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At least 1,333 records · Page 74
All sourcesNASA NTRSDOE OSTI
DOE OSTI2016

Detection of correlated fragments in a sequence of images by superimposed Fourier holograms

The problem of detecting correlated fragments in a sequence of images recorded by the superimposing holograms within the Fourier holography scheme with angular multiplication of a spatially modulated reference beam is considered. The approach to the solution of this problem is based on the properties of the variance of the image sum. It is shown that this problem can be solved by providing a constant distance between the signal and reference images when recording superimposed holograms and a partial mutual correlatedness of reference images. The detection efficiency is analysed from the point of view of estimated image data capacity, the degree of mutual correlation of reference images, and the hologram recording conditions. The results of a numerical experiment under the most complicated conditions (representation of images by realisations of homogeneous random fields) confirm the theoretical conclusions. (holographic memory)

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2017

Convergence of ray sequences of Frobenius-Padé approximants

Let σ-hat be a Cauchy transform of a possibly complex-valued Borel measure σ and {p_n} a system of orthonormal polynomials with respect to a measure μ, where supp(μ)∩supp(σ)=∅. An (m,n)th Frobenius-Padé approximant to σ-hat is a rational function P/Q, deg (P)≤m, deg (Q)≤n, such that the first m+n+1 Fourier coefficients of the remainder function Q σ-hat −P vanish when the form is developed into a series with respect to the polynomials p{sub n}. We investigate the convergence of the Frobenius-Padé approximants to σ-hat along ray sequences n/(n+m+1)→c>0, n−1≤m, when μ and σ are supported on intervals of the real line and their Radon-Nikodym derivatives with respect to the arcsine distribution of the corresponding interval are holomorphic functions. Bibliography: 30 titles. (paper)

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2012

The Era GTPase recognizes the GAUCACCUCC sequence and binds helix 45 near the 3; end of 16S rRNA

Era, composed of a GTPase domain and a K homology domain, is essential for bacterial cell viability. It is required for the maturation of 16S rRNA and assembly of the 30S ribosomal subunit. We showed previously that the protein recognizes nine nucleotides (1531{sup AUCACCUCC}1539) near the 3{prime} end of 16S rRNA, and that this recognition stimulates GTP-hydrolyzing activity of Era. In all three kingdoms of life, the 1530{sup GAUCA}1534 sequence and helix 45 (h45) (nucleotides 1506-1529) are highly conserved. It has been shown that the 1530{sup GA}1531 to 1530{sup AG}1531 double mutation severely affects the viability of bacteria. However, whether Era interacts with G1530 and/or h45 and whether such interactions (if any) contribute to the stimulation of Era's GTPase activity were not known. Here, we report two RNA structures that contain nucleotides 1506-1542 (RNA301), one in complex with Era and GDPNP (GNP), a nonhydrolysable GTP-analogue, and the other in complex with Era, GNP, and the KsgA methyltransferase. The structures show that Era recognizes 10 nucleotides, including G1530, and that Era also binds h45. Moreover, GTPase assay experiments show that G1530 does not stimulate Era's GTPase activity. Rather, A1531 and A1534 are most important for stimulation and h45 further contributes to the stimulation. Although G1530 does not contribute to the intrinsic GTPase activity of Era, its interaction with Era is important for binding and is essential for the protein to function, leading to the discovery of a new cold-sensitive phenotype of Era.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core

The burial of hydrophobic side chains in a protein core generally is thought to be the major ingredient for stable, cooperative folding. Here, we show that, for the snow flea antifreeze protein (sfAFP), stability and cooperativity can occur without a hydrophobic core, and without α-helices or β-sheets. We report sfAFP has low sequence complexity with 46% glycine and an interior filled only with backbone H-bonds between six polyproline 2 (PP2) helices. However, the protein folds in a kinetically two-state manner and is moderately stable at room temperature. We believe that a major part of the stability arises from the unusual match between residue-level PP2 dihedral angle bias in the unfolded state and PP2 helical structure in the native state. Additional stabilizing factors that compensate for the dearth of hydrophobic burial include shorter and stronger H-bonds, and increased entropy in the folded state. These results extend our understanding of the origins of cooperativity and stability in protein folding, including the balance between solvent and polypeptide chain entropies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

