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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 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Nonadditive gene expression is correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow ( Salix spp.)

Many studies have highlighted the complex and diverse basis for heterosis in inbred crops. Despite the lack of a consensus model, it is vital that we turn our attention to understanding heterosis in undomesticated, heterozygous, and polyploid species, such as willow (Salix spp.). Shrub willow is a dedicated energy crop bred to be fast-growing and high yielding on marginal land without competing with food crops. A trend in willow breeding is the consistent pattern of heterosis in triploids produced from crosses between diploid and tetraploid species. Here, we test whether differentially expressed genes are associated with heterosis in triploid families derived from diploid Salix purpurea, diploid Salix viminalis, and tetraploid Salix miyabeana parents. Three biological replicates of shoot tips from all family progeny and parents were collected after 12 weeks in the greenhouse and RNA extracted for RNA-Seq analysis. This study provides evidence that nonadditive patterns of gene expression are correlated with nonadditive phenotypic expression in interspecific triploid hybrids of willow. Expression-level dominance was most correlated with heterosis for biomass yield traits and was highly enriched for processes involved in starch and sucrose metabolism. In addition, there was a global dosage effect of parent alleles in triploid hybrids, with expression proportional to copy number variation. Importantly, differentially expressed genes between family parents were most predictive of heterosis for both field and greenhouse collected traits. Altogether, these data will be used to progress models of heterosis to complement the growing genomic resources available for the improvement of heterozygous perennial bioenergy crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Simulation of sugar kelp ( Saccharina latissima ) breeding guided by practices to accelerate genetic gains

Abstract Though Saccharina japonica cultivation has been established for many decades in East Asian countries, the domestication process of sugar kelp (Saccharina latissima) in the Northeast United States is still at its infancy. In this study, by using data from our breeding experience, we will demonstrate how obstacles for accelerated genetic gain can be assessed using simulation approaches that inform resource allocation decisions. Thus far, we have used 140 wild sporophytes that were sampled in 2018 from the northern Gulf of Maine to southern New England. From these sporophytes, we sampled gametophytes and made and evaluated over 600 progeny sporophytes from crosses among the gametophytes in 2019 and 2020. The biphasic life cycle of kelp gives a great advantage in selective breeding as we can potentially select both on the sporophytes and gametophytes. However, several obstacles exist, such as the amount of time it takes to complete a breeding cycle, the number of gametophytes that can be maintained in the laboratory, and whether positive selection can be conducted on farm-tested sporophytes. Using the Gulf of Maine population characteristics for heritability and effective population size, we simulated a founder population of 1,000 individuals and evaluated the impact of overcoming these obstacles on rate of genetic gain. Our results showed that key factors to improve current genetic gain rely mainly on our ability to induce reproduction of the best farm-tested sporophytes, and to accelerate the clonal vegetative growth of released gametophytes so that enough gametophyte biomass is ready for making crosses by the next growing season. Overcoming these challenges could improve rates of genetic gain more than 2-fold. Future research should focus on conditions favorable for inducing spring reproduction, and on increasing the amount of gametophyte tissue available in time to make fall crosses in the same year.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Genomics and Development of Lentinus tigrinus : A White-Rot Wood-Decaying Mushroom with Dimorphic Fruiting Bodies

Lentinus tigrinus is a species of wood-decaying fungi (Polyporales) that has an agaricoid form (a gilled mushroom) and a secotioid form (puffball-like, with enclosed spore-bearing structures). Previous studies suggested that the secotioid form is conferred by a recessive allele of a single locus. We sequenced the genomes of one agaricoid (Aga) strain and one secotioid (Sec) strain (39.53-39.88 Mb, with 15,581-15,380 genes, respectively). We mated the Sec and Aga monokaryons, genotyped the progeny, and performed bulked segregant analysis (BSA). We also fruited three Sec/Sec and three Aga/Aga dikaryons, and sampled transcriptomes at four developmental stages. Using BSA, we identified 105 top candidate genes with nonsynonymous SNPs that cosegregate with fruiting body phenotype. Transcriptome analyses of Sec/Sec versus Aga/Aga dikaryons identified 907 differentially expressed genes (DEGs) along four developmental stages. On the basis of BSA and DEGs, the top 25 candidate genes related to fruiting body development span 1.5 Mb (4% of the genome), possibly on a single chromosome, although the precise locus that controls the secotioid phenotype is unresolved. The top candidates include genes encoding a cytochrome P450 and an ATP-dependent RNA helicase, which may play a role in development, based on studies in other fungi.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Genetic mapping and prediction of flowering time and plant height in a maize Stiff Stalk MAGIC population

