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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 811 records · Page 45
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Whole-organism 3D quantitative characterization of zebrafish melanin by silver deposition micro-CT

We previously described X-ray histotomography, a high-resolution, non-destructive form of X-ray microtomography (micro-CT) imaging customized for three-dimensional (3D), digital histology, allowing quantitative, volumetric tissue and organismal phenotyping (Ding et al., 2019). Here, we have combined micro-CT with a novel application of ionic silver staining to characterize melanin distribution in whole zebrafish larvae. The resulting images enabled whole-body, computational analyses of regional melanin content and morphology. Normalized micro-CT reconstructions of silver-stained fish consistently reproduced pigment patterns seen by light microscopy, and further allowed direct quantitative comparisons of melanin content across wild-type and mutant samples, including subtle phenotypes not previously noticed. Silver staining of melanin for micro-CT provides proof-of-principle for whole-body, 3D computational phenomic analysis of a specific cell type at cellular resolution, with potential applications in other model organisms and melanocytic neoplasms. Advances such as this in whole-organism, high-resolution phenotyping provide superior context for studying the phenotypic effects of genetic, disease, and environmental variables.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1972

Concepts related to the origin of the genetic apparatus.

Since the genetic apparatus is composed of nucleic acid and protein, the origin of the apparatus involves the origin of polyaminoacids and of polynucleotides, separately or together. Laboratory models for the origins of the separate macromolecular types are considered. The origin of their joint synthesis, believed to have been necessary at a later stage, is also discussed. Proteins and nucleic acids appear to have definite relationships with each other in three major contemporary biological systems, including chromatin, ribosomes, and the protein synthesizing system using nucleic acid templates. Stages considered in connection with the flow of information in the early evolution of the apparatus are environment, protoprotein, protein, RNA, and DNA.

Lacey, J. C., Jr.↗
NASA NTRS2000

A Parallel Approach To Optimum Actuator Selection With a Genetic Algorithm

Recent discoveries in smart technologies have created a variety of aerodynamic actuators which have great potential to enable entirely new approaches to aerospace vehicle flight control. For a revolutionary concept such as a seamless aircraft with no moving control surfaces, there is a large set of candidate locations for placing actuators, resulting in a substantially larger number of combinations to examine in order to find an optimum placement satisfying the mission requirements. The placement of actuators on a wing determines the control effectiveness of the airplane. One approach to placement Maximizes the moments about the pitch, roll, and yaw axes, while minimizing the coupling. Genetic algorithms have been instrumental in achieving good solutions to discrete optimization problems, such as the actuator placement problem. As a proof of concept, a genetic has been developed to find the minimum number of actuators required to provide uncoupled pitch, roll, and yaw control for a simplified, untapered, unswept wing model. To find the optimum placement by searching all possible combinations would require 1,100 hours. Formulating the problem and as a multi-objective problem and modifying it to take advantage of the parallel processing capabilities of a multi-processor computer, reduces the optimization time to 22 hours.

Rogers, James L.↗
NASA NTRS2004

On the Use of CAD and Cartesian Methods for Aerodynamic Optimization

The objective for this paper is to present the development of an optimization capability for Curt3D, a Cartesian inviscid-flow analysis package. We present the construction of a new optimization framework and we focus on the following issues: 1) Component-based geometry parameterization approach using parametric-CAD models and CAPRI. A novel geometry server is introduced that addresses the issue of parallel efficiency while only sparingly consuming CAD resources; 2) The use of genetic and gradient-based algorithms for three-dimensional aerodynamic design problems. The influence of noise on the optimization methods is studied. Our goal is to create a responsive and automated framework that efficiently identifies design modifications that result in substantial performance improvements. In addition, we examine the architectural issues associated with the deployment of a CAD-based approach in a heterogeneous parallel computing environment that contains both CAD workstations and dedicated compute engines. We demonstrate the effectiveness of the framework for a design problem that features topology changes and complex geometry.

