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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 OSTI2019

Interaction of Structural Glycoprotein E2 of Classical Swine Fever Virus with Protein Phosphatase 1 Catalytic Subunit Beta (PPP1CB)

Classical swine fever virus (CSFV) E2 protein, the major virus structural glycoprotein, is an essential component of the viral envelope. E2 is involved in virus absorption, induction of a protective immune response and is critical for virulence in swine. Using the yeast two-hybrid system, we identified protein phosphatase 1 catalytic subunit beta (PPP1CB), which is part of the Protein Phosphatase 1 (PP1) complex, as a specific binding host partner for E2. We further confirmed the occurrence of this interaction in CSFV-infected swine cells by using two independent methodologies: Co-immunoprecipitation and Proximity Ligation Assay. In addition, we demonstrated that pharmacological activation of the PP1 pathway has a negative effect on CSFV replication while inhibition of the PP1 pathway or knockdown of PPP1CB by siRNA had no observed effect. Overall, our data suggests that the CSFV E2 and PPP1CB protein interact in infected cells, and that activation of the PP1 pathway decreases virus replication.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Molecular remodeling in Populus PdKOR RNAi roots profiled using LC-MS/MS proteomics

Plant endo-β-1,4-glucanases belonging to the Glycoside Hydrolase Family 9 have functional roles in cell wall biosynthesis and remodeling via endohydrolysis of (1→4)-β-D-glucosidic linkages. Modification of cell wall chemistry via RNAi-mediated downregulation of Populus deltoides KOR1 (PdKOR), a endo-β-1,4-glucanase gene, in Populus deltoides has been shown to have functional consequences for the composition of secondary metabolome and the ability of modified roots to interact with beneficial microbes. The molecular remodeling that underlies the observed differences at metabolic, physiological, and morphological levels in roots is not well understood. Here we used a LC-MS/MS-based proteome profiling approach to survey the molecular remodeling in root tissues of PdKOR and control plants. A total of 14316 peptides were identified and these mapped to 7139 P. deltoides proteins. Based on 90% sequence identity, the measured protein accessions represent 1187 functional protein groups. Analysis of GO categories and specific individual proteins showed differential expression of proteins relevant to plant-microbe interactions, cell wall chemistry, and metabolism. The new proteome dataset serves as a useful resource for deriving new hypotheses and empirical testing pertaining to functional roles of proteins and pathways in differential priming of plant roots to interactions with microbes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2018

The Spectrin-Actin-Based Periodic Cytoskeleton as a Conserved Nanoscale Scaffold and Ruler of the Neural Stem Cell Lineage

Through three-dimensional STORM super-resolution microscopy, we resolve the spectrin-actin-based membrane cytoskeleton of neural stem cells (NSCs) and NSC-derived neurons, astrocytes, and oligodendrocytes. We show that undifferentiated NSCs are capable of forming patches of locally periodic, one-dimensional (1D) membrane cytoskeleton with ~180 nm periodicity. Such periodic structures become increasingly ordered and long-ranging as the NSCs mature into terminally differentiated neuronal and glial cell types, and, during this process, distinct 1D periodic “strips” dominate the flat 2D membranes. Moreover, we report remarkable alignment of the periodic cytoskeletons between abutting cells at axon-axon and axon-oligodendrocyte contacts and identify two adhesion molecules, neurofascin and L1CAM, as candidates to drive this nanoscale alignment. We thus show that a conserved 1D periodic membrane cytoskeletal motif serves as a nanoscale scaffold and ruler to mediate the physical interactions between cell types of the NSC lineage.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Design and Development of Highly Potent HIV-1 Protease Inhibitors with a Crown-Like Oxotricyclic Core as the P2-Ligand To Combat Multidrug-Resistant HIV Variants

