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DOE OSTI2024

Topological quantum computation on a chiral Kondo chain

We describe the chiral Kondo chain model based on the symplectic Kondo effect and demonstrate that it has a quantum critical ground state populated by non-Abelian anyons. We show that the fusion channel of two arbitrary anyons can be detected by locally coupling the two anyons to an extra single channel of chiral current and measuring the corresponding conductance at a finite frequency. Based on such measurements, we propose that the chiral Kondo chain model with symplectic symmetry can be used for the implementation of measurement-only topological quantum computations, and it possesses several distinct features favorable for such applications. Furthermore, the sources and effects of errors in the proposed system are analyzed and possible material realizations are discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2021

Higher Compact Multiple Occurrence around Metal-poor M-dwarfs and Late-K-dwarfs

The planet–metallicity correlation serves as a potential link between exoplanet systems as we observe them today and the effects of bulk composition on the planet formation process. Many observers have noted a tendency for Jovian planets to form around stars with higher metallicities; however, there is no consensus on a trend for smaller planets. Here, we investigate the planet–metallicity correlation for rocky planets in single- and multi-planet systems around Kepler M-dwarf and late-K-dwarf stars. Due to molecular blanketing and the dim nature of these low-mass stars, it is difficult to make direct elemental abundance measurements via spectroscopy. We instead use a combination of accurate and uniformly measured parallaxes and photometry to obtain relative metallicities and validate this method with a subsample of spectroscopically determined metallicities. We use the Kolmogorov–Smirnov (K-S) test, Mann–Whitney U-test, and Anderson–Darling (AD) test to compare the compact multiple planetary systems with single-transiting planet systems and systems with no detected transiting planets. We find that the compact multiple planetary systems are derived from a statistically more metal-poor population, with a p-value of 0.015 in the K-S test, a p-value of 0.005 in the Mann–Whitney U-test, and a value of 2.574 in the AD test statistic, which exceeds the derived threshold for significance by a factor of 25. We conclude that metallicity plays a significant role in determining the architecture of rocky planet systems. Compact multiples either form more readily, or are more likely to survive on gigayear timescales, around metal-poor stars.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

BSE versus StarTrack: Implementations of new wind, remnant-formation, and natal-kick schemes in NBODY7 and their astrophysical consequences

As a result of their formation via massive single and binary stellar evolution, the masses of stellar-remnant black holes (BH) are subjects of great interest in this era of gravitational-wave detection from binary black hole (BBH) and binary neutron star merger events. In this work, we present new developments in the stellar-remnant formation and related schemes of the current N-body evolution program NBODY7. We demonstrate that the newly implemented stellar-wind and remnant-formation schemes in the stellar-evolutionary sector or BSE of the NBODY7 code, such as the “rapid” and the “delayed” supernova (SN) schemes along with an implementation of pulsational-pair-instability and pair-instability supernova (PPSN/PSN), now produce neutron star (NS) and BH masses that agree nearly perfectly, over large ranges of zero-age-main-sequence (ZAMS) mass and metallicity, with those from the widely recognised StarTrack population-synthesis program. We also demonstrate the new, recipe-based implementations of various widely debated mechanisms of natal kicks on NSs and BHs, such as “convection-asymmetry-driven”, “collapse-asymmetry-driven”, and “neutrino-emission-driven” kicks, in addition to a fully consistent implementation of the standard, fallback-dependent, momentum-conserving natal kick. All the above newly implemented schemes are also shared with the standalone versions of SSE and BSE. Furthermore, all these demonstrations are performed with both the updated standalone BSE and the updated NBODY7/BSE. When convolved with stellar and primordial-binary populations as observed in young massive clusters, such remnant-formation and natal-kick mechanisms crucially determine the accumulated number, mass, and mass distribution of the BHs retained in young massive, open, and globular clusters (GCs); these BHs would eventually become available for long-term dynamical processing. Among other conclusions, we find that although the newer, delayed SN remnant formation model gives birth to the largest number (mass) of BHs, the older remnant-formation schemes cause the largest number (mass) of BHs to survive in clusters, when incorporating SN material fallback onto the BHs. The SN material fallback also causes the convection-asymmetry-driven SN kick to effectively retain similar numbers and masses of BHs in clusters as for the standard, momentum-conserving kick. The collapse-asymmetry-driven SN kick would cause nearly all BHs to be retained in clusters irrespective of their mass, remnant-formation model, and metallicity, whereas the inference of a large population of BHs in GCs would potentially rule out the neutrino-driven SN kick mechanism. Pre-SN mergers of massive primordial binaries would potentially cause BH masses to deviate from the theoretical, single-star ZAMS to mass-remnant mass relation unless a substantial of the total merging stellar mass of up to ≈40% is lost during a merger process. In particular, such mergers, at low metallicities, have the potential to produce low-spinning BHs within the PSN mass gap that can be retained in a stellar cluster and be available for subsequent dynamical interactions. As recent studies indicate, the new remnant-formation modelling reassures us that young massive and open clusters would potentially contribute to the dynamical BBH merger detection rate to a similar extent as their more massive GC counterparts.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2022

