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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Temporal Dynamics of DNA Methylation Patterns in Response to Rearing Juvenile Steelhead (Oncorhynchus mykiss) in a Hatchery versus Simulated Stream Environment

Genetic selection is often implicated as the underlying cause of heritable phenotypic differences between hatchery and wild populations of steelhead trout (Oncorhynchus mykiss) that also differ in lifetime fitness. Developmental plasticity, which can also affect fitness, may be mediated by epigenetic mechanisms such as DNA methylation. Our previous study identified significant differences in DNA methylation between adult hatchery- and natural-origin steelhead from the same population that could not be distinguished by DNA sequence variation. In the current study, we tested whether hatchery-rearing conditions can influence patterns of DNA methylation in steelhead with known genetic backgrounds, and assessed the stability of these changes over time. Eyed-embryos from 22 families of Methow River steelhead were split across traditional hatchery tanks or a simulated stream-rearing environment for 8 months, followed by a second year in a common hatchery tank environment. Family assignments were made using a genetic parentage analysis to account for relatedness among individuals. DNA methylation patterns were examined in the liver, a relatively homogeneous organ that regulates metabolic processes and somatic growth, of juveniles at two time points: after eight months of rearing in either a tank or stream environment and after a subsequent year of rearing in a common tank environment. Further, we analyzed DNA methylation in the sperm of mature 2-year-old males from the earlier described treatments to assess the potential of environmentally-induced changes to be passed to offspring. Hepatic DNA methylation changes in response to hatchery versus stream-rearing in yearling fish were substantial, but few persisted after a second year in the tank environment. However, the early rearing environment appeared to affect how fish responded to developmental and environmental signals during the second year since novel DNA methylation differences were identified in the livers of hatchery versus stream-reared fish after a year of common tank rearing. Furthermore, we found profound differences in DNA methylation due to age, irrespective of rearing treatment. This could be due to smoltification associated changes in liver physiology after the second year of rearing. Although few rearing-treatment effects were observed in the sperm methylome, strong family effects were observed. These data suggest limited potential for intergenerational changes, but highlight the importance of understanding the effects of kinship among studied individuals in order to properly analyze and interpret DNA methylation data in natural populations. Our work is the first to study family effects and temporal dynamics of DNA methylation patterns in response to hatchery-rearing.

Gavery, Mackenzie R. (ORCID:0000000150103399)↗
DOE OSTI2023

Mutations in the Second Alternative Oxidase Gene: A New Approach to Group Aspergillus niger Strains

Alternative oxidase is a terminal oxidase in the branched mitochondrial electron transport chain of most fungi including Aspergillus niger (subgenus Circumdati, section Nigri). A second, paralogous aox gene (aoxB) is extant in some A. niger isolates but also present in two divergent species of the subgenus Nidulantes—A. calidoustus and A. implicatus—as well as in Penicillium swiecickii. Black aspergilli are cosmopolitan opportunistic fungi that can cause diverse mycoses and acute aspergillosis in immunocompromised individuals. Amongst the approximately 75 genome-sequenced A. niger strains, aoxB features considerable sequence variation. Five mutations were identified that rationally affect transcription or function or terminally modify the gene product. One mutant allele that occurs in CBS 513.88 and A. niger neotype strain CBS 554.65 involves a chromosomal deletion that removes exon 1 and intron 1 from aoxB. Another aoxB allele results from retrotransposon integration. Three other alleles result from point mutations: a missense mutation of the start codon, a frameshift, and a nonsense mutation. A. niger strain ATCC 1015 has a full-length aoxB gene. The A. niger sensu stricto complex can thus be subdivided into six taxa according to extant aoxB allele, which may facilitate rapid and accurate identification of individual species

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Systematic identification of cis -regulatory variants that cause gene expression differences in a yeast cross

