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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

A MULTIWAVELENGTH STUDY OF THREE HYBRID BLAZARS

We present multiwavelength imaging observations of PKS 1045−188, 8C 1849+670, and PKS 2216−038, three radio-loud active galactic nuclei from the MOJAVE-Chandra Sample that straddle the Fanaroff-Riley (FR) boundary between low- and high-power jets. These hybrid sources provide an excellent opportunity to study jet emission mechanisms and the influence of the external environment. We used archival VLA observations, and new Hubble and Chandra observations to identify and study the spectral properties of five knots in PKS 1045−188, two knots in 8C 1849+670, and three knots in PKS 2216−038. For the seven X-ray visible knots, we constructed and fit the broadband spectra using synchrotron and inverse Compton/cosmic microwave background (IC/CMB) emission models. In all cases, we found that the lack of detected optical emission ruled out the X-ray emission from the same electron population that produces radio emission. All three sources have high total extended radio power, similar to that of FR II sources. We find this is in good agreement with previously studied hybrid sources, where high-power hybrid sources emit X-rays via IC/CMB and the low-power hybrid sources emit X-rays via synchrotron emission. This supports the idea that it is total radio power rather than FR morphology that determines the X-ray emission mechanism. We found no significant asymmetries in the diffuse X-ray emission surrounding the host galaxies. Sources PKS 1045−188 and 8C 1849+670 show significant differences in their radio and X-ray termination points, which may result from the deceleration of highly relativistic bulk motion.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Structures of ligand-occupied β-Klotho complexes reveal a molecular mechanism underlying endocrine FGF specificity and activity

The three members of the endocrine fibroblast growth factor (FGF) family designated FGF19, FGF21, and FGF23 mediate their pleiotropic cellular effects by binding to and activating binary complexes composed of an FGF receptor (FGFR) bound to either α-Klotho or β-Klotho receptors. Structural analyses of ligandoccupied Klotho extracellular domains have provided important insights concerning mechanisms underlying the binding specificities of FGF21 and FGF23 to β-Klotho or α-Klotho, respectively. They have also demonstrated that Klotho proteins function as primary high-affinity receptors while FGFRs function as the catalytic subunits that mediate intracellular signaling. In this paper we describe the crystal structure the C-terminal tail of FGF19 (FGF19 CT ) bound to sKLB and demonstrate that FGF19 CT and FGF21 CT bind to the same binding site on sKLB, via a multiturn D-P motif to site 1 and via a SP- S motif to the pseudoglycoside hydrolase region (site 2). Binding affinities to sKLB and cellular stimulatory activities of FGF19 CT , FGF21 CT , and a variety of chimeric mutants to cells expressing β-Klotho together with FGFR1c or FGFR4 were also analyzed. These experiments as well as detailed comparison of the structures of free and ligand-occupied sKLB to the structure of ligandoccupied sKLA reveal a general mechanism for recognition of endocrine FGFs by Klotho proteins and regulatory interactions with FGFRs that control their pleiotropic cellular responses.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Plant root associated chitinases: structures and functions