Abstract The Stiff Stalk heterotic pool is a foundation of US maize seed parent germplasm and has been heavily utilized by both public and private maize breeders since its inception in the 1930s. Flowering time and plant height are critical characteristics for both inbred parents and their test crossed hybrid progeny. To study these traits, a 6-parent multiparent advanced generation intercross population was developed including maize inbred lines B73, B84, PHB47 (B37 type), LH145 (B14 type), PHJ40 (novel early Stiff Stalk), and NKH8431 (B73/B14 type). A set of 779 doubled haploid lines were evaluated for flowering time and plant height in 2 field replicates in 2016 and 2017, and a subset of 689 and 561 doubled haploid lines were crossed to 2 testers, respectively, and evaluated as hybrids in 2 locations in 2018 and 2019 using an incomplete block design. Markers were derived from a practical haplotype graph built from the founder whole genome assemblies and genotype-by-sequencing and exome capture-based sequencing of the population. Genetic mapping utilizing an update to R/qtl2 revealed differing profiles of significant loci for both traits between 635 of the DH lines and 2 sets of 570 and 471 derived hybrids. Genomic prediction was used to test the feasibility of predicting hybrid phenotypes based on the per se data. Predictive abilities were highest on direct models trained using the data they would predict (0.55–0.63), and indirect models trained using per se data to predict hybrid traits had slightly lower predictive abilities (0.49–0.55). Overall, this finding is consistent with the overlapping and nonoverlapping significant quantitative trait loci found within the per se and hybrid populations and suggests that selections for phenology traits can be made effectively on doubled haploid lines before hybrid data is available.

Genetics & Heredity↗
DOE OSTI2022

Reporter genes confer new-to-nature ornamental traits in plants

Ornamental plants (trees, shrubs, and herbs) beautify our urban and rural environments, enrich the quality of human life, and represent a vital component of the horticultural industry. The introduction of novel plant varieties and cultivars is critical to the ornamental horticultural industry [1]. To develop ornamental plants with desirable traits, different approaches, such as ploidy manipulation, interspecific hybridization, and physical/chemical mutagenesis, have been used for decades [2, 3]. However, the breeding of new ornamental varieties of trees and shrubs is a time- and labor-consuming process, because these plants may have a long juvenile growth period, large physical size, or altered floral structures, and consequently require long-term observations, large areas for progeny testing, and/or special equipment for pollination and/or seed collection [4].

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Fermentation Practices Select for Thermostable Endolysins in Phages

Endolysins are produced by (bacterio)phages and play a crucial role in degrading the bacterial cell wall and the subsequent release of new phage progeny. These lytic enzymes exhibit a remarkable diversity, often occurring in a multimodular form that combines different catalytic and cell wall-binding domains, even in phages infecting the same species. Yet, our current understanding lacks insight into how environmental factors and ecological niches may have influenced the evolution of these enzymes. In this study, we focused on phages infecting Streptococcus thermophilus, as this bacterial species has a well-defined and narrow ecological niche, namely, dairy fermentation. Among the endolysins found in phages targeting this species, we observed limited diversity, with a singular structural type dominating in most of identified S. thermophilus phages. Within this prevailing endolysin type, we discovered a novel and highly conserved calcium-binding motif. This motif proved to be crucial for the stability and activity of the enzyme at elevated temperatures. Ultimately, we demonstrated its positive selection within the host's environmental conditions, particularly under the temperature profiles encountered in the production of yogurt, mozzarella, and hard cheeses that rely on S. thermophilus.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The Number and Pattern of Viral Genomic Reassortments are not Necessarily Identifiable from Segment Trees

Reassortment is an evolutionary process common in viruses with segmented genomes. These viruses can swap whole genomic segments during cellular co-infection, giving rise to novel progeny formed from the mixture of parental segments. Since large-scale genome rearrangements have the potential to generate new phenotypes, reassortment is important to both evolutionary biology and public health research. However, statistical inference of the pattern of reassortment events from phylogenetic data is exceptionally difficult, potentially involving inference of general graphs in which individual segment trees are embedded. In this paper, we argue that, in general, the number and pattern of reassortment events are not identifiable from segment trees alone, even with theoretically ideal data. We call this fact the fundamental problem of reassortment, which we illustrate using the concept of the “first-infection tree,” a potentially counterfactual genealogy that would have been observed in the segment trees had no reassortment occurred. Further, we illustrate four additional problems that can arise logically in the inference of reassortment events and show, using simulated data, that these problems are not rare and can potentially distort our observation of reassortment even in small data sets. Finally, we discuss how existing methods can be augmented or adapted to account for not only the fundamental problem of reassortment, but also the four additional situations that can complicate the inference of reassortment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