In silico evidence for sequence-dependent nucleosome sliding

Significance The dynamic compaction of DNA into chromatin is essential for gene expression. Errors during compaction are associated with numerous diseases. Several molecular factors are known to affect chromatin dynamics, but their relative importance and the interplay between them are poorly understood. A detailed molecular model is used here to examine chromatin dynamics at the level of its most fundamental building block, namely the nucleosome. Nucleosome dynamics are demonstrated to be encoded in the DNA sequence itself, and key fundamental factors are uncovered that can significantly alter these dynamics at the molecular level. The results serve to complete a hitherto unavailable description of nucleosome dynamics by introducing previously unappreciated molecular processes, with the potential to influence macroscopic chromatin structure and genetics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Linking secondary metabolites to gene clusters through genome sequencing of six diverse Aspergillus species

Significance The genus of Aspergillus holds fungi relevant to plant and human pathology, food biotechnology, enzyme production, model organisms, and a selection of extremophiles. Here we present six whole-genome sequences that represent unexplored branches of the Aspergillus genus. The comparison of these genomes with previous genomes, coupled with extensive chemical analysis, has allowed us to identify genes for toxins, antibiotics, and anticancer compounds, as well as show that Aspergillus novofumigatus is potentially as pathogenic as Aspergillus fumigatus , and has an even more diverse set of secreted bioactive compounds. The findings are of interest to industrial biotechnology and basic research, as well as medical and clinical research.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Structure of the zinc-finger antiviral protein in complex with RNA reveals a mechanism for selective targeting of CG-rich viral sequences

Infection of animal cells by numerous viruses is detected and countered by a variety of means, including recognition of nonself nucleic acids. The zinc finger antiviral protein (ZAP) depletes cytoplasmic RNA that is recognized as foreign in mammalian cells by virtue of its elevated CG dinucleotide content compared with endogenous mRNAs. Here, we determined a crystal structure of a protein-RNA complex containing the N-terminal, 4-zinc finger human (h) ZAP RNA-binding domain (RBD) and a CG dinucleotide-containing RNA target. We report the structure reveals in molecular detail how hZAP is able to bind selectively to CG-rich RNA. Specifically, the 4 zinc fingers create a basic patch on the hZAP RBD surface. The highly basic second zinc finger contains a pocket that selectively accommodates CG dinucleotide bases. Structure guided mutagenesis, cross-linking immunoprecipitation sequencing assays, and RNA affinity assays show that the structurally defined CG-binding pocket is not required for RNA binding per se in human cells. However, the pocket is a crucial determinant of high-affinity, specific binding to CG dinucleotide-containing RNA. Moreover, variations in RNA-binding specificity among a panel of CG-binding pocket mutants quantitatively predict their selective antiviral activity against a CG-enriched HIV-1 strain. Overall, the hZAP RBD RNA structure provides an atomic-level explanation for how ZAP selectively targets foreign, CG-rich RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Untangling the sequence of events during the S 2 → S 3 transition in photosystem II and implications for the water oxidation mechanism

In oxygenic photosynthesis, light-driven oxidation of water to molecular oxygen is carried out by the oxygen-evolving complex (OEC) in photosystem II (PS II). Recently, we reported the room-temperature structures of PS II in the four (semi)stable S-states, S 1 , S 2 , S 3 , and S 0 , showing that a water molecule is inserted during the S 2 → S 3 transition, as a new bridging O(H)-ligand between Mn1 and Ca. To understand the sequence of events leading to the formation of this last stable intermediate state before O 2 formation, we recorded diffraction and Mn X-ray emission spectroscopy (XES) data at several time points during the S 2 → S 3 transition. At the electron acceptor site, changes due to the two-electron redox chemistry at the quinones, Q A and Q B , are observed. At the donor site, tyrosine Y Z and His190 H-bonded to it move by 50 µs after the second flash, and Glu189 moves away from Ca. This is followed by Mn1 and Mn4 moving apart, and the insertion of O X (H) at the open coordination site of Mn1. This water, possibly a ligand of Ca, could be supplied via a “water wheel”-like arrangement of five waters next to the OEC that is connected by a large channel to the bulk solvent. XES spectra show that Mn oxidation (τ of ∼350 µs) during the S 2 → S 3 transition mirrors the appearance of O X electron density. This indicates that the oxidation state change and the insertion of water as a bridging atom between Mn1 and Ca are highly correlated.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