Chitinases degrade chitin, a linear homopolymer of β-1,4-linked N-acetyl-D-glucosamine (GlcNAc) residues found in the cell walls of fungi and the exoskeletons of arthropods. They are secreted by the roots into the rhizosphere, a complex and dynamic environment where intense nutrient exchange occurs between plants and microbes. Here we modeled, expressed, purified, and characterized Zea mays and Oryza sativa root chitinases, and the chitinase of a symbiotic bacterium, Chitinophaga oryzae 1303 for their activities with chitin, di-, tri-, and tetra-saccharides and Aspergillus niger, with the goal of determining their role(s) in the rhizosphere and better understanding the molecular mechanisms underlying plant-microbe interactions. We show that Zea mays basic endochitinase (ZmChi19A) and Oryza sativa chitinase (OsChi19A) are from the GH19 chitinase family. The Chitinophaga oryzae 1303 chitinase (CspCh18A) belongs to the GH18 family. The three enzymes have similar apparent K M values of (20-40 µM) for the substrate 4-MU-GlcNAc 3 . They vary in their pH and temperature optima with OsChi19A activity optimal between pH 5–7 and 30–40°C while ZmChi19A and CspCh18A activities were optimal at pH 7-9 and 50–60°C. Modeling and site-directed mutation of ZmChi19A identified the catalytic cleft and the active residues E147 and E169 strategically positioned at ~8.6Å from each other in the folded protein. Cleavage of 4-MU-GlcNAc 3 was unaffected by the absence of the CBD but diminished in the absence of the flexible C-terminal domain. However, unlike for the soluble substrate, the CBD and the newly identified flexible C-terminal domain were vital for inhibiting Aspergillus niger growth. The results are consistent with the involvement of the plant chitinases in defense against pathogens like fungi that have chitin exoskeletons. In summary, we have characterized the functional features and structural domains necessary for the activity of two plant root chitinases that are believed to be involved in plant defense and a bacterial chitinase that, along with the plant chitinases, may participate in nutrient recycling in the rhizosphere.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Quasi-periodic Oscillations in Flares and Coronal Mass Ejections Associated with Magnetic Reconnection

We propose a mechanism for quasi-periodic oscillations of both coronal mass ejections (CMEs) and flare loops as related to magnetic reconnection in eruptive solar flares. We perform two-dimensional numerical MHD simulations of magnetic flux rope eruption, with three different values of the global Lundquist number. In the low Lundquist number run, no oscillatory behavior is found. In the moderate Lundquist number run, on the other hand, quasi-periodic oscillations are excited both at the bottom of the flux rope and at the flare loop top. In the high Lundquist number run, quasi-periodic oscillations are also excited; in the meanwhile, the dynamics become turbulent owing to the formation of multiple plasmoids in the reconnection current sheet. In high and moderate Lundquist number runs, thin reconnection jets collide with the flux rope bottom or flare loop top and dig them deeply. Steep oblique shocks are formed as termination shocks where reconnection jets are bent (rather than decelerated) in the horizontal direction, resulting in supersonic backflows. The structure becomes unstable, and quasi-periodic oscillations of supersonic backflows appear at locally confined high-beta regions at both the flux rope bottom and flare loop top. We compare the observational characteristics of quasi-periodic oscillations in erupting flux ropes, post-CME current sheets, flare ribbons, and light curves with corresponding dynamical structures found in our simulation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2019

Structures of ATP-bound DNA ligase D in a closed domain conformation reveal a network of amino acid and metal contacts to the ATP phosphates

DNA ligases are the sine qua non of genome integrity and essential for DNA replication and repair in all organisms. DNA ligases join 3'-OH and 5'-PO 4 ends via a series of three nucleotidyl transfer steps. In step 1, ligase reacts with ATP or NAD + to form a covalent ligase-(lysyl-N$ζ$)–AMP intermediate and release pyrophosphate (PP i ) or nicotinamide mononucleotide. In step 2, AMP is transferred from ligase-adenylate to the 5'-PO 4 DNA end to form a DNA-adenylate intermediate (AppDNA). In step 3, ligase catalyzes attack by a DNA 3'-OH on the DNA-adenylate to seal the two ends via a phosphodiester bond and release AMP. Eukaryal, archaeal, and many bacterial and viral DNA ligases are ATP-dependent. The catalytic core of ATP-dependent DNA ligases consists of an N-terminal nucleotidyltransferase domain fused to a C-terminal OB domain. Here we report crystal structures at 1.4–1.8 Å resolution of Mycobacterium tuberculosis LigD, an ATP-dependent DNA ligase dedicated to nonhomologous end joining, in complexes with ATP that highlight large movements of the OB domain (~50 Å), from a closed conformation in the ATP complex to an open conformation in the covalent ligase-AMP intermediate. The LigD·ATP structures revealed a network of amino acid contacts to the ATP phosphates that stabilize the transition state and orient the PP i leaving group. A complex with ATP and magnesium suggested a two-metal mechanism of lysine adenylylation driven by a catalytic Mg 2+ that engages the ATP $α$ phosphate and a second metal that bridges the ATP $β$ and $γ$ phosphates.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Discovering Blind Geothermal Systems in the Great Basin Region: An Integrated Geologic and Geophysical Approach for Establishing Geothermal Play Fairways: All Phases

