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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Influenza A viral burst size from thousands of infected single cells using droplet quantitative PCR (dqPCR)

An important aspect of how viruses spread and infect is the viral burst size, or the number of new viruses produced by each infected cell. Surprisingly, this value remains poorly characterized for influenza A virus (IAV), commonly known as the flu. In this study, we screened tens of thousands of cells using a microfluidic method called droplet quantitative PCR (dqPCR). The high-throughput capability of dqPCR enabled the measurement of a large population of infected cells producing progeny virus. By measuring the fully assembled and successfully released viruses from these infected cells, we discover that the viral burst sizes for both the seasonal H3N2 and the 2009 pandemic H1N1 strains vary significantly, with H3N2 ranging from 10 1 to 10 4 viruses per cell, and H1N1 ranging from 10 1 to 10 3 viruses per cell. Some infected cells produce average numbers of new viruses, while others generate extensive number of viruses. In fact, we find that only 10% of the single-cell infections are responsible for creating a significant portion of all the viruses. This small fraction produced approximately 60% of new viruses for H3N2 and 40% for H1N1. On average, each infected cell of the H3N2 flu strain produced 709 new viruses, whereas for H1N1, each infected cell produced 358 viruses. This novel method reveals insights into the flu virus and can lead to improved strategies for managing and preventing the spread of viruses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Application of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure

Introduction Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella , creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis. Methods We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism ( n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages. Results The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates ( n = 27) and singletons ( n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains). Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome. Discussion Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses.

Gao, Ruimin↗
DOE OSTI2021

Experimental evidence for recovery of mercury-contaminated fish populations

Anthropogenic releases of mercury (Hg) are a human health issue because the potent toxicant methylmercury (MeHg), formed primarily by microbial methylation of inorganic Hg in aquatic ecosystems, bioaccumulates to high concentrations in fish consumed by humans. Predicting the efficacy of Hg pollution controls on fish MeHg concentrations is complex because many factors influence the production and bioaccumulation of MeHg. Here we conducted a 15-year whole-ecosystem, single-factor experiment to determine the magnitude and timing of reductions in fish MeHg concentrations following reductions in Hg additions to a boreal lake and its watershed. During the seven-year addition phase, we applied enriched Hg isotopes to increase local Hg wet deposition rates fivefold. The Hg isotopes became increasingly incorporated into the food web as MeHg, predominantly from additions to the lake because most of those in the watershed remained there. Thereafter, isotopic additions were stopped, resulting in an approximately 100% reduction in Hg loading to the lake. The concentration of labelled MeHg quickly decreased by up to 91% in lower trophic level organisms, initiating rapid decreases of 38–76% of MeHg concentration in large-bodied fish populations in eight years. Although Hg loading from watersheds may not decline in step with lowering deposition rates, this experiment clearly demonstrates that any reduction in Hg loadings to lakes, whether from direct deposition or runoff, will have immediate benefits to fish consumers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Observation of Long-Lived UV-Induced Fluorescence from Environmental Materials Using the HVeV Detector as Developed for SuperCDMS

Here, we describe recent experiments using a SuperCDMS HVeV single-charge sensitive detector illuminated with an ultraviolet LED (275 nm) and a monochromatic laser(650 nm) using a dual fiber optic system installed in a small dilution refrigerator at Stanford University. We observed a population of fluorescence background events after UV exposure but not after exposure to the laser source. The fluorescence was likely due to scattered UV photons absorbed outside the detector. We discuss the possibility of fluorescence being a contributor to the low energy excess background observed in above-ground Dark Matter experiments.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Single-cell measurement of plasmid copy number and promoter activity

Abstract Accurate measurements of promoter activities are crucial for predictably building genetic systems. Here we report a method to simultaneously count plasmid DNA, RNA transcripts, and protein expression in single living bacteria. From these data, the activity of a promoter in units of RNAP/s can be inferred. This work facilitates the reporting of promoters in absolute units, the variability in their activity across a population, and their quantitative toll on cellular resources, all of which provide critical insights for cellular engineering.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Jet quenching in the glasma phase: Medium-induced radiation

