Karyotypic diversity in four species of the genus Gymnotus Linnaeus, 1758 (Teleostei, Gymnotiformes, Gymnotidae): physical mapping of ribosomal genes and telomeric sequences

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Genetic structure of the ornamental tetra fish species Piabucus melanostomus Holmberg, 1891 (CHARACIDAE, IGUANODECTINAE) in the Brazilian Pantanal wetlands inferred by mitochondrial DNA sequences

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

Chromosomal mapping of rDNAs and H3 histone sequences in the grasshopper rhammatocerus brasiliensis (acrididae, gomphocerinae): extensive chromosomal dispersion and co-localization of 5S rDNA/H3 histone clusters in the A complement and B chromosome

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Genetic variability of porcine parvovirus isolates revealed by analysis of partial sequences of the structural coding gene VP2

The 3'-terminal 853 nt (and the putative 283 aa) sequence of the VP2-encoding gene from 29 field strains of porcine parvovirus (PPV) were determined and compared both to each other and with other published sequences. Sequences were examined using maximum-parsimony and statistical analyses for nucleotide diversity and sequence variability. Among the nucleotide sequences of the PPV field strains, 26 polymorphic sites were encountered; 22 polymorphic sites were detected in the putative amino acid sequence. Mapping polymorphic sites of protein data onto the three-dimensional (3D) structure of PPV VP2 revealed that almost all substitutions were located on the external surface of the viral capsid. Mapping amino acid substitutions to the alignment between PPV VP2 sequences and the 3D structure of canine parvovirus (CPV) capsid, many PPV substitutions were observed to map to regions of recognized antigenicity and/or to contain phenotypically important residues for CPV and other parvoviruses. In spite of the high sequence similarity, genetic analysis has shown the existence of at least two virus lineages among the samples. In conclusion, these results highlight the need for close surveillance on PPV genetic drift, with an assessment of its potential ability to modify the antigenic make-up of the virus.

Phylogenetic relationships in genus Arachis based on ITS and 5.8S rDNA sequences

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

Phylogeny of leafcutter ants in the genus Atta Fabricius (Formicidae: Attini) based on mitochondrial and nuclear DNA sequences

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

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)

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.

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.

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.

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.