Nemec, M.↗
NASA NTRS2006

Development of Standardized Lunar Regolith Simulant Materials

Lunar exploration requires scientific and engineering studies using standardized testing procedures that ultimately support flight certification of technologies and hardware. It is necessary to anticipate the range of source materials and environmental constraints that are expected on the Moon and Mars, and to evaluate in-situ resource utilization (ISRU) coupled with testing and development. We describe here the development of standardized lunar regolith simulant (SLRS) materials that are traceable inter-laboratory standards for testing and technology development. These SLRS materials must simulate the lunar regolith in terms of physical, chemical, and mineralogical properties. A summary of these issues is contained in the 2005 Workshop on Lunar Regolith Simulant Materials [l]. Lunar mare basalt simulants MLS-1 and JSC-1 were developed in the late 1980s. MLS-1 approximates an Apollo 11 high-Ti basalt, and was produced by milling of a holocrystalline, coarse-grained intrusive gabbro (Fig. 1). JSC-1 approximates an Apollo 14 basalt with a relatively low-Ti content, and was obtained from a glassy volcanic ash (Fig. 2). Supplies of MLS-1 and JSC-1 have been exhausted and these materials are no longer available. No highland anorthosite simulant was previously developed. Upcoming lunar polar missions thus require the identification, assessment, and development of both mare and highland simulants. A lunar regolith simulant is manufactured from terrestrial components for the purpose of simulating the physical and chemical properties of the lunar regolith. Significant challenges exist in the identification of appropriate terrestrial source materials. Lunar materials formed under comparatively reducing conditions in the absence of water, and were modified by meteorite impact events. Terrestrial materials formed under more oxidizing conditions with significantly greater access to water, and were modified by a wide range of weathering processes. The composition space of lunar materials can be modeled by mixing programs utilizing a low-Ti basalt, ilmenite, KREEP component, high-Ca anorthosite, and meteoritic components. This approach has been used for genetic studies of lunar samples via chemical and modal analysis. A reduced composition space may be appropriate for simulant development, but it is necessary to determine the controlling properties that affect the physical, chemical and mineralogical components of the simulant.

Carpenter, P.↗
NASA NTRS2002

Development of Three-Dimensional Multicellular Tissue-Like Constructs for Mutational Analysis Using Macroporous Microcarriers

A three-dimensional (3-D), tissue-like model was developed for the genotoxic assessment of space environment. In previous experiments, we found that culturing mammalian cells in a NASA-designed bioreactor, using Cytodex-3 beads as a scaffold, generated 3-D multicellular spheroids. In an effort to generate scaffold-free spheroids, we developed a new 3-D tissue-like model by coculturing fibroblast and epithelial cell in a NASA bioreactor using macroporous Cultispher-S(TradeMark) microcarriers. Big Blue(Registered Trademark) Rat 2(Lambda) fibroblasts, genetically engineered to contain multiple copies (>60 copies/cell) of the Lac I target gene, were cocultured with radio-sensitive human epithelial cells, H184F5. Over an 8-day period, samples were periodically examined by microscopy and histology to confirm cell attachment, growth, and viability. Immunohistochemistry and western analysis were used to evaluate the expression of specific cytoskeletal and adhesion proteins. Key cell culture parameters (glucose, pH, and lactate concentrations) were monitored daily. Controls were two-dimensional mono layers of fibroblast or epithelial cells cultured in T-flasks. Analysis of 3-D spheroids from the bioreactor suggests fibroblast cells attached to and completely covered the bead surface and inner channels by day 3 in the bioreactor. Treatment of the 3-day spheroids with dispase II dissolved the Cultisphers(TradeMark) and produced multicellular, bead-less constructs. Immunohistochemistry confirmed the presence of vi.mentin, cytokeratin and E-cadherin in treated spheroids. Examination of the dispase II treated spheroids with transmission electron microscopy (TEM) also showed the presence of desmosomes. These results suggest that the controlled enzymatic degradation of an artificial matrix in the low shear environment of the NASA-designed bioreactor can produce 3-D tissue-like spheroids. 2