Inspired by the recent considerations of parton momentum broadening in the glasma phase, we study the medium-induced soft gluon radiation of jet partons at early times in heavy-ion collisions. The glasma state is assumed to be comprised of independent color domains with homogenous longitudinal fields that vary event by event, and we further complete this model with an event-averaging procedure accounting for the finite correlation length. Using this description, we evaluate the rate of medium-induced radiation from an energetic parton at midrapidity in the glasma phase. We mainly focus on SU(2) color fields for simplicity, also referring to the U(1) case and comparing with the Baier, Dokshitzer, Mueller, Peigné, Schiff, and Zakharov rate to gain further insight. Our results show that there is an intricate interplay of the synchrotron-like radiation in a single color domain with the destructive interference between different color domains, after the medium averaging is performed. Thus, we find that the emission rate is sensitive to the matter structure, decreasing for a glasma state populated by smaller color domains—i.e., for a glasma with a larger characteristic saturation scale. Our approach can be applied to more realistic backgrounds, and it sets the stage for the modeling of jet evolution in the early stages of heavy-ion collisions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Cosmological Simulations of Stellar Halos with Gaia Sausage–Enceladus Analogs: Two Sausages, One Bun?

Observations of the Milky Way’s stellar halo find that it is predominantly comprised of a radially biased population of stars, dubbed the Gaia Sausage–Enceladus, or GSE. These stars are thought to be debris from dwarf galaxy accretion early in the Milky Way’s history. Though typically considered to be from a single merger, it is possible that the GSE debris has multiple sources. To investigate this possibility, we use the IllustrisTNG50 simulation to identify stellar accretion histories in 98 Milky Way analogs—the largest sample for which such an identification has been performed—and find GSE-like debris in 32, with two-merger GSEs accounting for a third of these cases. Distinguishing single-merger GSEs from two-merger GSEs is difficult in common kinematic spaces, but differences are more evident through chemical abundances and star formation histories. This is because single-merger GSEs are typically accreted more recently than the galaxies in two-merger GSEs: the median infall times (with 16th and 84th percentiles) are $5.{9}_{-2.0}^{+3.3}$ and $10.{7}_{-3.7}^{+1.2}$ Gyr ago for single- and two-merger scenarios, respectively. The systematic shifts in abundances and ages that occur as a result suggest that efforts in modeling these aspects of the stellar halo prove ever-important in understanding its assembly.

galactic archaeology↗
DOE OSTI2022

Application of wideband pulsed high-frequency EPR to molecular quantum spin science

This presentation provides an overview of a range of new applications in the area of molecular quantum spin science that are now possible at the US National High Magnetic Field Laboratory as a result of the development of a wideband, high-power 94 GHz pulsed EPR spectrometer. Here, this instrument allows true Fourier-transform detected experiments spanning a 1 GHz instantaneous bandwidth, akin to what has been possible in NMR for several decades. The presentation will begin by describing experiments on a nitroxide radical using chirped pulses, enabling acquisition of the full spectrum in a single sequence, thus providing a very efficient and convenient means to measure the field orientation dependence of the spin-lattice relaxation time, T 1 . This will be followed by a discussion of a coherent population transfer protocol involving the 2S + 1 = 8 Zeeman levels associated with the spin S = 7/2 Gd 3+ ion, potentially paving the way towards implementation of well-known quantum search algorithms. It will also be shown how the use of chirped pulses provides a route to achieving highly non-thermal spin populations, suggesting novel initialization schemes.