DNA damage in cells exhibiting radiation-induced genomic instability

Cells exhibiting radiation induced genomic instability exhibit varied spectra of genetic and chromosomal aberrations. Even so, oxidative stress remains a common theme in the initiation and/or perpetuation of this phenomenon. Isolated oxidatively modified bases, abasic sites, DNA single strand breaks and clustered DNA damage are induced in normal mammalian cultured cells and tissues due to endogenous reactive oxygen species generated during normal cellular metabolism in an aerobic environment. While sparse DNA damage may be easily repaired, clustered DNA damage may lead to persistent cytotoxic or mutagenic events that can lead to genomic instability. In this study, we tested the hypothesis that DNA damage signatures characterised by altered levels of endogenous, potentially mutagenic, types of DNA damage and chromosomal breakage are related to radiation-induced genomic instability and persistent oxidative stress phenotypes observed in the chromosomally unstable progeny of irradiated cells. The measurement of oxypurine, oxypyrimidine and abasic site endogenous DNA damage showed differences in non-double-strand breaks (DSB) clusters among the three of the four unstable clones evaluated as compared to genomically stable clones and the parental cell line. These three unstable clones also had increased levels of DSB clusters. The results of this study demonstrate that each unstable cell line has a unique spectrum of persistent damage and lead us to speculate that alterations in DNA damage signaling and repair may be related to the perpetuation of genomic instability.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Lessons learned on the presentation of scan data

Technicians performed a radiological survey of a surplus metal tank to support disposition planning at an Oak Ridge, Tennessee site. The survey included radiation scans to identify contamination and, if identified, define the boundary and magnitude of contamination. Fixed-point 1-minute measurements were also collected at randomly selected locations for comparison against the site's free release limit of 5,000 disintegrations per minute per 100 cm² (dpm/100 cm²) (0.83 Bq/cm²). Scan data were recorded using a data logger as a means to document surveyor observation - logged data captured at 1-second intervals and converted to counts per minute (cpm) by the data logger software were presented in the project report. Both the qualitative scan data (in cpm) and the quantitative direct measurement (in dpm/100 cm²) were reported for completeness, so stakeholders had all available information to support disposition decisions. However, a new stakeholder - introduced to the project at the reporting phase of work - used the instrument efficiency and background data to convert the scan data from cpm to dpm/100 cm², then compared the converted results to the site limit. Many of the converted values exceeded 5,000 dpm/100 cm². This resulted in delays in tank disposition and additional project costs which could have been avoided if the proper use and interpretation of scan data, and implications of radon progeny buildup on oxidized metal surfaces, had been better communicated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2018

EVALUATION OF AN UPWARD TREND IN BACKGROUND COUNT RATES FROM A STACK PARTICULATE CONTINUOUS AIR MONITOR

The Pacific Northwest National Laboratory (PNNL) operates the Radiochemical Processing Laboratory (RPL), which is a multi-purpose, non-reactor nuclear research facility. Regulations require both continuous sampling and monitoring of radioactive particulates and tritium gas in the exhaust from the main stack. Releases of other radioactive gases, including planned releases of radon, are tracked separately in a database and reported. During the 2015 calibration of the RPL stack continuous air monitor (CAM), measured alpha and beta background count rates were much higher than expected, especially when compared to count rates from previous calibrations. The source of the higher background count rates was examined by trending of historical CAM measurements and a comparison to the sampler data. The analysis revealed that the sample results showed no increase in emissions, whereas the CAM showed a steady increase in count rates. Ultimately, the CAM filter was analyzed and found to contain higher-than-normal background levels of 220Rn progeny. Assessments were performed to determine the cause of the increased background values, including reviews of building research activities, radioactive material usage and storage, adequacy of procedures, and the potential for internal CAM contamination. Project reviews determined that a research activity involving 228Th was left in a semi-stored state, resulting in 220Rn being released from a hot cell into the exhaust system. The 228Th source material was subsequently repackaged and contained resulting in a decrease of CAM background count rates. An estimate of the 220Rn release was made and the contribution to the annual offsite dose from the facility was calculated. The released activity and reported dose results were well below the permit limits for the facility.

