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At least 901 records · Page 50

A single amino acid change led to structural and functional differentiation of PvHd1 to control flowering in switchgrass

Abstract Switchgrass, a forage and bioenergy crop, occurs as two main ecotypes with different but overlapping ranges of adaptation. The two ecotypes differ in a range of characteristics, including flowering time. Flowering time determines the duration of vegetative development and therefore biomass accumulation, a key trait in bioenergy crops. No causal variants for flowering time differences between switchgrass ecotypes have, as yet, been identified. In this study, we mapped a robust flowering time quantitative trait locus (QTL) on chromosome 4K in a biparental F2 population and characterized the flowering-associated transcription factor gene PvHd1, an ortholog of CONSTANS in Arabidopsis and Heading date 1 in rice, as the underlying causal gene. Protein modeling predicted that a serine to glycine substitution at position 35 (p.S35G) in B-Box domain 1 greatly altered the global structure of the PvHd1 protein. The predicted variation in protein compactness was supported in vitro by a 4 °C shift in denaturation temperature. Overexpressing the PvHd1-p.35S allele in a late-flowering CONSTANS-null Arabidopsis mutant rescued earlier flowering, whereas PvHd1-p.35G had a reduced ability to promote flowering, demonstrating that the structural variation led to functional divergence. Our findings provide us with a tool to manipulate the timing of floral transition in switchgrass cultivars and, potentially, expand their cultivation range.

59 BASIC BIOLOGICAL SCIENCES↗

Functional Data Analysis for Extracting the Intrinsic Dimensionality of Spectra: Application to Chemical Homogeneity in the Open Cluster M67

High-resolution spectroscopic surveys of the Milky Way have entered the Big Data regime and have opened avenues for solving outstanding questions in Galactic archeology. However, exploiting their full potential is limited by complex systematics, whose characterization has not received much attention in modern spectroscopic analyses. In this work, we present a novel method to disentangle the component of spectral data space intrinsic to the stars from that due to systematics. Using functional principal component analysis on a sample of 18,933 giant spectra from APOGEE, we find that the intrinsic structure above the level of observational uncertainties requires ≈10 functional principal components (FPCs). Our FPCs can reduce the dimensionality of spectra, remove systematics, and impute masked wavelengths, thereby enabling accurate studies of stellar populations. To demonstrate the applicability of our FPCs, we use them to infer stellar parameters and abundances of 28 giants in the open cluster M67. We employ Sequential Neural Likelihood, a simulation-based Bayesian inference method that learns likelihood functions using neural density estimators, to incorporate non-Gaussian effects in spectral likelihoods. By hierarchically combining the inferred abundances, we limit the spread of the following elements in M67: Fe ≲ 0.02 dex; C ≲ 0.03 dex; O, Mg, Si, Ni ≲ 0.04 dex; Ca ≲ 0.05 dex; N, Al ≲ 0.07 dex (at 68% confidence). Our constraints suggest a lack of self-pollution by core-collapse supernovae in M67, which has promising implications for the future of chemical tagging to understand the star formation history and dynamical evolution of the Milky Way.

79 ASTRONOMY AND ASTROPHYSICS↗

In Situ Structural Observation of a Substrate- and Peroxide-Bound High-Spin Ferric-Hydroperoxo Intermediate in the P450 Enzyme CYP121

The P450 enzyme CYP121 from Mycobacterium tuberculosis catalyzes a carbon–carbon (C–C) bond coupling cyclization of the dityrosine substrate containing a diketopiperazine ring, cyclo(l-tyrosine-l-tyrosine) (cYY). An unusual high-spin (S = 5/2) ferric intermediate maximizes its population in less than 5 ms in the rapid freeze-quenching study of CYP121 during the shunt reaction with peracetic acid or hydrogen peroxide in acetic acid solution. Here, we show that this intermediate can also be observed in the crystalline state by EPR spectroscopy. By developing an on-demand-rapid-mixing method for time-resolved serial femtosecond crystallography with X-ray free-electron laser (tr-SFX-XFEL) technology covering the millisecond time domain and without freezing, we structurally monitored the reaction in situ at room temperature. After a 200 ms peracetic acid reaction with the cocrystallized enzyme–substrate microcrystal slurry, a ferric-hydroperoxo intermediate is observed, and its structure is determined at 1.85 Å resolution. The structure shows a hydroperoxyl ligand between the heme and the native substrate, cYY. The oxygen atoms of the hydroperoxo are 2.5 and 3.2 Å from the iron ion. The end-on binding ligand adopts a near-side-on geometry and is weakly associated with the iron ion, causing the unusual high-spin state. This compound 0 intermediate, spectroscopically and structurally observed during the catalytic shunt pathway, reveals a unique binding mode that deviates from the end-on compound 0 intermediates in other heme enzymes. The hydroperoxyl ligand is only 2.9 Å from the bound cYY, suggesting an active oxidant role of the intermediate for direct substrate oxidation in the nonhydroxylation C–C bond coupling chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Soil pH influences the structure of virus communities at local and global scales

