A stratigraphic chart of the Late Carboniferous/Permian succession of the eastern border of the Parana Basin, Brazil, South America

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

PrimerSNP: a web tool for whole-genome selection of allele-specific and common primers of phylogenetically-related bacterial genomic sequences

Background: The increasing number of genomic sequences of bacteria makes it possible to select unique SNPs of a particular strain/species at the whole genome level and thus design specific primers based on the SNPs. The high similarity of genomic sequences among phylogenetically-related bacteria requires the identification of the few loci in the genome that can serve as unique markers for strain differentiation. PrimerSNP attempts to identify reliable strain-specific markers, on which specific primers are designed for pathogen detection purpose.Results: PrimerSNP is an online tool to design primers based on strain specific SNPs for multiple strains/species of microorganisms at the whole genome level. The allele-specific primers could distinguish query sequences of one strain from other homologous sequences by standard PCR reaction. Additionally, PrimerSNP provides a feature for designing common primers that can amplify all the homologous sequences of multiple strains/species of microorganisms. PrimerSNP is freely available at http://cropdisease.ars.usda.gov/similar to primer.Conclusion: PrimerSNP is a high-throughput specific primer generation tool for the differentiation of phylogenetically-related strains/species. Experimental validation showed that this software had a successful prediction rate of 80.4 - 100% for strain specific primer design.

Seqüência Ordovício-Siluriana e Devoniana no Flanco Norte da Bacia do Paraná

Two stratigraphic sequences characterize the basal units of the Paraná basin. The Ordovician-Silurian sequence overlie directly the Neoproterozoic basement and consists of a 55m-thick unit of coarse-grained sandstones, diamictites, fossiliferous shales and fine-grained micaceous sandstones. The Alto Garças Formation constitutes the base of the sequence and is made of coarse-grained, massive and reddish sandstones associated with conglomeratic lenses. Diamictites with pebbles of diverse composition in siltic and arenaceous matrix were deposited during the Ordovician-Silurian glaciation. Whenever the basal sandstones are absent, the diamictites directly overlie the basement. The diamictites were previously included in the Vila Maria Formation. However our study revealed that they are part of the Iapó Formation. A transgressive event following the glaciation is marked by the deposition of the Vila Maria Formation, which is characterized by fossiliferous (mollusks, brachiopods, cryptospores and microplankton) and laminated shales and siltstones, grading upward to fine-grained micaceous sandstones with hummocky cross stratification. Layers containing trace fossils (Anthrophycus) occur at the transition between the siltstones and the sandstones. The Devonian sequence is represented by 80-170 meters thick sandstones of the Furnas Formation (lower unit) and a sucession of sandstones, siltstones and shales of the Ponta Grossa Formation (upper unit). Unlike other areas of the Paraná Basin, the Ponta Grossa Formation is characterized by coarsening-upward succession beginning with fine sandstones and grading upward to coarse and very-coarse sandstone beds. Cretaceous modifying tectonics affected the Paleozoic sequences, which are cut by a series of faults, in some cases showing displacements greater than 500 meters.

Conserved sequences in the β subunit of archaeal and eukaryal translation initiation factor 2 (elF2), absent from elF5, mediate interaction with elF2γ

The eukaryotic translation initiation factor 2 (eIF2) binds the methionyl-initiator tRNA in a GTP-dependent mode. This complex associates with the 40 S ribosomal particle, which then, with the aid of other factors, binds to the 5' end of the mRNA and migrates to the first AUG codon, where eIF5 promotes GTP hydrolysis, followed by the formation of the 80 S ribosome. Here we provide a comparative sequence analysis of the β subunit of eIF2 and its archaeal counterpart (aIF2β). aIF2β differs from eIF2β in not possessing an N-terminal extension implicated in binding RNA, eIF5 and eIF2B. The remaining sequences are highly conserved, and are shared with eIF5. Previously isolated mutations in the yeast eIF2β, which allow initiation of translation at UUG codons due to the uncovering of an intrinsic GTPase activity in eIF2, involve residues that are conserved in aIF2β, but not in eIF5. We show that the sequence of eIF2B homologous to aIF2β is sufficient for binding eIF2γ, the only subunit with which it interacts, and comprises, at the most, 78 residues, eIF5 does not interact with eIF2γ, despite its similarity with eIF2β, probably because of a gap in homology in this region. These observations have implications for the evolution of the mechanism of translation initiation.