47 OTHER INSTRUMENTATION↗
DOE OSTI2021

Regional Relative Risk, a Physics-Based Metric for Characterizing Airborne Infectious Disease Transmission

Airborne infectious disease transmission events occur over a wide range of spatial scales and can be an important means of disease transmission. Physics- and biology-based models can assist in predicting airborne transmission events, overall disease incidence, and disease control strategy efficacy. We describe a new theory that extends current approaches for the case in which an individual is infected by a single airborne particle, including the scenario in which numerous infectious particles are present in the air but only one causes infection. A single infectious particle can contain more than one pathogenic microorganism and be physically larger than the pathogen itself. This approach allows robust relative risk estimates even when there is wide variation in (i) individual exposures and (ii) the individual response to that exposure (the pathogen dose-response function can take any mathematical form and vary by individual). Based on this theory, we propose the regional relative risk—a new metric, distinct from the traditional relative risk metric, that compares the risk between two regions. In theory, these regions can range from individual rooms to large geographic areas. In this paper, we apply the regional relative risk metric to outdoor disease transmission events over spatial scales ranging from 50 m to 20 km, demonstrating that in many common cases minimal input information is required to use the metric. Also, we demonstrate that the model predictions are consistent with data from prior outbreaks. Future efforts could apply and validate this theory for other spatial scales, such as transmission within indoor environments. This work provides context for (i) the initial stages of an airborne disease outbreak and (ii) larger-scale disease spread, including unexpected low-probability disease “sparks” that potentially affect remote populations, a key practical issue in controlling airborne disease outbreaks.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Triboelectric backgrounds to radio-based polar ultra-high energy neutrino (UHEN) experiments

Here, in the hopes of observing the highest-energy neutrinos (E EeV) populating the Universe, both past (RICE, AURA, ANITA) and current (RNO-G, ARIANNA, ARA and TAROGE-M) polar-sited experiments exploit the impulsive radio emission produced by neutrino interactions. In such experiments, rare single event candidates must be unambiguously identified above backgrounds. Background rejection strategies to date primarily target thermal noise fluctuations and also impulsive radio-frequency signals of anthropogenic origin. In this paper, we consider the possibility that ‘fake’ neutrino signals may also be generated naturally via the ‘triboelectric effect.’ This broadly describes any process in which force applied at a boundary layer results in displacement of surface charge, leading to the production of an electrostatic potential difference V. Wind blowing over granular surfaces such as snow can induce such a potential difference, with subsequent coronal discharge. Discharges over timescales as short as nanoseconds can then lead to radio-frequency emissions at characteristic MHz–GHz frequencies. Using data from various past (RICE, AURA, SATRA, ANITA) and current (RNO-G, ARIANNA and ARA) neutrino experiments, we find evidence for such backgrounds, which are generally characterized by: (a) a threshold wind velocity which likely depends on the experimental trigger criteria and layout; for the experiments considered herein, this value is typically $\mathscr{O}$(10 m/s), (b) frequency spectra generally shifted to the low-end of the frequency regime to which current radio experiments are typically sensitive (100–200 MHz), (c) for the strongest background signals, an apparent preference for discharges from above-surface structures, although the presence of more isotropic, lower amplitude triboelectric discharges cannot be excluded.

Background rejection↗
DOE OSTI2023

Midlatitude Ozone Depletion and Air Quality Impacts from Industrial Halogen Emissions in the Great Salt Lake Basin

We report aircraft observations of extreme levels of HCl and the dihalogens Cl 2 , Br 2 , and BrCl in an industrial plume near the Great Salt Lake, Utah. Complete depletion of O 3 was observed concurrently with halogen enhancements as a direct result of photochemically produced halogen radicals. Observed fluxes for Cl 2 , HCl, and NO x agreed with facility-reported emissions inventories. Bromine emissions are not required to be reported in the inventory, but are estimated as 173 Mg year –1 Br 2 and 949 Mg year –1 BrCl, representing a major uncounted oxidant source. A zero-dimensional photochemical box model reproduced the observed O 3 depletions and demonstrated that bromine radical cycling was principally responsible for the rapid O 3 depletion. Inclusion of observed halogen emissions in both the box model and a 3D chemical model showed significant increases in oxidants and particulate matter (PM 2.5 ) in the populated regions of the Great Salt Lake Basin, where winter PM 2.5 is among the most severe air quality issues in the U.S. The model shows regional PM 2.5 increases of 10%–25% attributable to this single industrial halogen source, demonstrating the impact of underreported industrial bromine emissions on oxidation sources and air quality within a major urban area of the western U.S.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Spatio-temporal dynamics of Hendra virus in Australia reveal stable maintenance of diverse viral clades among Pteropus bats