The influence of biotic and abiotic factors on viral communities across environmental gradients in soil is relatively unknown. While soil pH strongly influences microbial community structure, it is unclear whether there is a similar influence on soil viruses. In this study, prokaryotic and viral communities were characterized in soils from a long-term pH-manipulated soil gradient (pH 4.5 and 7.5), and viral populations also compared to those of other soils ranging in pH (4.0–7.5). Viral communities were significantly influenced by pH at the local scale with 99% of viral operational taxonomic units restricted to pH 4.5 or 7.5 soil only. Analysis of viromes from six other European and North American soil systems demonstrated that a selection of viral clusters from acidic and neutral pH soils were more associated with those from the local gradient pH 4.5 or 7.5 soils, respectively. While direct pH effects on virion integrity and indirect selection via host composition were not distinguished, the results reveal that soil pH is a factor in structuring viral communities at local and global scales.

59 BASIC BIOLOGICAL SCIENCES↗

Crystallization of ApoA1 and ApoE4 Nanolipoprotein Particles and Initial XFEL-Based Structural Studies

Nanolipoprotein particles (NLPs), also called “nanodiscs”, are discoidal particles with a patch of lipid bilayer corralled by apolipoproteins. NLPs have long been of interest due to both their utility as membrane-model systems into which membrane proteins can be inserted and solubilized and their physiological role in lipid and cholesterol transport via high-density lipoprotein (HDL) and low-density lipoprotein (LDL) maturation, which are important for human health. Serial femtosecond crystallography (SFX) at X-ray free electron lasers (XFELs) is a powerful approach for structural biology of membrane proteins, which are traditionally difficult to crystallize as large single crystals capable of producing high-quality diffraction suitable for structure determination. To facilitate understanding of the specific role of two apolipoprotein/lipid complexes, ApoA1 and ApoE4, in lipid binding and HDL/LDL particle maturation dynamics, and to develop new SFX methods involving NLP membrane protein encapsulation, we have prepared and crystallized homogeneous populations of ApoA1 and ApoE4 NLPs. Crystallization of empty NLPs yields semi-ordered objects that appear crystalline and give highly anisotropic and diffuse X-ray diffraction, similar to fiber diffraction. Several unit cell parameters were approximately determined for both NLPs from these measurements. Thus, low-background, sample conservative methods of delivery are critical. Here we implemented a fixed target sample delivery scheme utilizing the Roadrunner fast-scanning system and ultra-thin polymer/graphene support films, providing a low-volume, low-background approach to membrane protein SFX. This study represents initial steps in obtaining structural information for ApoA1 and ApoE4 NLPs and developing this system as a supporting scaffold for future structural studies of membrane proteins crystalized in a native lipid environment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The fluorescence of cometary OH

A new solar spectral atlas, improved oscillator strengths, and additional transitions have been incorporated in calculations of the fluorescent equilibrium of the OH molecule in comets as a function of heliocentric distance and radial velocity. Comparisons of detailed, ultraviolet band profiles have been made with the observed, high-resolution spectra of eight comets. While a purely fluorescent equilibrium calculation is sufficient to reproduce the major variations seen in the band structure from one comet to another, some collisional quenching of the inversion of the X2II3/2 Lambda-doublet ground state is required to match the detailed features. The relative population inversion of the upper and lower levels of the ground state is also calculated as a function of both distance and velocity, with the results being consistent with 18 cm radio observations. Predictions of the infrared OH vibrational bands are made; the 1-0 band should be observable if a sufficiently high spectral resolution is employed.