Most geothermal resources in the Great Basin region of the western USA are blind, and thus the discovery of new commercial-grade systems requires synthesis of favorable characteristics for geothermal activity. The geothermal play fairway concept involves integration of multiple parameters indicative of geothermal activity to identify promising areas for new development. This project integrated multiple datasets to apply the play fairway concept and assess geothermal potential in a large region of the Great Basin in Nevada. It is therefore referred to as the Nevada play fairway project. This project was a strong collaborative effort between several organizations, led by the Nevada Bureau of Mines and Geology at the University of Nevada, Reno, but with key support from the U.S. Geological Survey, ATLAS Geosciences, Inc,, Hi-Q Geophysical, Inc., Lawrence Berkeley National Laboratory, Utah Geological Survey, and Innovative Geothermal Ltd. In Budget Period 1 of this project, available data for nine geologic, geochemical, and geophysical parameters were initially synthesized to produce a new detailed geothermal potential map of 96,000 km2 from west-central to eastern Nevada. These parameters were grouped into subsets and individually weighted to delineate rankings for local permeability, intermediate permeability, regional permeability, and thermal potential, which collectively defined geothermal play fairways (i.e., most likely locations for significant geothermal fluid flow). This initial work was aimed at reducing the risks in regional exploration and therefore facilitating discovery of new commercial-grade systems in blind settings, as well as in areas with surface expressions of geothermal activity. Budget Period 2 of the project involved detailed analysis of some of the most promising areas identified in Phase 1. Twenty-four highly prospective areas, including both known undeveloped systems and previously undiscovered potential blind systems, were identified for further analysis. After reconnaissance of these areas, five of the most promising sites were selected for detailed studies. Multiple techniques were employed in the detailed studies, including geologic mapping, shallow temperature surveys, gravity surveys, Lidar, geochemical studies, seismic reflection analysis, and 3D modeling. The goal of the detailed studies was to identify specific areas with the highest likelihood for high permeability and thermal fluids, such that drill sites could be targeted. Three main sets of predictive maps were generated for each detailed study area: 1) play fairway maps, 2) play fairway error maps, and 3) direct evidence maps. Local- and intermediate-scale permeability models were revised to reflect results of the detailed geologic, geophysical, and geochemical analyses. Budget Period 3 of the project involved more detailed geophysical analyses and temperature-gradient (TG) drilling in southeastern Gabbs Valley and northern Granite Springs Valley, deemed the two most promising sites, with the goal of providing preliminary validation of the play fairway methodology. In southeastern Gabbs Valley, the collocation of a favorable structural setting (displacement transfer zone and fault intersections), Quaternary faults, intersecting and terminating gravity gradients, magnetic low, shallow (2 m) temperature anomaly, low resistivity anomaly, and promising geothermometry from nearby water wells provided evidence for a blind system. Drilling of six TG holes defines an apparent geothermal system at this locality with temperatures as high as 124°C at 152 m. This system is blind, with no surface hot springs, fumaroles, or paleo-geothermal deposits. For northern Granite Springs Valley, a favorable structural setting (termination of a major Quaternary normal fault), terminating gravity gradient, magnetic gradient, newly discovered sinter deposits, nearby warm water wells, previously drilled TG holes in the vicinity, and promising geothermometry suggest a hidden system. Drilling of six new TG holes yields temperatures of ~96°C at ~250 m, suggesting the presence of a geothermal system. Major lessons learned in the course of this project include: 1) initially identified sites commonly include multiple favorable structural settings at a finer scale; 2) promising sites in Cenozoic basins cannot be recognized without detailed geophysical surveys; and 3) play fairway analysis should be refined as the exploration program vectors into the most promising sites and finer-scale data are acquired. In addition to producing copious amounts of data, this project resulted in 16 published papers, 10 abstracts, more than 40 presentations across the U.S. and abroad (including several keynote addresses), 2 Masters theses, and 7 media reports.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