Hendra virus (HeV) was discovered in 1994 in Australia. Limited genomic data have hindered comprehensive understanding of HeV’s evolutionary dynamics. Here, in this work, we recovered 48 HeV genomes from bats and 9 from horses from Australia between 2016 and 2020, revealing four distinct clades. Each clade was distributed over a large spatial area with multiple clades co-circulating within a single bat roost on the same day and over consecutive years. The diversity and temporal stability of co-circulating clades suggest that viral dynamics are driven by episodic shedding of existing lineages maintained at the population level, rather than immune-driven strain-replacement dynamics. HeV isolates of different clades displayed variation in phenotypic properties but minimal antigenic differences. We provide an overview of evolutionary dynamics, phenotypic properties and assessment of countermeasures for HeV, and provide insights into the processes that maintain virus diversity in bats and influence the potential for viral emergence.

genetic variation↗
DOE OSTI2021

Ultrafast sorting: Excimeric π–π stacking distinguishes pyrene-N-methylacetamide isomers on the ultrafast time scale

Pyrene based molecules are inclined to form excimers through self-association upon photoexcitation. In this work, the pyrene core is functionalized with N-methylacetamide group at the position 1 or 2, to develop pyren-1-methylacetamide (PyMA1) and pyren-2- methylacetamide (PyMA2), respectively. The introduction of methylacetamide group was believed to help having hydrogen bonded excimers in close aggregation. Upon photoexcitation, PyMA1 and PyMA2, at 1.0mM in toluene, have formed predominantly static and dynamic excimers, respectively. The transient absorption (TA) measurements over fs-ps regime (fs-TA) showed that the formation of static excimers is an ultrafast process (~560fs) whereas, the dynamic excimers formed in much slower time scale (~65ps). Finally, single crystal X-ray diffraction studies show that for PyMA2 the overlap between the pyrene moieties (~42%) are better than PyMA1 (~17%) in ground state at 80K, which also reflected in the respective lifetimes and population percentages of excimers.

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

Magnetic anisotropy and two-dimensional short-range chemical ordering in Ba 1−𝑥 ⁢Na 𝑥 ⁢Fe 2 ⁢As 2

A true understanding of the properties of pnictide superconductors requires the development of high-quality materials and performing measurements designed to unravel their intrinsic properties and short-range nematic correlations which are often obscured by extrinsic effects such as poor crystallinity, inhomogeneity, domain formation, and twinning. Here, in this paper, we report the systematic growth of high-quality Na-substituted BaFe 2 As 2 single crystals and their characterization using pulsed magnetic fields x-ray diffraction and x-ray diffuse scattering. Analysis of the properties and compositions of the highest-quality crystals shows that their actual Na stoichiometry is about 50-60% of the nominal content and that the targeted production of crystals with specific compositions is accessible. We derived a reliable equation to estimate the Na stoichiometry based on the measured superconducting T c of these materials. Attempting to force spin reorientation and induce tetragonality, orthorhombic Ba 1-x Na x Fe 2 As 2 single crystals subjected to out-of-plane magnetic fields up to 31.4T are found to exhibit strong in-plane magnetic anisotropy demonstrated by the insufficiency of such high fields in manipulating the relative population of their twinned domains or in suppressing the orthorhombic order. Broad x-ray diffuse-intensity rods observed at temperatures between 30 and 300 K uncover short-range structural correlations. Local structure modeling together with 3D-Δ pair-distribution function mapping of real-space interatomic vectors show that the diffuse scattering arises from in-plane short-range chemical correlations of the Ba and Na atoms coupled with short-range atomic displacements within the same plane due to an effective size difference between the two atomic species.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Steelhead ( Oncorhynchus mykiss ) lineages and sexes show variable patterns of association of adult migration timing and age‐at‐maturity traits with two genomic regions