Sequence variation in regulatory DNA alters gene expression and shapes genetically complex traits. However, the identification of individual, causal regulatory variants is challenging. Here, we used a massively parallel reporter assay to measure the cis-regulatory consequences of 5832 natural DNA variants in the promoters of 2503 genes in the yeast Saccharomyces cerevisiae. We identified 451 causal variants, which underlie genetic loci known to affect gene expression. Several promoters harbored multiple causal variants. In five promoters, pairs of variants showed non-additive, epistatic interactions. Causal variants were enriched at conserved nucleotides, tended to have low derived allele frequency, and were depleted from promoters of essential genes, which is consistent with the action of negative selection. Causal variants were also enriched for alterations in transcription factor binding sites. Models integrating these features provided modest, but statistically significant, ability to predict causal variants. This work revealed a complex molecular basis for cis-acting regulatory variation.

60 APPLIED LIFE SCIENCES↗
NASA NTRS1977

Static behavior and the effects of thermal cycling in hybrid laminates

Static stiffness, strength and ultimate strain after thermal cycling were investigated for graphite/Kevlar 49/epoxy and graphite/S-glass/epoxy angle-ply laminates. Tensile stress-strain curves to failure and uniaxial tensile properties were determined, and theoretical predictions of modulus, Poisson's ratio and ultimate strain, based on linear lamination theory, constituent ply properties and measured strength, were made. No significant influence on tensile stress properties due to stacking sequence variations was observed. In general, specimens containing two 0-degree Kevlar or S-glass plies were found to behave linearly to failure, while specimens containing 4 0-degree Kevlar or S-glass plies showed some nonlinear behavior.

Liber, T. M.↗
NASA NTRS1978

Premix fuels study applicable to duct burner conditions for a variable cycle engine

Emission levels and performance of a premixing Jet-A/air duct burner were measured at reference conditions representative of take-off and cruise for a variable cycle engine. In a parametric variation sequence of tests, data were obtained at inlet temperatures of 400, 500 and 600K at equivalence ratios varying from 0.9 to the lean stability limit. Ignition was achieved at all the reference conditions although the CO levels were very high. Significant nonuniformity across the combustor was observed for the emissions at the take-off condition. At a reference Mach number of 0.117 and an inlet temperature of 600K, corresponding to a simulated cruise condition, the NOx emission level was approximately 1 gm/kg-fuel.

Venkataramani, K. S.↗
NASA NTRS1993

Damage tolerance of pressurized graphite/epoxy tape cylinders under uniaxial and biaxial loading

The damage tolerance behavior of internally pressurized, axially slit, graphite/epoxy tape cylinders was investigated. Specifically, the effects of axial stress, structural anisotropy, and subcritical damage were considered. In addition, the limitations of a methodology which uses coupon fracture data to predict cylinder failure were explored. This predictive methodology was previously shown to be valid for quasi-isotropic fabric and tape cylinders but invalid for structurally anisotropic (+/-45/90)(sub s) and (+/-45/0)(sub s) cylinders. The effects of axial stress and structural anisotropy were assessed by testing tape cylinders with (90/0/+/-45)(sub s), (+/-45/90)(sub s), and (+/-45/0)(sub s) layups in a uniaxial test apparatus, specially designed and built for this work, and comparing the results to previous tests conducted in biaxial loading. Structural anisotropy effects were also investigated by testing cylinders with the quasi-isotropic (0/+/-45/90)(sub s) layup which is a stacking sequence variation of the previously tested (90/0/+/-45)(sub s) layup with higher D(sub 16) and D(sub 26) terms but comparable D(sub 16) and D(sub 26) to D(sub 11) ratios. All cylinders tested and used for comparison are made from AS4/3501-6 graphite/epoxy tape and have a diameter of 305 mm. Cylinder slit lengths range from 12.7 to 50.8 mm. Failure pressures are lower for the uniaxially loaded cylinders in all cases. The smallest percent failure pressure decreases are observed for the (+/-45/90)(sub s) cylinders, while the greatest such decreases are observed for the (+/-45/0)(sub s) cylinders. The relative effects of the axial stress on the cylinder failure pressures do not correlate with the degree of structural coupling. The predictive methodology is not applicable for uniaxially loaded (+/-45/90)(sub s) and (+/-45/0)(sub s) cylinders, may be applicable for uniaxially loaded (90/0/+/-45)(sub s) cylinders, and is applicable for the biaxially loaded (90/0/+/-45)(sub s) and (0/+/-45/90)(sub s) cylinders. This indicates that the ratios of D(sub 16) and D(sub 26) to D(sub 11), as opposed to the absolute magnitudes of D(sub 16) and D(sub 26), may be important in the failure of these cylinders and in the applicability of the methodology. Discontinuities observed in the slit tip hoop strains for all the cylinders tested indicate that subcritical damage can play an important role in the failure of tape cylinders. This role varies with layup and loading condition and is likely coupled to the effects of structural anisotropy. Biaxial failure pressures may exceed the uniaxial values because the axial stress contributes to the formation of 0 deg ply splitting (accompanied by delamination) or similar stress-mitigating subcritical damage. The failure behavior of similar cylinders can also vary as a result of differences in the role of subcritical damage as observed for the case of a biaxially loaded (90/0/+/-45)(sub s) cylinder with a 12.7 mm slit. For this case, the methodology is valid when the initial coupon and cylinder fracture modes agree. However, the methodology underpredicts the failure pressure of the cylinder when a circumferential fracture path, suggestive of a 0 deg ply split, occurs at one slit tip. Thus, the failure behavior of some tape cylinders may be highly sensitive to the initial subcritical damage mechanism. Finite element analyses are recommended to determine how structural anisotropy and axial stress modify the slit tip stress states in cylinders from those found in flat plates since similarity of these stress states is a fundamental assumption of the current predictive methodology.

