Can the chemical composition of the whole body of a goat be estimated from parts of its body?

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

Sequencing wasp venom peptides by endopeptidase digestion and nested collision-induced dissociation/post-source decay methods

A method incorporating nested collision-induced dissociation/post-source decay (CID/PSD) combined with endopeptidase digestion is described as an approach to determine the sequence of N-terminally modified peptides. The information from immonium and related ions observed in the CID/PSD spectrum was used for the selection of a suitable endopeptidase for the digestion of peptides. Rapid and reliable assignment of peptide sequence was performed by the comparison of CID/PSD spectra of both intact and endopeptidese-digested peptide fragments, since the assignments of the observed fragment ions to either N- or C-terminal ions can thus be carried out unambiguously. This nested CID/PSD method was applied to the sequence determination of two peptides from the solitary wasps Anoplius samariensis and Batozonellus maculifrons (pompilid wasps), which could not be sequenced by the Edman method due to N-terminal modification. Copyright (C) 2002 John Wiley Sons, Ltd.

Identification of polymorphisms in the 5 '-untranslated region of the TAFI gene: relationship with plasma TAFI levels and risk of venous thrombosis

Background and Objectives. Thrombin activatable fibrinolysis inhibitor (TAFI) plays an important role in hemostasis, functioning as a potent fibrinolysis inhibitor. TAFI gene variations may contribute to plasma TAFI levels and thrombotic risk.Design and Methods. We sequenced a 2083-bp region of the 5 ' -regulatory region of the TAFI gene in 127 healthy subjects searching for variations, and correlated identified polymorphisms with plasma TAFI levels. TAFI polymorphisms were examined as risk factors for venous thrombosis by determining their prevalence in 388 patients with deep venous thrombosis (DVT) and in 388 controls.Results. Seven novel polymorphisms were identified: -152 A/G, -438 A/G, -530 C/T, -1053 T/C, -1102 T/G, -1690 G/A, and -1925 T/C. -152 A/G, -530 C/T and -1925 T/C were found to be in strong linkage disequilibrium, as were the -438 A/G, -1053 T/C, -1102 T/G and -1690 G/A, Plasma TAFI levels were higher in -43866/-1053CC/-1102GG/-1690AA homozygotes than In -438AG/-1053TC/-1102TG/-1690GA heterozygotes, and -438AA/-1053TT/-1102TT/-1690GG homozygotes had the lowest TAFI levels (p=0.0003). TAFI concentrations in -152AA/-530CC/-1925TT homozygotes were somewhat higher but not significantly different from levels observed for -152AG/-530CT/-1925TC heterozygotes, Taken in combination, -438AG/-1053TC/-1102TG/-1690GA and -438AA/-1053TT/-1102TT/-1690GG yielded an OR for DVT of 0.8 (95%CI: 0.6-1). in subjects aged < 35 years the OR was 0.7 (95%CI: 0.5-1.1), the OR for -152AG/-530CT/-1925TC was 1 (95%CI: 0.5-2.2) in the whole group of patients and controls, whereas in subjects aged <35 years the OR was 0.1 (95%CI: 0.02-0.9).Interpretation and Conclusions. Polymorphisms in the TAFI promoter determine plasma antigen levels and may influence the risk of venous thrombophilia. <(c)>2001, Ferrata Storti Foundation.

Association of free amino acids with caries experience and mutans streptococci levels in whole saliva of children with early childhood caries