Understanding the evolution of double perovskite band structure upon dimensional reduction

Recent investigations into the effects of dimensional reduction on halide double perovskites have revealed an intriguing change in band structure when the three-dimensional (3D) perovskite is reduced to a two-dimensional (2D) perovskite with inorganic sheets of monolayer thickness (n = 1). The indirect bandgap of 3D Cs 2 AgBiBr 6 becomes direct in the n = 1 perovskite whereas the direct bandgap of 3D Cs 2 AgTlBr 6 becomes indirect at the n = 1 limit. Here, we apply a linear combination of atomic orbitals approach to uncover the orbital basis for this bandgap symmetry transition with dimensional reduction. We adapt our previously established method for predicting band structures of 3D double perovskites for application to their 2D congeners, emphasizing new considerations required for the 2D lattice. In particular, we consider the inequivalence of the terminal and bridging halides and the consequences of applying translational symmetry only along two dimensions. The valence and conduction bands of the layered perovskites can be derived from symmetry adapted linear combinations of halide p orbitals propagated across the 2D lattice. The dispersion of each band is then determined by the bonding and antibonding interactions of the metal and halide orbitals, thus affording predictions of the essential features of the band structure. We demonstrate this analysis for 2D Ag–Bi and Ag–Tl perovskites with sheets of mono- and bilayer thickness, establishing a detailed understanding of their band structures, which enables us to identify the key factors that drive the bandgap symmetry transitions observed at the n = 1 limit. Importantly, these insights also allow us to make the general prediction that direct → indirect or indirect → direct bandgap transitions in the monolayer limit are most likely in double perovskite compositions that involve participation of metal d orbitals at the band edges or that have no metal-orbital contributions to the valence band, laying the groundwork for the targeted realization of this phenomenon.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2010

An intact SAM-dependent methyltransferase fold is encoded by the human endothelin-converting enzyme-2 gene

A recent survey of protein expression patterns in patients with Alzheimer's disease (AD) has identified ece2 (chromosome: 3; Locations: 3q27.1) as the most significantly downregulated gene within the tested group. ece2 encodes endothelin-converting enzyme ECE2, a metalloprotease with a role in neuropeptide processing. Deficiency in the highly homologous ECE1 has earlier been linked to increased levels of AD-related {beta}-amyloid peptide in mice, consistent with a role for ECE in the degradation of that peptide. Initially, ECE2 was presumed to resemble ECE1, in that it comprises a single transmembrane region of {approx}20 residues flanked by a small amino-terminal cytosolic segment and a carboxy-terminal lumenar peptidase domain. The carboxy-terminal domain has significant sequence similarity to both neutral endopeptidase, for which an X-ray structure has been determined, and Kell blood group protein. After their initial discovery, multiple isoforms of ECE1 and ECE2 were discovered, generated by alternative splicing of multiple exons. The originally described ece2 transcript, RefSeq NM{_}174046, contains the amino-terminal cytosolic portion followed by the transmembrane region and peptidase domain (Fig. 1, isoform B). Another ece2 transcript, available from the Mammalian Gene Collection under MGC2408 (Fig. 1, isoform C), RefSeq accession NM{_}032331, is predicted to be translated into a 255 residue peptide with low but detectable sequence similarity to known S-adenosyl-L-methionine (SAM)-dependent methyltransferases (SAM-MTs), such as the hypothetical protein TT1324 from Thermus thermophilis, PDB code 2GS9, which shares 30% amino acid sequence identity with ECE2 over 138 residues of the sequence. Intriguingly, another 'elongated' ece2 transcript (Fig. 1, isoform A) (RefSeq NM{_}014693) contains an amino-terminal portion of the putative SAM-MT domain, the transmembrane domain, and the protease domain. This suggests the possibility for coexistence of the putative SAM-MT and protease domains in a single polypeptide and their transmembrane interplay. Although sequence conservation across the SAM-MT family is weak, the structural fold is highly conserved. The most conserved part of this fold is the SAM-binding subdomain, which is shared between MGC2408 and hypothetical protein TT1324. Typically, the SAM-binding subdomain is flanked by a variable Nterminal extension and, at the C-terminus, by a substrate- binding subdomain, which varies enormously in size but preserves a conserved topology with three antiparallel b-strands. The 'elongated' transcript of ece2 lacks this substrate-binding subdomain. To test the hypothesis that the 255 residue ece2 gene product MGC2408 represents a complete SAM-MT fold, we have determined a crystal structure of this protein in the presence of SAH.