Priest, Stacy Marie↗
NASA NTRS1999

Molecular evidence of simian virus 40 infections in children

Recent studies have detected simian virus 40 (SV40) DNA in certain human tumors and normal tissues. The significance of human infections by SV40, which was first discovered as a contaminant of poliovirus vaccines used between 1955 and 1963, remains unknown. The occurrence of SV40 infections in unselected hospitalized children was evaluated. Polymerase chain reaction and DNA sequence analyses were done on archival tissue specimens from patients positive for SV40 neutralizing antibody. SV40 DNA was identified in samples from 4 of 20 children (1 Wilms' tumor, 3 transplanted kidney samples). Sequence variation among SV40 regulatory regions ruled out laboratory contamination of specimens. This study shows the presence of SV40 infections in pediatric patients born after 1982.

Non-NASA Center↗
NASA NTRS2013

Characterization of Microbial Communities Found in Bioreactor Effluent

The purpose of this investigation was to examine microbial communities of simulated wastewater effluent from hollow fiber membrane bioreactors collected from the Space Life Science Laboratory and Texas Technical University. Microbes were characterized using quantitative polymerase chain reaction where a total count of bacteria and fungi were determined. The primers that were used to determine the total count of bacteria and fungi were targeted for 16S rDNA genes and the internal transcribed spacer, respectively. PCR products were detected with SYBR Green I fluorescent dye and a melting curve analysis was performed to identify unique melt profiles resulting from DNA sequence variations from each species of the community. Results from both the total bacteria and total fungi count assays showed that distinct populations were present in isolates from these bioreactors. This was exhibited by variation in the number of peaks observed on the melting curve analysis graph. Further analysis of these results using species-specific primers will shed light on exactly which microbes are present in these effluents. Information gained from this study will enable the design of a system that can efficiently monitor microbes that play a role in the biogeochemical cycling of nitrogen in wastewater on the International Space Station to assist in the design of a sustainable system capable of converting this nutrient.