radon, 220Rn, environmental assessment, air monito↗
DOE OSTI2026

Distribution of Natural Radionuclides at the Nevada National Security Site

According to the United Nations Scientific Committee on the Effects of Atomic Radiation (UNSCEAR) publications, contributions of terrestrial gamma doses are mainly from the presence of 40 K, and of 238 U and 232 Th together with their progeny in various rocks and soils. A survey of soil distributions of radionuclides 40 K, 238 U, and 232 Th was performed at the Nevada National Security Site (NNSS) using in situ gamma-ray spectrometry with a high-purity germanium (HPGe) detector. The average activity concentrations of 40 K, 238 U, and 232 Th in natural soils at the NNSS are 867 Bq kg -1 (range from 150 ± 8 to 1297 ± 56 Bq kg -1 ), 50 Bq kg -1 (range from 29 ± 3 to 74 ± 8 Bq kg -1 ), and 56 Bq kg -1 (range from 11 ± 2 to 96 ± 10 Bq kg -1 ), respectively. The concentration at each location is significantly associated with its geological lithology. The terrestrial gamma dose rates around the NNSS were estimated from 26 to 144 nSv h -1 with mean value of 93 nSv h -1 . In conclusion, our results provide useful information about the natural background radiation and radiological effects of naturally occurring radionuclides at the NNSS.

environmental assessment↗
DOE OSTI2024

The reproduction number and its probability distribution for stochastic viral dynamics

We consider stochastic models of individual infected cells. The reproduction number, R, is understood as a random variable representing the number of new cells infected by one initial infected cell in an otherwise susceptible (target cell) population. Variability in R results partly from heterogeneity in the viral burst size (the number of viral progeny generated from an infected cell during its lifetime), which depends on the distribution of cellular lifetimes and on the mechanism of virion release. We analyse viral dynamics models with an eclipse phase: the period of time after a cell is infected but before it is capable of releasing virions. The duration of the eclipse, or the subsequent infectious, phase is non-exponential, but composed of stages. We derive the probability distribution of the reproduction number for these viral dynamics models, and show it is a negative binomial distribution in the case of constant viral release from infectious cells, and under the assumption of an excess of target cells. In a deterministic model, the ultimate in-host establishment or extinction of the viral infection depends entirely on whether the mean reproduction number is greater than, or less than, one, respectively. Here, the probability of extinction is determined by the probability distribution of R, not simply its mean value. In particular, we show that in some cases the probability of infection is not an increasing function of the mean reproduction number.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Ground-state and decay properties of neutron-rich 106 Nb

The ground-state properties of neutron-rich 106 Nb and its β decay into 106 Mo have been studied using the CARIBU radioactive-ion-beam facility at Argonne National Laboratory. Niobium-106 ions were extracted from a 252 Cf fission source and mass separated before being delivered as low-energy beams to the Canadian Penning Trap, as well as the X-Array and SATURN β-decay-spectroscopy station. The measured 106 Nb ground-state mass excess of –66202.0(13) keV is consistent with a recent measurement but has three times better precision; this work also rules out the existence of a second long-lived, β-decaying state in 106 Nb above 5 keV in excitation energy. The decay half-life of 106 Nb was measured to be 1.097(21) s, which is 8% longer than the adopted value. Here, the level scheme of the decay progeny, 106 Mo, has been expanded up to ≈ 4 MeV. The distribution of decay strength and considerable population of excited states in 106 Mo of J ≥ 3 emphasizes the need to revise the adopted J π = 1 – ground-state spin-parity assignment of 106 Nb; it is more likely to be J ≥ 3.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Analog-antianalog isospin mixing in 47 K 𝛽−decay

Here, we have measured the isospin mixing of the 𝐼 𝜋 =1/2 + , 𝐸 𝑥 = 2.599 MeV state in nearly doubly magic 47 Ca with the isobaric analog 1/2 + state of 47 K . Using the TRIUMF atom trap for 𝛽 decay, we have measured a nonzero asymmetry of the progeny 47 Ca with respect to the initial 47 K spin polarization, which together with the 𝛽 asymmetry implies a nonzero ratio of Fermi to Gamow-Teller matrix elements 𝑦 = 0.098 ± 0.037 for the 1/2 + → 1/2 + transition. Interpreting 𝑦 as mixing between this state and the isobaric analog state implies a Coulomb matrix element magnitude 101 ± 37 keV. This relatively large matrix element supports a model from the literature of analog-antianalog isospin mixing, which predicts large matrix elements in cases involving excess neutrons over protons occupying more than one major shell. The result supports pursuing a search for time-reversal odd, parity-even, isovector interactions using a correlation in 47 K 𝛽 decay.