Targeting the Bet-Hedging Strategy with an Inhibitor of Bacterial Efflux Capacity Enhances Antibiotic Efficiency and Ameliorates Bacterial Persistence In Vitro

Persistence is a bet-hedging strategy in bacterial populations that increases antibiotic tolerance and leads to the establishment of latent infections. In this study, we demonstrated that a synthetic non-toxic taxane-based reversal agent (tRA), developed as an inhibitor of ABC transporter systems in mammalian cancer cells, enhanced antibiotic killing of persister populations from different pathogens, including Burkholderia, Pseudomonas, Francisella, and Yersinia. Acting as an inhibitor of bacterial efflux at 100 nM, tRA99020 enhanced antibiotic efficiency and suppressed the production of natural products of Burkholderia species polyketide synthase (PKS) function. We demonstrate that the metabolites produced by PKS in response to stress by different antibiotics act as inhibitors of mammalian histone deacetylase activity and stimulate cell death. Applying a single-molecule fluorescence in situ hybridization (smFISH) assay, we analyzed on a single-cell level the activation profiles of the persistence regulating pks gene in Burkholderia thailandensis treated with tRA99020 and antibiotics. We posit that a multi-pronged approach encompassing antibiotic therapies and inhibition of efflux systems and fatty acid catabolism will be required for efficient eradication of persistent bacterial populations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

Microbes play fundamental roles in shaping natural ecosystem properties and functions, but do so under constraints imposed by their viral predators. However, studying viruses in nature can be challenging due to low biomass and the lack of universal gene markers. Though metagenomic short-read sequencing has greatly improved our virus ecology toolkit—and revealed many critical ecosystem roles for viruses—microdiverse populations and fine-scale genomic traits are missed. Some of these microdiverse populations are abundant and the missed regions may be of interest for identifying selection pressures that underpin evolutionary constraints associated with hosts and environments. Though long-read sequencing promises complete virus genomes on single reads, it currently suffers from high DNA requirements and sequencing errors that limit accurate gene prediction. Here we introduce VirION2, an integrated short- and long-read metagenomic wet-lab and informatics pipeline that updates our previous method (VirION) to further enhance the utility of long-read viral metagenomics. Using a viral mock community, we first optimized laboratory protocols (polymerase choice, DNA shearing size, PCR cycling) to enable 76% longer reads (now median length of 6,965 bp) from 100-fold less input DNA (now 1 nanogram). Using a virome from a natural seawater sample, we compared viromes generated with VirION2 against other library preparation options (unamplified, original VirION, and short-read), and optimized downstream informatics for improved long-read error correction and assembly. VirION2 assemblies combined with short-read based data (‘enhanced’ viromes), provided significant improvements over VirION libraries in the recovery of longer and more complete viral genomes, and our optimized error-correction strategy using long- and short-read data achieved 99.97% accuracy. In the seawater virome, VirION2 assemblies captured 5,161 viral populations (including all of the virus populations observed in the other assemblies), 30% of which were uniquely assembled through inclusion of long-reads, and 22% of the top 10% most abundant virus populations derived from assembly of long-reads. Viral populations unique to VirION2 assemblies had significantly higher microdiversity means, which may explain why short-read virome approaches failed to capture them. These findings suggest the VirION2 sample prep and workflow can help researchers better investigate the virosphere, even from challenging low-biomass samples. Our new protocols are available to the research community on protocols.io as a ‘living document’ to facilitate dissemination of updates to keep pace with the rapid evolution of long-read sequencing technology.

