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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 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

A Review of Coccidioides Research, Outstanding Questions in the Field, and Contributions by Women Scientists

Abstract Purpose of Review Coccidioidomycosis is an infectious disease that gained clinical significance in the early 20th century. Many of the foundational contributions to coccidioidomycosis research, including the discovery of the fungal disease agent, Coccidioides spp., were made by women. We review recent progress in Coccidioides research and big questions remaining in the field, while highlighting some of the contributions from women. Recent Findings New molecular-based techniques provide a promising method for detecting Coccidioides, which can help determine the dominate reservoir host and ideal environmental conditions for growth. Genetic and genomic analyses have allowed an understanding of population structure, species level diversity, and evolutionary histories. We present a current, comprehensive genome list, where women contributed many of these entries. Several efforts to develop a coccidioidomycosis vaccine are underway. Summary Women continue to pioneer research on Coccidioides, including the relationships between the fungi and the environment, genetics, and clinical observations. Significant questions remain in the field of Coccidioides, including the main host reservoir, the relationships between genotypic and phenotypic variation, and the underlying cause for chronic clinical coccidioidomycosis cases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Population Structure of White Sturgeon (Acipenser transmontanus) in the Columbia River Inferred from Single-Nucleotide Polymorphisms

White sturgeon (Acipenser transmontanus) are the largest freshwater fish in North America, with reproducing populations in the Sacramento-San Joaquin, Fraser, and Columbia River Basins. Of these, the Columbia River is the largest, but it is also highly fragmented by hydroelectric dams, and many segments are characterized by declining abundance and persistent recruitment failure. Efforts to conserve and supplement these fish requires an understanding of their spatial genetic structure. Here, we assembled a large set of samples from throughout the Columbia River Basin, along with representative collections from adjacent basins, and genotyped them using a panel of 325 single-nucleotide markers. Results from individual- and group-based analyses of these data indicate that white sturgeon in the uppermost Columbia River Basin, in the Kootenai and upper Snake Rivers, are the most distinct, while the remaining populations downstream in the basin can be described as a genetic gradient consistent with an isolation-by-distance effect. Notably, the population in the lowest reaches of the Columbia River is more distinct from the middle or upper reaches than from outside basins, and suggests historically a higher or more recent gene exchange through coastal routes than with populations in the interior Columbia Basin. Nonetheless, proximal reaches were generally only marginally or non-significantly divergent, suggesting that transplanting larvae or juveniles from nearby sources poses relatively little risk of outbreeding depression. Indeed, we inferred examples of dispersal between reaches via close-kin mark-recapture and genetic mark-recapture that indicate movement between nearby reaches is not unusual. Samples from the Kootenai and upper Snake Rivers exhibited notably lower genetic diversity than the remaining samples as a result of population bottlenecks, genetic drift, and/or historical divergence. Conservation actions, such as supplementation, are underway to maintain population viability and will require balanced efforts to increase demographic abundance while maintaining genetic diversity.

Willis, Stuart C.↗
DOE OSTI2024

Parallel Variable Population Multi-Objective Optimizer (pvpmoo) v1.0

This is a parallel variable population multi-objective optimizer with an adaptive unified differential evolution algorithm or a genetic algorithm. It can also be used for single objective optimization. Some features of this code include: 1) The population size varies from generation to generation to save the total # of objective function evaluations. 2) The population is uniformly distributed to a number of parallel processors for simultaneous objective function evaluation. 3) The objective function evaluation can be attained from an external simulation program with control variables in its input file and objectives calculated from its output files. 4) The optimizer includes an adaptive unified differential evolution algorithm and a real value genetic algorithm. The parameters in the unified differential evolution algorithm can be chosen to attain any mutation schemes in the published literature.