36 MATERIALS SCIENCE↗
DOE OSTI2016

Structural and Kinetic Analysis of Miscoding Opposite the DNA Adduct 1, N 6 -Ethenodeoxyadenosine by Human Translesion DNA Polymerase $η$

1, N 6 -Ethenodeoxyadenosine (1, N 6 -ϵdA) is the major etheno lesion formed in the reaction of DNA with epoxides substituted with good leaving groups ( e.g. vinyl chloride epoxide). This lesion is also formed endogenously in DNA from lipid oxidation. Recombinant human DNA polymerase η (hpol η) can replicate oligonucleotide templates containing 1, N 6 -ϵdA. In steady-state kinetic analysis, hpol η preferred to incorporate dATP and dGTP, compared with dTTP. Mass spectral analysis of incorporation products also showed preferred purine (A, G) incorporation and extensive –1 frameshifts, suggesting pairing of the inserted purine and slippage before further replication. Five x-ray crystal structures of hpol η ternary complexes were determined, three at the insertion and two at the extension stage. We report two insertion complexes revealed incoming non-hydrolyzable dATP or dGTP analogs not pairing with but instead in a staggered configuration relative to 1, N 6 -ϵdA in the anti conformation, thus opposite the 5'-T in the template, explaining the proclivity for frameshift misincorporation. In another insertion complex, dTTP was positioned opposite 1, N 6 -ϵdA, and the adduct base was in the syn conformation, with formation of two hydrogen bonds. At the extension stage, with either an incorporated dA or dT opposite 1, N 6 -ϵdA and 2'-deoxythymidine-5'-[(α,β)-imido]triphosphate opposite the 5'-A, the 3'-terminal nucleoside of the primer was disordered, consistent with the tendency not to incorporate dTTP opposite 1, N 6 -ϵdA. Collectively, the results show a preference for purine pairing opposite 1, N 6 -ϵdA and for –1 frameshifts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Structures of vertebrate R2 retrotransposon complexes during target-primed reverse transcription and after second-strand nicking

R2 retrotransposons are site-specific eukaryotic non–long terminal repeat retrotransposons that copy and paste into gene loci encoding ribosomal RNAs. Recently, we demonstrated that avian A-clade R2 proteins achieve efficient and precise insertion of transgenes into their native safe-harbor loci in human cells. The features of A-clade R2 proteins that support gene insertion are not well characterized. Here, we report high-resolution cryo–electron microscopy structures of two vertebrate A-clade R2 proteins at the initiation of target-primed reverse transcription and after cDNA synthesis and second-strand nicking. Using biochemical and cellular assays, we illuminate the basis for high selectivity of template use and unique roles for each of the three zinc-finger domains in nucleic acid recognition. Reverse transcriptase active site architecture is reinforced by an unanticipated insertion motif specific to vertebrate A-clade R2 proteins. Our work provides the first insights into A-clade R2 protein structure during gene insertion and may enable future improvement and adaptation of R2-based systems for precise transgene insertion.