Long-reads↗

DOE OSTI2022

Whole-Genome Resequencing to Evaluate Life History Variation in Anadromous Migration of Oncorhynchus mykiss

Anadromous fish experience physiological modifications necessary to migrate between vastly different freshwater and marine environments, but some species such as Oncorhynchus mykiss demonstrate variation in life history strategies with some individuals remaining exclusively resident in freshwater, whereas others undergo anadromous migration. Because there is limited understanding of genes involved in this life history variation across populations of this species, we evaluated the genomic difference between known anadromous ( n = 39) and resident ( n = 78) Oncorhynchus mykiss collected from the Klickitat River, WA, USA, with whole-genome resequencing methods. Sequencing of these collections yielded 5.64 million single-nucleotide polymorphisms that were tested for significant differences between resident and anadromous groups along with previously identified candidate gene regions. Although a few regions of the genome were marginally significant, there was one region on chromosome Omy12 that provided the most consistent signal of association with anadromy near two annotated genes in the reference assembly: COP9 signalosome complex subunit 6 (CSN6) and NACHT, LRR, and PYD domain–containing protein 3 (NLRP3). Previously identified candidate genes for anadromy within the inversion region of chromosome Omy05 in coastal steelhead and rainbow trout were not informative for this population as shown in previous studies. Results indicate that the significant region on chromosome Omy12 may represent a minor effect gene for male anadromy and suggests that this life history variation in Oncorhynchus mykiss is more strongly driven by other mechanisms related to environmental rearing such as epigenetic modification, gene expression, and phenotypic plasticity. Further studies into regulatory mechanisms of this trait are needed to understand drivers of anadromy in populations of this protected species.

Collins, Erin E.↗

DOE OSTI2023

Waffle Homes: Utilizing Aerial Imagery of Unfinished Buildings to Determine Average Room Size

A primary function of the Population Density Tables Project (PDT) at Oak Ridge National Laboratory is to produce residential population densities per 1000 sq. ft. for each country and their associated first-level administrative units. This is accomplished by utilizing the average size of different types of dwelling areas (urban, rural, single-family, multi-family, etc.) and the average household size provided by a country’s Census or statistical bureau records. This data is available for the majority of Europe, North America, and large swathes of Asia, but is less easily found in Africa and South America. In these regions, Censuses generally report dwelling area by number of rooms, which poses the challenging question of how we can translate number of rooms to dwelling size when no dwelling size areas are available with which to compare. Using sub-meter resolution satellite imagery of Accra, Ghana, this challenge can be tackled using imagery of roofless buildings currently under construction that show the interior floor plan of the dwelling. A sample of buildings from the different neighborhoods of Accra can be digitized to provide an estimate and range of average room sizes of dwellings. This average room size can then be translated to a total dwelling area using the "number of rooms occupied by a household" variable from the Ghanaian Census. This intermediate step between average dwelling size and number of rooms occupied, fills the missing link that prevents PDT from continually producing new population densities for countries where dwelling size is unavailable through any official means.

