A repeated GGA motif is critical for the activity and stability of the riboregulator RsmY of Pseudomonas fluorescens.

The riboregulator RsmY of Pseudomonas fluorescens strain CHA0 is an example of small regulatory RNAs belonging to the global Rsm/Csr regulatory systems controlling diverse cellular processes such as glycogen accumulation, motility, or formation of extracellular products in various bacteria. By binding multiple molecules of the small regulatory protein RsmA, RsmY relieves the negative effect of RsmA on the translation of several target genes involved in the biocontrol properties of strain CHA0. RsmY and functionally related riboregulators have repeated GGA motifs predicted to be exposed in single-stranded regions, notably in the loops of hairpins. The secondary structure of RsmY was corroborated by in vivo cleavage with lead acetate. RsmY mutants lacking three or five (out of six) of the GGA motifs showed reduced ability to derepress the expression of target genes in vivo and failed to bind the RsmA protein efficiently in vitro. The absence of GGA motifs in RsmY mutants resulted in reduced abundance of these transcripts and in a shorter half-life (< or = 6 min as compared with 27 min for wild type RsmY). These results suggest that both the interaction of RsmY with RsmA and the stability of RsmY strongly depend on the GGA repeats and that the ability of RsmY to interact with small regulatory proteins such as RsmA may protect this RNA from degradation.

First principles LDA+U and GGA+U study of cerium oxides: Dependence on the effective U-parameter

The electronic structure and properties of cerium oxides (CeO2 and Ce2O3) have been studied in the framework of the LDA+U and GGA(PW91)+U implementations of density functional theory. The dependence of selected observables of these materials on the effective U parameter has been investigated in detail. The examined properties include lattice constants, bulk moduli, density of states, and formation energies of CeO2 and Ce2O3. For CeO2, the LDA+U results are in better agreement with experiment than the GGA+U results whereas for the computationally more demanding Ce2O3 both approaches give comparable accuracy. Furthermore, as expected, Ce2O3 is much more sensitive to the choice of the U value. Generally, the PW91 functional provides an optimal agreement with experiment at lower U energies than LDA does. In order to achieve a balanced description of both kinds of materials, and also of nonstoichiometric CeO2¿x phases, an appropriate choice of U is suggested for LDA+U and GGA+U schemes. Nevertheless, an optimum value appears to be property dependent, especially for Ce2O3. Optimum U values are found to be, in general, larger than values determined previously in a self-consistent way.

First principles LDA+U and GGA+U study of cerium oxides: Dependence on the effective U-parameter

The electronic structure and properties of cerium oxides (CeO2 and Ce2O3) have been studied in the framework of the LDA+U and GGA(PW91)+U implementations of density functional theory. The dependence of selected observables of these materials on the effective U parameter has been investigated in detail. The examined properties include lattice constants, bulk moduli, density of states, and formation energies of CeO2 and Ce2O3. For CeO2, the LDA+U results are in better agreement with experiment than the GGA+U results whereas for the computationally more demanding Ce2O3 both approaches give comparable accuracy. Furthermore, as expected, Ce2O3 is much more sensitive to the choice of the U value. Generally, the PW91 functional provides an optimal agreement with experiment at lower U energies than LDA does. In order to achieve a balanced description of both kinds of materials, and also of nonstoichiometric CeO2¿x phases, an appropriate choice of U is suggested for LDA+U and GGA+U schemes. Nevertheless, an optimum value appears to be property dependent, especially for Ce2O3. Optimum U values are found to be, in general, larger than values determined previously in a self-consistent way.

LDA or GGA? A combined experimental inelastic neutron scattering and ab initio lattice dynamics study of alkali metal hydrides

In a previous work, we carried out inelastic neutron scattering (INS) spectroscopy experiments and preliminary first principles calculations on alkali metal hydrides. The complete series of alkali metal hydrides, LiH, NaH, KH, RbH and CsH was measured in the high-resolution TOSCA INS spectrometer at ISIS. Here, we present the results of ab initio electronic structure calculations of the properties of the alkali metal hydrides using both the local density approximation (LDA) and the generalized gradient approximation (GGA), using the Perdew–Burke–Ernzerhof (PBE) parameterization. Properties calculated were lattice parameters, bulk moduli, dielectric constants, effective charges, electronic densities and inelastic neutron scattering (INS) spectra. We took advantage of the currently available computer power to use full lattice dynamics theory to calculate thermodynamic properties for these materials. For the alkali metal hydrides (LiH, NaH, KH, RbH and CsH) using lattice dynamics, we found that the INS spectra calculated using LDA agreed better with the experimental data than the spectra calculated using GGA. Both zero-point effects and thermal contributions to free energies had an important effect on INS and several thermodynamic properties.