Science & Technology - Other Topics↗
DOE OSTI2021

SPRUCE Diurnal and Seasonal Patterns of Water Potential in S1 Bog and SPRUCE Experimental Plot Vegetation beginning in 2010

This data set reports on water potential from excised terminal shoots or leaves (Mainthemum only) of vegetation at the SPRUCE site located in the S1 bog. Pretreatment measurements were collected from outside plots within the S1 bog. Post treatments were collected from inside SPRUCE plots. Water potential was measured on the overstory canopy species, consisting of the evergreen Picea mariana (Mill.) B.S.P. (black spruce) and deciduous Larix laricina (Du Roi) K. Koch (tamarack) trees, and ericaceous shrubs < 1 m tall, consisting of the evergreen Rhododendron groenlandicum (Oeder) Kron & Judd (Labrador tea) and Chamaedaphne calyculata (L.) Moench. (leatherleaf). Some measurement campaigns also included the evergreen Kalmia polifolia, Wangenh. (bog laurel), the deciduous Vaccinium angustifolium (Aiton) (blueberry), and the herbaceous Maianthemum trifolium (L.) Sloboda (three-leaf false Solomon’s seal). This dataset contains one data file in comma-separated (*.csv) format. This is the second release of water potential data from the site with additional data from 2018 and 2019. These data cover 2010-06-22 to 2019-07-16. Further results will be added to this data set and released to the public periodically as quality assurance and publication of results are accomplished. There are 10 experimental plots in SPRUCE: five temperature treatments (+0, +2.25, +4.5, +6.75, +9°C) at ambient CO2, and the same five temperature treatments at elevated CO2 (+500 ppm). These data span the pre- and post-treatment periods when enclosed plots were exposed to warming and elevated carbon dioxide (CO2) within the SPRUCE experiment. The pretreatment samples were collected from south end of the S1 bog prior to SPRUCE boardwalk construction, then throughout the bog once the boardwalks were completed.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2011

Generic Repository Concepts and Thermal Analysis for Advanced Fuel Cycles

The current posture of the used nuclear fuel management program in the U.S. following termination of the Yucca Mountain Project, is to pursue research and development (R&D) of generic (i.e., non-site specific) technologies for storage, transportation and disposal. Disposal R&D is directed toward understanding and demonstrating the performance of reference geologic disposal concepts selected to represent the current state-of-the-art in geologic disposal. One of the principal constraints on waste packaging and emplacement in a geologic repository is management of the waste-generated heat. This paper describes the selection of reference disposal concepts, and thermal management strategies for waste from advanced fuel cycles. A geologic disposal concept for spent nuclear fuel (SNF) or high-level waste (HLW) consists of three components: waste inventory, geologic setting, and concept of operations. A set of reference geologic disposal concepts has been developed by the U.S. Department of Energy (DOE) Used Fuel Disposition Campaign, for crystalline rock, clay/shale, bedded salt, and deep borehole (crystalline basement) geologic settings. We performed thermal analysis of these concepts using waste inventory cases representing a range of advanced fuel cycles. Concepts of operation consisting of emplacement mode, repository layout, and engineered barrier descriptions, were selected based on international progress and previous experience in the U.S. repository program. All of the disposal concepts selected for this study use enclosed emplacement modes, whereby waste packages are in direct contact with encapsulating engineered or natural materials. The encapsulating materials (typically clay-based or rock salt) have low intrinsic permeability and plastic rheology that closes voids so that low permeability is maintained. Uniformly low permeability also contributes to chemically reducing conditions common in soft clay, shale, and salt formations. Enclosed modes are associated with temperature constraints that limit changes to the encapsulating materials, and they generally have less capacity to dissipate heat from the waste package and its immediate surroundings than open modes such as that proposed for a repository at Yucca Mountain, Nevada. Open emplacement modes can be ventilated for many years prior to permanent closure of the repository, limiting peak temperatures both before and after closure, and combining storage and disposal functions in the same facility. Open emplacement modes may be practically limited to unsaturated host formations, unless emplacement tunnels are effectively sealed everywhere prior to repository closure. Thermal analysis of disposal concepts and waste inventory cases has identified important relationships between waste package size and capacity, and the duration of surface decay storage needed to meet temperature constraints. For example, the choice of salt as the host medium expedites the schedule for geologic disposal by approximately 50 yr (other factors held constant) thereby reducing future reliance on surface decay storage. Rock salt has greater thermal conductivity and stability at higher temperatures than other media considered. Alternatively, the choice of salt permits the use of significantly larger waste packages for SNF. The following sections describe the selection of reference waste inventories, geologic settings, and concepts of operation, and summarize the results from the thermal analysis.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2010

