Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction

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

A systematization for one-loop 4D Feynman integrals

We present a strategy for the systematization of manipulations and calculations involving divergent (or not) Feynman integrals, typical of the one-loop perturbative solutions of QFT, where the use of an explicit regularization is avoided. Two types of systematization are adopted. The divergent parts are put in terms of a small number of standard objects, and a set of structure functions for the finite parts is also defined. Some important properties of the finite structures, specially useful in the verification of relations among Green's functions, are identified. We show that, in fundamental (renormalizable) theories, all the finite parts of two-, three- and four-point functions can be written in terms of only three basic functions while the divergent parts require (only) five objects. The final results obtained within the proposed strategy can be easily converted into those corresponding to any specific regularization technique providing an unified point of view for the treatment of divergent Feynman integrals. Examples of physical amplitudes evaluation and their corresponding symmetry relations verification are presented as well as generalizations of our results for the treatment of Green's functions having an arbitrary number of points are considered.

Chiral aspects of hadron structure

Chiral loop corrections for hadronic properties are considered in a constituent quark model. It is emphasized that the correct implementation of such corrections requires a sum over intermediate hadronic states. The leading non-analytic corrections are very important for baryon magnetic moments and explain the failure of the sum rule (mu(Sigma+) + 2 mu(Sigma-))/mu(A) = -1 predicted by the constituent quark model. (C) 2000 Elsevier B.V. B.V. All rights reserved.

Four-fermion contact interactions at one-loop and the new atomic parity violation results.

We investigate the possibility that four-fermion contact interactions give rise to the observed deviation from the Standard Model prediction for the weak charge of cesium, through one-loop contributions. We show that the presence of loops involving the third generation quarks can explain such deviation.

The higher grading structure of the WKI hierarchy and the two-component short pulse equation

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the "Mfold Web Server" simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of "Dinamelt Web Server". The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors. (C) 2011 Elsevier B.V. All rights reserved.

Uncertainties in the prediction of spatial variability of soil CO2 emissions and related properties

A emissão de CO2 do solo apresenta alta variabilidade espacial, devido à grande dependência espacial observada nas propriedades do solo que a influenciam. Neste estudo, objetivou-se: caracterizar e relacionar a variabilidade espacial da respiração do solo e propriedades relacionadas; avaliar a acurácia dos resultados fornecidos pelo método da krigagem ordinária e simulação sequencial gaussiana; e avaliar a incerteza na predição da variabilidade espacial da emissão de CO2 do solo e demais propriedades utilizando a simulação sequencial gaussiana. O estudo foi conduzido em uma malha amostral irregular com 141 pontos, instalada sobre a cultura de cana-de-açúcar. Nesses pontos foram avaliados a emissão de CO2 do solo, a temperatura do solo, a porosidade livre de água, o teor de matéria orgânica e a densidade do solo. Todas as variáveis apresentaram estrutura de dependência espacial. A emissão de CO2 do solo mostrou correlações positivas com a matéria orgânica (r = 0,25, p < 0,05) e a porosidade livre de água (r = 0,27, p <0,01) e negativa com a densidade do solo (r = -0,41, p < 0,01). No entanto, quando os valores estimados espacialmente (N=8833) são considerados, a porosidade livre de água passa a ser a principal variável responsável pelas características espaciais da respiração do solo, apresentando correlação de 0,26 (p < 0,01). As simulações individuais propiciaram, para todas as variáveis analisadas, melhor reprodução das funções de distribuição acumuladas e dos variogramas, em comparação à krigagem e estimativa E-type. As maiores incertezas na predição da emissão de CO2 estiveram associadas às regiões da área estudada com maiores valores observados e estimados, produzindo estimativas, ao longo do período estudado, de 0,18 a 1,85 t CO2 ha-1, dependendo dos diferentes cenários simulados. O conhecimento das incertezas gerado por meio dos diferentes cenários de estimativa pode ser incluído em inventários de gases do efeito estufa, resultando em estimativas mais conservadoras do potencial de emissão desses gases.