Jordan, Jacqueline A.↗
DOE OSTI2024

Modeling plasticity-mediated void growth at the single crystal scale: A physics-informed machine learning approach

Modeling the evolution of voids during plastic flow as well as their effects on plastic dissipation is critical for both component manufacturing and lifetime estimation purposes. To this end, we propose a rate-dependent constitutive model to homogenize the effects of semi-randomly distributed voids on single crystal plasticity whilst capturing void interaction and plastic anisotropy. Here, this present work focuses on the case of face centered cubic crystals to introduce an anisotropic gauge function applicable within the crystal plasticity formalism. The approach combines analytical methods to describe the micromechanics of the system in combination with symbolic regression to capture analytically intractable mechanisms from data. The hybrid framework uses a physics-informed genetic programming-based symbolic regression algorithm to solve a multiform optimization problem simultaneously producing a new gauge function and a new strain rate equation. This is also a multi-objective optimization problem with many competing objectives. A new search and selection step is introduced to the genetic algorithm that promotes convergence toward a global solution that better satisfies all the objectives. Overall, the symbolic equations produced leverage data-driven methods to achieve greater accuracy than comparable alternatives on an analytically intractable problem while maintaining model transparency.

36 MATERIALS SCIENCE↗
DOE OSTI2023

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Characterization of Caenorhabditis elegans sphingomyelin synthases through heterologous expression

Sphingomyelin (SM) is a major component of mammalian cell membranes and particularly abundant in the myelin sheath that surrounds nerve fibers. Its production is catalyzed by SM synthases SMS1 and SMS2, which interconvert phosphatidylcholine and ceramide to diacylglycerol and SM in the Golgi and at the plasma membrane, respectively. As the lipids participating in this reaction fulfill both structural and signaling functions, SMS enzymes have considerable potential to influence diverse important cellular processes. The nematode Caenorhabditis elegans is an attractive model for studying both animal development and human disease. The organism contains five SMS homologues but none of these have been characterized in any detail. Here, we carried out the first systematic analysis of SMS family members in C. elegans . Using heterologous expression systems, genetic ablation, metabolic labeling and lipidome analyses, we show that C. elegans harbors at least three distinct SM synthases and one ceramide phosphoethanolamine (CPE) synthase. Moreover, C. elegans SMS family members have partially overlapping but also unique sub-cellular distributions and together occupy all principal compartments of the secretory pathway. Our findings shed light on crucial aspects of sphingolipid metabolism in a valuable animal model and opens avenues for exploring the role of SM and its metabolic intermediates in organismal development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

High-throughput genetic engineering of nonmodel and undomesticated bacteria via iterative site-specific genome integration

Efficient genome engineering is critical to understand and use microbial functions. Despite recent development of tools such as CRISPR-Cas gene editing, efficient integration of exogenous DNA with well-characterized functions remains limited to model bacteria. Here, we describe serine recombinase–assisted genome engineering, or SAGE, an easy-to-use, highly efficient, and extensible technology that enables selection marker–free, site-specific genome integration of up to 10 DNA constructs, often with efficiency on par with or superior to replicating plasmids. SAGE uses no replicating plasmids and thus lacks the host range limitations of other genome engineering technologies. We demonstrate the value of SAGE by characterizing genome integration efficiency in five bacteria that span multiple taxonomy groups and biotechnology applications and by identifying more than 95 heterologous promoters in each host with consistent transcription across environmental and genetic contexts. We anticipate that SAGE will rapidly expand the number of industrial and environmental bacteria compatible with high-throughput genetics and synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The genotype-phenotype landscape of an allosteric protein