Woody, Carson↗

DOE OSTI2024

The hyperplane of early-type galaxies: using stellar population properties to increase the precision and accuracy of the fundamental plane as a distance indicator

ABSTRACT We use deep spectroscopy from the SAMI (Sydney-AAO Multi-object Integral) Galaxy Survey to explore the precision of the fundamental plane (FP) of early-type galaxies as a distance indicator for future single-fibre spectroscopy surveys. We study the optimal trade-off between sample size and signal-to-noise ratio (SNR), and investigate which additional observables can be used to construct hyperplanes with smaller intrinsic scatter than the FP. We add increasing levels of random noise (parametrized as effective exposure time) to the SAMI spectra to study the effect of increasing measurement uncertainties on the FP- and hyperplane-inferred distances. We find that, using direct-fit methods, the values of the FP and hyperplane best-fitting coefficients depend on the spectral SNR, and reach asymptotic values for a mean $\langle \mathrm{ SNR} \rangle =40\, \mathrm{\mathring{\rm A}}^{-1}$. As additional variables for the FP we consider three stellar-population observables: light-weighted age, stellar mass-to-light ratio, and a novel combination of Lick indices ($I_\mathrm{age}$). For an $\langle \mathrm{ SNR} \rangle =45~\mathrm{\mathring{\rm A}}^{-1}$ (equivalent to 1-h exposure on a 4-m telescope), all three hyperplanes outperform the FP as distance indicators. Being an empirical spectral index, $I_\mathrm{age}$ avoids the model-dependent uncertainties and bias underlying age and mass-to-light ratio measurements, yet yields a 10 per cent reduction of the median distance uncertainty compared to the FP. We also find that, as a by-product, the $I_\mathrm{age}$ hyperplane removes most of the reported environment bias of the FP. After accounting for the different SNR, these conclusions also apply to a 50 times larger sample from SDSS-III (Sloan Digital Sky Survey). However, in this case, only $\mathrm{ age}$ removes the environment bias.

D’Eugenio, Francesco (ORCID:0000000323888172)↗

DOE OSTI2025

Predicting the Galactic population of free-floating planets from realistic initial conditions

ABSTRACT We present the first prediction for the mass distribution function of Galactic free-floating planets (FFPs) that aims to accurately include the relative contributions of multiple formation pathways and stellar populations. We derive our predicted distribution from dedicated simulations of planet birth, growth, migration, and ejection around circumbinary systems and extend these results to also include the contributions from single and wide binary systems. Our resulting FFP mass distribution shows several distinct features, including a strong peak at ${\sim} 8\, {\rm M}_{\oplus }$ arising from the transition between pebble and gas accretion regimes and a trough at ${\sim} 1\, {\rm M}_{\oplus }$ due to the shift in the dominant ejection process from planet–planet scattering to ejection through interactions with stars in circumbinary systems. We find that interactions with the central binary in close circumbinary systems are likely the dominant progenitor for FFPs more massive than Earth, leading to a steep power-law dependence in mass that agrees well with existing observations. In contrast, we find planet–planet scattering events in single and wide binary systems likely produce the majority of planets at Mars mass and below, resulting in a shallower power-law dependence. Our results suggest that existing extrapolations into the sub-terrestrial mass range may significantly overestimate the true FFP abundance. The features we predict in the mass distribution of FFPs will be detectable by upcoming space-based microlensing surveys and, if observed, will provide key insight into the origins of FFPs and the environments in which they form.

Coleman, Gavin A. L. (ORCID:0000000151118963)↗

DOE OSTI2024

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [ Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink’s yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height ( Dw1 and Dw2 ) and the YELLOW SEED1 locus ( Y1 ) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