Qiang, Ji↗
NASA NTRS2000

Realizing the potential of rapid-cycling Brassica as a model system for use in plant biology research

Rapid-cycling Brassica populations were initially developed as a model for probing the genetic basis of plant disease. Paul Williams and co-workers selected accessions of the six main species for short time to flower and rapid seed maturation. Over multiple generations of breeding and selection, rapid-cycling populations of each of the six species were developed. Because of their close relationship with economically important Brassica species, rapid-cycling Brassica populations, especially those of B. rapa (RCBr) and B. oleracea, have seen wide application in plant and crop physiology investigations. Adding to the popularity of these small, short-lived plants for research applications is their extensive use in K-12 education and outreach.

Review, Tutorial↗
NASA NTRS2019

Nasa GeneLab Computomics Reveal Horizontal Gene Transfer on International Space Station Environmental Metagenomes

Prokaryotic lifeforms can be observed to demonstrate many keen adaptive advantages, perhaps facilitated by a nature simplistic relative to divergent domains of life. In particular, decompartmentalized gene expression facilitates adaptation by allowing free exchange of genetic material, albeit at the cost of increased susceptibility to genetic damage. Thus, these lifeforms must compensate by embracing diverse investment strategies in an attempt to “brute force” the evolvability equation through precipitous genesis, lean metabolic efficiency, and sheer population. This prokaryotic archetype also enables symbiotic relationships with secondary mobile genetic elements known as plasmids, which have been shown to drive evolution on rapid temporal scales through processes such as conjugation and transformation. This study attempts to decipher whether these mechanisms of horizontal gene transfer (HGT) are major factors in determining prokaryote fitness within a unique isolated environment, the International Space Station (ISS). The ISS Microbial Tracking (MT) project has generated a wealth of data concerning the successive reigns of microbial genera that appear to thrive amidst harsh conditions for life. Despite relatively higher doses of ionizing radiation as compared to Earth, complications associated with microgravity, and the anti-microbial mélange deployed, microbial life still persists in this environment. The NASA GeneLab serves as a data repository and analysis platform to enable researchers to access space flight factor related data. With the use of GeneLab’s modern computational suites (computomics), phylogenetic and functional genomic investigations of HGT events were conducted on the data generated from the MT-1 project. The putative data concerning the plasmid population (plasmidome) of the ISS was algorithmically derived and compared to those of habitats with similar environmental dynamics- such as living quarters and hospitals- to investigate whether these HGT elements may play crucial role(s) in shaping the microbiome of this closed habitat that serves as the only inhabited structure in space.

Bense, Nicholas↗
DOE OSTI2023

Whole-genome sequencing distinguishes the two most common giant kelp ecomorphs

Abstract Giant kelp, Macrocystis pyrifera, exists as distinct morphological variants—or “ecomorphs”—in different populations, yet the mechanism for this variation is uncertain, and environmental drivers for either adaptive or plastic phenotypes have not been identified. The ecomorphs Macrocystis “pyrifera” and M. “integrifolia” are distributed throughout temperate waters of North and South America with almost no geographic overlap and exhibit an incongruous, non-mirrored, distribution across the equator. This study evaluates the degree of genetic divergence between M. “pyrifera” and M. “integrifolia” across 18 populations in Chile and California using whole-genome sequencing and single-nucleotide polymorphism markers. Our results based on a principal component analysis, admixture clustering by genetic similarity, and phylogenetic inference demonstrate that M. “pyrifera” and M. “integrifolia” are genetically distinguishable. Analyses reveal separation by Northern and Southern Hemispheres and between morphs within hemispheres, suggesting that the convergent “integrifolia” morphology arose separately in each hemisphere. This is the first study to use whole-genome sequencing to understand genetic divergence in giant kelp ecomorphs, identifying 83 potential genes under selection and providing novel insights about Macrocystis evolution that were not evident with previous genetic techniques. Future studies are needed to uncover the environmental forces driving local adaptation and presumed convergent evolution of these morphs.

