Correntes críticas e comportamento dinâmico dos vórtices em fitas supercondutoras do tipo II com arranjos conformes de centros de aprisionamento

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Conformational changes in a hyperthermostable glycoside hydrolase: enzymatic activity is a consequence of the loop dynamics and protonation balance

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Distribution of neutral prilocaine in a phospholipid bilayer: Insights from molecular dynamics simulations

In this work, we report a 20-ns constant pressure molecular dynamics simulation of prilocaine (PLC), in amine-amide local anesthetic, in a hydrated liquid crystal bilayer of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine. The partition of PLC induces the lateral expansion of the bilayer and a concomitant contraction in its thickness. PLC molecules are preferentially found in the hydrophobic acyl chains region, with a maximum probability at similar to 12 angstrom from the center of the bilayer (between the C(4) and C(5) methylene groups). A decrease in the acyl chain segmental order parameter, vertical bar S-CD vertical bar, compared to neat bilayers, is found, in good agreement with experimental H-2-NMR studies. The decrease in vertical bar S-CD vertical bar induced by PLC is attributed to a larger accessible volume per lipid in the acyl chain region. (C) 2008 Wiley Periodicals, Inc.

Time-periodic perturbation of a Lienard equation with an unbounded homoclinic loop

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Variability of the conserved V3 loop tip motif in HIV-1 subtype B isolates collected from Brazilian and French patients

The diversity of the V3 loop tip motif sequences of HIV-1 subtype B was analyzed in patients from Botucatu (Brazil) and Montpellier (France). Overall, 37 tetrameric tip motifs were identified, 28 and 17 of them being recognized in Brazilian and French patients, respectively. The GPGR (P) motif was predominant in French but not in Brazilian patients (53.5% vs 31.0%), whereas the GWGR (W) motif was frequent in Brazilian patients (23.0%) and absent in French patients. Three tip motif groups were considered: P, W, and non-P non-W groups. The distribution of HIV-1 isolates into the three groups was significantly different between isolates from Botucatu and from Montpellier (P < 0.001). A higher proportion of CXCR4-using HIV-1 (X4 variants) was observed in the non-P non-W group as compared with the P group (37.5% vs 19.1%), and no X4 variant was identified in the W group (P < 0.001). The higher proportion of X4 variants in the non-P non-W group was essentially observed among the patients from Montpellier, who have been infected with HIV-1 for a longer period of time than those from Botucatu. Among patients from Montpellier, CD4+ cell counts were lower in patients belonging to the non-P non-W group than in those belonging to the P group (24 cells/µL vs 197 cells/µL; P = 0.005). Taken together, the results suggest that variability of the V3 loop tip motif may be related to HIV-1 coreceptor usage and to disease progression. However, as analyzed by a bioinformatic method, the substitution of the V3 loop tip motif of the subtype B consensus sequence with the different tip motifs identified in the present study was not sufficient to induce a change in HIV-1 coreceptor usage.

Visual detection of turkey coronavirus RNA in tissues and feces by reverse-transcription loop-mediated isothermal amplification (RT-LAMP) with hydroxynaphthol blue dye

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Correlation of temperature induced conformation change with optimum catalytic activity in the recombinant G/11 xylanase A from Bacillus subtilis strain 168 (1A1)

The 1.7 angstrom resolution crystal structure of recombinant family G/11 beta-1,4-xylanase (rXynA) from Bacillus subtilis 1A1 shows a jellyroll fold in which two curved P-sheets form the active-site and substrate-binding cleft. The onset of thermal denaturation of rXynA occurs at 328 K, in excellent agreement with the optimum catalytic temperature. Molecular dynamics simulations at temperatures of 298-328 K demonstrate that below the optimum temperature the thumb loop and palm domain adopt a closed conformation. However, at 328 K these two domains separate facilitating substrate access to the active-site pocket, thereby accounting for the optimum catalytic temperature of the rXynA. (c) 2005 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

One loop conformal invariance of the superstring in an AdS(5) x S-5 background

It is proven that the pure spinor superstring in an AdS(5) x S-5 background remains conformally invariant at one loop level in the sigma model perturbation theory.

Massless and massive one-loop three-point functions in negative dimensional approach

In this article we present the complete massless and massive one-loop triangle diagram results using the negative dimensional integration method (NDIM). We consider the following cases: massless internal fields; one massive, two massive with the same mass m and three equal masses for the virtual particles. Our results are given in terms of hypergeometric and hypergeometric-type functions of the external momenta (and masses for the massive cases) where the propagators in the Feynman integrals are raised to arbitrary exponents and the dimension of the space-time is D. Our approach reproduces the known results; it produces other solutions as yet unknown in the literature as well. These new solutions occur naturally in the context of NDIM revealing a promising technique to solve Feynman integrals in quantum field theories.

NDIM achievements: massive, arbitrary tensor rank and N-loop insertions in Feynman integrals

One of the main difficulties in studying quantum field theory, in the perturbative regime, is the calculation of D-dimensional Feynman integrals. In general, one introduces the so-called Feynman parameters and, associated with them, the cumbersome parametric integrals. Solving these integrals beyond the one-loop level can be a difficult task. The negative-dimensional integration method (NDIM) is a technique whereby such a problem is dramatically reduced. We present the calculation of two-loop integrals in three different cases: scalar ones with three different masses, massless with arbitrary tensor rank, with and N insertions of a two-loop diagram.

Kaon condensation and lambda-nucleon loop in the relativistic mean-field approach

The possibility of kaon condensation in high-density symmetric nuclear matter is investigated including both s- and p-wave kaon-baryon interactions within the relativistic mean-field (RMF) theory. Above a certain density, we have a collective (D) over bar (S) state carrying the same quantum numbers as the antikaon. The appearance of the (K) over bar (S) state is caused by the time component of the axial-vector interaction between kaons and baryons. It is shown that the system becomes unstable with respect to condensation of K-(K) over bar (S) pairs. We consider how the effective baryon masses affect the kaon self-energy coming from the time component of the axial-vector interaction. Also, the role of the spatial component of the axial-vector interaction on the possible existence of the collective kaonic states is discussed in connection with A-mixing effects in the ground state of high-density matter: Implications of K (K) over bar (S) condensation for high-energy heavy-ion collisions are briefly mentioned. (c) 2005 Elsevier B.V. All rights reserved.

The two-loop massless (lambda/4!)phi(4) model in nontranslational invariant domain

We study the (lambda/4!)phi(4) massless scalar field theory in a four-dimensional Euclidean space, where all but one of the coordinates are unbounded. We are considering Dirichlet boundary conditions in two hyperplanes, breaking the translation invariance of the system. We show how to implement the perturbative renormalization up to two-loop level of the theory. First, analyzing the full two and four-point functions at the one-loop level, we show that the bulk counterterms are sufficient to render the theory finite. Meanwhile, at the two-loop level, we must also introduce surface counterterms in the bare Lagrangian in order to make finite the full two and also four-point Schwinger functions. (c) 2006 American Institute of Physics.

NOISE and ULTRAVIOLET DIVERGENCES IN SIMULATIONS of GINZBURG-LANDAU-LANGEVIN TYPE of EQUATIONS

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)