Analysis of the Crystal Structure of the ExsC.ExsE Complex Reveals Distinctive Binding Interactions of the Pseudomonas aeruginosa Type III Secretion Chaperone ExsC with ExsE and ExsD

Pseudomonas aeruginosa, like many Gram-negative bacterial pathogens, requires its type III secretion system (T3SS) to facilitate acute infections. In P. aeruginosa, the expression of all T3SS-related genes is regulated by the transcriptional activator ExsA. A signaling cascade involving ExsA and three additional proteins, ExsC, ExsD, and ExsE, directly ties the upregulation of ExsA-mediated transcription to the activation of the type III secretion apparatus. In order to characterize the events underlying the signaling process, the crystal structure of the T3SS chaperone ExsC in complex with its cognate effector ExsE has been determined. The structure reveals critical contacts that mediate the interactions between these two proteins. Particularly striking is the presence of two Arg-X-Val-X-Arg motifs in ExsE that form identical interactions along opposite sides of an ExsC dimer. The structure also provides insights into the interactions of ExsC with the antiactivator protein ExsD. It was shown that the amino-terminal 46 residues of ExsD are sufficient for ExsC binding. On the basis of these findings, a new model for the ExsC {center_dot} ExsD complex is proposed to explain its distinctive 2:2 stoichiometry and why ExsC displays a weaker affinity for ExsD than for ExsE.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Structure and immune recognition of trimeric pre-fusion HIV-1 Env

The human immunodeficiency virus type 1 (HIV-1) envelope (Env) spike, comprising three gp120 and three gp41 subunits, is a conformational machine that facilitates HIV-1 entry by rearranging from a mature unliganded state, through receptor-bound intermediates, to a post-fusion state. As the sole viral antigen on the HIV-1 virion surface, Env is both the target of neutralizing antibodies and a focus of vaccine efforts. Here we report the structure at 3.5 Å resolution for an HIV-1 Env trimer captured in a mature closed state by antibodies PGT122 and 35O22. This structure reveals the pre-fusion conformation of gp41, indicates rearrangements needed for fusion activation, and defines parameters of immune evasion and immune recognition. Pre-fusion gp41 encircles amino- and carboxy-terminal strands of gp120 with four helices that form a membrane-proximal collar, fastened by insertion of a fusion peptide-proximal methionine into a gp41-tryptophan clasp. Spike rearrangements required for entry involve opening the clasp and expelling the termini. In conclusion, N-linked glycosylation and sequence-variable regions cover the pre-fusion closed spike; we used chronic cohorts to map the prevalence and location of effective HIV-1-neutralizing responses, which were distinguished by their recognition of N-linked glycan and tolerance for epitope-sequence variation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