Environmental Sciences & Ecology↗
DOE OSTI2022

One hundred years into the study of ecotypes, new advances are being made through large-scale field experiments in perennial plant systems

A hundred years after Turesson first clearly described how locally adaptive variation is distributed within species, plant biologists are making major breakthroughs in our understanding of mechanisms underlying adaptation from local populations to the scale of continents. Although the genetics of local adaptation has typically been studied in smaller reciprocal transplant experiments, here it is being evaluated with whole genomes in large-scale networks of common garden experiments with perennial switchgrass and poplar trees. These studies support the hypothesis that a complex combination of loci, both with and without adaptive trade-offs, underlies local adaptation and that hybridization and adaptive introgression play a key role in the evolution of these species. Future studies incorporating high-throughput phenotyping, gene expression, and modeling will be used to predict responses of these species to climate change.

Trade-off↗
DOE OSTI2025

scRNA seq of an F1 cross of Marek’s disease resistant and susceptible chickens identifies allele specific expression signatures enriched in transcription modulators

Abstract Marek’s disease (MD), a T cell lymphoma disease in chickens, is caused by the Marek’s disease virus (MDV) found ubiquitously in the poultry industry. Genetically resistant Line 6 3 (L6) and susceptible Line 7 2 (L7) chickens have been instrumental to research on avian immune system response to MDV infection. In this study we characterized molecular signatures unique to splenic immune cell types across different genetic backgrounds 6 days after infection. Using three populations, L6, L7, and an F1 cross between L6xL7, we evaluated the immune cell transcriptome of responding cell types using single cell RNA sequencing. Several MDV genes were found expressed mainly in cytotoxic T cells while ICP4 and MEQ MDV genes were expressed across infected cell types. Using the F1 we quantified allele specific expression (ASE) of biallelic SNPs and found biased expression of parental alleles specific to immune cell subtypes. We identified 22 SNPs with ASE in response to MDV infection mapped to gene rich regions surrounding 59 genes of critical importance for chromatin remodeling and transcriptional regulation. Histone deacetylase genes (HDAC1 and HDAC8) had increased expression of L6 alleles, while small nuclear RNA genes (SNORA68 and SNORA72) expressed higher levels of L7 alleles with infection in T cell subsets. SNPs with ASE also mapped genes important for an adequate immune response including GNLY (cytotoxic activity) and PDIA3 (component of MHC class I peptide loading complex), and genes known to promote viral replication (MCM5 and EIF3M). These results show that functional variants associated with susceptibility to MD may have a bigger impact in subsets of immune cell types, and by characterizing the transcriptomes of these subtypes we can unravel molecular signatures specific to MD genomic resistance.

Science & Technology - Other Topics↗
DOE OSTI2021

Genomic reconstruction of fossil and living microorganisms in ancient Siberian permafrost

Abstract Background Total DNA (intracellular, iDNA and extracellular, eDNA) from ancient permafrost records the mixed genetic repository of the past and present microbial populations through geological time. Given the exceptional preservation of eDNA under perennial frozen conditions, typical metagenomic sequencing of total DNA precludes the discrimination between fossil and living microorganisms in ancient cryogenic environments. DNA repair protocols were combined with high throughput sequencing (HTS) of separate iDNA and eDNA fraction to reconstruct metagenome-assembled genomes (MAGs) from ancient microbial DNA entrapped in Siberian coastal permafrost. Results Despite the severe DNA damage in ancient permafrost, the coupling of DNA repair and HTS resulted in a total of 52 MAGs from sediments across a chronosequence (26–120 kyr). These MAGs were compared with those derived from the same samples but without utilizing DNA repair protocols. The MAGs from the youngest stratum showed minimal DNA damage and thus likely originated from viable, active microbial species. Many MAGs from the older and deeper sediment appear related to past aerobic microbial populations that had died upon freezing. MAGs from anaerobic lineages, including Asgard archaea, however exhibited minimal DNA damage and likely represent extant living microorganisms that have become adapted to the cryogenic and anoxic environments. The integration of aspartic acid racemization modeling and metaproteomics further constrained the metabolic status of the living microbial populations. Collectively, combining DNA repair protocols with HTS unveiled the adaptive strategies of microbes to long-term survivability in ancient permafrost. Conclusions Our results indicated that coupling of DNA repair protocols with simultaneous sequencing of iDNA and eDNA fractions enabled the assembly of MAGs from past and living microorganisms in ancient permafrost. The genomic reconstruction from the past and extant microbial populations expanded our understanding about the microbial successions and biogeochemical alterations from the past paleoenvironment to the present-day frozen state. Furthermore, we provided genomic insights into long-term survival mechanisms of microorganisms under cryogenic conditions through geological time. The combined strategies in this study can be extrapolated to examine other ancient non-permafrost environments and constrain the search for past and extant extraterrestrial life in permafrost and ice deposits on Mars.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Selecting Minimal Motion Primitive Libraries with Genetic Algorithms