DNA affinity purification sequencing and transcriptional profiling reveal new aspects of nitrogen regulation in a filamentous fungus

Significance Microorganisms have evolved transcriptional networks to prioritize utilization of available nutrient sources. For filamentous fungi, such as Neurospora crassa , this entails distinguishing between a variety of organic and inorganic nitrogen sources. Here, we transcriptionally profiled the response of N. crassa to a variety of nitrogen sources and used DNA affinity purification sequencing to characterize the role of regulatory genes and their direct downstream targets. We identified a transcription factor responsible for regulating genes involved in amino acid and mannose metabolism. By comparing the genes regulated by transcription factors that regulate specific nitrogen utilization pathways and transcription factors that regulate utilization of all nitrogen sources that require metabolic processing before utilization, we revealed aspects of the nitrogen regulatory network.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deciphering the evolution of flavin-dependent monooxygenase stereoselectivity using ancestral sequence reconstruction

Controlling the selectivity of a reaction is critical for target-oriented synthesis. Accessing complementary selectivity profiles enables divergent synthetic strategies, but is challenging to achieve in biocatalytic reactions given enzymes’ innate preferences of a single selectivity. Thus, it is critical to understand the structural features that control selectivity in biocatalytic reactions to achieve tunable selectivity. Here, we investigate the structural features that control the stereoselectivity in an oxidative dearomatization reaction that is key to making azaphilone natural products. Crystal structures of enantiocomplementary biocatalysts guided the development of multiple hypotheses centered on the structural features that control the stereochemical outcome of the reaction; however, in many cases, direct substitutions of active site residues in natural proteins led to inactive enzymes. Ancestral sequence reconstruction (ASR) and resurrection were employed as an alternative strategy to probe the impact of each residue on the stereochemical outcome of the dearomatization reaction. These studies suggest that two mechanisms are active in controlling the stereochemical outcome of the oxidative dearomatization reaction: one involving multiple active site residues in AzaH and the other dominated by a single Phe to Tyr switch in TropB and AfoD. Moreover, this study suggests that the flavin-dependent monooxygenases (FDMOs) adopt simple and flexible strategies to control stereoselectivity, which has led to stereocomplementary azaphilone natural products produced by fungi. This paradigm of combining ASR and resurrection with mutational and computational studies showcases sets of tools for understanding enzyme mechanisms and provides a solid foundation for future protein engineering efforts.

Science & Technology - Other Topics↗
DOE OSTI2024

Dissecting neurofilament tail sequence-phosphorylation-structure relationships with multicomponent reconstituted protein brushes

