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At least 523 records · Page 29

Assignment of function to a domain of unknown function: DUF1537 is a new kinase family in catabolic pathways for acid sugars

Using a large-scale “genomic enzymology” approach, we ( i ) assigned novel ATP-dependent four-carbon acid sugar kinase functions to members of the DUF1537 protein family (domain of unknown function; Pfam families PF07005 and PF17042) and ( ii ) discovered novel catabolic pathways for d -threonate, l -threonate, and d -erythronate. The experimentally determined ligand specificities of several solute binding proteins (SBPs) for TRAP (tripartite ATP-independent permease) transporters for four-carbon acids, including d -erythronate and l -erythronate, were used to constrain the substrates for the catabolic pathways that degrade the SBP ligands to intermediates in central carbon metabolism. Sequence similarity networks and genome neighborhood networks were used to identify the enzyme components of the pathways. Conserved genome neighborhoods encoded SBPs as well as permease components of the TRAP transporters, members of the DUF1537 family, and a member of the 4-hydroxy- l -threonine 4-phosphate dehydrogenase (PdxA) oxidative decarboxylase, class II aldolase, or ribulose 1,5-bisphosphate carboxylase/oxygenase, large subunit (RuBisCO) superfamily. Because the characterized substrates of members of the PdxA, class II aldolase, and RuBisCO superfamilies are phosphorylated, we postulated that the members of the DUF1537 family are novel ATP-dependent kinases that participate in catabolic pathways for four-carbon acid sugars. We determined that ( i ) the DUF1537/PdxA pair participates in a pathway for the conversion of d -threonate to dihydroxyacetone phosphate and CO 2 and ( ii ) the DUF1537/class II aldolase pair participates in pathways for the conversion of d -erythronate and l -threonate (epimers at carbon-3) to dihydroxyacetone phosphate and CO 2 . As a result, the physiological importance of these pathways was demonstrated in vivo by phenotypic and genetic analyses.

59 BASIC BIOLOGICAL SCIENCES↗

THE LUMINOSITY FUNCTION OF FERMI-DETECTED FLAT-SPECTRUM RADIO QUASARS

Fermi has provided the largest sample of {gamma}-ray-selected blazars to date. In this work we use a complete sample of flat spectrum radio quasars (FSRQs) detected during the first year of operation to determine the luminosity function (LF) and its evolution with cosmic time. The number density of FSRQs grows dramatically up to redshift {approx}0.5-2.0 and declines thereafter. The redshift of the peak in the density is luminosity dependent, with more luminous sources peaking at earlier times; thus the LF of {gamma}-ray FSRQs follows a luminosity-dependent density evolution similar to that of radio-quiet active galactic nuclei. Also, using data from the Swift Burst Alert Telescope we derive the average spectral energy distribution (SED) of FSRQs in the 10 keV-300 GeV band and show that there is no correlation between the luminosity at the peak of the {gamma}-ray emission component and its peak frequency. Using this luminosity-independent SED with the derived LF allows us to predict that the contribution of FSRQs to the Fermi isotropic {gamma}-ray background is 9.3{sup +1.6}{sub -1.0}% ({+-}3% systematic uncertainty) in the 0.1-100 GeV band. Finally we determine the LF of unbeamed FSRQs, finding that FSRQs have an average Lorentz factor of {gamma} = 11.7{sup +3.3}{sub -2.2}, that most are seen within 5 Degree-Sign of the jet axis, and that they represent only {approx}0.1% of the parent population.

79 ASTRONOMY AND ASTROPHYSICS↗

THE SDSS-II SUPERNOVA SURVEY: PARAMETERIZING THE TYPE Ia SUPERNOVA RATE AS A FUNCTION OF HOST GALAXY PROPERTIES

Using data from the Sloan Digital Sky Supernova Survey-II (SDSS-II SN Survey), we measure the rate of Type Ia supernovae (SNe Ia) as a function of galaxy properties at intermediate redshift. A sample of 342 SNe Ia with 0.05 < z < 0.25 is constructed. Using broadband photometry and redshifts, we use the PEGASE.2 spectral energy distributions to estimate host galaxy stellar masses and recent star formation rates (SFRs). We find that the rate of SNe Ia per unit stellar mass is significantly higher (by a factor of {approx}30) in highly star-forming galaxies compared to passive galaxies. When parameterizing the SN Ia rate (SNR{sub Ia}) based on host galaxy properties, we find that the rate of SNe Ia in passive galaxies is not linearly proportional to the stellar mass; instead an SNR{sub Ia}{proportional_to}M{sup 0.68} is favored. However, such a parameterization does not describe the observed SNR{sub Ia} in star-forming galaxies. The SNR{sub Ia} in star-forming galaxies is well fitted by SNR{sub Ia} = (0.41 {+-} 0.15) Multiplication-Sign 10{sup -10} M{sup 0.72{+-}0.15} + (0.65 {+-} 0.25) Multiplication-Sign 10{sup -3}SFR{sup 1.01{+-}0.22} (statistical errors only), where M is the host galaxy stellar mass (in M{sub Sun }) and SFR is the SFR (in M{sub Sun} yr{sup -1}). We show that our results, for SNe Ia in passive galaxies, are consistent with those at higher redshifts (favoring SNR{sub Ia}{proportional_to}M) when accounting for the difference in the ages of our galaxies. This suggests that the rate of SNe Ia is correlated with the age of the stellar population. The MLCS extinction parameter, A{sub V} , is similar in passive and moderately star-forming galaxies, but we find indications that it is smaller, on average, in highly star-forming galaxies. This result appears to be driven by a deficit of the reddest (A{sub V} > 0.15) SNe Ia in highly star-forming galaxies. We consider that the high levels of dust in these systems may be obscuring the reddest and faintest SNe Ia.