Design, synthesis, and evaluation of a new class of exceptionally potent HIV-1 protease inhibitors are reported. Inhibitor 5 displayed superior antiviral activity and drug-resistance profiles. In fact, this inhibitor showed several orders of magnitude improved antiviral activity over the FDA approved drug darunavir. This inhibitor incorporates an unprecedented 6–5–5 ring-fused crown-like tetrahydropyranofuran as the P2 ligand and an aminobenzothiazole as the P2' ligand with the (R)-hydroxyethylsulfonamide isostere. The crown-like P2 ligand for this inhibitor has been synthesized efficiently in an optically active form using a chiral Diels–Alder catalyst providing a key intermediate in high enantiomeric purity. Furthermore, two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Nanoporous silica-based protocells at multiple scales for designs of life and nanomedicine

In this study, various protocell models have been constructed de novo with the bottom-up approach. Here we describe a silica-based protocell composed of a nanoporous amorphous silica core encapsulated within a lipid bilayer built by self-assembly that provides for independent definition of cell interior and the surface membrane. In this review, we will first describe the essential features of this architecture and then summarize the current development of silica-based protocells at both micro- and nanoscale with diverse functionalities. As the structure of the silica is relatively static, silica-core protocells do not have the ability to change shape, but their interior structure provides a highly crowded and, in some cases, authentic scaffold upon which biomolecular components and systems could be reconstituted. In basic research, the larger protocells based on precise silica replicas of cells could be developed into geometrically realistic bioreactor platforms to enable cellular functions like coupled biochemical reactions, while in translational research smaller protocells based on mesoporous silica nanoparticles are being developed for targeted nanomedicine. Ultimately we see two different motivations for protocell research and development: (1) to emulate life in order to understand it; and (2) to use biomimicry to engineer desired cellular interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2011

An Insight into the Interaction Mode Between CheB and Chemoreceptor from Two Crystal Structures of CheB Methylesterase Catalytic Domain

We have determined 2.2 {angstrom} resolution crystal structure of Thermotoga maritima CheB methylesterase domain to provide insight into the interaction mode between CheB and chemoreceptors. T. maritima CheB methylesterase domain has identical topology of a modified doubly-wound {alpha}/{beta} fold that was observed from the previously reported Salmonella typhimurium counterpart, but the analysis of the electrostatic potential surface near the catalytic triad indicated considerable charge distribution difference. As the CheB demethylation consensus sites of the chemoreceptors, the CheB substrate, are not uniquely conserved between T. maritima and S. typhimurium, such surfaces with differing electrostatic properties may reflect CheB regions that mediate protein-protein interaction. Via the computational docking of the two T. maritima and S. typhimurium CheB structures to the respective T. maritima and Escherichia coli chemoreceptors, we propose a CheB:chemoreceptor interaction mode.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deep learning-enabled natural language processing to identify directional pharmacokinetic drug–drug interactions

Background. During drug development, it is essential to gather information about the change of clinical exposure of a drug (object) due to the pharmacokinetic (PK) drug-drug interactions (DDIs) with another drug (precipitant). While many natural language processing (NLP) methods for DDI have been published, most were designed to evaluate if (and what kind of) DDI relationships exist in the text, without identifying the direction of DDI (object vs. precipitant drug). Here we present a method for the automatic identification of the directionality of a PK DDI from literature or drug labels. Methods. We reannotated the Text Analysis Conference (TAC) DDI track 2019 corpus for identifying the direction of a PK DDI and evaluated the performance of a fine-tuned BioBERT model on this task by following the training and validation steps prespecified by TAC. Results. This initial attempt showed the model achieved an F-score of 0.82 in identifying sentences as containing PK DDI and an F-score of 0.97 in identifying object versus precipitant drugs in those sentences. Discussion and conclusion. Despite a growing list of NLP methods for DDI extraction, most of them use a common set of corpora to perform general purpose tasks (e.g., classifying a sentence into one of several fixed DDI categories). There is a lack of coordination between the drug development and biomedical informatics method development community to develop corpora and methods to perform specific tasks (e.g., extract clinical exposure changes due to PK DDI). We hope that our effort can encourage such a coordination so that more “fit for purpose” NLP methods could be developed and used to facilitate the drug development process.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Insight into industrial hemp ( Cannabis sativa L.) root exudation composition in a simulated soil environment: a rhizosphere-on-a-chip study