Prediction of cassava starch edible film properties by chemometric analysis of infrared spectra

Cassava starch has been shown to make transparent and colorless flexible films without any previous chemical treatment. The functional properties of edible films are influenced by starch properties, including chain conformation, molecular bonding, crystallinity, and water content. Fourier-transform infrared (FTIR) spectroscopy in combination with attenuated total reflectance (ATR) has been applied for the elucidation of the structure and conformation of carbohydrates. This technique associated with chemometric data processing could indicate the relationship between the structural parameters and the functional properties of cassava starch-based edible films. Successful prediction of the functional properties values of the starch-based films was achieved by partial least squares regression data. The results showed that presence of the hydroxyl group on carbon 6 of the cyclic part of glucose is directly correlated with the functional properties of cassava starch films.

A structure-activity relationship study of quinone compounds with trypanocidal activity

A set of 25 quinone compounds with anti-trypanocidal activity was studied by using the density functional theory (DFT) method in order to calculate atomic and molecular properties to be correlated with the biological activity. The chemometric methods principal component analysis (PCA), hierarchical cluster analysis (HCA), stepwise discriminant analysis (SDA), Kth nearest neighbor (KNN) and soft independent modeling of class analogy (SIMCA) were used to obtain possible relationships between the calculated descriptors and the biological activity studied and to predict the anti-trypanocidal activity of new quinone compounds from a prediction set. Four descriptors were responsible for the separation between the active and inactive compounds: T-5 (torsion angle), QTS1 (sum of absolute values of the atomic charges), VOLS2 (volume of the substituent at region B) and HOMO-1 (energy of the molecular orbital below HOMO). These descriptors give information on the kind of interaction that occurs between the compounds and the biological receptor. The prediction study was done with a set of three new compounds by using the PCA, HCA, SDA, KNN and SIMCA methods and two of them were predicted as active against the Trypanosoma cruzi. (c) 2005 Elsevier SAS. All rights reserved.

Prediction and spatial variability of soil dynamic properties in sugar cane fields of São Paulo State Brazil

The objective of this work was to model and diagnose the spatial variability of soil load support capacity (SLSC) in sugar cane crop fields, as well as to evaluate the management impact on São Paulo State soil structure. The investigated variables were: pressure preconsolidation (sigma(p)), apparent cohesion () and internal friction angle (). The conclusions from the results were that the models and spatial dependence maps constitute important tools in the prediction and location of the mechanical internal strength of soils cultivated with sugar cane. They will help future soil management decisions so that soil structure sustainability will not be compromised.

Crystal structure of a novel myotoxic Arg49 phospholipase A(2) homolog (zhaoermiatoxin) from Zhaoermia mangshanensis snake venom: Insights into Arg49 coordination and the role of Lys122 in the polarization of the C-terminus

The venom of Zhaoermia mangshanensis, encountered solely in Mt Mang in China's Hunan Province, exhibits coagulant, phosphodiesterase, L-amino acid oxidase, kallikrein, phospholipase A(2) and myotoxic activities. The catalytically inactive PLA(2) homolog referred to as zhaoermiatoxin is highly myotoxic and displays high myonecrotic and edema activities. Zhaoermiatoxin possesses a molecular weight of 13,972 Da, consists of 121 amino-acid residues crosslinked by seven disulfide bridges and shares high sequence homology with Lys49-PLA(2)s from the distantly related Asian pitvipers. However, zhaoermiatoxin possesses an arginine residue at position 49 instead of a lysine, thereby suggesting a secondary Lys49 -> Arg substitution which results in a catalytically inactive protein. We have determined the first crystal structure of zhaoermiatoxin, an Arg49-PLA(2), from Zhaoermia mangshanensis venom at 2.05 A resolution, which represents a novel member of phospholipase A(2) family. In this structure, unlike the Lys49 PLA(2)s, the C-terminus is well ordered and an unexpected non-polarized state of the putative calcium-binding loop due to the flip of Lys122 towards the bulk solvent is observed. The orientation of the Arg-49 side chain results in a similar binding mode to that observed in the Lys49 PLA(2)s; however, the guadinidium group is tri-coordinated by carbonyl oxygen atoms of the putative calcium-binding loop, whereas the N zeta atom of lysine is tetra-coordinated as a result of the different conformation adopted by the putative calcium-binding loop. (c) 2008 Elsevier Ltd. All rights reserved.