Neurofilaments (NFs) are multisubunit, bottlebrush-shaped intermediate filaments abundant in the axonal cytoskeleton. Each NF subunit contains a long intrinsically disordered tail domain, which protrudes from the NF core to form a “brush” surrounding each NF. Precisely how the tails’ variable charge patterns and repetitive phosphorylation sites mediate their conformation within the brush remains an open question in axonal biology. We address this problem by grafting recombinant NF tail protein constructs NF-Light, -Medium, and -Heavy (NFL, NFM, and NFH) to surfaces, yielding protein brushes of defined stoichiometry that can be phosphorylated in vitro. Atomic force microscopy measurements reveal that brush height depends on composition monotonically but not always linearly for binary NFL:NFM or NFL:NFH systems, and that NFM-based brushes are highly extended, while brushes incorporating the much larger NFH are surprisingly compact even after multisite phosphorylation. Complementary self-consistent field theory (SCFT) predicts multilayer brush morphologies for NFM and phosphorylated NFH brushes. Further experiments and SCFT analysis with designed mutants reveal that N-terminal negative charges in the NFH tail repel phosphorylated residues to generate the multilayer morphology, while the C-terminal charge-neutral region contributes to multilayer brush morphology but not total brush height. Charge-shuffled NFM variants show that charge segregation promotes brush collapse near physiological ionic strengths. Collectively, this study supports a role for NFM in establishing a dynamic range for NF brush conformation, lending insight into previous in vitro and in vivo findings. More broadly, this work establishes a platform for dissecting contributions of disordered protein sequence to conformation at interfaces.

Science & Technology - Other Topics↗
DOE OSTI2015

The Replication Focus Targeting Sequence (RFTS) Domain Is a DNA-competitive Inhibitor of Dnmt1

Dnmt1 (DNA methyltransferase 1) is the principal enzyme responsible for maintenance of cytosine methylation at CpG dinucleotides in the mammalian genome. The N-terminal replication focus targeting sequence (RFTS) domain of Dnmt1 has been implicated in subcellular localization, protein association, and catalytic function. However, progress in understanding its function has been limited by the lack of assays for and a structure of this domain. Here, we show that the naked DNA- and polynucleosome-binding activities of Dnmt1 are inhibited by the RFTS domain, which functions by virtue of binding the catalytic domain to the exclusion of DNA. Kinetic analysis with a fluorogenic DNA substrate established the RFTS domain as a 600-fold inhibitor of Dnmt1 enzymatic activity. The crystal structure of the RFTS domain reveals a novel fold and supports a mechanism in which an RFTS-targeted Dnmt1-binding protein, such as Uhrf1, may activate Dnmt1 for DNA binding.

Syeda, Farisa↗
DOE OSTI2013

THE EVOLUTION OF DUSTY STAR FORMATION IN GALAXY CLUSTERS TO z = 1: SPITZER INFRARED OBSERVATIONS OF THE FIRST RED-SEQUENCE CLUSTER SURVEY

We present the results of an infrared (IR) study of high-redshift galaxy clusters with the MIPS camera on board the Spitzer Space Telescope. We have assembled a sample of 42 clusters from the Red-Sequence Cluster Survey-1 over the redshift range 0.3 < z < 1.0 and spanning an approximate range in mass of 10{sup 14-15} M {sub ☉}. We statistically measure the number of IR-luminous galaxies in clusters above a fixed inferred IR luminosity of 2 × 10{sup 11} M {sub ☉}, assuming a star forming galaxy template, per unit cluster mass and find it increases to higher redshift. Fitting a simple power-law we measure evolution of (1 + z){sup 5.1±1.9} over the range 0.3 < z < 1.0. These results are tied to the adoption of a single star forming galaxy template; the presence of active galactic nuclei, and an evolution in their relative contribution to the mid-IR galaxy emission, will alter the overall number counts per cluster and their rate of evolution. Under the star formation assumption we infer the approximate total star formation rate per unit cluster mass (ΣSFR/M {sub cluster}). The evolution is similar, with ΣSFR/M {sub cluster} ∼ (1 + z){sup 5.4±1.9}. We show that this can be accounted for by the evolution of the IR-bright field population over the same redshift range; that is, the evolution can be attributed entirely to the change in the in-falling field galaxy population. We show that the ΣSFR/M {sub cluster} (binned over all redshift) decreases with increasing cluster mass with a slope (ΣSFR/M{sub cluster}∼M{sub cluster}{sup -1.5±0.4}) consistent with the dependence of the stellar-to-total mass per unit cluster mass seen locally. The inferred star formation seen here could produce ∼5%-10% of the total stellar mass in massive clusters at z = 0, but we cannot constrain the descendant population, nor how rapidly the star-formation must shut-down once the galaxies have entered the cluster environment. Finally, we show a clear decrease in the number of IR-bright galaxies per unit optical galaxy in the cluster cores, confirming star formation continues to avoid the highest density regions of the universe at z ∼ 0.75 (the average redshift of the high-redshift clusters). While several previous studies appear to show enhanced star formation in high-redshift clusters relative to the field we note that these papers have not accounted for the overall increase in galaxy or dark matter density at the location of clusters. Once this is done, clusters at z ∼ 0.75 have the same or less star formation per unit mass or galaxy as the field.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2014