Flowe, Candice↗
NASA NTRS1992

Magnetic susceptibility variations in Loess sequences and their relationship to astronomical forcing

The long, well-exposed and often continuous sequences of loess found throughout the world are generally thought to provide an excellent opportunity for studying long-term, large-scale environmental change during the last few million years. In recent years, the most fruitful loess studies have been those involving the deposits of the loess in China. One of the most intriguing results of that work has been the discovery of an apparent correlation between variations in the magnetic susceptibility of the loess sequence and the oxygen isotope record of the deep sea. This correlation implies that magnetic susceptibility variations are being driven by astronomical parameters. However, the basic data have been interpreted in various ways by different authors, most of whom assumed that the magnetic minerals in the loess have not been affected by post-depositional processes. Using a chemical extraction procedure that allows us to separate the contribution of secondary pedogenic magnetic minerals from primary inherited magnetic minerals, we have found that the magnetic susceptibility of the Chinese paleosols is largely due to a pedogenic component which is present to a lesser degree in the loess. We have also found that the smaller inherited component of the magnetic susceptibility is about the same in the paleosols and the loess. These results demonstrate the need for additional study of the processes that create magnetic susceptibility variations in order to interpret properly the role of astronomical forcing in producing these variations.

Verosub, Kenneth L.↗
DOE OSTI2018

Investigation of inter- and intraspecies variation through genome sequencing of Aspergillus section Nigri

Aspergillus section Nigri comprises filamentous fungi relevant to biomedicine, bioenergy, health, and biotechnology. In order to learn more about fungal speciation, as well as potential for applications in biotechnology and biomedicine, we sequenced 23 genomes de novo, forming a full genome compendium for the section (26 species), as well as six A. niger isolates. This allowed us to quantify both inter- and intra-species genomic variation. We further predicted 17,903 CAZymes and 2,717 secondary metabolite gene clusters, which we condensed into 455 distinct families corresponding to compound classes, 49% of which are only found in single species. We performed metabolomics and genetic engineering to correlate genotypes to phenotypes, as demonstrated for the metabolite aurasperone, and by heterologous transfer of citrate production to A. nidulans. Experimental and computational analyses all supported a role in speciation for secondary metabolism and regulators and allowed us to propose a three-step model for fungal speciation.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1985

Stellar activity cycles

The variety of stellar chromospheric and coronal activity provides a framework for understanding solar and stellar magnetic activity. It is pointed out that the recognition of an 11-yr periodicity within the record of sunspot numbers is a relatively recent discovery of just over a century ago. The solar activity cycle is examined, taking into account the sunspot cycle, and solar dynamo models. Time-averaged stellar chromospheric activity levels are considered along with long-term activity fluctuations of cool stars. Attention is given to the direct measurement of stellar magnetic fields, solar luminosity variations, the RS Canum Venaticorum and BY Draconis variables, continuum variations in lower main sequence stars, chromospheric variations in lower main sequence stars, and chromospheric variations in evolved stars.

Baliunas, S. L.↗
NASA NTRS1995

Chromospheric variations in main-sequence stars

The fluxes in passbands 0.1 nm wide and centered on the Ca II H and K emission cores have been monitored in 111 stars of spectral type F2-M2 on or near the main sequence in a continuation of an observing program started by O. C. Wilson. Most of the measurements began in 1966, with observations scheduled monthly until 1980, when observations were schedueld sevral times per week. The records, with a long-term precision of about 1.5%, display fluctuations that can be idntified with variations on timescales similar to the 11 yr cycle of solar activity as well as axial rotation, and the growth and decay of emitting regions. We present the records of chromospheric emission and general conclusions about variations in surface magnetic activity on timescales greater than 1 yr but less than a few decades. The results for stars of spectral type G0-K5 V indicate a pattern of change in rotation and chromospheric activity on an evolutionary timescale, in which (1) young stars exhibit high average levels of activity, rapid rotation rates, no Maunder minimum phase and rarely display a smooth, cyclic variation; (2) stars of intermediate age (approximately 1-2 Gyr for 1 solar mass) have moderate levels of activity and rotation rates, and occasional smooth cycles; and (3) stars as old as the Sun and older have slower rotation rates, lower activity levels and smooth cycles with occasional Maunder minimum-phases.

