Cytogenetic mapping of the W chromosome in the genus Leporinus (Teleostei, Anostomidae) using a highly repetitive DNA sequence

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

Relation of pretreatment sequence diversity in NS5A region of HCV genotype 1 with immune response between pegylated-INF/ribavirin therapy outcomes

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Characterization of generalized Bessel polynomials in terms of polynomial inequalities

Generalized Bessel polynomials (GBPs) are characterized as the extremal polynomials in certain inequalities in L-2 norm of Markov type. (C) 1998 Academic Press.

Amino acid sequence of a myotoxic Lys49-phospholipase A(2) homologue from the venom of Cerrophidion (Bothrops) godmani

The complete amino acid sequence of myotoxin II (godMT-II), a myotoxic phospholipase A( 2 )(PLA(2)) homologue from the venom of the Central American crotaline snake Cerrophidion (Bothrops) godmani, was determined by direct protein sequencing methods. GodMT-II is a class II PLA, showing a Lys instead of Asp at position 49. An additional substitution in the calcium binding loop region (Asn instead of Tyr at position 28) suggests the lack of enzymatic activity observed in this toxin is due to loss of its ability to bind the co-factor Ca2+, since the residues involved in forming the catalytic network of PLA(2)s (His-48, Tyr-52 and Asp-99) an conserved in godMT-II. This myotoxin shows highest sequence homology with other Lys-49 PLA(2)s from Bothrops, Agkistrodon and Trimeresurus species, suggesting that they constitute a conserved family of proteins, yet in contrast presents lower homology with Bothrops asper myotoxin III, a catalytically-active PLA(2). The C-terminal region of godMT-II, which is rich in cationic and hydrophobic residues, shares high sequence homology to the corresponding region in the myotoxin II from B. asper, which has been proposed to play an important role in the Ca2+-independent membrane damaging activity. (C) 1998 Elsevier B.V. B.V. All rights reserved.

Amino acid sequence and crystal structure of BaP1, a metalloproteinase from Bothrops asper snake venom that exerts multiple tissue-damaging activities

BaP1 is a 22.7-kD P-I-type zinc-dependent metalloproteinase isolated from the venom of the snake Bothrops asper, a medically relevant species in Central America. This enzyme exerts multiple tissue-damaging activities, including hemorrhage, myonecrosis, dermonecrosis, blistering, and edema. BaP1 is a single chain of 202 amino acids that shows highest sequence identity with metalloproteinases isolated front the venoms of snakes of the subfamily Crotalinae. It has six Cys residues involved in three disulfide bridges (Cys 117-Cys 197, Cys 159-Cys 181, Cys 157-Cys 164). It has the consensus sequence H(142)E(143)XXH(146)XXGXXH(152), as well as the sequence C164I165M166, which characterize the metzincin superfamily of metalloproteinases. The active-site cleft separates a major subdomain (residues 1-152), comprising four a-helices and a five-stranded beta-sheet, from the minor subdomain, which is formed by a single a-helix and several loops. The catalytic zinc ion is coordinated by the N-epsilon2 nitrogen atoms of His 142, His 146, and His 152, in addition to a solvent water molecule, which in turn is bound to Glu 143. Several conserved residues contribute to the formation of the hydrophobic pocket, and Met 166 serves as a hydrophobic base for the active-site groups. Sequence and structural comparisons of hemorrhagic and nonhemorrhagic P-I metalloproteinases from snake venoms revealed differences in several regions. In particular, the loop comprising residues 153 to 176 has marked structural differences between metalloproteinases with very different hemorrhagic activities. Because this region lies in close proximity to the active-site microenvironment, it may influence the interaction of these enzymes with physiologically relevant substrates in the extracellular matrix.

Using genetic algorithm to design protein sequence

In this work, genetic algorithms concepts along with a rotamer library for proteins side chains are used to optimize the tertiary structure of the hydrophobic core of Cytochrome b(562) starting from the known PDB structure of its backbone which is kept fixed while the side chains of the hydrophobic core are allowed to adopt the conformations present in the rotamer library. The atoms of the side chains forming the core interact via van der Waals energy. Besides the prediction of the native core structure, it is also suggested a set of different amino acid sequences for this core. Comparison between these new cores and the native are made in terms of their volumes, van der Waals energies values and the numbers of contacts made by the side chains forming the cores. This paper proves that genetic algorithms area efficient to design new sequence for the protein core. (C) 2007 Elsevier B.V. All rights reserved.