High-energy emissions from the gamma-ray binary LS 5039

We study mechanisms of multi-wavelength emissions (X-ray, GeV, and TeV gamma-rays) from the gamma-ray binary LS 5039. This paper is composed of two parts. In the first part, we report on results of observational analysis using 4 yr data of the Fermi Large Area Telescope. Due to the improvement of instrumental response function and increase of the statistics, the observational uncertainties of the spectrum in the ∼100-300 MeV bands and >10 GeV bands are significantly improved. The present data analysis suggests that the 0.1-100 GeV emissions from LS 5039 contain three different components: (1) the first component contributes to <1 GeV emissions around superior conjunction, (2) the second component dominates in the 1-10 GeV energy bands, and (3) the third component is compatible with the lower-energy tail of the TeV emissions. In the second part, we develop an emission model to explain the properties of the phase-resolved emissions in multi-wavelength observations. Assuming that LS 5039 includes a pulsar, we argue that emissions from both the magnetospheric outer gap and the inverse-Compton scattering process of cold-relativistic pulsar wind contribute to the observed GeV emissions. We assume that the pulsar is wrapped by two kinds of termination shock: Shock-I due to the interaction between the pulsar wind and the stellar wind and Shock-II due to the effect of the orbital motion. We propose that the X-rays are produced by the synchrotron radiation at the Shock-I region and the TeV gamma-rays are produced by the inverse-Compton scattering process at the Shock-II region.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

SU-F-19A-04: Dosimetric Evaluation of a Novel CT/MR Compatible Fletcher Applicator for Intracavitary Brachytherapy of the Cervix Uteri

Purpose: To validate a Monte Carlo model and evaluate the dosimetric capabilities of a novel commercial CT/MR compatible Fletcher applicator for cervical cancer brachytherapy. Methods: MCNPX 2.7.0 was used to model the Fletcher CT/MR shielded applicator (FA) and 192Ir HDR source. Energy deposition was calculated with a track length estimator modified by an energy-dependent heating function. A high density polystyrene phantom was constructed with three film pockets for validation of the MCNPX model. Three planes of data were calculated with the MCNPX model corresponding to the three film planes in phantom. The planes were located 1 cm from the most anterior, posterior, and medial extents of the FA right ovoid. Unshielded distributions were calculated by modeling the shielded cells as air instead of the tungsten alloy. A third order polynomial fit to the OD to dose curve was used to convert OD of the three film planes to dose. Each film and MCNPX plane dose distribution was normalized to a point 2 cm from the center of the film plane and in a region of low dose gradient. MCNPX and film were overlaid and compared with a distance-to-agreement criterion of (±2%/±2mm). Shielded and unshielded distributions were overlaid and a percent shielded plot was created. Results: 85.2%, 97.1%, and 96.6% of the MCNPX points passed the (±2%/±2mm) criterion respectively for the anterior, lateral, and posterior film comparison planes. A majority of the points in the anterior plane that exceeded the DTA criterion were either along edges of where the film was cut or near the terminal edges of the film. The percent shielded matrices indicated that the maximum % shielding was 50%. Conclusion: These data confirm the validity of the FA Monte Carlo model. The FA ovoid can shield up to 50% of the dose in the anteroposterior direction.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Global 3D Radiation Magnetohydrodynamic Simulations of Accretion onto a Stellar-mass Black Hole at Sub- and Near-critical Accretion Rates

We present global 3D radiation magnetohydrodynamic simulations of accretion onto a 6.62 solar-mass black hole, with quasi-steady-state accretion rates reaching 0.016–0.9 times the critical accretion rate, which is defined as the accretion rate for powering the Eddington luminosity, assuming a 10% radiative efficiency, in three different runs. The simulations show no sign of thermal instability over hundreds of thermal timescales at 10 r g . The energy dissipation occurs close to the mid-plane in the near-critical runs and near the disk surface in the low–accretion rate run. The total radiative luminosity inside ~20 r g is about 1%–30% of the Eddington limit, with radiative efficiencies of about 6% and 3%, respectively, in the sub- and near-critical accretion regimes. In both cases, self-consistent turbulence generated by the magnetorotational instability leads to angular momentum transfer, and the disk is supported by magnetic pressure. Outflows from the central low-density funnel, with a terminal velocity of ~0.1c, are seen only in the near-critical runs. We conclude that these magnetic pressure–dominated disks are thermally stable and thicker than the α disk, and that the effective temperature profiles are much flatter than those in the α disks. The magnetic pressures of these disks are comparable within an order of magnitude to the previous analytical magnetic pressure–dominated disk model.

79 ASTRONOMY AND ASTROPHYSICS↗