75 Å resolution. X : K pairs have significant propeller twist angles, similar to those observed for A:T pairs, and a calculated hydrogen bonding pairing energy that is weaker than that of A:T. Thus, although inclusion of X : K pairs results in a duplex DNA structure that is globally similar to that of an analogous G:C structure, the X : K pairs locally and energetically more closely resemble A:T pairs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Source of Rate Acceleration for Carbocation Cyclization in Biomimetic Supramolecular Cages

The results of quantum chemical and molecular dynamics calculations reveal that polyanionic gallium-based cages accelerate cyclization reactions of pentadienyl alcohols as a result of substrate cage interactions, preferential binding of reactive conformations of substrate/H 3 O + pairs, and increased substrate basicity. However, the increase in basicity dominates. Here, experimental structure–activity relationship studies in which the metal vertices and overall charge of the cage are varied confirm the model derived via calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

The Campylobacter jejuni CiaD effector co-opts the host cell protein IQGAP1 to promote cell entry

Campylobacter jejuni is a foodborne pathogen that binds to and invades the epithelial cells lining the human intestinal tract. Maximal invasion of host cells by C. jejuni requires cell binding as well as delivery of the Cia proteins (Campylobacter invasion antigens) to the host cell cytosol via the flagellum. Here, we show that CiaD binds to the host cell protein IQGAP1 (a Ras GTPase-activating-like protein), thus displacing RacGAP1 from the IQGAP1 complex. This, in turn, leads to the unconstrained activity of the small GTPase Rac1, which is known to have roles in actin reorganization and internalization of C. jejuni. Our results represent the identification of a host cell protein targeted by a flagellar secreted effector protein and demonstrate that C. jejuni-stimulated Rac signaling is dependent on IQGAP1.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Fusion and fission events regulate endosome maturation and viral escape

Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators

Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirR DTS ) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirR DTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae . Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Moving beyond the constraints of chemistry via crystal structure discovery with isotropic multiwell pair potentials

The rigid constraints of chemistry-dictated by quantum mechanics and the discrete nature of the atom-limit the set of observable atomic crystal structures. What structures are possible in the absence of these constraints? Here, we systematically crystallize one-component systems of particles interacting with isotropic multiwell pair potentials. We investigate two tunable families of pairwise interaction potentials. Our simulations self-assemble a multitude of crystal structures ranging from basic lattices to complex networks. Sixteen of the structures have natural analogs spanning all coordination numbers found in inorganic chemistry. Fifteen more are hitherto unknown and occupy the space between covalent and metallic coordination environments. The discovered crystal structures constitute targets for self-assembly and expand our understanding of what a crystal structure can look like.

crystal structures↗
DOE OSTI2020

Modular protein-oligonucleotide signal exchange

Abstract While many methods are available to measure the concentrations of proteins in solution, the development of a method to quantitatively report both increases and decreases in different protein concentrations in real-time using changes in the concentrations of other molecules, such as DNA outputs, has remained a challenge. Here, we present a biomolecular reaction process that reports the concentration of an input protein in situ as the concentration of an output DNA oligonucleotide strand. This method uses DNA oligonucleotide aptamers that bind either to a specific protein selectively or to a complementary DNA oligonucleotide reversibly using toehold-mediated DNA strand-displacement. It is possible to choose the sequence of output strand almost independent of the sensing protein. Using this strategy, we implemented four different exchange processes to report the concentrations of clinically relevant human α-thrombin and vascular endothelial growth factor using changes in concentrations of DNA oligonucleotide outputs. These exchange processes can operate in tandem such that the same or different output signals can indicate changes in concentration of distinct or identical input proteins. The simplicity of our approach suggests a pathway to build devices that can direct diverse output responses in response to changes in concentrations of specific proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot

Fungal mineral weathering regulates the bioavailability of inorganic nutrients from mineral surfaces to organic matter and increase the bioavailable fraction of nutrients. Such weathering strategies are classified as biomechanical or biochemical. In the case of fungal uptake of mineral nutrients through biochemical weathering, it is widely hypothesized that uptake of inorganic nutrients occurs through organic acid chelation, but such processes have not been directly visualized. This is in part due to challenges in probing the complex and heterogeneous soil environment. Here, using an epoxy-based, mineral-doped soil micromodel platform, which emulates soil mineralogy and porosity, we visualize the molecular mechanisms of mineral weathering. Mass spectrometry imaging revealed differences in the distribution of fungal exudates, citric acid, and tartaric acid on the soil micromodels in presence of minerals. Citric acid was detected closer to the nutrient-rich inoculation point, whereas tartaric acid was highly abundant away from inoculation point. This suggested that the organic acid exuded by the fungi depended on the proximity from the carbon-rich organic substrate at the point of inoculation. Using a combination of X-ray fluorescence and X-ray near edge structure analysis, we identified citric acid- and tartaric acid-bound K within fungal hyphae networks grown in the presence of minerals. Combined, our results provide direct evidence that fungi uptake and transport mineral derived nutrient organic acid chelation. The results of this study provided unprecedented visualization of fungal uptake and transport of K + , while resolving the indirect weathering mechanism of fungal K uptake from mineral interfaces.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18

Bacteriophages are useful nonantibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identified Phaeobacter virus MD18 , a phage antagonist of Phaeobacter inhibens , a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggested that Phaeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identified genes that modulate host susceptibility to phage MD18 and implicated the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Ectomycorrhizal fungi alter soil food webs and the functional potential of bacterial communities

Most of Earth’s trees rely on critical soil nutrients that ectomycorrhizal fungi (EcMF) liberate and provide, and all of Earth’s land plants associate with bacteria that help them survive in nature. Yet, our understanding of how the presence of EcMF modifies soil bacterial communities, soil food webs, and root chemistry requires direct experimental evidence to comprehend the effects that EcMF may generate in the belowground plant microbiome. To this end, we grew Pinus muricata plants in soils that were either inoculated with EcMF and native forest bacterial communities or only native bacterial communities. We then profiled the soil bacterial communities, applied metabolomics and lipidomics, and linked omics data sets to understand how the presence of EcMF modifies belowground biogeochemistry, bacterial community structure, and their functional potential. We found that the presence of EcMF (i) enriches soil bacteria linked to enhanced plant growth in nature, (ii) alters the quantity and composition of lipid and non-lipid soil metabolites, and (iii) modifies plant root chemistry toward pathogen suppression, enzymatic conservation, and reactive oxygen species scavenging. Using this multi-omic approach, we therefore show that this widespread fungal symbiosis may be a common factor for structuring soil food webs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Fungal Hyphosphere Microbiomes Are Distinct from Surrounding Substrates and Show Consistent Association Patterns

Fungi and bacteria are the most abundant and diverse organisms in soils (perhaps more so than any other habitat on earth), and together these microorganisms contribute to broad soil ecosystem processes. There is a suite of bacteria that appears consistently within the physical space called the hyphosphere, the area of influence surrounding fungal hyphae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

Gyrokinetic Particle Simulation of Turbulent Transport in Burning Plasmas

In this project, we have developed techniques for visualizing large-scale time-varying multivariate particle and field data produced by the GPS_TTBP team. Our basic approach to particle data visualization is to provide the user with an intuitive interactive interface for exploring the data. We have designed a multivariate filtering interface for scientists to effortlessly isolate those particles of interest for revealing structures in densely packed particles as well as the temporal behaviors of selected particles. With such a visualization system, scientists on the GPS-TTBP project can validate known relationships and temporal trends, and possibly gain new insights in their simulations. We have tested the system using over several millions of particles on a single PC. We will also need to address the scalability of the system to handle billions of particles using a cluster of PCs. To visualize the field data, we choose to use direct volume rendering. Because the data provided by PPPL is on a curvilinear mesh, several processing steps have to be taken. The mesh is curvilinear in nature, following the shape of a deformed torus. Additionally, in order to properly interpolate between the given slices we cannot use simple linear interpolation in Cartesian space but instead have to interpolate along the magnetic field lines given to us by the scientists. With these limitations, building a system that can provide an accurate visualization of the dataset is quite a challenge to overcome. In the end we use a combination of deformation methods such as deformation textures in order to fit a normal torus into their deformed torus, allowing us to store the data in toroidal coordinates in order to take advantage of modern GPUs to perform the interpolation along the field lines for us. The resulting new rendering capability produces visualizations at a quality and detail level previously not available to the scientists at the PPPL. In summary, in this project we have successfully created new capabilities for the scientists to visualize their 3D data at higher accuracy and quality, enhancing their ability to evaluate the simulations and understand the modeled phenomena.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Position Papers for Inverse Methods for Complex Systems under Uncertainty Workshop