beta decay↗
DOE OSTI2024

Subsurface cosmogenic and radiogenic production of 42 Ar

Radioactive decays from 42 Ar and its progeny 42 K are potential background sources in large-scale liquid-argon-based neutrino and dark matter experiments. In the atmosphere, 42 Ar is produced primarily by cosmogenic activation on 40 Ar. The use of low radioactivity argon from cosmogenically shielded underground sources can expand the reach and sensitivity of liquid-argon-based rare event searches. We estimate 42 Ar production underground by nuclear reactions induced by natural radioactivity and cosmic-ray muon-induced interactions. At 3,000 mwe, 42 Ar production rate is 1.8×10 -3 atoms per ton of crust per year, 7 orders of magnitude smaller than the 39 Ar production rate at a similar depth in the crust. In conclusion, by comparing the calculated production rate of 42 Ar to that of 39 Ar for which the concentration has been measured in an underground gas sample, we estimate the activity of 42 Ar in gas extracted from 3,000 mwe depth to be less than two decays per ton of argon per year.

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2017

First measurement of surface nuclear recoil background for argon dark matter searches

Here, one major background in direct searches for weakly interacting massive particles (WIMPs) comes from the deposition of radon progeny on detector surfaces. A dangerous surface background is the 20 6Pb nuclear recoils produced by 210 Po decays. In this paper, we report the first characterization of this background in liquid argon. The scintillation signal of low energy Pb recoils is measured to be highly quenched in argon, and we estimate that the 103 keV 206 Pb recoil background will produce a signal equal to that of a ~5 keV (30 keV) electron recoil ( 40 Ar recoil). In addition, we demonstrate that this dangerous 210 Po surface background can be suppressed, using pulse shape discrimination methods, by a factor of ~100 or higher, which can make argon dark matter detectors near background-free and enhance their potential for discovery of medium- and high-mass WIMPs. Lastly, we also discuss the impact on other low background experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2016

The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2

Traditional marker-based mapping and next-generation sequencing was used to determine that the Arabidopsis (Arabidopsis thaliana) low cell wall arabinose mutant murus5 (mur5) encodes a defective allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2 (RGP2). Marker analysis of 13 F2 confirmed mutant progeny from a recombinant mapping population gave a rough map position on the upper arm of chromosome 5, and deep sequencing of DNA from these 13 lines gave five candidate genes with G→A (C→T) transitions predicted to result in amino acid changes. Of these five, only insertional mutant alleles of RGP2, a gene that encodes a UDP-arabinose mutase that interconverts UDP-arabinopyranose and UDP-arabinofuranose, exhibited the low cell wall arabinose phenotype. The identities of mur5 and two SALK insertional alleles were confirmed by allelism tests and overexpression of wild-type RGP2 complementary DNA placed under the control of the 35S promoter in the three alleles. The mur5 mutation results in the conversion of cysteine-257 to tyrosine-257 within a conserved hydrophobic cluster predicted to be distal to the active site and essential for protein stability and possible heterodimerization with other isoforms of RGP.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

A System for Dosage-Based Functional Genomics in Poplar

Altering gene dosage through variation in gene copy number is a powerful approach to addressing questions regarding gene regulation, quantitative trait loci, and heterosis, but one that is not easily applied to sexually transmitted species. Elite poplar (Populus spp) varieties are created through interspecific hybridization, followed by clonal propagation. Altered gene dosage relationships are believed to contribute to hybrid performance. Clonal propagation allows for replication and maintenance of meiotically unstable ploidy or structural variants and provides an alternative approach to investigating gene dosage effects not possible in sexually propagated species. Here, we built a genome-wide structural variation system for dosage-based functional genomics and breeding of poplar. We pollinated Populus deltoides with gamma-irradiated Populus nigra pollen to produce >500 F1 seedlings containing dosage lesions in the form of deletions and insertions of chromosomal segments (indel mutations). Using high-precision dosage analysis, we detected indel mutations in ~55% of the progeny. These indels varied in length, position, and number per individual, cumulatively tiling >99% of the genome, with an average of 10 indels per gene. Combined with future phenotype and transcriptome data, this population will provide an excellent resource for creating and characterizing dosage-based variation in poplar, including the contribution of dosage to quantitative traits and heterosis.

59 BASIC BIOLOGICAL SCIENCES↗