Molecular and cytogenetic analysis of the telomeric (TTAGGG)n repetitive sequences in the Nile tilapia, Oreochromis niloticus (Teleostei: Cichlidae)

The majority of chromosomes in Oreochromis niloticus, as with most fish karyotyped to date, cannot be individually identified owing to their small size. As a first step in establishing a physical map for this important aquaculture species of tilapia we have analyzed the location of the vertebrate telomeric repeat sequence, (TTAGGG)n, in O. niloticus. Southern blot hybridization analysis and a Bal31 sensitivity assay confirm that the vertebrate telomeric repeat is indeed present at O. niloticus chromosomal ends with repeat tracts extending for 4-10 kb on chromosomal ends in erythrocytes. Fluorescent in situ hybridization revealed that (TTAGGG)n is found not only at telomeres, but also at two interstitial loci on chromosome 1. These data support the hypothesis that chromosome 1, which is significantly larger than all the other chromosomes in the karyotype, was produced by the fusion of three chromosomes and explain the overall reduction of chromosomal number from the ancestral teleost karyotype of 2n=48 to 2n=44 observed in tilapia.

Phylogenetic relationships among genera Eucalyptus and Corymbia species based on rnDNA internal transcribed spacers sequences

Phylogenetio relationships between Eucalyptus species, subgenus Symphyomyrtus (sections Adnataria, Exsertaria, Maldenaria, and Transversaria), and Corymbia species (sections Politaria and Ocharia) were established based on the sequence of Internal transcribed rDNA spacers (ITS1 and ITS2). The species analyzed were obtained from a collection kept in Brazil. Fragments obtained using primers ITS1 and ITS2 were sequenced and part of the sequence of ITS1 and ITS2 and the complete sequence of 5.8S rDNA were used in the analysis. ITSs and 5.8S rDNA sequences from E. globulus ssp. globulus and A. bakeri (Genus Angophora) were downloaded from the Genbank database and included in the analysis. Psidlum guajava was the selected outgroup used. The sequence alignment and a Neighbor-joining tree were obtained using Clustal X. Few variations were detected in the 5.8S rDNA sequences obtained, occurring mainly between Eucalyptus and Corymbia, thus defining these genera. Variations in ITS sequences occurred in all investigated species. Phylogenetic analysis showed a clear separation between the genera Corymbia and Eucalyptus. A bakeri was more closely related to species belonging to genus Corymbia. Regarding the subgenus Symphyomyrtus (Genus Eucalyptus), only species from section Maidenaria grouped together according to their common section. This could have been caused by the removal of natural reproductive barriers when these species were introduced In Brazil, with a consequent Increase in the rate of interspecific crossings and Introgression events.

Estratigrafia de seqüências das formações Taciba e Rio Bonito (Membro Triunfo) na região de Mafra/SC, leste da Bacia do Paraná