bioenergy association panel↗

DOE OSTI2021

Understanding the Origin of Structural Diversity of DNA Double Helix

Deciphering the contribution of DNA subunits to the variability of its 3D structure represents an important step toward the elucidation of DNA functions at the atomic level. In the pursuit of that goal, our previous studies revealed that the essential conformational characteristics of the most populated “canonic” BI and AI conformational families of Watson–Crick duplexes, including the sequence dependence of their 3D structure, preexist in the local energy minima of the elemental single-chain fragments, deoxydinucleoside monophosphates (dDMPs). Those computations have uncovered important sequence-dependent regularity in the superposition of neighbor bases. The present work expands our studies to new minimal fragments of DNA with Watson–Crick nucleoside pairs that differ from canonic families in the torsion angles of the sugar-phosphate backbone (SPB). To address this objective, computations have been performed on dDMPs, cdDMPs (complementary dDMPs), and minimal fragments of SPBs of respective systems by using methods of molecular and quantum mechanics. These computations reveal that the conformations of dDMPs and cdDMPs having torsion angles of SPB corresponding to the local energy minima of separate minimal units of SPB exhibit sequence-dependent characteristics representative of canonic families. In contrast, conformations of dDMP and cdDMP with SPB torsions being far from the local minima of separate SPB units exhibit more complex sequence dependence.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2023

Diverse Chemo-Dynamical Properties of Nitrogen-Rich Stars Identified from Low-Resolution Spectra

The second generation of stars in the globular clusters (GCs) of the Milky Way (MW) exhibit unusually high N, Na, or Al, compared to typical Galactic halo stars at similar metallicities. The halo field stars enhanced with such elements are believed to have originated in disrupted GCs or escaped from existing GCs. We identify such stars in the metallicity range –3.0 < [Fe/H] < 0.0 from a sample of ~ 36,800 giant stars observed in the Sloan Digital Sky Survey and Large Sky Area Multi-Object Fiber Spectroscopic Telescope survey, and present their dynamical properties. The N-rich population (NRP) and N-normal population (NNP) among our giant sample do not exhibit similarities in either in their metallicity distribution function (MDF) or dynamical properties. We find that, even though the MDF of the NRP looks similar to that of the MW’s GCs in the range of [Fe/H] < –1.0, our analysis of the dynamical properties does not indicate similarities between them in the same metallicity range, implying that the escaped members from existing GCs may account for a small fraction of our N-rich stars, or the orbits of the present GCs have been altered by the dynamical friction of the MW. We also find a significant increase in the fraction of N-rich stars in the halo field in the very metal-poor (VMP; [Fe/H] < –2.0) regime, comprising up to ~ 20% of the fraction of the N-rich stars below [Fe/H] = –2.5, hinting that partially or fully destroyed VMP GCs may have in some degree contributed to the Galactic halo. A more detailed dynamical analysis of the NRP reveals that our sample of N-rich stars do not share a single common origin. Although a substantial fraction of the N-rich stars seem to originate from the GCs formed in situ, more than 60% of them are not associated with those of typical Galactic populations, but probably have extragalactic origins associated with Gaia Sausage/Enceladus, Sequoia, and Sagittarius dwarf galaxies, as well as with presently unrecognized progenitors.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

An Ab Initio Electronic Structure Investigation of the Ground and Excited States of ScH + , YH + , and LaH +

Multireference configuration interaction (MRCI), Davidson-corrected MRCI (MRCI+Q), coupled-cluster singles, doubles, and perturbative triples [CCSD(T)], and frozen-core full configuration interaction (fcFCI) calculations were carried out using large, correlation-consistent basis sets to investigate the excited states of the Sc atom and the spin–free and spin–orbit coupled potential energy profiles, energetics, spectroscopic constants, and electron populations of low-lying states of MH + (M = Sc, Y, La). The core electron correlation effects, complete basis set effects, and spin–orbit coupling effects were also evaluated. The first four electronic states of all MH + are 1 2 Δ, 1 2 Σ + , 1 2 Π, and 2 2 Σ + with 1σ 2 1δ 1 , 1σ 2 2σ 1 , 1σ 2 1π 1 , and 1σ 2 3σ 1 single-reference electron configurations, respectively. These states of MH + can be represented by the M 2+ H – ionic structure. The ground states of ScH + , YH + , and LaH + are 1 2 Δ 3/2 , 1 2 Σ + 1/2 , and 1 2 Δ 3/2 with 55.45, 60.54, and 62.34 kcal/mol bond energies, respectively. The core electron correlation was found to be vital for gaining accurate predictions on the ground and excited state properties of MH + . The spin–orbit coupling effects are minor for ScH + but become substantial moving to YH + and LaH + . Overall, the results of this work are in good agreement with the limited set of experimental findings of MH + available in the literature and will be of use for future investigations. Furthermore, the theoretical approaches, findings, and trends reported here are expected to aid studies of similar species.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2023

