Phylogenetic relationships of Pseudis and Lysapsus (Anura, Hylidae, Hylinae) inferred from mitochondrial and nuclear gene sequences

The previous uncertain placement of Lysapsus and Pseudis within the neobatrachians was recently resolved by molecular and morphological studies, which supported them as members of the Hylinae subfamily. Their inter- and intrageneric relationships, however, have long been under debate and no studies shed light on these questions. Aiming to elucidate such questions, this paper used 3.2 kb comprising the mitochondrial genes 12S, tRNA valine, 16S and cytochrome b, and the nuclear exon 1 coding for rhodopsin, to all representatives of both genera (except to two subspecies of Pseudis paradoxa). The results identified three major clades: the clade 1 was composed by Lysapsus species and subspecies; clade 2 included the subspecies of the Pseudis paradoxa (Pseudis paradoxa paradoxa, P. paradoxa platensis and P. paradoxa occidentalis), P. fusca, P. bolbodactyla and P. tocantins, and clade 3 was composed by Pseudis southern Brazil species (Pseudis cardosoi and P. minuta). As closely related taxa we found Pseudis minuta + P. cardosoi; P. tocantins + P. fusca, and the subspecies within each genus. Evidence that Pseudis is not monophyletic with respect to Lysapsus was found and we suggest Lysapsus to be a junior synonym of Pseudis. Based on pair-wise comparison among gene sequences, we also suggest that the subspecies of Pseudis paradoxa and Lysapsus limellum must be considered as full species. (c) the Willi Hennig Society 2007.

A phylogenetic analysis of Pleurodema (Anura: Leptodactylidae: Leiuperinae) based on mitochondrial and nuclear gene sequences, with comments on the evolution of anuran foam nests

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

L-orthogonal polynomials associated with related measures

A positive measure psi defined on [a, b] such that its moments mu(n) = integral(b)(a)t(n) d psi(t) exist for n = 0, +/-1, +/-2. can be called a strong positive measure on [a, b] When 0 <= a < b <= infinity the sequence of polynomials {Q(n)} defined by integral(b)(a) t(-n+s) Q(n)(t) d psi(t) = 0, s = 0, ., n - 1, exist and they are referred here as L-orthogonal polynomials We look at the connection between two sequences of L-orthogonal polynomials {Q(n)((1))} and {Q(n)((0))} associated with two closely related strong positive measures and th defined on [a, b]. To be precise, the measures are related to each other by (t - kappa) d psi(1)(t) = gamma d psi(0)(t). where (t - kappa)/gamma is positive when t is an element of (n, 6). As applications of our study. numerical generation of new L-orthogonal polynomials and monotonicity properties of the zeros of a certain class of L-orthogonal polynomials are looked at. (C) 2010 IMACS Published by Elsevier B V All rights reserved

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.

Deglaciation sequences in the Permo-Carboniferous Itarare Group, Parana Basin, southern Brazil

The Late Carboniferous-Early Permian Itarare Group is a thick glacial unit of the Parana Basin. Five unconformity-bounded sequences have been defined in the eastern outcrop belt and recognized in well logs along 400 km across the central portion of the basin. Deglaciation sequences are present in the whole succession and represent the bulk of the stratigraphic record. The fining-upward vertical facies succession is characteristic of a retrogradational stacking pattern and corresponds to the stratigraphic record of major ice-retreat phases. Laterally discontinuous subglacial tillites and boulder beds occur at the base of the sequences. When these subglacial facies are absent, deglaciation sequences lie directly on the basal disconformities. Commonly present in the lowermost portions of the deglaciation sequences, polymictic conglomerates and cross-bedded sandstones are generated in subaqueous proximal outwash fans in front of retreating glaciers. The overlying assemblage of diamictites, parallel-bedded and rippled sandstones, and Bouma-like facies sequences are interpreted as deposits of distal outwash fan lobes. The tops of the deglaciation sequences are positioned in clay-rich marine horizons that show little (fine-laminated facies with dropstones) or no evidence of glacial influence on the deposition and likely represent periods of maximum ice retreat. (c) 2006 Elsevier Ltd. All rights reserved.

Structuralism and the Applicability of Mathematics

In this paper I argue for the view that structuralism offers the best perspective for an acceptable account of the applicability of mathematics in the empirical sciences. Structuralism, as I understand it, is the view that mathematics is not the science of a particular type of objects, but of structural properties of arbitrary domains of entities, regardless of whether they are actually existing, merely presupposed or only intentionally intended.

VERIFICATION of THE PRESENCE of CAPSULE GENE SEQUENCES IN NASOPHARYNGEAL ISOLATES of NONTYPEABLE HAEMOPHILUS INFLUENZAE FROM HEALTHY CHILDREN AT A BRAZILIAN DAY CARE CENTER

Cinqüenta e oito cepas de Haemophilus influenzae foram isoladas da nasofaringe de crianças saudáveis que freqüentam uma creche, e através da técnica de Southern blot foi pesquisada nas cepas acapsuladas a presença de seqüências do gene capsular. Sete cepas (12%) caracterizadas sorologicamente como acapsuladas mostraram homologia com seqüências específicas da cápsula. Uma cepa foi caracterizada com uma linhagem H. influenzae tipo b cápsula deficiente.

Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences

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

Comparative genomic hybridization analysis detects frequent over-representation of DNA sequences at 3q, 7p, and 8q in head and neck carcinomas

Comparative genomic hybridization (CGH) was used to identify chromosomal imbalances in 19 samples of squamous cell carcinoma of the head and neck (HNSCC). The chromosome arms most often or er-represented were 3q (48%), 8q (42%), and 7p (32%); in many cases, these changes were observed at high copy number. Other commonly over-represented sites were 1q, 2q, 6p, 6q, and 18q. The most frequently under-represented segments were 3p and 22q. Loss of heterozygosity of two polymorphic microsatellite loci from chromosome 22 was observed in two tongue tumors, in agreement with the CGH analysis. Gains of 1q and 2q material were detected in patients exhibiting a clinical history of recurrence and/or metastasis followed by terminal disease. This association suggests that gain of 1q and 2q map be a new marker of head and neck tumors with a refractory clinical response. (C) 2000 Elsevier B.V. All rights reserved.

Correlations between differences in amino-terminal sequences and different hemolytic activity of sticholysins

Sticholysins I and II (St I and St II) are cytolysins produced by the sea anemone Stichodactyla helianthus. In spite of their 93% sequence homology, St II is more hemolytic against human erythrocytes than St 1. In order to establish the possible causes of this difference, we studied the hemolytic activity of synthetic peptides containing sequences from the N-termini of both proteins. The results demonstrated that the differences in hemolytic activity of the toxins could be ascribed at least partly to differences in their N-termini. (c) 2007 Elsevier Ltd. All rights reserved.

Szego polynomials: some relations to L-orthogonal and orthogonal polynomials

We consider the real Szego polynomials and obtain some relations to certain self inversive orthogonal L-polynomials defined on the unit circle and corresponding symmetric orthogonal polynomials on real intervals. We also consider the polynomials obtained when the coefficients in the recurrence relations satisfied by the self inversive orthogonal L-polynomials are rotated. (C) 2002 Elsevier B.V. B.V. All rights reserved.

Correlation between the mobility of spin-labeled peptide chains and resin solvation: An approach to optimize the synthesis of aggregating sequences

Resin solvation properties affect the efficiency of the coupling reactions in solid-phase peptide synthesis. Here we report a novel approach to evaluate resin solvation properties, making use of spin label electron paramagnetic resonance (EPR) spectroscopy. The aggregating VVLGAAIV and ING sequences were assembled in benzhydrylamine-resin with different amino group contents (up to 2.6 mmol/g) to examine the extent of chain association within the beads. These model peptidyl-resins were first labeled at their N-terminus with the amino acid spin label 2,2,6,6-tetramethylpiperidine-N-oxyl-4-amino-4-carboxylic acid (Toac). Their solvation properties in different solvents were estimated, either by bead swelling measurement or by assessing the dynamics of their polymeric matrixes through the analysis of Toac EPR spectra, and were correlated with the yield of the acylation reaction. In most cases the coupling rate was found to depend on bead swelling. Comparatively, the EPR approach was more effective. Line shape analysis allowed the detection of more than one peptide chain population, which influenced the reaction. The results demonstrated the unique potential of EPR spectroscopy not only for improving the yield of peptide synthesis, even in challenging conditions, but also for other relevant polymer-supported methodologies in chemistry and biology.

Companion orthogonal polynomials: some applications

In this paper the recurrence relations of symmetric orthogonal polynomials whose measures are related to each other in a certain way are considered. Many of the relations satisfied by the coefficients of the recurrence relations are exposed. The results are applied to obtain, for example, information regarding certain Sobolev orthogonal polynomials and regarding the measures of certain orthogonal polynomial sequences with twin periodic recurrence coefficients. (C) 2001 IMACS. Published by Elsevier B.V. B.V. All rights reserved.

GENETIC INTERRELATIONSHIPS OF PROTEOLYTIC CLOSTRIDIUM-BOTULINUM TYPE-A, TYPE-B, AND TYPE-F AND OTHER MEMBERS OF THE CLOSTRIDIUM-BOTULINUM COMPLEX AS REVEALED BY SMALL-SUBUNIT RIBOSOMAL-RNA GENE-SEQUENCES

The phylogenetic interrelationships of members of the Clostridium botulinum complex of species was investigated by direct sequencing of their 16S rRNA genes. Comparative analysis of the 16S rRNA sequences demonstrated the presence of four phylogenetically distinct lineages corresponding to: i) proteolytic C. botulinum types Al B, and F, and C. sporogenes, ii) saccharolytic types B, E and F, iii) types C and D and C. novyi type A, and iv) type G and C. subterminale. The phylogenetic groupings obtained from the 16S rRNA were in complete agreement with the four divisions recognised within the 'species complex' on the basis of phenotypic criteria.