Allostery is a fundamental biophysical mechanism that underlies cellular sensing, signaling, and metabolism. Yet a quantitative understanding of allosteric genotype-phenotype relationships remains elusive. Here, we report the large-scale measurement of the genotype-phenotype landscape for an allosteric protein: the lac repressor from Escherichia coli , LacI. Using a method that combines long-read and short-read DNA sequencing, we quantitatively measure the dose-response curves for nearly 10 5 variants of the LacI genetic sensor. The resulting data provide a quantitative map of the effect of amino acid substitutions on LacI allostery and reveal systematic sequence-structure-function relationships. We find that in many cases, allosteric phenotypes can be quantitatively predicted with additive or neural-network models, but unpredictable changes also occur. For example, we were surprised to discover a new band-stop phenotype that challenges conventional models of allostery and that emerges from combinations of nearly silent amino acid substitutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The impact of long-range dispersal on gene surfing

Range expansions lead to distinctive patterns of genetic variation in populations, even in the absence of selection. These patterns and their genetic consequences have been well studied for populations advancing through successive short-ranged migration events. However, most populations harbor some degree of long-range dispersal, experiencing rare yet consequential migration events over arbitrarily long distances. Although dispersal is known to strongly affect spatial genetic structure during range expansions, the resulting patterns and their impact on neutral diversity remain poorly understood. Here, we systematically study the consequences of long-range dispersal on patterns of neutral variation during range expansion in a class of dispersal models which spans the extremes of local (effectively short-ranged) and global (effectively well-mixed) migration. We find that sufficiently long-ranged dispersal leaves behind a mosaic of monoallelic patches, whose number and size are highly sensitive to the distribution of dispersal distances. We develop a coarse-grained model which connects statistical features of these spatial patterns to the evolution of neutral diversity during the range expansion. We show that growth mechanisms that appear qualitatively similar can engender vastly different outcomes for diversity: Depending on the tail of the dispersal distance distribution, diversity can be either preserved (i.e., many variants survive) or lost (i.e., one variant dominates) at long times. Our results highlight the impact of spatial and migratory structure on genetic variation during processes as varied as range expansions, species invasions, epidemics, and the spread of beneficial mutations in established populations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection

The United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response. We identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions. The NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Neuromuscular Junction Model Optimized for Electrical Platforms

Neuromuscular junctions (NMJs), specialized synapses between motor neurons and muscle fibers, are essential for muscle activity. A simple and reproducible cell-based in vitro NMJ platform is needed to test the impact of chemicals on the neuron-muscle communication. Our platform utilizes genetically modified neurons and muscle cells, optimized culture conditions, and commercially available multielectrode array system for recording action potentials. Neuronal cells (NSC34) were optogenetically modified with channelrhodopsin chimera to allow for simultaneous, light-mediated, millisecond-precise activation of neuronal population. This signal is propagated through functional synapses to the muscle fibers. Muscle cells (C2C12) were modified by incorporating gap junction protein (Connexin-43) to improve intracellular communication without affecting muscle differentiation. This communication between muscle fibers resulted in better signal propagation and signal strength. Optimized culture medium facilitated the growth and differentiation of both cell types together. Our system was validated using vecuronium, a muscle relaxant, which abolished the muscle response. This in vitro model provides a unique tool for establishing a NMJ platform that is easy to record and analyze. Potential applications include nondestructive long-term screening of drugs affecting the NMJ.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Cell-Free Protein Synthesis for High-Throughput Biosynthetic Pathway Prototyping

Biological systems provide a sustainable and complimentary approach to synthesizing useful chemical products. Metabolic engineers seeking to establish economically viable biosynthesis platforms strive to increase product titers, rates, and yields. Despite continued advances in genetic tools and metabolic engineering techniques, cellular workflows remain limited in throughput. It may take months to test dozens of unique pathway designs even in a robust model organism, such as Escherichia coli. In contrast, cell-free protein synthesis enables the rapid generation of enzyme libraries that can be combined to reconstitute metabolic pathways in vitro for biochemical synthesis in days rather than weeks. Cell-free reactions thereby enable comparison of hundreds to thousands of unique combinations of enzyme homologs and concentrations, which can quickly identify the most productive pathway variants to test in vivo or further characterize in vitro. Furthermore, this cell-free pathway prototyping strategy provides a complementary approach to accelerate cellular metabolic engineering efforts toward highly productive strains for metabolite production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Influence of particle size on NIR spectroscopic characterization of sorghum biomass for the biofuel industry