Motion primitives allow for application of discrete search algorithms to rapidly produce trajectories in complex continuous space. The maneuver automaton (MA) provides an elegant formulation for creating a primitive library based on trims and maneuvers. However, performance is fundamentally limited by the contents of the primitive library. If the library is too sparse, performance can be poor in terms of path cost, whereas a library that is too large can increase run time. This work outlines new methods for using genetic algorithms to prune a primitive library. The proposed methods balance the path cost and planning time while maintaining the reachability of the MA. The genetic algorithm in this paper evaluates and mutates populations of motion primitive libraries to optimize both objectives. Here, we illustrate the performance of these methods with a simulated study using a nonlinear medium-fidelity F-16 model. We optimize a library with the presented algorithm for obstacle-free navigation and a nap-of-the-Earth navigation task. In the obstacle-free navigation task, we show a tradeoff of a 10.16% higher planning cost for a 96.63% improvement in run time. In the nap-of-the-Earth task, we show a tradeoff of a 9.712% higher planning cost for a 92.06% improvement in run time.

42 ENGINEERING↗
DOE OSTI2021

Genetics and Genomics of Pathogen Resistance in Switchgrass

This project investigates the genetic and genomic bases of resistance/tolerance to disease in switchgrass (Panicum virgatum) populations developed as bioenergy feedstock. The focus is placed populations adapted to the Central Great Plains derived from the hybridization of upland and lowland ecotypes, represented by cultivars Summer and Kanlow, respectively. Resistance was investigated against the rust disease caused by the fungus Puccinia novo-panici (syn. P emaculata) and mosaic disease caused by the virus complex of Panicum mosaic virus and its satellite. Objectives of the project were: 1) to elucidate the genetic and genomic bases of resistance/tolerance in locally adapted upland and lowland switchgrass breeding populations with contrasting disease symptoms under field conditions; 2) determine the molecular underpinnings of why cv Kanlow has broad resistance/tolerance to pathogens; and 3) discover the molecular differences that permit systemic viral infections in some switchgrass plants but not in other genetically-related plants.

09 BIOMASS FUELS↗
DOE OSTI2025

Spatial Replication Is Important for Developing Landscape Genetic Inferences for a Wetland Salamander

Habitat fragmentation is a pressing threat to wildlife populations, and maintenance of gene flow between populations is an essential goal of conservation. Resistance surfaces have emerged as an important tool for modelling connectivity and developing management strategies to mitigate effects of habitat fragmentation. However, recent studies have noted inconsistencies in the factors most strongly associated with connectivity across different landscapes. Thus, replication of genetic-based resistance surface optimisation across landscapes may be necessary for making robust conclusions about the influence of environmental variables. Accordingly, replication represents a substantive challenge and opportunity in the field of landscape genetics. In this study, we conducted replicated landscape genetic analyses across five landscapes in Tennessee and Kentucky for a threatened wetland amphibian, the four-toed salamander (Hemidactylium scutatum). We tested multiple hypotheses of how different landscape features that could directly affect small, desiccation-intolerant amphibians (e.g., canopy cover) influenced gene flow and assessed the appropriate scale at which to model different features. We found some concordance in the landscape features that influenced gene flow (e.g., a common importance of forest cover and topography), but also some differences—potentially owing to the difference in variability of predictors across landscapes. We also found discordance in the scale of effect of different features across landscapes. In conclusion, our work emphasises that flat areas of moist forest not bisected by roads may be important for H. scutatum conservation, and our replicated design allows us to identify relationships that would have been missed if only using one study site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Novel candidate genes for lignin structure identified through genome-wide association study of naturally varying Populus trichocarpa