Electronic charge transfer between ceria surfaces and gold adatoms: a GGA+U investigation

We use density functional theory calculations with Hubbard corrections (DFT+U) to investigate electronic aspects of the interaction between ceria surfaces and gold atoms. Our results show that Au adatoms at the (111) surface of ceria can adopt Au0, Au+ or Au� electronic configurations depending on the adsorption site. The strongest adsorption sites are on top of the surface oxygen and in a bridge position between two surface oxygen atoms, and in both cases charge transfer from the gold atom to one of the Ce cations at the surface is involved. Adsorption at other sites, including the hollow sites of the surface, and an O–Ce bridging site, is weaker and does not involve charge transfer. Adsorption at an oxygen vacancy site is very strong and involves the formation of an Au� anion. We argue that the ability of gold atoms to stabilise oxygen vacancies at the ceria surface by moving into the vacancy site and attracting the excess electrons of the defect could be responsible for the enhanced reducibility of ceria surfaces in the presence of gold. Finally, we rationalise the differences in charge transfer behaviour from site to site in terms of the electrostatic potential at the surface and the coordination of the species.

GaMnAs: Position of Mn-d levels and majority spin band gap predicted from GGA-1/2 calculations

Among all magnetic semiconductors, GaMnAs seems to be the most important one. In this work, we present accurate first-principles calculations of GaMnAs within the GGA-1/2 approach: We concentrate our efforts in obtaining the position of the peak of Mn-d levels in the valence band and also the majority spin band gap. For the position of the Mn-d peak, we find a value of 3.3 eV below the Fermi level, in good agreement with the most recent experimental results of 3.5 and 3.7 eV. An analytical expression that fits the calculated E-g(x) for majority spin is derived in order to provide ready access to the band gap for the composition range from 0 to 0.25. We found a value of 3.9 eV for the gap bowing parameter. The results agree well with the most recent experimental data. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4718602]

Digital magnetic heterostructures based on GaN using GGA-1/2 approach

We present ab-initio calculations of seven digital magnetic heterostructures, GaN delta-doped with V, Cr, Mn, Fe, Co, Ni, and Cu, forming two-dimensional systems. Only GaN delta-doped with V or Cr present a ferromagnetic ground state with high Curie temperatures. For both, to better describe the electronic properties, we used the GGA-1/2 approach. The ground state of GaN/Cr resulted in a two dimensional half-metal, with 100% spin polarization. For GaN/V, we obtained an insulating state: integer magnetic moment of 2.0 mu(B), a minority spin gap of 3.0 eV close to the gap of GaN, but a majority spin gap of 0.34 eV. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4751285]

Yeast Gga Coat Proteins Function with Clathrin in Golgi to Endosome Transport

Gga proteins represent a newly recognized, evolutionarily conserved protein family with homology to the “ear” domain of the clathrin adaptor AP-1 γ subunit. Yeast cells contain two Gga proteins, Gga1p and Gga2p, that have been proposed to act in transport between the trans-Golgi network and endosomes. Here we provide genetic and physical evidence that yeast Gga proteins function in trans-Golgi network clathrin coats. Deletion of Gga2p (gga2Δ), the major Gga protein, accentuates growth and α-factor maturation defects in cells carrying a temperature-sensitive allele of the clathrin heavy chain gene. Cells carrying either gga2Δ or a deletion of the AP-1 β subunit gene (apl2Δ) alone are phenotypically normal, but cells carrying both gga2Δ and apl2Δ are defective in growth, α-factor maturation, and transport of carboxypeptidase S to the vacuole. Disruption of both GGA genes and APL2 results in cells so severely compromised in growth that they form only microcolonies. Gga proteins can bind clathrin in vitro and cofractionate with clathrin-coated vesicles. Our results indicate that yeast Gga proteins play an important role in cargo-selective clathrin-mediated protein traffic from the trans-Golgi network to endosomes.