Study of Structure and Properties of Bi4Ti3O12 Prepared by Mechanochemical Syntheses

Bi4Ti3O12 powder was synthesized from bismuth oxide and titanium oxide. Mixture of oxides was milled in zirconium oxide jar in the planetary ball-mill during 1, 3 and 6 h. Extended time of milling directed to formation of higher amount of titanates perovskite phase. Bi4Ti3O12 was formed between 1 and 3 h of milling time. The phase formation of Bi4Ti3O12, crystal structure and powder particle size were followed by XRD, Raman spectroscopy and SEM analysis. After milling for various times the powders were compacted by pressing and isothermal sintering. Sample milled for 3 h and subsequently sintered at 1000C for 24 h exhibit a hysteresis loop, confirming that the synthesized material possesses ferroelectric properties. All results affect that the structure Bi4Ti3O12 is strongly dependent on the milling time.

Feynman integrals with tensorial structure in the negative dimensional integration scheme

The negative-dimensional integration method (NDIM) is revealing itself as a very useful technique for computing massless and/or massive Feynman integrals, covariant and noncovanant alike. Up until now however, the illustrative calculations done using such method have been mostly covariant scalar integrals/without numerator factors. We show here how those integrals with tensorial structures also can be handled straightforwardly and easily. However, contrary to the absence of significant features in the usual approach, here the NDIM also allows us to come across surprising unsuspected bonuses. Toward this end, we present two alternative ways of working out the integrals and illustrate them by taking the easiest Feynman integrals in this category that emerge in the computation of a standard one-loop self-energy diagram. One of the novel and heretofore unsuspected bonuses is that there are degeneracies in the way one can express the final result for the referred Feynman integral.

Structure of tick anticoagulant peptide at 1.6 Å resolution complexed with bovine pancreatic trypsin inhibitor

The structure of tick anticoagulant peptide (TAP) has been determined by X-ray crystallography at t.6 Å resolution complexed with bovine pancreatic trypsin inhibitor (BPTI). The TAP-BPTI crystals are tetragonal, a = b = 46.87, c = 50.35 Å, space group P41, four complexes per unit cell. The TAP molecules are highly dipolar and form an intermolecular helical array along the c-axis with a diameter of about 45 Å. Individual TAP units interact in a head-to-tail fashion, the positive end of one molecule associating with the distal negative end of another, and vice versa. The BPTI molecules have a uniformly distributed positively charged surface that interacts extensively through 14 hydrogen bonds and two hydrogen bonded salt bridges with the helical groove around the helical TAP chains. Comparing the structure of TAP in TAP-BPTI with TAP bound to factor Xa(Xa) suggests a massive reorganization in the N-terminal tetrapeptide and the first disulfide loop of TAP (CyS5(T)- Cys 15(T)) upon binding to Xa. The Tyr1(T)OH atom of TAP moves 14.2 Å to interact with Asp189 of the S1 specificity site, Arg3(T)CZ moves 5.0 Å with the guanidinium group forming a cation-π-electron complex in the S4 subsite of Xa, while Lys7(T)NZ differs in position by 10.6 Å in TAP-BPTI and TAP-Xa, all of which indicates a different pre-Xa-bound conformation for the N- terminal of TAP in its native state. In contrast to TAP, the BPTI structure of TAP-BPTI is practically the same as all those of previously determined structures of BPTI, only arginine and lysine side-chain conformations showing significant differences.

Can four-fermion contact interactions at one-loop explain the new atomic parity violation results?

We investigate the possibility that four-fermion contact interactions give rise to the observed deviation from the standard model prediction for the weak charge of cesium, through one-loop contributions. We show that the presence of loops involving the third generation quarks can explain such a deviation.