Orbital motion in pre-main sequence binaries

We present results from our ongoing program to map the visual orbits of pre-main sequence (PMS) binaries in the Taurus star forming region using adaptive optics imaging at the Keck Observatory. We combine our results with measurements reported in the literature to analyze the orbital motion for each binary. We present preliminary orbits for DF Tau, T Tau S, ZZ Tau, and the Pleiades binary HBC 351. Seven additional binaries show curvature in their relative motion. Currently, we can place lower limits on the orbital periods for these systems; full solutions will be possible with more orbital coverage. Five other binaries show motion that is indistinguishable from linear motion. We suspect that these systems are bound and might show curvature with additional measurements in the future. The observations reported herein lay critical groundwork toward the goal of measuring precise masses for low-mass PMS stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2011

MAGNETIC INTERACTIONS IN PRE-MAIN-SEQUENCE BINARIES

Young stars typically have strong magnetic fields, so that the magnetospheres of newly formed close binaries can interact, dissipate energy, and produce synchrotron radiation. The V773 Tau A binary system, a pair of T Tauri stars with a 51 day orbit, displays such a signature, with peak emission taking place near periastron. This paper proposes that the observed emission arises from the change in energy stored in the composite magnetic field of the system. We model the fields using the leading order (dipole) components and show that this picture is consistent with current observations. In this model, the observed radiation accounts for a fraction of the available energy of interaction between the magnetic fields from the two stars. Assuming antisymmetry, we compute the interaction energy E{sub int} as a function of the stellar radii, the stellar magnetic field strengths, the binary semimajor axis, and orbital eccentricity, all of which can be measured independently of the synchrotron radiation. The variability in time and energetics of the synchrotron radiation depend on the details of the annihilation of magnetic fields through reconnection events, which generate electric fields that accelerate charged particles, and how those charged particles, especially fast electrons, are removed from the interaction region. However, the major qualitative features are well described by the background changes in the global magnetic configuration driven by the orbital motion. The theory can be tested by observing a collection of pre-main-sequence binary systems.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

STELLAR DIAMETERS AND TEMPERATURES. I. MAIN-SEQUENCE A, F, AND G STARS

We have executed a survey of nearby, main-sequence A-, F-, and G-type stars with the CHARA Array, successfully measuring the angular diameters of forty-four stars with an average precision of {approx}1.5%. We present new measures of the bolometric flux, which in turn leads to an empirical determination of the effective temperature for the stars observed. In addition, these CHARA-determined temperatures, radii, and luminosities are fit to Yonsei-Yale model isochrones to constrain the masses and ages of the stars. These results are compared to indirect estimates of these quantities obtained by collecting photometry of the stars and applying them to model atmospheres and evolutionary isochrones. We find that for most cases, the models overestimate the effective temperature by {approx}1.5%-4% when compared to our directly measured values. The overestimated temperatures and underestimated radii in these works appear to cause an additional offset in the star's surface gravity measurements, which consequently yield higher masses and younger ages, in particular for stars with masses greater than {approx}1.3 M{sub Sun }. Additionally, we compare our measurements to a large sample of eclipsing binary stars, and excellent agreement is seen within both data sets. Finally, we present temperature relations with respect to (B - V) and (V - K) colors as well as spectral type, showing that calibration of effective temperatures with errors {approx}1% is now possible from interferometric angular diameters of stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

