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.

Analytical optimization of spread and change of exponential decay of generalized Wannier functions in one dimension

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Bacterial leaching of uranium ore from Figueira-PR, Brazil, at laboratory and pilot scale

A bacterial leaching program was carried out in order to evaluate the potential of applying this process to leach uranium from the ore of Figueira-PR, Brazil. The experiments were carried out in shake flasks, column percolation (laboratory and semipilot scale) and in heap leaching. In shake flasks and in column percolation experiments at laboratory scale, bacterial activity on the ore was confirmed: approximately 60% of uranium was leached, against around 30% in sterilized controls. Column percolation experiments at semipilot scale and heap leaching (850 tons of ore) showed uranium extractions of approximately 50%. In both experiments, a complementary sulfuric acid attack, after the bacterial leaching phase, was necessary to reach this level of uranium extraction.

The interaction between vitamin K nutriture and warfarin administration in patients with bacterial overgrowth due to atrophic gastritis

Atrophic gastritis patients have intestinal bacterial overgrowth which could produce menaquinones. The aim of this study was to evaluate the interaction between a diet low in phylloquinone and minidoses of warfarin in subjects with and without bacterial overgrowth. Subjects with atrophic gastritis (indicated by serum pepsinogen ratio) and healthy volunteers were studied while fed a restrictive phylloquinone diet and while receiving a minidose of warfarin. Coagulation times, serum osteocalcin, serum undercarboxylated osteocalcin, plasma phylloquinone, plasma K-epoxide, plasma undercarboxylated prothrombin (PIVKA)-II and urinary gamma-carboxyglutamic acid (Gla) were measured. At baseline, there were no differences between groups for any variable measured. Comparisons between baseline and post intervention in both groups, showed significant increases in circulating levels of K-epoxide, PIVKA II and undercarboxylated osteocalcin. However, no differences were observed when comparisons were made between groups. Our data do not support the hypothesis that bacterial synthesis of menaquinones in patients with bacterial overgrowth due to atrophic gastritis confers considerable resistance to the effect of warfarin.

Decay of protons and neutrons induced by acceleration

We investigate the decay of accelerated protons and neutrons. Calculations are carried out in the inertial and coaccelerated frames. Particle interpretation of these processes are quite different in each frame but the decay rates are verified to agree in both cases. For the sake of simplicity our calculations are performed in a two-dimensional spacetime since our conclusions are not conceptually affected by this. ©1999 The American Physical Society.

Comment on Majoron emitting neutrinoless double beta decay in the electroweak chiral gauge extensions

We point out that if the Majoron-like scheme is implemented within a 3-3-1 model, there must exist at least three different mass scales for the scalar vacuum expectation values in the model. ©1999 The American Physical Society.

Weak decay of uniformly accelerated protons and related processes

We investigate the weak interaction emission of spin-1/2 fermions from accelerated currents. As particular applications, we analyze the decay of uniformly accelerated protons and neutrons, and the neutrino-antineutrino emission from uniformly accelerated electrons. The possible relevance of our results to astrophysics is also discussed.

Decay of accelerated protons and the existence of the Fulling-Davies-Unruh effect

A theoretic-oriented strategy was taken to address the weak decay of uniformly accelerated protons. The decay of uniformly accelerated p+'s was analyzed using standard quantum field theory (QFT). It was shown that the FDU effect is essential to reproduce the proper decay rate in the uniformly accelerated frame.