Oxidative DNA damage induced by S(IV) in the presence of Cu(II) and Cu(I) complexes

The DNA damage induced by S(IV) in the presence of some Cu(II) complexes in air saturated solution was investigated. The addition of S(IV) to an air saturated solution containing CuII GGA (GGA = glycylglycyl-L-alanine), CuII G3 (G3 = triglycine) or CuII G4 (G4 = tetraglycine) and Ni(II) traces, causes rapid formation of the respective Cu(III) complex, with simultaneous O2 uptake and S(IV) oxidation. SO3•- and HO• were detected by EPR-spin trapping experiments. The DNA strand breaks were attributed to the oxysulfur radicals formed. In the reduction of Cu(II)/BCA (BCA = 4,4' dicarboxy-2-2'-biquinoline) by S(IV), with CuI BCA complex formation, there is the possible formation of carbon centered radical of BCA or peroxyl radical (ROO•) capable of oxidizing DNA bases. The intensity of DNA damage in the presence of these Cu(II) complexes and S(IV) (10-300 µmol L-1) followed the order: CuII BCA ∼ CuII G4 ∼ Cu(II) (added as Cu(NO3)2) > CuII G3 ∼ CuII GGA. Specifically for CuII BCA the damage occurred even at lower S(IV) concentration (0.1 µmol L-1). For the Cu(II) complexes with glycylglycylhistidine, glycylhistidylglycine, glycylhistidyllysine and glycylglycyltyrosylarginine the Cu(III) formation and the DNA damage was not observed.

Systematic investigation of a family of gradient-dependent functionals for solids

Eleven density functionals are compared with regard to their performance for the lattice constants of solids. We consider standard functionals, such as the local-density approximation and the Perdew-Burke-Ernzerhof (PBE) generalized-gradient approximation (GGA), as well as variations of PBE GGA, such as PBEsol and similar functionals, PBE-type functionals employing a tighter Lieb-Oxford bound, and combinations thereof. On a test set of 60 solids, we perform a system-by-system analysis for selected functionals and a full statistical analysis for all of them. The impact of restoring the gradient expansion and of tightening the Lieb-Oxford bound is discussed, and confronted with previous results obtained from other codes, functionals or test sets. No functional is uniformly good for all investigated systems, but surprisingly, and pleasingly, the simplest possible modifications to PBE turn out to have the most beneficial effect on its performance. The atomization energy of molecules was also considered and on a testing set of six molecules, we found that the PBE functional is clearly the best, the others leading to strong overbinding.

Gradient-dependent density functionals of the Perdew-Burke-Ernzerhof type for atoms, molecules, and solids

One of the standard generalized-gradient approximations (GGAs) in use in modern electronic-structure theory [Perdew-Burke-Ernzerhof (PBE) GGA] and a recently proposed modification designed specifically for solids (PBEsol) are identified as particular members of a family of functionals taking their parameters from different properties of homogeneous or inhomogeneous electron liquids. Three further members of this family are constructed and tested, together with the original PBE and PBEsol, for atoms, molecules, and solids. We find that PBE, in spite of its popularity in solid-state physics and quantum chemistry, is not always the best performing member of the family and that PBEsol, in spite of having been constructed specifically for solids, is not the best for solids. The performance of GGAs for finite systems is found to sensitively depend on the choice of constraints stemming from infinite systems. Guidelines both for users and for developers of density functionals emerge from this work.

The role of electron localization in the atomic structure of transition-metal 13-atom clusters: the example of Co(13), Rh(13), and Hf(13)

The crystalline structure of transition-metals (TM) has been widely known for several decades, however, our knowledge on the atomic structure of TM clusters is still far from satisfactory, which compromises an atomistic understanding of the reactivity of TM clusters. For example, almost all density functional theory (DFT) calculations for TM clusters have been based on local (local density approximation-LDA) and semilocal (generalized gradient approximation-GGA) exchange-correlation functionals, however, it is well known that plain DFT fails to correct the self-interaction error, which affects the properties of several systems. To improve our basic understanding of the atomic and electronic properties of TM clusters, we report a DFT study within two nonlocal functionals, namely, the hybrid HSE (Heyd, Scuseria, and Ernzerhof) and GGA + U functionals, of the structural and electronic properties of the Co(13), Rh(13), and Hf(13) clusters. For Co(13) and Rh(13), we found that improved exchange-correlation functionals decrease the stability of open structures such as the hexagonal bilayer (HBL) and double simple-cubic (DSC) compared with the compact icosahedron (ICO) structure, however, DFT-GGA, DFT-GGA + U, and DFT-HSE yield very similar results for Hf(13). Thus, our results suggest that the DSC structure obtained by several plain DFT calculations for Rh(13) can be improved by the use of improved functionals. Using the sd hybridization analysis, we found that a strong hybridization favors compact structures, and hence, a correct description of the sd hybridization is crucial for the relative energy stability. For example, the sd hybridization decreases for HBL and DSC and increases for ICO in the case of Co(13) and Rh(13), while for Hf(13), the sd hybridization decreases for all configurations, and hence, it does not affect the relative stability among open and compact configurations.