Review of particle deposition to and removal from clothing, skin, and hair after a radioactive airborne dispersal event

Explosive Radiological Dispersal Devices (RDD) – aka dirty bombs – are seen as a credible method to carry out a radiological terror attack. After exploding a radioactive source, the radionuclide-laden plume will be blown downwind of ground zero, with particles falling out and potentially depositing on people caught in and under the cloud. Some of these people may not show any sign of radiation sickness and therefore not realize they have been contaminated and may take the radioactive particulate with them on their daily activities, thus spreading the radioactive particulate outside the initially contaminated area. This paper reviews the scientific literature to better understand the rate at which particulate deposits on and is removed from the different “surfaces” of a person, i.e., hair, skin, and clothing. Prior research indicates that: 1) particle deposition is usually higher on skin than on hair and clothing; 2) particle deposition is greater for a person with higher skin moisture, 3) stronger wind increases the deposition flux onto a person, and 4) the fraction of particulate deposited on the hair, skin, and clothing respectively depends on the length of the hair, assuming all the hair surface is available for deposition. The studies taken into consideration show that the largest uncertainty in particulate deposition onto a person is due to clothing type because of the different possible weave arrangements and tightness which translate into differences in actual surface area and surface roughness. A factor of 2-to-20 variation in deposition rate was found. Removal of the particulate from the contaminated person may be due to wind, a person's movement, and/or contact transfer, i.e., by touching a different clean surface. Experiments show that the majority of the particulate is resuspended within 2–6 h mostly depending on the intensity of physical activity. The largest uncertainty in particulate removal from skin depends on the skin moisture, transfer rate of single-contact, and how many objects/people a person touches per hour. No data for hair were found for particle removal and resuspension. The studies considered did not utilize radionuclides directly; however, data on adhesion of radioactive vs. their non-radioactive counterpart have shown that the uncertainty due to the radioactivity of the particles is lower than that due to other factors. In conclusion, an idealized scenario involving a single building in the path of the cloud showed the impact of building-influenced flow on the cloud transport path and mixing, which affects the radiological dose the downwind population is exposed to and consequently the health effects.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2024

Remarkably High Internal Transcribed Spacer Haplotype Diversity of the Fungal Select Agent Coniothyrium glycines Discovered Throughout Its Range in Sub-Saharan Africa

Red leaf blotch of soybean, caused by the fungus Coniothyrium glycines, is a foliar disease characterized by blotching, necrosis, and defoliation that has only been reported from Africa. The species is listed as a Select Agent by the Federal Select Agent Program due to its potentially devastating impacts to soybean production should it spread to the United States. Despite its potential import, very few isolates are available for study. Herein, we obtained 96 new C. glycines isolates from six soybean-producing countries throughout sub-Saharan Africa. Along with 12 previously collected ones, we sequenced each at the internal transcribed spacer (ITS) region. Between all isolates, we identified a total of 28 single-nucleotide polymorphisms and 23 haplotypes. One hypothesis to explain the tremendous diversity uncovered at the ITS—which is generally conserved within a species—is that our current species concept of C. glycines is too broad and that there may be multiple species that cause red leaf blotch. Zambia contained the highest haplotype diversity, a significant fraction of which remains unsampled. Most haplotypes were specific to a single country, except for two, which were found in Zambia and either neighboring Mozambique or Zimbabwe. This geographic specificity indicates that the ITS region may be useful for identifying source populations or routes of transmission should this pathogen spread beyond Africa. The observed geographic partitioning of this pathogen is likely the result of millions of years of replication on little-studied native hosts, given that soybean has only been cultivated in Africa since the early 1900s.