Abstract As life history diversity plays a critical role in supporting the resilience of exploited populations, understanding the genetic basis of those life history variations is important for conservation management. However, effective application requires a robust understanding of the strength and universality of genetic associations. Here, we examine genetic variation of single nucleotide polymorphisms in genomic regions previously associated with migration phenology and age‐at‐maturity in steelhead ( Oncorhynchus mykiss ) from the Columbia River. We found chromosome 28 markers (GREB1L, ROCK1 genes) explained significant variance in migration timing in both coastal and inland steelhead. However, strength of association was much greater in coastal than inland steelhead ( R 2 0.51 vs. 0.08), suggesting that genomic background and challenging inland migration pathways may act to moderate effects of this region. Further, we found that chromosome 25 candidate markers (SIX6 gene) were significantly associated with age and size at first return migration for inland steelhead, and this pattern was mediated by sex in a predictable pattern (males R 2 = 0.139–0.170; females R 2 = 0.096–0.111). While this encourages using these candidate regions in predicting life history characteristics, we suggest that stock‐specific associations and haplotype frequencies will be useful in guiding implementation of genetic assays to inform management.

Willis, Stuart C.↗
DOE OSTI2021

Trends in Spitzer Secondary Eclipses

It is well established that the magnitude of the incident stellar flux is the single most important factor in determining the day–night temperature gradients and atmospheric chemistries of short-period gas giant planets. However, it is likely that other factors, such as planet-to-planet variations in atmospheric metallicity, C/O ratio, and cloud properties, also contribute to the observed diversity of infrared spectra for this population of planets. In this study, we present new 3.6 and 4.5 μm secondary eclipse measurements for five transiting gas giant planets: HAT-P-5b, HAT-P-38b, WASP-7b, WASP-72b, and WASP-127b. We detect eclipses in at least one bandpass for all five planets and confirm circular orbits for all planets except WASP-7b, which shows evidence for a nonzero eccentricity. Building on the work of Garhart et al., we place these new planets into a broader context by comparing them with the sample of all planets with measured Spitzer secondary eclipses. We find that incident flux is the single most important factor for determining the atmospheric chemistry and circulation patterns of short-period gas giant planets. Although we might also expect surface gravity and host star metallicity to play a secondary role, we find no evidence for correlations with either of these two variables.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Efficient mutagenesis and genotyping of maize inbreds using biolistics, multiplex CRISPR/Cas9 editing, and Indel-Selective PCR

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Data for "Efficient Mutagenesis and Genotyping of Maize Inbreds Using Biolistics, Multiplex CRISPR/Cas9 Editing, and Indel-Selective PCR"

CRISPR/Cas9 based genome editing has advanced our understanding of a myriad of important biological phenomena. Important challenges to multiplex genome editing in maize include assembly of large complex DNA constructs, few genotypes with efficient transformation systems, and costly/labor-intensive genotyping methods. Here we present an approach for multiplex CRISPR/Cas9 genome editing system that delivers a single compact DNA construct via biolistics to Type I embryogenic calli, followed by a novel efficient genotyping assay to identify desirable editing outcomes. We first demonstrate the creation of heritable mutations at multiple target sites within the same gene. Next, we successfully created individual and stacked mutations for multiple members of a gene family. Genome sequencing found off-target mutations are rare. Multiplex genome editing was achieved for both the highly transformable inbred line H99 and Illinois Low Protein1 (ILP1), a genotype where transformation has not previously been reported. In addition to screening transformation events for deletion alleles by PCR, we also designed PCR assays that selectively amplify deletion or insertion of a single nucleotide, the most common outcome from DNA repair of CRISPR/Cas9 breaks by non-homologous end-joining. The Indel-Selective PCR (IS-PCR) method enabled rapid tracking of multiple edited alleles in progeny populations. The ‘end to end’ pipeline presented here for multiplexed CRISPR/Cas9 mutagenesis can be applied to accelerate maize functional genomics in a broader diversity of genetic backgrounds.

gene editing↗