79 ASTRONOMY AND ASTROPHYSICS↗

Impacts of nitrogen addition on switchgrass root-associated diazotrophic community structure and function

ABSTRACT Cellulosic bioenergy crops, like switchgrass (Panicum virgatum), have potential for growth on lands unsuitable for food production coupled with potential for climate mitigation. Sustainability of these systems lies in identifying conditions that promote high biomass yields on marginal lands under low-input agricultural practices. Associative nitrogen fixation (ANF) is a potentially important nitrogen (N) source for these crops, yet ANF contributions to plant N, especially under fertilizer N addition are unclear. In this study, we assess structure (nifH) and function (ANF) of switchgrass root-associated diazotrophic communities to long-term and short-term N additions using soil from three marginal land sites. ANF rates were variable and often unexpectedly high, sometimes 10× greater than reported in the literature, and did not respond in repeatable ways to long-term or short-term N. We found few impacts of N addition on root-associated diazotrophic community structure or membership. Instead, we found a very consistent root-associated diazotrophic community even though switchgrass seeds were germinated in soil from field sites with distinct diazotrophic communities. Ultimately, this work demonstrates that root-associated diazotrophic communities have the potential to contribute to switchgrass N demands, independent of N addition, and this may be driven by selection of the diazotrophic community by switchgrass roots.

Microbiology↗

Electronic and magnetic properties of T i 4 O 7 predicted by self-interaction-corrected density functional theory

Understanding electronic properties of substoichiometric phases of titanium oxide such as Magneli phase Ti 4 O 7 is crucial in designing and modeling resistive switching devices. Here we present our study on Magneli phase Ti 4 O 7 together with rutile TiO 2 and Ti 2 O 3 using density functional theory methods with atomic-orbital-based self-interaction correction (ASIC). We predict a new antiferromagnetic (AF) ground state in the low temperature (LT) phase, and we explain energy difference with a competing AF state using a Heisenberg model. The predicted energy ordering of these states in the LT phase is calculated to be robust in a wide range of modeled isotropic strain. We have also investigated the dependence of the electronic structures of the Ti-O phases on stoichiometry. The splitting of titanium t 2g orbitals is enhanced with increasing oxygen deficiency as Ti-O is reduced. Furthermore, the electronic properties of all these phases can be reasonably well described by applying ASIC with a "standard" value for transition metal oxides of the empirical parameter alpha of 0.5 representing the magnitude of the applied self-interaction correction.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Two-dimensional ferroelectric topological insulators in functionalized atomically thin bismuth layers

We introduce a class of two-dimensional (2D) materials that possess coexisting ferroelectric and topologically insulating orders. Such ferroelectric topological insulators (FETIs) occur in noncentrosymmetric atomic layer structures with strong spin-orbit coupling (SOC). Here, we showcase a prototype 2D FETI in an atomically thin bismuth layer functionalized by CH 2 OH, which exhibits a large ferroelectric polarization that is switchable by a ligand molecule rotation mechanism and a strong SOC that drives a band inversion leading to the topologically insulating state. An external electric field that switches the ferroelectric polarization also tunes the spin texture in the underlying atomic lattice. Moreover, the functionalized bismuth layer exhibits an additional quantum order driven by the valley splitting at the K and K' points in the Brillouin zone stemming from the symmetry breaking and strong SOC in the system, resulting in a remarkable state of matter with the simultaneous presence of the quantum spin Hall and quantum valley Hall effect. These phenomena are predicted to exist in other similarly constructed 2D FETIs, thereby offering a unique quantum material platform for discovering novel physics and exploring innovative applications.

2-dimensional systems↗

Examination of the low-energy enhancement of the γ -ray strength function of Fe 56

A model-independent technique was used to determine the gamma-ray strength function (gamma SF) of Fe-56 down to gamma-ray energies less than 1 MeV for the first time with GRETINA using the (p, p') reaction at 16MeV. No difference was observed in the energy dependence of the gamma SF built on 2(+) and 4(+) final states, supporting the Brink hypothesis. In addition, angular distribution and polarization measurements were performed. The angular distributions are consistent with dipole radiation. The polarization results show a small bias towards magnetic character in the region of the enhancement.

Jones, M. D.↗

Valence-quark distribution functions in the kaon and pion

We describe expressions for pion and kaon dressed-quark distribution functions that incorporate contributions from gluons which bind quarks into these mesons and hence overcome a flaw of the commonly used handbag approximation. The distributions therewith obtained are purely valence in character, ensuring that dressed quarks carry all the meson’s momentum at a characteristic hadronic scale and vanish as ( 1 - x ) 2 when Bjorken- x → 1 . Comparing such distributions within the pion and kaon, it is apparent that the size of S U ( 3 ) -flavor symmetry breaking in meson parton distribution functions is modulated by the flavor dependence of dynamical chiral symmetry breaking. Corrections to these leading-order formulas may be divided into two classes, responsible for shifting dressed-quark momentum into glue and sea quarks. Working with available empirical information, we build an algebraic framework that is capable of expressing the principal impact of both classes of corrections. This enables a realistic comparison with experiment which allows us to identify and highlight basic features of measurable pion and kaon valence-quark distributions. We find that whereas roughly two thirds of the pion’s light-front momentum is carried by valence dressed quarks at a characteristic hadronic scale; this fraction rises to 95% in the kaon; evolving distributions with these features to a scale typical of available Drell-Yan data produces a kaon-to-pion ratio of u -quark distributions that is in agreement with the single existing data set, and predicts a u -quark distribution within the pion that agrees with a modern reappraisal of π N Drell-Yan data. Precise new data are essential in order to validate this reappraisal and because a single modest-quality measurement of the kaon-to-pion ratio cannot be considered definitive.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