Populus is a promising lignocellulosic feedstock for biofuels and bioproducts. However, the cell wall biopolymer lignin is a major barrier in conversion of biomass to biofuels. To investigate the variability and underlying genetic basis of the complex structure of lignin, a population of 409 three-year-old, naturally varying Populus trichocarpa genotypes were characterized by heteronuclear single quantum coherence (HSQC) nuclear magnetic resonance (NMR). A subsequent genome-wide association study (GWAS) was conducted using approximately 8.3 million single nucleotide polymorphisms (SNPs), which identified 756 genes that were significantly associated (−log 10 ( p -value)>6) with at least one lignin phenotype. Several promising candidate genes were identified, many of which have not previously been reported to be associated with lignin or cell wall biosynthesis. These results provide a resource for gaining insights into the molecular mechanisms of lignin biosynthesis and new targets for future genetic improvement in poplar.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Genome_shuffling_enables_quantitative_trait_locus_mapping_in_Bacillus_subtilis

Genetic mapping is a powerful tool for eukaryotic genetics that has only been applied to bacteria in limited circumstances. Quantitative trait locus (QTL) mapping generally relies on sexual recombination to break linkages between genes, yet bacteria rarely undergo sufficient homologous recombination to generate suitable mapping populations. In this work, we used iterative biparental genome shuffling by protoplast fusion inBacillus subtilisto generate a population of bacteria with substantial random recombination throughout their genomes. Individual shuffled progeny were arrayed in well plates, resequenced, and characterized for a range of complex phenotypes including spore germination and swarming motility. Genetic mapping of the resulting phenotypes identified high-confidence QTLs of moderate size (∼10 kb), and these associations were validated through targeted genetic swaps. ThisB. subtilisQTL population can easily be used to map additional phenotypes, and the general approach for QTL mapping is applicable in a wide range of bacteria.

Bacillus subtilis↗
DOE OSTI2022

Breeding Realistic D‐Brane Models

Abstract Intersecting branes provide a useful mechanism to construct particle physics models from string theory with a wide variety of desirable characteristics. The landscape of such models can be enormous, and navigating towards regions which are most phenomenologically interesting is potentially challenging. Machine learning techniques can be used to efficiently construct large numbers of consistent and phenomenologically desirable models. In this work we phrase the problem of finding consistent intersecting D‐brane models in terms of genetic algorithms, which mimic natural selection to evolve a population collectively towards optimal solutions. For a four‐dimensional supersymmetric type IIA orientifold with intersecting D6‐branes, we demonstrate that unique, fully consistent models can be easily constructed, and, by a judicious choice of search environment and hyper‐parameters, of the found models contain the desired Standard Model gauge group factor. Having a sizable sample allows us to draw some preliminary landscape statistics of intersecting brane models both with and without the restriction of having the Standard Model gauge factor.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Population Genomic Analyses Reveal Connectivity via Human-Mediated Transport across Populus Plantations in North America and an Undescribed Subpopulation of Sphaerulina musiva