THE HERSCHEL REFERENCE SURVEY: DUST IN EARLY-TYPE GALAXIES AND ACROSS THE HUBBLE SEQUENCE

We present Herschel observations of 62 early-type galaxies (ETGs), including 39 galaxies morphologically classified as S0+S0a and 23 galaxies classified as ellipticals using SPIRE at 250, 350, and 500 {mu}m as part of the volume-limited Herschel Reference Survey (HRS). We detect dust emission in 24% of the ellipticals and 62% of the S0s. The mean temperature of the dust is (T{sub d} ) = 23.9 {+-} 0.8 K, warmer than that found for late-type galaxies in the Virgo Cluster. The mean dust mass for the entire detected early-type sample is logM{sub d} = 6.1 {+-} 0.1 M{sub Sun} with a mean dust-to-stellar-mass ratio of log(M{sub d} /M{sub *}) = -4.3 {+-} 0.1. Including the non-detections, these parameters are logM{sub d} = 5.6 {+-} 0.1 and log(M{sub d} /M{sub *}) = -5.1 {+-} 0.1, respectively. The average dust-to-stellar-mass ratio for the early-type sample is fifty times lower, with larger dispersion, than the spiral galaxies observed as part of the HRS, and there is an order-of-magnitude decline in M{sub d} /M{sub *} between the S0s and ellipticals. We use UV and optical photometry to show that virtually all the galaxies lie close to the red sequence yet the large number of detections of cool dust, the gas-to-dust ratios, and the ratios of far-infrared to radio emission all suggest that many ETGs contain a cool interstellar medium similar to that in late-type galaxies. We show that the sizes of the dust sources in S0s are much smaller than those in early-type spirals and the decrease in the dust-to-stellar-mass ratio from early-type spirals to S0s cannot simply be explained by an increase in the bulge-to-disk ratio. These results suggest that the disks in S0s contain much less dust (and presumably gas) than the disks of early-type spirals and this cannot be explained simply by current environmental effects, such as ram-pressure stripping. The wide range in the dust-to-stellar-mass ratio for ETGs and the lack of a correlation between dust mass and optical luminosity suggest that much of the dust in the ETGs detected by Herschel has been acquired as the result of interactions, although we show these are unlikely to have had a major effect on the stellar masses of the ETGs. The Herschel observations tentatively suggest that in the most massive systems, the mass of interstellar medium is unconnected to the evolution of the stellar populations in these galaxies.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2012

ASSEMBLY OF THE RED SEQUENCE IN INFRARED-SELECTED GALAXY CLUSTERS FROM THE IRAC SHALLOW CLUSTER SURVEY

We present results for the assembly and star formation histories (SFHs) of massive ({approx}L*) red sequence galaxies (RSGs) in 11 spectroscopically confirmed, infrared-selected galaxy clusters at 1.0 < z < 1.5, the precursors to present-day massive clusters with M {approx} 10{sup 15} M{sub Sun }. Using rest-frame optical photometry, we investigate evolution in the color and scatter of the RSG population, comparing with models of possible SFHs. In contrast to studies of central cluster galaxies at lower redshift (z < 1), these data are clearly inconsistent with the continued evolution of stars formed and assembled primarily at a single, much earlier time. Specifically, we find that the colors of massive cluster galaxies at z Almost-Equal-To 1.5 imply that the bulk of star formation occurred at z {approx} 3, whereas by z Almost-Equal-To 1 their colors imply formation at z {approx} 2; therefore these galaxies exhibit approximately the same luminosity-weighted stellar age at 1 < z < 1.5. This likely reflects star formation that occurs over an extended period, the effects of significant progenitor bias, or both. Our results generally indicate that massive cluster galaxy populations began forming a significant mass of stars at z {approx}> 4, contained some red spheroids by z Almost-Equal-To 1.5, and were actively assembling much of their final mass during 1 < z < 2 in the form of younger stars. Qualitatively, the slopes of the cluster color-magnitude relations are consistent with no significant evolution relative to local clusters.

79 ASTRONOMY AND ASTROPHYSICS↗