Schleicher, David G.↗

Non-parabolic hydrodynamic formulations for the simulation of inhomogeneous semiconductor devices

Hydrodynamic models are becoming prevalent design tools for small scale devices and other devices in which high energy effects can dominate transport. Most current hydrodynamic models use a parabolic band approximation to obtain fairly simple conservation equations. Interest in accounting for band structure effects in hydrodynamic device simulation has begun to grow since parabolic models can not fully describe the transport in state of the art devices due to the distribution populating non-parabolic states within the band. This paper presents two different non-parabolic formulations of the hydrodynamic model suitable for the simulation of inhomogeneous semiconductor devices. The first formulation uses the Kane dispersion relationship (hk)(exp 2)/2m = W(1 + alpha(W)). The second formulation makes use of a power law ((hk)(exp 2)/2m = xW(sup y)) for the dispersion relation. Hydrodynamic models which use the first formulation rely on the binomial expansion to obtain moment equations with closed form coefficients. This limits the energy range over which the model is valid. The power law formulation readily produces closed form coefficients similar to those obtained using the parabolic band approximation. However, the fitting parameters (x,y) are only valid over a limited energy range. The physical significance of the band non-parabolicity is discussed as well as the advantages/disadvantages and approximations of the two non-parabolic models. A companion paper describes device simulations based on the three dispersion relationships: parabolic, Kane dispersion, and power low dispersion.

Smith, Arlynn W.↗

An Aerodynamic Analysis of a Spinning Missile with Dithering Canards

A generic spinning missile with dithering canards is used to demonstrate the utility of an overset structured grid approach for simulating the aerodynamics of rolling airframe missile systems. The approach is used to generate a modest aerodynamic database for the generic missile. The database is populated with solutions to the Euler and Navier-Stokes equations. It is used to evaluate grid resolution requirements for accurate prediction of instantaneous missile loads and the relative aerodynamic significance of angle-of-attack, canard pitching sequence, viscous effects, and roll-rate effects. A novel analytical method for inter- and extrapolation of database results is also given.

Meakin, Robert L.↗

Mercuryʼs Circumsolar Dust Ring as an Imprint of a Recent Impact

A circumsolar dust ring has been recently discovered close to the orbit of Mercury. There are currently no hypotheses for the origin of this ring in the literature, so we explore four different origin scenarios here: the dust originated from (1) the sporadic meteoroid complex that comprises the major portion of the Zodiacal Cloud, (2) recent asteroidal/cometary activity, (3) hypothetical dust-generating bodies locked in mean-motion resonances beyond Mercury, and (4) bodies co-orbiting with Mercury. We find that only scenario (4) reproduces the observed structure and location of Mercury's dust ring. However, the lifetimes of Mercury's co-orbitals (<20 Ma) preclude a primordial origin of the co-orbiting source population due to dynamical instabilities and meteoroid bombardment, demanding a recent event feeding the observed dust ring. We find that an impact on Mercury can eject debris into the co-orbital resonance. We estimate the ages of six candidate impacts that formed craters larger than 40 km in diameter using high-resolution spacecraft data from MESSENGER and find two craters with estimated surface ages younger than 50 Ma. We find that the amount of mass transported from Mercury's surface into the co-orbital resonance from these two impacts is several orders of magnitude smaller than what is needed to explain the magnitude of Mercury's ring inferred from remote sensing. Therefore we suggest that numerous younger, smaller impacts collectively contributed to the origin of the ring. We conclude that the recent impact hypothesis for the origin of Mercury's dust ring is a viable scenario, whose validity can be constrained by future inner solar system missions.

