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.

Immunohistochemical characterisation of probable intravascular haematopoiesis in the vasa rectae of the renal medulla in acute tubular necrosis

Immunohistochemistry was applied to identify the nature of the nucleated cells that accumulate in the vasa rectae of the corticomedullary junction in acute tubular necrosis. In all 6 cases studied, there were intravascular cells that reacted with monoclonal antibodies to erythroblast, macrophages, myeloid cells, T and B lymphocytes and rare megakaryocytes. The findings are consistent with the occurrence of intravascular haematopoiesis in the renal medulia in acute tubular necrosis.

Effects of HCl on the ultrasound catalyzed TEOS hydrolysis as determined by a calorimetric study

The acid catalyzed and ultrasound stimulated hydrolysis of solventless tetraethoxysilane-water mixtures was studied at 39°C as a function of HCl added to the mixtures (log[HCl]-1 ranged from 0.8 to 2.0), The reaction was carried out in a specially designed device, in which a steady state heat flow is maintained, while sonication is taking place, if no reaction is expected to occur. The exothermal hydrolysis reaction causes an increasing temperature (ΔTt) as a function of the reaction time, t. The isothermal hydrolysis rate constant, k, has been evaluated from the experimental ΔTt versus t data, after corrections for the increasing temperature effects, by using a method resulting from our theoretical modeling based on a dissolution and reaction mechanism. The hydrolysis rate constant fits closely a k α [H+] law as expected for this kind of hydrogen-ion catalyzed reaction.

Calibration of therapeutic ultrasound equipment

Temporal and spatial acoustic intensity (SATA) of therapeutic ultrasound (US) equipment should be monitored periodically. In order to evaluate the conditions of US equipment in use in the city of Piracicaba-Sao Paulo, Brazil, 31 machines - representing all Brazilian manufacturers - were analysed under continuous and pulsed conditions at a frequency of 1 MHz. Data about temporal and spatial acoustic intensity were collected and the use of equipment was surveyed. Intensities of 0.1, 0.2, 0.5, 0.8, 1.0, 1.5, 2.0, 2.5 and 3.0 Wcm -2, indicated on the equipment panel were analysed using a previously calibrated digital radiation pressure scale, model UPM-DT-1 (Ohmic Instruments Co). The acoustic intensity (I) results were expressed as superior and inferior quartile ranges for transducers with metal surfaces of 9 cm 2 and an effective radiation area (ERA) Of 4 cm 2. The results under continuous conditions were: I 0.1 = -20.0% and -96%. I 0.2 = -3.1% and -83.7%. I 0.5 = -35.0% and -86.5%. I 0.8 = -37.5% and -71.0%. I 2.5 = -49.0% and -69.5%. I 3.0 = -58.1% and -77.6%. For pulsed conditions, intensities were: I 0.1 = -40.0% and -86.2%. I 1.0 = -50.0% and -86.5%. I 1.5 = -62.5% and -82.5%. I 2.0 = -62.5% and -81.6%. I 2.5 = -64.7% and -88.8%. I 3.0 = -87.1% and -94.8%. In reply to the questionnaire drawn up to check the conditions of use of equipment, all users reported the use of hydrosoluble gel as a coupling medium and none had carried out previous calibrations. Most users used intensities in the range of 0.4. to 1.0 Wcm -2 and used machines for 300 to 400 minutes per week. The majority of machines had been bought during the previous seven years and weekly use ranged from less than 100 minutes to 700 minutes (11 hours 40 minutes). Findings confirm previous observations of discrepancy between the intensity indicated on the equipment panel and that emitted by the transducer and highlight the necessity for periodic evaluations of US equipment.

Structural changes induced by ultrasound during aging of the boehmite phase

Structural changes induced by ultrasound during the aging of the aluminum monohydroxide (boehmite) were studied by means of X-ray diffraction (XRD) and nitrogen adsorption. The BET surface area and the pore volume of the ultrasound stimulated hydroxide (HU) are about 40% less than those of the non-stimulated one (HS). The mean pore size practically does not change, while the mean crystallite size (L) is about 25% greater in the HU system. The increase of L alone is not enough to account for the surface area diminution, suggesting that the sonication also induces compaction by elimination of some porosity. The sonication of the precursor hydroxide does not seem to play an apparent role in the structural properties of the resulting calcinated γ-alumina. © 1997 Elsevier Science B.V.