Microfluidic technologies provide a reduced complexity and soil-free environment to study plant-soil interactions at the microscale. Traditionally used for model plants such as Arabidopsis thaliana, this study represents the first application of a rhizosphere-on-a-chip (RhizoChip) to investigate root exudation in industrial hemp (Cannabis sativa L.), an agronomic crop with growing economic importance. By incorporating soil-like minerals (kaolinite, potassium feldspar, and biotite), the RhizoChip addresses limitations of previous research. Hemp seedlings grown in mineral-containing chips exhibited significant root growth, emphasizing the critical role of minerals in root development. Using untargeted metabolomics, 170 compounds were identified, including organic acids, amino acids, and secondary metabolites, with distinct profiles across conditions. Metabolic pathway analysis revealed activity in amino acid metabolism, the citric acid cycle, and secondary metabolite biosynthesis. In conclusion, this study highlights the RhizoChip's potential for long-term studies of root exudates in non-model crops and offers insights into rhizosphere processes with implications for sustainable agriculture.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1994

Climatology and natural variability of the global hydrologic cycle in the GLA atmospheric general circulation model

Time average climatology and low-frequency variabilities of the global hydrologic cycle (GHC) in the Goddard Laboratory for Atmospheres (GLA) general circulation model (GCM) were investigated in the present work. A 730-day experiment was conducted with the GLA GCM forced by insolation, sea surface temperature, and ice-snow undergoing climatological annual cycles. Ifluences of interactive soil moisture on time average climatology and natural variability of the GHC were also investigated by conducting 365-day experiments with and without interactive soil moisture. Insolation, sea surface temperature, and ice-snow were fixed at their July levels in the latter two experiments. Results show that the model's time average hydrologic cycle variables for July in all three experiments agree reasonably well with observations. Except in the case of precipitable water, the zonal average climates of the annual cycle experiment and the two perpetual July experiments are alike, i.e., their differences are within limits of the natural variability of the model's climate. Statistics of various components of the GHC, i.e., water vapor, evaporation, and precipitation, are significantly affected by the presence of interactive soil moisture. A long-term trend is found in the principal empirical modes of variability of ground wetness, evaporation, and sensible heat. Dominant modes of variability of these quantities over land are physically consistent with one another and with land surface energy balance requirements. The dominant mode of precipitation variability is found to be closely related to organized convection over the tropical western Pacific Ocean. The precipitation variability has timescales in the range of 2 to 3 months and can be identified with the stationary component of the Madden-Julian Oscillation. The precipitation mode is not sensitive to the presence of interactive soil moisture but is closely linked to both the rotational and divergent components of atmospheric moisture transport. The present results indicate that globally coherent natural variability of the GHC in the GLA GCM has two basic timescales in the absence of annual cycles of external forcings: a long-term trend associated with atmosphere-soil moisture interaction which affects the model atmosphere mostly over midlatitude continental regions and a large-scale 2- to 3-month variability associated with atmospheric moist processes over the western Pacific Ocean.

Lau, K.-M.↗
DOE OSTI2017

Peptide recognition by heterochromatin protein 1 (HP1) chromoshadow domains revisited: Plasticity in the pseudosymmetric histone binding site of human HP1