Petr Pokorny↗

On the magnetic structure of the quiet transition region

Existing models of the quiet chromosphere-corona transition region predict a distribution of emission measure over temperature that agrees with observation for a T greater than about 100,000 K. These 'network' models assume that all magnetic field lines that emerge from the photosphere extend into and are in thermal contact with the corona. It is shown that the observed fine-scale structure of the photospheric magnetic network instead suggests a two-component picture in which magnetic funnels that open into the corona emerge from only a fraction of the network. The gas that makes up the hotter transition region is mostly contained within these funnels, as in standard models, but, because the funnels are more constricted in our picture, the heat flowing into the cooler transition region from the corona is reduced by up to an order of magnitude. The remainder of the network is occupied by a population of low-lying loops with lengths less than about 10,000 km. It is proposed that the cooler transition region is mainly located within such loops, which are magnetically insulated from the corona and must, therefore, be heated internally. The fine-scale structure of ultraviolet spectroheliograms is consistent with this proposal, and theoretical models of internally heated loops can explain the behavior of the emission measure below a T of aobut 100,000 K.

Rabin, D.↗

Observations of the impact of starbursts on the interstellar medium in dwarf galaxies

Dwarf galaxies play a crucial role in our understanding of the formation and evolution of galaxies, and the concept of supernova-driven mass outflows is a vital ingredient in theories of the structure and evolution of dwarf galaxies. Despite the theoretical importance of these outflows, there is a very limited amount of direct observational evidence for their existence. We have therefore begun a detailed multi-wave-band search for outflows in dwarf (M(sub B) greater than or = -18) galaxies with extensive recent or ongoing centrally concentrated star formation. We report the first results of this search in the present paper. Observations of the ionized gas in dwarf amorphous galaxies with centrally concentrated populations of massive stars provide evidence for the large-scale expansion of their expansion of their ionized interstellar media. Fabry-Perot H alpha images reveal the presence of kiloparsec-scale 'superbubbles' and filaments which tend to be oriented along the galaxy minor axis. These structures are comparable in size to the chracteristic optical sizes of the galaxies, and dominate the morphology of the galaxies at low surface brightness in H alpha. Since expanding structure of this size and velocity are not observed in all low-mass galaxies with recent or ongoing star formation, we suggest that we are witnessing transient events that likely have a relatively low 'duty cycle' in such galaxies. That is, we argue that the particular galaxies in the present paper have had significantly elevated star formation rates over the past 10(exp 7)-10(exp 8) yr (i.e., these are starburst or young poststarburst systems). This interpretation is consistent with the optical colors and emission-line properties of these galaxies.

Marlowe, Amanda T.↗

Low spin spectroscopy of neutron-rich Cl 43 , 44 , 45 via β - and β n decay

In this article, β - decay studies of neutron-rich isotopes 43,45 S performed at the National Superconducting Cyclotron Laboratory are reported. β -delayed $\gamma$ transitions were detected by an array of 16 clover detectors surrounding the Beta Counting Station, which consists of a 40×40 double-sided silicon strip detector followed by a single-sided silicon strip detector. β -decay half-lives were extracted for 43,45 S by correlating implants and decays in the pixelated implant detector and by considering further coincidences with $\gamma$ transitions in the daughter nuclei. Further, the level structures of 43,45 Cl are expanded by the addition of 20 and 8 new $\gamma$ transitions in 43 Cl and 45 Cl respectively, and core-excited negative-parity states were observed in both nuclei for the first time. For 45 S, a large fraction of the β -decay strength was observed feeding neutron-unbound states in 45 Cl, which, decaying by delayed neutrons, populated excited states in the β ⁢1⁢ n daughter, 44 Cl. Experimental observations were compared to detailed shell-model calculations using the SDPFSDG-MU interaction to highlight the role of the diminished N = 28 neutron shell gap and the near degeneracy of the proton s 1/2 and d 3/2 orbitals in the structure of the neutron-rich Cl isotopes. The current work also provides further support to a ground-state spin-parity assignment of 3/2 + in 45 Cl.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Relics of interspecific hybridization retained in the genome of a drought-adapted peanut cultivar

Peanut (Arachis hypogaea L.) is a globally important oil and food crop frequently grown in arid, semi-arid, or dryland environments. Improving drought tolerance is a key goal for peanut crop improvement efforts. Here, we present the genome assembly and gene model annotation for “Line8,” a peanut genotype bred from drought-tolerant cultivars. Our assembly and annotation are the most contiguous and complete peanut genome resources currently available. The high contiguity of the Line8 assembly allowed us to explore structural variation both between peanut genotypes and subgenomes. We detect several large inversions between Line8 and other peanut genome assemblies, and there is a trend for the inversions between more genetically diverged genotypes to have higher gene content. We also relate patterns of subgenome exchange to structural variation between Line8 homeologous chromosomes. Unexpectedly, we discover that Line8 harbors an introgression from A.cardenasii, a diploid peanut relative and important donor of disease resistance alleles to peanut breeding populations. The fully resolved sequences of both haplotypes in this introgression provide the first in situ characterization of A.cardenasii candidate alleles that can be leveraged for future targeted improvement efforts. The completeness of our genome will support peanut biotechnology and broader research into the evolution of hybridization and polyploidy.