The ability to solve inverse problems – inferring unknown parameters, structures, or states of a system from observed data – is essential for advancing scientific discovery and innovation capabilities for the DOE mission. Basic research needs and challenges are particularly acute in emerging areas such as the interactive, data-driven, modeling and simulation of digital twins; decision support for experiments at DOE scientific user facilities; and for other complex systems and workflows. Inverse problems are at the heart of understanding and controlling complex systems due to factors such as observational data with varying modalities and fidelities, inherent uncertainties in physical measurements and numerical models, and the computational demands of rapid and high-fidelity simulations. The convergence of recent scientific computing trends – scientific machine learning, artificial intelligence, and computing advances such as exascale computing – is creating unprecedented opportunities. These advancements offer the potential to revolutionize how we approach inverse problems to extract actionable insights with the required level of accuracy and computational efficiency. This workshop and the Call for Position Papers are vital steps in bringing together experts to collectively explore and identify the new computational and mathematical directions needed in inverse methods for complex systems under uncertainty.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

Community Structure and Function of High-Temperature Chlorophototrophic Microbial Mats Inhabiting Diverse Geothermal Environments

Six phototrophic microbial mat communities from different geothermal springs (YNP) were studied using metagenome sequencing and geochemical analyses. The primary goals of this work were to determine differences in community composition of high-temperature phototrophic mats distributed across the Yellowstone geothermal ecosystem, and to identify metabolic attributes of predominant organisms present in these communities that may correlate with environmental attributes important in niche differentiation. Random shotgun metagenome sequences from six phototrophic communities (average ~53 Mbp/site) were subjected to multiple taxonomic, phylogenetic, and functional analyses. All methods, including G + C content distribution, MEGAN analyses, and oligonucleotide frequency based clustering, provided strong support for the dominant community members present in each site. Cyanobacteria were only observed in non-sulfidic sites; de novo assemblies were obtained for Synechococcus-like populations at Chocolate Pots (CP_7) and Fischerella-like populations at White Creek (WC_6). Chloroflexi-like sequences (esp. Roseiflexus and/or Chloroflexus spp.) were observed in all six samples and contained genes involved in bacteriochlorophyll biosynthesis and the 3-hydroxypropionate carbon fixation pathway. Other major sequence assemblies were obtained for a Chlorobiales population from CP_7 (proposed family Thermochlorobacteriaceae), and an anoxygenic, sulfur-oxidizing Thermochromatium-like (Gamma-proteobacteria) population from Bath Lake Vista Annex (BLVA_20). Additional sequence coverage is necessary to establish more complete assemblies of other novel bacteria in these sites (e.g., Bacteroidetes and Firmicutes); however, current assemblies suggested that several of these organisms play important roles in heterotrophic and fermentative metabolisms. Definitive linkages were established between several of the dominant phylotypes present in these habitats and important functional processes such as photosynthesis, carbon fixation, sulfur oxidation, and fermentation.

54 ENVIRONMENTAL SCIENCES↗
NASA NTRS1972

A study and classification of non-linear high frequency ionospheric instabilities by coupled mode theory.

Two basic high-frequency ionospheric instabilities are discussed - i.e., the three-wave parametric interaction, and the oscillating two-stream instability. In the parametric instability, the ion-acoustic wave has a complex frequency, whereas in the oscillating two-stream instability the ion-acoustic frequency is purely imaginary. The parametric instability is shown to be the only one whose threshold depends on the ion collision frequency. A coupled-mode theory is proposed which permits study and classification of high-frequency instabilities on a unified basis.

Harker, K. J.↗