The Taciba and Rio Bonito (lower Triunfo Mbr) formations are divided into six depositional sequences based on cores, gamma-ray and electrical logs from shallow drillings from northern Santa Catarina State, Each sequence is formed by two systems tracts, a lower one, sandy (lowstand) and an upper one, shaly (highstand). The Taciba Formation has three sequences, S 0 to S 0 sequence S 0 has a thick turbidite sandstone at the base (Rio Segredo Member) that pinches out towards the eastern margin and even disappears in the Mafra outcrop area. Sequence S 1 varies from a thin fluvial-estuarine system to a thick turbidite sandstone of a channelized fan system; S 1 upper shaly system tract is marine in well PP-11, and it is glacially-influenced in well PP-10. Sequence S 2 is a thick sand-stone body of shallow marine origin, but restricted to one well (PP-11); its upper shaly tract is dominated by massive siltstones intercalated with thin, distal tempestites. The lower Triunfo Member (or Taciba-Triunfo transition) begins with the arrival of deltaic clastics of sequence S 3 lower tract, coarsening-up from medial- to proximal delta front sandstones. Sequence S 4 is quite similar to S 3, both showing sand-stone progradation from north to south, as opposed to the southwest-sourced transgressive diamictites. Sequence S 5 consists of fluvial deposits at well PP-12, and two transgressive cycles from wells PP-11 to PP-9, each one of them composed of fluvial-estuarine to marine systems. Well PP-10 is an exception, where the lower cycle presents deglaciation to marine deposits.

Comparative analysis of noncoding sequences of orthologous bovine and human gene pairs

Genomic sequence comparison across species has enabled the elucidation of important coding and regulatory sequences encoded within DNA. Of particular interest are the noncoding regulatory sequences, which influence gene transcriptional and posttranscriptional processes. A phylogenetic footprinting strategy was employed to identify noncoding conservation patterns of 39 human and bovine orthologous genes. Seventy-three conserved noncoding sequences were identified that shared greater than 70% identity over at least 100 bp. Thirteen of these conserved sequences were also identified in the mouse genome. Evolutionary conservation of noncoding sequences across diverse species may have functional significance, and these conserved sequences may be good candidates for regulatory elements.

Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences

The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.

Phylogenetic analysis of flatfish (order pleuronectiformes) based on mitochondrial 16s rDNA sequences

The phylogenetic relationships of the order Pleuronectiformes are controversial and at some crucial points remain unresolved. To date most phylogenetic studies on this order have been based on morpho-anatomical criteria, whereas only a few sequence comparisons based studies have been reported. In the present study, the phylogenetic relationships of 30 flatfish species pertaining to seven different families were examined by sequence analysis of the first half of the 16S mitochondrial DNA gene. The results obtained did not support percoids as the sister group of pleuronectiforms. The monophyletic origin of most families analyzed, Soleidae, Scophthalmidae, Achiridae, Pleuronectidae and Bothidae, was strongly supported, except for Paralichthyidae which was clearly subdivided into two groups, one of them associated with high confidence to Pleuronectidae. The analysis of the 16S rRNA gene also suggested the monophyly of Pleuronectiforms as the most probable hypothesis and consistently supported some major interfamily groupings.

Ciclos e seqüências deposicionais das formações Rio da Batateira e Santana (Andar Alagoas), Bacia do Araripe, Brasil

The Rio da Batateira e Santana formations, the latter with Crato, Ipubi and Romualdo members (Alagoas Stage, Aptian), were studied in four cored and logged wells from the eastern portion of Araripe Basin, Northeastern Brazil. The investigated section is 230 m-thick, and PS-14 well is the most representative, because it is the only one which sampled the evaporites of Ipubi Member. Nine facies cycles were identified, being formed by siliciclastics (estuarine, deltaic and lacustrine), mixed lithologies (lacustrine), carbonates, black shales and marls (lacustrine), and gypsum-anhydrite (lacustrine evaporite). The ordering of facies cycles furnished six depositional sequences. They were formed by siliciclastic, regressive-transgressive R-T cycles (S1 and S4, corresponding to Rio da Batateira Formation and to Santana Formation/Romualdo Member), by siliciclastics and carbonates, R-T cycles (S2, S3.1 and S3.2, corresponding to Crato Member), and by siliciclastic-carbonate, R-T cycles followed by evaporitic cycles (S3.3, referred to Ipubi Member). The last cycles correspond to concentration-dilution, C-D cycles of marine brines, which precipitated gypsum in the restricted lacustrine basin.