Baliunas, S. L.↗
DOE OSTI2025

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Data for "Design of Diverse, Functional Mitochondrial Targeting Sequences Across Eukaryotic Organisms Using Variational Autoencoder"

Mitochondria play a key role in energy production and metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we leverage a Variational Autoencoder to design novel mitochondrial targeting sequences. In silico analysis reveals that a high fraction of the generated peptides (90.14%) are functional and possess features important for mitochondrial targeting. We characterize artificial peptides in four eukaryotic organisms and, as a proof-of-concept, demonstrate their utility in increasing 3-hydroxypropionic acid titers through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Moreover, we employ latent space interpolation to shed light on the evolutionary origins of dual-targeting sequences. Overall, our work demonstrates the potential of generative artificial intelligence for both fundamental research and practical applications in mitochondrial biology.

AI/ML↗
DOE OSTI2020

Organic amendments change soil organic C structure and microbial community but not total organic matter on sub-decadal scales

Organic C has many benefits for soil, but it is depleted by tillage and crop harvest, and especially so for biofuel crops. Accordingly, strategies such as partially retaining stover or planting a cover crop can help ameliorate the negative effect of C removal. We used a long-term field experiment to study the impacts of stover retention and planting cover crop on soil organic matter (SOM), its extractable components and the soil microbial community. SOM chemical composition characterization was determined by electrospray ionization (ESI) coupled with Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) in sequential water, methanol (MeOH), and chloroform (CHCl3) extracts. The characteristics of the soil bacterial community were measured by phospholipid fatty acid (PLFA), real-time quantitative PCR, and 16S rRNA gene sequence. The variations in total SOM content, total microbial biomass, and bacterial population were slight among treatments, but SOM chemical compounds, arbuscular mycorrhizal fungi (AMF) biomass, and bacterial structure changed significantly, and especially so in the coupled application of stover retention and cover crop. Specifically, stover retention enriched more lignin-like compounds in soil, whereas cover crop enriched more condensed hydrocarbons, and had more compounds with an aromaticity index (AI) >0.5. The bacterial community was not altered by the cover crop, but the corn stover retention increased the relative abundances of Myxococcales (Deltaproteobacteria) and decreased that of Actinobacteria. Redundancy analysis (RDA) further unveiled that the bacterial community in the stover treatments had significantly positive association with CHCl3-extracted chemical classes, i.e. unsaturated hydrocarbon and lipid with the coupled application (stover and cover crop), and lignin and protein with the single corn stover treatment. Taken together, our study shows how different C addition practices influence the molecular composition of SOM and the structure of soil microbial communities.

Xu, Jiangbin↗
DOE OSTI2020

Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)

Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Data-driven prediction of geometry- and toolpath sequence-dependent intra-layer process conditions variations in laser powder bed fusion

Geometrical features and toolpath sequence are two important factors that cause process condition variations, such as variations in the meltpool temperature or meltpool size, that might lead to undesired material properties in the laser powder bed fusion (LPBF) process. Due to the high dynamics and complex physics of the LPBF process, it is difficult to predict variations in process conditions with simulations alone. Advances in measurement technology and computational technologies open up new possibilities for smart manufacturing. In this paper, a data-driven method to predict intra-layer variations in the processing conditions that source from the toolpath sequence and part geometry is presented. The approach is demonstrated using two-color on-axis pyrometer measurements. Three demonstration cases are presented in which it is demonstrated (1) how the trained predictive model can be used as a filter to ease the interpretation of process variations and discover patterns related to toolpath and part geometry, and (2) how to generate predictions that can be used for feedforward control, i.e., for adjusting laser power or scanning speed along the toolpath using a meltpool temperature prediction model generated based on on-axis measurements. Results show that the developed prediction model is able to meaningfully predict process variations resulted from toolpath sequence and geometry. Predictions are aligned with the results from the related work of others and for the case of 180° laser path turnarounds in our high-speed X-ray imaging experiments. In conclusion, the potential issues related to the current maturity status of the process and measuring equipment that could in practice affect the performance of the proposed solutions are also discussed.

42 ENGINEERING↗
NASA NTRS1991

LinkFinder: An expert system that constructs phylogenic trees

An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

Inglehart, James↗