Preliminary functional characterization, cloning and primary sequence of Fastuosain, a cysteine peptidase isolated from fruits of Bromelia fastuosa

The present work reports the characterization of Fastuosain, a novel cysteine protease of 25kDa, purified from the unripe fruits of Bromelia fastuosa, a wild South American Bromeliaceae. Proteolytic activity, measured using casein and synthetic substrates, was dependent on the presence of thiol reagents, having maximum activity at pH 7.0. The present work reports cDNA cloning of Fastuosain; cDNA was amplified by PCR using specific primers. The product was 1096pb long. Mature fastuosain has 217 residues, and with the proregion has a total length of 324 residues. Its primary sequence showed high homology with ananain(74%), stem bromelain (66%) and papain (44%).

Completion of the Nucleotide Sequence of a Brazilian Isolate of Southern bean mosaic virus

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

Multitrace operators and the generalized AdS/CFT prescription

We show that multitrace interactions can be consistently incorporated into an extended AdS conformal field theory (CFT) prescription involving the inclusion of generalized boundary conditions and a modified Legendre transform prescription. We find new and consistent results by considering a self-contained formulation which relates the quantization of the bulk theory to the AdS/CFT correspondence and the perturbation at the boundary by double-trace interactions. We show that there exist particular double-trace perturbations for which irregular modes are allowed to propagate as well as the regular ones. We perform a detailed analysis of many different possible situations, for both minimally and nonminimally coupled cases. In all situations, we make use of a new constraint which is found by requiring consistency. In the particular nonminimally coupled case, the natural extension of the Gibbons-Hawking surface term is generated.

New thought experiment to test the generalized second law of thermodynamics

We propose an extension of the original thought experiment proposed by Geroch, which sparked much of the actual debate and interest on black hole thermodynamics, and show that the generalized second law of thermodynamics is in compliance with it.

Mathematical models of generalized diffusion

We discuss in this paper equations describing processes involving non-linear and higher-order diffusion. We focus on a particular case (u(t) = 2 lambda (2)(uu(x))(x) + lambda (2)u(xxxx)), which is put into analogy with the KdV equation. A balance of nonlinearity and higher-order diffusion enables the existence of self-similar solutions, describing diffusive shocks. These shocks are continuous solutions with a discontinuous higher-order derivative at the shock front. We argue that they play a role analogous to the soliton solutions in the dispersive case. We also discuss several physical instances where such equations are relevant.

Generalized non-abelian Toda models of dyonic type

The construction of a class of non-abelian Toda models admiting dyonic type soliton solutions is reviewed.

Generalized sine-Gordon/massive Thirring models and soliton/particle correspondences

We consider a real Lagrangian off-critical submodel describing the soliton sector of the so-called conformal affine sl(3)((1)) Toda model coupled to matter fields. The theory is treated as a constrained system in the context of Faddeev-Jackiw and the symplectic schemes. We exhibit the parent Lagrangian nature of the model from which generalizations of the sine-Gordon (GSG) or the massive Thirring (GMT) models are derivable. The dual description of the model is further emphasized by providing the relationships between bilinears of GMT spinors and relevant expressions of the GSG fields. In this way we exhibit the strong/weak coupling phases and the (generalized) soliton/particle correspondences of the model. The sl(n)((1)) case is also outlined. (C) 2002 American Institute of Physics.

Laguerre moments and generalized functions

Here we explore the link between the moments of the Laguerre polynomials or Laguerre moments and the generalized functions (as the Dirac delta-function and its derivatives), presenting several interesting relations. A useful application is related to a procedure for calculating mean values in quantum optics that makes use of the so-called quasi-probabilities. One of them, the P-distribution, can be represented by a sum over Laguerre moments when the electromagnetic field is in a photon-number state. Consequently, the P-distribution can be expressed in terms of Dirac delta-function and derivatives. More specifically, we found a direct relation between P-distributions and the Laguerre factorial moments.

Generalized squeezing operators, bipartite Wigner functions and entanglement via Wehrl's entropy functionals

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)