NIR spectroscopy is a rapid and accurate green technology for high-throughput biomass characterization, including sorghum (Sorghum bicolor), a promising energy crop for the biofuel industry. This study assessed the influence of particle size on NIR spectroscopic analysis (wavelength range: 867–2535 nm) of sorghum biomass composition. Grown under field conditions, a total of 113 types of genetically diverse sorghum accessions were dried, ground, and sieved (<250, 250–600, 600–850, and > 850 µm particle size) for developing partial least square regression (PLSR) prediction models for moisture, ash, extractive, glucan, xylan, acid-soluble lignin (ASL), acid-insoluble lignin (AIL), and total lignin (ASL + AIL). Overall, smaller particle sizes provided better model performance, while no single particle size provided the best performance for all the selected components. With only 9 selected bands and 4 latent variables (LVs), the best PLSR model was obtained for moisture with particle size of 600–850 µm with the square root of the coefficient of determination (R) of 0.85, the ratio of prediction to deviation (RPD) of 2.2, and the root mean square error (RMSE) of 0.46 % in external validation. Similar model performances were also obtained for ash, extractive, glucan, and xylan. This study showed that size reduction could effectively improve NIR spectroscopic analysis for lipid-producing sorghum biomass for the biofuel industry.

09 BIOMASS FUELS↗
DOE OSTI2020

A genetic algorithm approach for reconstructing spectral content from filtered x-ray diode array spectrometers

Filtered diode array spectrometers are routinely employed to infer the temporal evolution of spectral power from x-ray sources, but uniquely extracting spectral content from a finite set of broad, spectrally overlapping channel spectral sensitivities is decidedly nontrivial in these under-determined systems. Here, we present the use of genetic algorithms to reconstruct a probabilistic spectral intensity distribution and compare to the traditional approach most commonly found in the literature. Unlike many of the previously published models, spectral reconstructions from this approach are neither limited by basis functional forms nor do they require a priori spectral knowledge. While the original intent of such measurements was to diagnose the temporal evolution of spectral power from quasi-blackbody radiation sources—where the exact details of spectral content were not thought to be crucial—we demonstrate that this new technique can greatly enhance the utility of the diagnostic by providing more physical spectra and improved robustness to hardware configuration for even strongly non-Planckian distributions.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Inferring demographic and selective histories from population genomic data using a 2-step approach in species with coding-sparse genomes: an application to human data

Abstract The demographic history of a population, and the distribution of fitness effects (DFE) of newly arising mutations in functional genomic regions, are fundamental factors dictating both genetic variation and evolutionary trajectories. Although both demographic and DFE inference has been performed extensively in humans, these approaches have generally either been limited to simple demographic models involving a single population, or, where a complex population history has been inferred, without accounting for the potentially confounding effects of selection at linked sites. Taking advantage of the coding-sparse nature of the genome, we propose a 2-step approach in which coalescent simulations are first used to infer a complex multi-population demographic model, utilizing large non-functional regions that are likely free from the effects of background selection. We then use forward-in-time simulations to perform DFE inference in functional regions, conditional on the complex demography inferred and utilizing expected background selection effects in the estimation procedure. Throughout, recombination and mutation rate maps were used to account for the underlying empirical rate heterogeneity across the human genome. Importantly, within this framework it is possible to utilize and fit multiple aspects of the data, and this inference scheme represents a generalized approach for such large-scale inference in species with coding-sparse genomes.

Soni, Vivak (ORCID:0000000294969562)↗