Taxonomic and phylogenetic relationships between neotropical species of ticks from genus Amblyomma (Acari: Ixodidae) inferred from second internal transcribed spacer sequences of rDNA

The accurate specific identification of ticks is essential for the study, control and prevention of tick-borne diseases. Herein, we determined ribosomal nucleotide sequences of the second internal transcribed spacer (ITS2) of 15 Neotropical hard tick species of the genus Amblyomma Koch found in Brazil. Most of the studied ticks accidentally parasite humans and potentially act as vectors of zoonoses. Lengths of the ITS2 sequences ranged from 956 to 1,207 bp, whereas GC content varied from 62.4 to 66.9%. A matrix of ITS2 divergence was calculated with the ITS2 sequence data obtained showing divergence levels varying from 1.5 to 28.8%. The analysis indicated that this molecular marker can be useful for Amblyomma-specific identification. Phylogenetic inferences based on the ITS2 sequences were used to assess some issues in subgenus taxonomy. © 2007 Entomological Society of America.

Nuclear mitochondrial-like sequences in ants: Evidence from Atta cephalotes (Formicidae: Attini)

Nuclear mitochondrial-like sequences (numts) are copies of mitochondrial DNA that have migrated to the genomic DNA. We present the first characterization of numts in ants, these numts being homologues to a mitochondrial DNA fragment containing loci the 3′ portion of the cytochrome oxidase I gene, an intergenic spacer, the tRNA leucine gene and the 5′ portion of the cytochrome oxidase II gene. All 67 specimens of Atta cephalotes (Hymenoptera: Formicidae: Attini) investigated had these homologues, which are within two monophyletic groups that we called numt1 and numt2. Numt1 and numt2 sequences are less variable than mitochondrial sequences and released from the severe purifying selection constraining the evolution of mitochondrial genes. Their formation probably involved bottlenecks related to two distinct transfer events of ancient and fast evolving mitochondrial DNA fragments to comparative slowly evolving nuclear DNA regions. © 2007 The Authors.

Facies sedimentares e ambientes deposicionais da Formação Barbalha no vale do cariri, bacia do araripe, nordeste do Brasil

The Aptian Barbalha Formation represents the first unit of the post-rift sequence of the Araripe Basin and crops out at the slopes of the Aranpe plateau in the eastern part ot Aranpe Basin. The unit has also been named Kio da Batateira Formation, but this name is here used in its original definition as Batateira Beds, an interval of great lateral continuity and characterized by the presence of bituminous shales of the Alagoas Stage (P-270 palynological biozone). This paper presents the results of a stratigraphic analysis carried out along the outcrop belt in order to establish the facies architecture and to interpret deposicional environments of the siliciclastic Barbalha Formation. Detailed stratigraphic vertical sections were measured and correlated. They allowed the recognition of two depositional sequences characterized by fining upward arrangement of facies, beginning with fluvial deposits and ending with lacustrine deposits at their tops. The end of the first cycle is represented by black shales and brecciated limestones of the Batateira Beds that record a geologic event of regional magnitude and serve as meaningful long-distance stratigraphic mark. The second deposicional sequence overlies disconformably the Batateira Beds and begins with clast-supported conglomerates, which are covered by a succession of fluvial sandstones and minor intervals of pelitic rocks. The sandstone content diminishes towards the top and the upper part of the unit is characterized by the presence of ostracode-rich green shales. The Barbalha Formation is conformably overlaid by Late Aptian lacustrine limestones belonging to the Crato Member of the Santana Formation.

Weak mixing and eigenvalues for arnoux-rauzy sequences

We define by simple conditions two wide subclasses of the socalled Arnoux-Rauzy systems; the elements of the first one share the property of (measure-theoretic) weak mixing, thus we generalize and improve a counterexample to the conjecture that these systems are codings of rotations; those of the second one have eigenvalues, which was known hitherto only for a very small set of examples.