60 APPLIED LIFE SCIENCES↗

Population Aging and Heat Exposure in the 21st Century: Which U.S. Regions Are at Greatest Risk and Why?

Abstract Background and Objectives The co-occurring trends of population aging and climate change mean that rising numbers of U.S. older adults are at risk of intensifying heat exposure. We estimate county-level variations in older populations’ heat exposure in the early (1995–2014) and mid (2050) 21st century. We identify the extent to which rising exposures are attributable to climate change versus population aging. Research Design and Methods We estimate older adults’ heat exposure in 3,109 counties in the 48 contiguous U.S. states. Analyses use NASA NEX Global Daily Downscaled Product (NEX-GDDP-CMIP6) climate data and county-level projections for the size and distribution of the U.S. age 69+ population. Results Population aging and rising temperatures are documented throughout the United States, with particular “hotspots” in the Deep South, Florida, and parts of the rural Midwest. Increases in heat exposure by 2050 will be especially steep in historically colder regions with large older populations in New England, the upper Midwest, and rural Mountain regions. Rising temperatures are driving exposure in historically colder regions, whereas population aging is driving exposure in historically warm southern regions. Discussion and Implications Interventions to address the impacts of temperature extremes on older adult well-being should consider the geographic distribution and drivers of this exposure. In historically cooler areas where climate change is driving exposures, investments in warning systems may be productive, whereas investments in health care and social services infrastructures are essential in historically hot regions where exposures are driven by population aging.

60 APPLIED LIFE SCIENCES↗

A GALAH view of the chemical homogeneity and ages of stellar strings identified in Gaia

ABSTRACT The advent of Gaia has led to the discovery of nearly 300 elongated stellar associations (called ‘strings’) spanning hundreds of parsecs in length and mere tens of parsecs in width. These newfound populations present an excellent laboratory for studying the assembly process of the Milky Way thin disc. In this work, we use data from GALAH DR3 to investigate the chemical distributions and ages of 18 newfound stellar populations, 10 of which are strings and 8 of which are compact in morphology. We estimate the intrinsic abundance dispersions in [X/H] of each population and compare them with those of both their local fields and the open cluster (OC) M 67. We find that all but one of these groups are more chemically homogeneous than their local fields. Furthermore, half of the strings, namely Theias 139, 169, 216, 303, and 309, have intrinsic [X/H] dispersions that range between 0.01 and 0.07 dex in most elements, equivalent to those of many OCs. These results provide important new observational constraints on star formation and the chemical homogeneity of the local interstellar medium (ISM). We investigate each population’s Li and chemical clock abundances (e.g. [Sc/Ba], [Ca/Ba], [Ti/Ba], and [Mg/Y]) and find that the ages suggested by chemistry generally support the isochronal ages in all but six structures. This work highlights the unique advantages that chemistry holds in the study of kinematically related stellar groups.

79 ASTRONOMY AND ASTROPHYSICS↗

Recombination smooths the time-signal disrupted by latency in within-host HIV phylogenies