Heterochromatin protein 1 (HP1), a highly conserved non-histone chromosomal protein in eukaryotes, plays important roles in the regulation of gene transcription. Each of the three human homologs of HP1 includes a chromoshadow domain (CSD). The CSD interacts with various proteins bearing the PXVXL motif but also with a region of histone H3 that bears the similar PXXVXL motif. The latter interaction has not yet been resolved in atomic detail. Here we demonstrate that the CSDs of all three human HP1 homologs have comparable affinities to the PXXVXL motif of histone H3. The HP1 C-terminal extension enhances the affinity, as does the increasing length of the H3 peptide. The crystal structure of the human HP1γ CSD (CSDγ) in complex with an H3 peptide suggests that recognition of H3 by CSDγ to some extent resembles CSD-PXVXL interaction. Nevertheless, the prolyl residue of the PXXVXL motif appears to play a role distinct from that of Pro in the known HP1β CSD-PXVXL complexes. Lastly, we consequently generalize the historical CSD-PXVXL interaction model and expand the search scope for additional CSD binding partners.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Elongation factor 4 remodels the A-site tRNA on the ribosome

During translation, a plethora of protein factors bind to the ribosome and regulate protein synthesis. Many of those factors are guanosine triphosphatases (GTPases), proteins that catalyze the hydrolysis of guanosine 5'-triphosphate (GTP) to promote conformational changes. Despite numerous studies, the function of elongation factor 4 (EF-4/LepA), a highly conserved translational GTPase, has remained elusive. Here, we present the crystal structure at 2.6-Å resolution of the Thermus thermophilus 70S ribosome bound to EF-4 with a nonhydrolyzable GTP analog and A-, P-, and E-site tRNAs. The structure reveals the interactions of EF-4 with the A-site tRNA, including contacts between the C-terminal domain (CTD) of EF-4 and the acceptor helical stem of the tRNA. Remarkably, EF-4 induces a distortion of the A-site tRNA, allowing it to interact simultaneously with EF-4 and the decoding center of the ribosome. Furthermore, the structure provides insights into the tRNA-remodeling function of EF-4 on the ribosome and suggests that the displacement of the CCA-end of the A-site tRNA away from the peptidyl transferase center (PTC) is functionally significant.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1983

Radar image interpretation techniques applied to sea ice geophysical problems

The geophysical science problems in the sea ice area which at present concern understanding the ice budget, where ice is formed, how thick it grows and where it melts, and the processes which control the interaction of air-sea and ice at the ice margins is discussed. The science problems relate to basic questions of sea ice: how much is there, thickness, drift rate, production rate, determination of the morphology of the ice margin, storms feeling for the ice, storms and influence at the margin to alter the pack, and ocean response to a storm at the margin. Some of these questions are descriptive and some require complex modeling of interactions between the ice, the ocean, the atmosphere and the radiation fields. All involve measurements of the character of the ice pack, and SAR plays a significant role in the measurements.

Carsey, F. D.↗
NASA NTRS1982

Development and application of the GIM code for the Cyber 203 computer

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.

Stainaker, J. F.↗
DOE OSTI2021

Simultaneous Discovery of Positive and Negative Interactions Among Rhizosphere Bacteria Using Microwell Recovery Arrays

Understanding microbe-microbe interactions is critical to predict microbiome function and to construct communities for desired outcomes. Investigation of these interactions poses a significant challenge due to the lack of suitable experimental tools available. Here we present the microwell recovery array (MRA), a new technology platform that screens interactions across a microbiome to uncover higher-order strain combinations that inhibit or promote the function of a focal species. One experimental trial generates 10 4 microbial communities that contain the focal species and a distinct random sample of uncharacterized cells from plant rhizosphere. Cells are sequentially recovered from individual wells that display highest or lowest levels of focal species growth using a high-resolution photopolymer extraction system. Interacting species are then identified and putative interactions are validated. Using this approach, we screen the poplar rhizosphere for strains affecting the growth of Pantoea sp. YR343, a plant growth promoting bacteria isolated from Populus deltoides rhizosphere. In one screen, we montiored 3,600 microwells within the array to uncover multiple antagonistic Stenotrophomonas strains and a set of Enterobacter strains that promoted YR343 growth. The later demonstrates the unique ability of the platform to discover multi-membered consortia that generate emergent outcomes, thereby expanding the range of phenotypes that can be characterized from microbiomes. This knowledge will aid in the development of consortia for Populus production, while the platform offers a new approach for screening and discovery of microbial interactions, applicable to any microbiome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Dynamic interactions at the mineral–organic matter interface