Lack of Association Between a 3 ` UTR VNTR Polymorphism of Dopamine Transporter Gene (SLC6A3) and ADHD in a Brazilian Sample of Adult Patients

Objective: To investigate a possible association between a 3`UTR VNTR polymorphism of the dopamine transporter gene (SLC6A3) and ADHD in a Brazilian sample of adult patients. Method: Study Case-control with 102 ADHD adult outpatients (DSM-IV criteria) and 479 healthy controls. The primers` sequence used were: 3`UTR-Forward: 5`TGT GGT GAT GGG AAC GGC CTG AG 3` and 3`UTR-Reverse: 5`CTT CCT GGA GGT CAC GGC TCA AGG 3`. Alleles of the 3`UTR were coded according to their number of repeats: 6- repeat 320 bp (allele 6), 8- repeat 400 bp (allele 8), 9-repeat 480 bp (allele 9), 10- repeat 480 bp (allele 10), and 11- repeat 520 bp (allele 11). Results: There were no allelic (chi(2) = 2.67, 5df, p = .75) and genotypic (chi(2) = 7.20, 1df, p = .61) association between adult ADHD and VNTR 3`UTR polymorphism of SLC6A3. Conclusion: Our findings do not support SLC6A3 as marker genetic susceptibility factor in adult ADHD. More comprehensive polymorphism coverage within the SLC6A3 region should be conducted in larger samples, including comparisons in clinical subgroups, and in samples with different ethnic backgrounds. (J. of Att. Dis. 2011; 15(4) 305-309)

Optimization of the Sybr Green real time PCR for the detection of Human Herpes Virus type 6 (HHV-6)

HHV-6 is the etiological agent of Exanthem subitum which is considered the sixth most frequent disease in infancy. In immuno-compromised hosts, reactivation of latent HHV-6 infection may cause severe acute disease. We developed a Sybr Green Real Time PCR for HHV-6 and compared the results with nested conventional PCR. A 214 pb PCR derived fragment was cloned using pGEM-T easy from Promega system. Subsequently, serial dilutions were made in a pool of negative leucocytes from 10-6 ng/µL (equivalent to 2465.8 molecules/µL) to 10-9 (equivalent to 2.46 molecules/µL). Dilutions of the plasmid were amplified by Sybr Green Real Time PCR, using primers HHV3 (5' TTG TGC GGG TCC GTT CCC ATC ATA 3)'and HHV4 (5' TCG GGA TAG AAA AAC CTA ATC CCT 3') and by conventional nested PCR using primers HHV1 (outer): 5'CAA TGC TTT TCT AGC CGC CTC TTC 3'; HHV2 (outer): 5' ACA TCT ATA ATT TTA GAC GAT CCC 3'; HHV3 (inner) and HHV4 (inner) 3'. The detection threshold was determined by plasmid serial dilutions. Threshold for Sybr Green real time PCR was 24.6 molecules/µL and for the nested PCR was 2.46 molecules/µL. We chose the Real Time PCR for diagnosing and quantifying HHV-6 DNA from samples using the new Sybr Green chemistry due to its sensitivity and lower risk of contamination.

Genetic parameters and mapping quantitative trait loci associated with tibia traits in broilers.

Abstract: Selection among broilers for performance traits is resulting in locomotion problems and bone disorders, once skeletal structure is not strong enough to support body weight in broilers with high growth rates. In this study, genetic parameters were estimated for body weight at 42 days of age (BW42), and tibia traits (length, width, and weight) in a population of broiler chickens. Quantitative trait loci (QTL) were identified for tibia traits to expand our knowledge of the genetic architecture of the broiler population. Genetic correlations ranged from 0.56 +/- 0.18 (between tibia length and BW42) to 0.89 +/- 0.06 (between tibia width and weight), suggesting that these traits are either controlled by pleiotropic genes or by genes that are in linkage disequilibrium. For QTL mapping, the genome was scanned with 127 microsatellites, representing a coverage of 2630 cM. Eight QTL were mapped on Gallus gallus chromosomes (GGA): GGA1, GGA4, GGA6, GGA13, and GGA24. The QTL regions for tibia length and weight were mapped on GGA1, between LEI0079 and MCW145 markers. The gene DACH1 is located in this region; this gene acts to form the apical ectodermal ridge, responsible for limb development. Body weight at 42 days of age was included in the model as a covariate for selection effect of bone traits. Two QTL were found for tibia weight on GGA2 and GGA4, and one for tibia width on GGA3. Information originating from these QTL will assist in the search for candidate genes for these bone traits in future studies.