Within-host HIV evolution involves several features that may disrupt standard phylogenetic reconstruction. One important feature is re-activation of latently integrated provirus, which has the potential to disrupt the temporal signal, leading to variation in the branch lengths and apparent evolutionary rates in a tree. Yet, real within-host HIV phylogenies tend to show clear, ladder-like trees structured by the time of sampling. Another important feature is recombination, which violates the fundamental assumption that evolutionary history can be represented by a single bifurcating tree. Thus, recombination complicates the within-host HIV dynamic by mixing genomes and creating evolutionary loop structures that cannot be represented in bifurcating trees. In this paper, we develop a coalescent-based simulator of within-host HIV evolution that includes latency, recombination, and effective population size dynamics that allows us to study the relationship between the true, complex genealogy of within-host HIV evolution, encoded as an Ancestral Recombination Graph (ARG), and the observed phylogenetic tree. To compare our ARG results to the familiar phylogeny format, we calculate the expected bifurcating tree after decomposing the ARG into all unique site trees, their combined distance matrix, and the overall corresponding bifurcating tree. While latency and recombination separately disrupt the phylogenetic signal, remarkably, we find that recombination recovers the temporal signal of within-host HIV evolution caused by latency by mixing fragments of old, latent genomes into the contemporary population. In effect, recombination averages over extant heterogeneity, whether it stems from mixed time-signals or population bottlenecks. Further, we establish that the signals of latency and recombination can be observed in phylogenetic trees despite being an incorrect representation of the true evolutionary history. Using an Approximate Bayesian Computation method, we develop a set of statistical probes to tune our simulation model to nine longitudinally-sampled within-host HIV phylogenies. Because ARGs are exceedingly difficult to infer from real HIV data, our simulation system allows investigating effects of latency, recombination, and population size bottlenecks by matching decomposed ARGs to real data as observed in standard phylogenies.

59 BASIC BIOLOGICAL SCIENCES↗

Spectroscopy of states in 136 Ba using the 138 Ba(p,t) reaction

Background: The 136 Ba isotope is the daughter nucleus in 136 Xe $ββ$ decay. It also lies in a shape transitional region of the nuclear chart, making it a suitable candidate to test a variety of nuclear models. Purpose: To obtain spectroscopic information on states in 136 Ba, which will allow a better understanding of its low-lying structure. These data may prove useful to constrain future 136 Xe → 136 Ba neutrinoless $ββ$ decay matrix element calculations. Methods: Here, a 138 Ba(p, t) reaction was used to populate states in 136 Ba up to approximately 4.6 MeV in excitation energy. The tritons were detected using a high-resolution Q3D magnetic spectrograph. A distorted wave Born approximation analysis was performed for the measured triton angular distributions. Results: 102 excited states in 136 Ba were observed, out of which 52 are reported for the first time. Definite spin-parity assignments are made for 26 newly observed states, while previously ambiguous assignments for ten other states are resolved. Together with other available data, the results are used to determine level densities in 136 Ba. These were compared with theory predictions, obtained using shell model calculations with Hamiltonians previously used for 136 Xe neutrinoless $ββ$ decay matrix element evaluations. Conclusions: The shell model predicted level densities agree reasonably well for the two Hamiltonians. However the results for theory and experiment are found to agree only at lower energies, diverging from one another for the higher lying states, with the discrepancy increasing with energy. This is presumably because of lower production cross sections for a majority of the higher-lying predicted states and the experimental limitations in resolving a large number of nearly degenerate states predicted by the theory.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

PacWave South SeaRAY k2 Risk Registers

The SeaRAY is a deployable power system for maritime sensors, monitoring equipment, communications, unmanned underwater vehicles, and other similar payloads. This project is to design, deliver, and test a prototype low-power WEC that lowers the total cost of ownership and provides robust, new capabilities for customers in the maritime environment. Failure Modes, Effects, and Criticality Analysis (FMECA) is conducted to systematically identify all potential failure modes and their effects on the system, and to analyze the criticality of each risk based on the likelihood of the event and the severity of the impact. Actions may then be recommended to mitigate the criticality of a risk, either by reducing the likelihood of the risk or the severity of its impact. Risk assessment is executed iteratively as an integral part of the design process. By incorporating risk assessment early in the development cycle, mitigation of risk can be achieved cost effectively. The actions recommended to mitigate risk may be subsequently executed, and as the design progresses the risk assessment is reviewed and revised. Review of the risk assessment is integrated into structured design reviews, ensuring that critical risks are comprehended and that the Project will not progress to e.g. fabrication while intolerable risks remain. The risk assessment process results in the population and maintenance of Risk Registers (RRs). Each major system (and as needed, subsystem) will have a distinct RR. This allows each system or subsystem to be assessed individually, rendering the RRs to a manageable size for review.

16 TIDAL AND WAVE POWER↗