Monolithic diphasic gels of mullite by sol-gel process under ultrasound stimulation

Diphasic gel in the mullite composition was prepared from a colloidal sol of boehmite mixed with a hydrolyzed tetraethoxisilane (TEOS) solution. The boehmite sol was obtained by peptization of a poorly crystallized or very small mean crystallite size (∼34 Å) precipitate, resulting from the reaction between solutions of aluminum sulfate and sodium hydroxide. Ultrasound was utilized in the processes of the TEOS hydrolysis and the boehmite peptization, and also for complete homogenization of the mixture to gel. The wet gel is almost clear and monolithic. The gel transparency is lost on drying, when syneresis has ended, so that the interlinked pore structure starts to empty and is recovered upon water re-absorption. Cracking closely accompanies this critical drying process. Differential thermal analysis (DTA) and X-ray diffraction (XRD) show that the solid structure of the gel is composed of an amorphous silica phase, as a matrix, and a colloidal sized crystalline phase of boehmite. Upon heat treatment, the boehmite phase within the gel closely follows the same transition sequence as in pure alumina shifted towards higher temperatures. Orthorhombic mullite formation was detected at 1300°C. © 1998 Elsevier Science B.V. All rights reserved.

Effects of Chronic Physical Activity and of Ultrasound Treatment on Bone Consolidation

The objective of this study was to investigate the effects of ultrasound treatment and physical exercise on the velocity of bone consolidation and resistance to deformation. We performed osteotomy in the upper third of the right tibia of rats. Physical training consisted of swimming 1 h per day with a load of 5% b.w. for 30 days. Therapy with medium-intensity ultrasound was applied daily on the damaged area. Wistar rats were divided into the following groups: osteotomized sedentary animals with no ultrasound treatment (1.OSnUS), osteotomized trained animals with no ultrasound treatment (2.OTnUS), osteotomized sedentary animals with ultrasound treatment (3.OSwUS). and osteotomized trained animals with ultrasound treatment (4.OTwUS). The animals were sacrificed for the following analyses: muscle glycogen, serum alkaline phosphatase at the 5th, 10th, 20th, and 30th days, test of maximum resistance to flexion, rupture flexion and mean tibial rigidity at the 30th day. Muscle glycogen was increased at the 20th day: alkaline phosphatase was elevated at the 5th and 20th days in groups 3.OSwUS and 4.OTwUS. and decreased at the 10th day. Groups1.OSnUS and 2.OTnUS did not show significant variations. In the mechanical resistance tests, we noted that ultrasound therapy and the association of physical activity used in the present study showed significant differences in bone resistance and bone rigidity after 30 days of treatment. These facts suggest that ultrasound or physical activity, or their combination may accelerate the process of bone tissue repair.

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.

The influence of ultrasound on the retention of cast posts cemented with different agents

Aim: The aim of this study was to evaluate the influence of ultrasound during the removal of posts cemented with either zinc phosphate cement, glass ionomer cement or resin cement. Methodology: Eighty-four single-rooted teeth were prepared and after cementation of cast posts, they were randomly divided into six groups of 14. Groups 1, 2 and 3 did not receive ultrasonic vibration, whilst groups 4, 5 and 6 received ultrasonic vibration for 10 min. The force necessary for post removal was determined using a universal testing machine. Results were statistically analysed using ANOVA and Tukey tests (5%). Results: The application of ultrasonic vibration reduced the retention provided by zinc phosphate and glass ionomer cements by 39% and 33%, respectively. Conclusions: A statistically significant reduction in the force necessary to remove posts cemented with zinc phosphate and glass ionomer cements occurred following application of ultrasound. The application of ultrasonic vibration did not influence the retention of cast posts cemented with resin cement.

Characterization of lubricating oil using ultrasound

This paper presents an ultrasonic method to measure small concentrations of water in lubricating oil. It uses an ultrasonic measurement cell composed by a piezoceramic emitter (5 and 10 MHz), and a large aperture PVDF receiver that eliminates diffraction effects. The propagation velocity, attenuation coefficient and density of several samples of water-in-oil emulsion were measured. The concentrations of water of the samples were in the range of 0 to 5% in volume, and the results showed that these low concentrations can be discriminated within a resolution of 0.2% in the studied range, using the measurement of the propagation velocity.

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.

Effects of low-intensity pulsed ultrasound on wound healing in corneas of dogs following keratoplasty

The effects of low-intensity pulsed ultrasound on wound healing were evaluated at the graft-cornea transition in dogs following lamellar keratoplasty using tunica vaginalis preserved in 98% glycerin. Twenty-one dogs were subdivided into three groups of seven animals. The first group (W/US) received daily treatment of low-intensity pulsed ultrasound (20 mW/cm 2) for 15 min for the first 10 days post surgery. The second group (N/US) was submitted to the same procedure but with the ultrasound apparatus turned off. The third group, the control (CO), underwent the surgical procedure only. The animals were clinically evaluated during the initial (1-15 days), intermediate (16-30 days) and late (31-120 days) postoperative period. The corneas were evaluated by light microscopy at 1, 3, 7, 15, 30, 60 and 120 days after surgery. Clinically, there were no differences which would promote an advantage to any of the treatments. Light microscopy, however, revealed more extensive vascularization and more advanced wound healing in the W/US group, as well as a tendency towards early graft incorporation. Based on the present results, low-intensity pulsed ultrasound shows advantages, especially in situations where trophic support is a mandatory condition, facilitating better graft incorporation and rapid recovery of stromal organization.

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.