Minerals are widely assumed to protect organic matter (OM) from degradation in the environment, promoting the persistence of carbon in soil and sediments. In this Review, we describe the mechanisms and processes operating at the mineral–organic interface as they relate to OM transformation dynamics. A broad set of interactions occur, with minerals adsorbing organic compounds to their surfaces and/or acting as catalysts for organic reactions. Minerals can serve as redox partners for OM through direct electron transfer or by generating reactive oxygen species, which then oxidize OM. Finally, the compartmentalization of soil and sediment by minerals creates unique microsites that host diverse microbial communities. Acknowledgement of this multiplicity of interactions suggests that the general assumption that the mineral matrix provides a protective function for OM is overly simplistic. Future work must recognize adsorption as a condition for further reactions instead of as a final destination for organic adsorbates, and should consider the spatial and functional complexity that is characteristic of the environments where mineral–OM interactions are observed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Nitrogen addition alters soil fungal communities, but root fungal communities are resistant to change

Plants are colonized by numerous microorganisms serving important symbiotic functions that are vital to plant growth and success. Understanding and harnessing these interactions will be useful in both managed and natural ecosystems faced with global change, but it is still unclear how variation in environmental conditions and soils influence the trajectory of these interactions. In this study, we examine how nitrogen addition alters plant-fungal interactions within two species of Populus - Populus deltoides and P. trichocarpa. In this experiment, we manipulated plant host, starting soil (native vs. away for each tree species), and nitrogen addition in a fully factorial replicated design. After ~10 weeks of growth, we destructively harvested the plants and characterized plant growth factors and the soil and root endosphere fungal communities using targeted amplicon sequencing of the ITS2 gene region. Overall, we found nitrogen addition altered plant growth factors, e.g., plant height, chlorophyll density, and plant N content. Interestingly, nitrogen addition resulted in a lower fungal alpha diversity in soils but not plant roots. Further, there was an interactive effect of tree species, soil origin, and nitrogen addition on soil fungal community composition. Starting soils collected from Oregon and West Virginia were dominated by the ectomycorrhizal fungi Inocybe (55.8% relative abundance), but interestingly when P. deltoides was grown in its native West Virginia soil, the roots selected for a high abundance of the arbuscular mycorrhizal fungi, Rhizophagus. These results highlight the importance of soil origin and plant species on establishing plant-fungal interactions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Effect of Composition and Local Environment on CO 2 Adsorption on Nickel and Magnesium Oxide Solid Solutions

CO 2 adsorption energies on the (100) surfaces of a nickel oxide doped with Mg, magnesium oxide doped with Ni, and their 50:50 solid solution were calculated using density functional theory. The composition and atomic arrangement of the adsorption site was varied to understand how the local environment affects CO 2 adsorption and the basicity of the surfaces at the atomic level. The dispersive and electronic contributions to the adsorption energies were quantified, and the results indicate that the variation of the adsorption energy with adsorption site configuration and metal composition is dominated by electronic interactions. Interestingly, for magnesium oxide doped with nickel, a single substitution can create stronger CO 2 binding sites, which implies stronger basic sites, even though nickel oxide is less basic than magnesium oxide. The effect of double substitution at the binding site can be reasonably approximated by summing the effects of single substitutions. Furthermore, this work provides guidance for the preparation of metal oxides with tailored Lewis basicity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1988

Frontogenesis over a mountain ridge

The interaction of developing two-dimensional cold and warm frontal systems with a mesoscale mountain ridge is examined. The basic equations and a scale analysis which isolates the parameters that describe the flow are discussed, and the governing equations and techniques used to solve the problem are presented. Frontal development in the absence of topography and features of the steady mountain flow field are considered. Model results are presented on the interaction of cold and warm fronts with topography.

Zehnder, Joseph A.↗