Domestication of plant species has affected the evolutionary dynamics of plant pathogens in agriculture and forestry. A model system for studying the consequences of plant domestication on the evolution of an emergent plant disease is the fungal pathogen Sphaerulina musiva. This ascomycete causes leaf spot and stem canker disease of Populus spp. and their hybrids. A population genomics approach was used to determine the degree of population structure and evidence for selection on the North American population of S. musiva. In total, 122 samples of the fungus were genotyped identifying 120,016 single-nucleotide polymorphisms after quality filtering. In North America, S. musiva has low to moderate degrees of differentiation among locations. Three main genetic clusters were detected: southeastern United States, midwestern United States and Canada, and a new British Columbia cluster (BC2). Population genomics suggest that BC2 is a novel genetic cluster from central British Columbia, clearly differentiated from previously reported S. musiva from coastal British Columbia, and the product of a single migration event. Phenotypic measurements from greenhouse experiments indicate lower aggressiveness of BC2 on Populus trichocarpa. In summary, S. musiva has geographic structure across broad regions indicative of gene flow among clusters. The interconnectedness of the North American S. musiva populations across large geographic distances further supports the hypothesis of anthropogenic-facilitated transport of the pathogen.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Genomic Analysis of the Natural Variation of Fatty Acid Composition in Seed Oils of Camelina sativa

Camelina sativa is an oilseed crop that has shown strong promise as a biofuel feedstock. The profile of fatty acids greatly influences the oil quality; however, genetic mechanisms that determine the natural variation of fatty acid composition in camelina are not fully understood. A genome wide association study (GWAS) was performed to uncover genetic loci that may contribute to the contents of major fatty acids such as oleic and linolenic acids in camelina seed. Two approaches were taken to improve the GWAS efficiency. First, growing a diversity panel of 212 accessions in four locations and two nitrogen fertilization conditions revealed great variation in fatty acid contents in seeds. Second, using an improved reference genome, abundant markers, including 203,320 single nucleotide polymorphisms (SNPs) and 99,067 insertions/deletions (indels), were developed, which refined the population structure of the diversity panel. GWAS resulted in 118 genetic markers across 31 trait/treatment conditions. Closely linked markers were determined based on linkage decay and by comparing secondarily associated markers when highly associated ones were removed. Candidate genes were examined by comparing the pangenomes of 12 high-quality reference genomes. This study provides new resources to understand seed lipid metabolism and improve camelina oils through molecular breeding.

Life Sciences & Biomedicine - Other Topics↗
DOE OSTI2022

Light-Level Geolocation of the LANL Population of Western Bluebirds

Options for tracking and reconstructing animal movement are increasingly accessible due to rapidly decreasing costs, smaller sizes, and a proliferation of analytical inference techniques (Rutz and Hays, 2009; Wikelski et al., 2007). A wide variety of options exists for determining movement patterns of animals—from high-resolution pinpoint ARGOS satellite tags to time-consuming and logistically challenging radio telemetry. One option, light-level geolocation, offers small, affordable devices with long battery lives known as global location sensors (GLS), making them ideal for gathering preliminary migratory data. Geolocation works by inferring patterns of animal movement from light-level transitions between day and night (Hill and Braun, 2001). The recent advances in tracking technologies allow biologists to zoom in on migratory behavior, delineating heretofore-unidentified intraspecific migratory behavior (Delmore et al., 2012). The ubiquity of migratory divides (populations within a species that exhibit different migratory patterns) remains largely unknown, but their existence can lead to favorable demographic metrics (e.g., genetic diversity) in conservation contexts (Møller et al., 2011) and necessitate the development of population-specific conservation plans (Delmore et al., 2012). Delimiting the populations within a species that migrate and the extent of their migrations relative to individuals that remain resident across a species’ range has important evolutionary, ecological, and conservation implications. Within this context, Los Alamos National Laboratory (LANL) biologists have leveraged the local Avian Nestbox Network (ANN; Fair and Myers, 2002) to evaluate the migratory behaviors of a common local bird species, the Western Bluebird (Sialia mexicana).

47 OTHER INSTRUMENTATION↗