Plant Sciences↗

DOE OSTI2021

The Binary INformation from Open Clusters Using SEDs (BINOCS) Project: Reliable Photometric Mass Determinations of Binary Star Systems in Clusters

We introduce a new binary detection technique, Binary INformation from Open Clusters using SEDs (binocs), which we show is able to determine reliable stellar multiplicity and masses over a much larger mass range than current approaches. This new technique determines accurate component masses of binary and single systems of the open clusters’ main sequence by comparing observed magnitudes from multiple photometric filters to synthetic star spectral energy distributions (SEDs), allowing us to systematically probe the binary population for low-mass stars in clusters for eight well-studied open clusters. We provide new deep, infrared photometric catalogs (1.2–8.0 μm) for the key open clusters NGC 1960 (M36), NGC 2099 (M37), NGC 2420, and NGC 2682 (M67), using observations from NOAO/NEWFIRM and Spitzer/IRAC. Using these deep multiwavelength catalogs, the binocs method is applied to these clusters to determine accurate component masses for unresolved cluster binaries. We explore binary fractions as a function of cluster age, Galactic location, and metallicity.

47 OTHER INSTRUMENTATION↗

DOE OSTI2022

Low Pathogenicity H7N3 Avian Influenza Viruses Have Higher Within-Host Genetic Diversity Than a Closely Related High Pathogenicity H7N3 Virus in Infected Turkeys and Chickens

Within-host viral diversity offers a view into the early stages of viral evolution occurring after a virus infects a host. In recent years, advances in deep sequencing have allowed for routine identification of low-frequency variants, which are important sources of viral genetic diversity and can potentially emerge as a major virus population under certain conditions. We examined within-host viral diversity in turkeys and chickens experimentally infected with closely related H7N3 avian influenza viruses (AIVs), specifically one high pathogenicity AIV (HPAIV) and two low pathogenicity AIV (LPAIVs) with different neuraminidase protein stalk lengths. Consistent with the high mutation rates of AIVs, an abundance of intra-host single nucleotide variants (iSNVs) at low frequencies of 2–10% was observed in all samples collected. Furthermore, a small number of common iSNVs were observed between turkeys and chickens, and between directly inoculated and contact-exposed birds. Notably, the LPAIVs have significantly higher iSNV diversities and frequencies of nonsynonymous changes than the HPAIV in both turkeys and chickens. These findings highlight the dynamics of AIV populations within hosts and the potential impact of genetic changes, including mutations in the hemagglutinin gene that confers the high pathogenicity pathotype, on AIV virus populations and evolution.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Role of dipole-forbidden autoionizing resonances in nonresonant one-color two-photon single ionization of N 2

We present an experimental and theoretical energy- and angle-resolved study on the photoionization dynamics of non-resonant one-color two-photon single valence ionization of neutral N$_2$ molecules. Using 9.3 eV photons produced via high harmonic generation and a 3-D momentum imaging spectrometer, we detect the photoelectrons and ions produced from one-color two-photon ionization in coincidence. Photoionization of N$_2$ populates the X $^2\Sigma^+_g$, A $^2\Pi_u$, and B $^2\Sigma^+_u$ ionic states of N$_2^+$, where the photoelectron angular distributions associated with the X $^2\Sigma^+_g$ and A $^2\Pi_u$ states both vary with changes in photoelectron kinetic energy of only a few hundred meV. We attribute the rapid evolution in the photoelectron angular distributions to the excitation and decay of dipole-forbidden autoionizing resonances that belong to series of different symmetries, all of which are members of the Hopfield series, and compete with the direct two-photon single ionization.

74 ATOMIC AND MOLECULAR PHYSICS↗