Objective: The aim of the present study was to identify the free amino acid content in whole saliva of children with (CE) and without early childhood caries (CF) (ECC), correlating these findings with caries experience and mutans streptococci (MS) levels in saliva.Design: Seventy-eight healthy children, both genders, 6-71 months age, were selected to participate in the study. Following examination for dmft scores calculation, unstimulated whole saliva was collected from all 78 participants, stored at -80 degrees C, and used for amino acid analysis, on a Biochem 20 plus amino acid analyzer. Stimulated whole saliva was collected from 52 children, transported, diluted and plated on MSB agar medium for detection of MS in cfu/mL.Results: Forty different free amino acids were identified in whole saliva, with great variation in their concentration. A statistically significant relation was found between caries experience and the presence of free proline and glycine. While proline (p = 0.0182) was more frequently absent in the CF group, the absence of glycine (p = 0.0397) was more often observed in the CE group. In the presence of higher levels of MS, free glycine reduced the risk of experiencing dental caries (p = 0.0419). Conversely, the presence of proline was found to increase the risk of experiencing the disease (p = 0.0492).Conclusions: The presence of free proline and absence of free glycine in children with ECC, highly contaminated with MS, increased the chances of experiencing dental caries in the present population. Further studies are needed to better understand this phenomenon. (C) 2008 Elsevier Ltd. All rights reserved.

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.

Simple and versatile heterodyne whole-field interferometer for phase optics characterization

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Copy number variation of individual cattle genomes using next-generation sequencing

Copy number variations (CNVs) affect a wide range of phenotypic traits; however, CNVs in or near segmental duplication regions are often intractable. Using a read depth approach based on next-generation sequencing, we examined genome-wide copy number differences among five taurine (three Angus, one Holstein, and one Hereford) and one indicine (Nelore) cattle. Within mapped chromosomal sequence, we identified 1265 CNV regions comprising similar to 55.6-Mbp sequence-476 of which (similar to 38%) have not previously been reported. We validated this sequence-based CNV call set with array comparative genomic hybridization (aCGH), quantitative PCR (qPCR), and fluorescent in situ hybridization (FISH), achieving a validation rate of 82% and a false positive rate of 8%. We further estimated absolute copy numbers for genomic segments and annotated genes in each individual. Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (similar to 52%, chi(2) test; P-value <0.05). In contrast, genes related to pathogen- and parasite-resistance, such as CATHL4 and ULBP17, were highly duplicated in the Nelore individual relative to the taurine cattle, while genes involved in lipid transport and metabolism, including APOL3 and FABP2, were highly duplicated in the beef breeds. These CNV regions also harbor genes like BPIFA2A (BSP30A) and WC1, suggesting that some CNVs may be associated with breed-specific differences in adaptation, health, and production traits. By providing the first individualized cattle CNV and segmental duplication maps and genome-wide gene copy number estimates, we enable future CNV studies into highly duplicated regions in the cattle genome.

Chemistry of Biotites and Whole Rocks from the Rapakivi Itu Complex (Late Precambrian), State of São Paulo, SE Brazil

Chemical analyses for biotites and their host rocks from the Cabreúva (three facies) and Salto (five facies) intrusions from the multiple-centered rapakivi Itu Complex, State of São Paulo, Brazil, are presented and compared. The Cabreúva intrusion comprises different kinds of mainly even-grained biotite and hornblende-bearing syenogranites, monzogranites and quartz syenites and the Salto intrusion several types of mainly porphyritic biotite syenogranites, some of them hornblende-bearing. The biotites from the Salto intrusion (S-micas) show a more restricted composition than those from the Cabreúva intrusion (C-micas). This reflects the chemical variability of the two bodies which is smaller in the Salto intrusion and larger in the Cabreúva pluton. In the AlIV x Fet/(Fet+Mg) diagram the S- and C-micas show similar AlIV contents, around 2.2-2.3, but C-micas have higher Fet/(Fet+Mg) ratios (0.7-0.9) compared to those of S-micas (0.5-0.6). In the Mg:(Al+Fe+3+Ti):(Fe+2+Mn) diagram the S-micas are defined as Fe+2-biotites and the C-micas occupy the area between the Fe+2-biotites and the siderophyllite/lepidomelane fields, slightly overlapping the latter. In the Al2O3 × FeOt, MgO × FeOt, Al2O3 x MgO and Alt x Mg diagrams, the S-micas always lie on the calc-alkaline/alkaline boundary (or in the subalkaline field) whereas the C-micas systematically plot in the alkaline field, reflecting the higher alkalis content of the Cabreúva intrusion. In the Fet/(Fet+Mg) x SiO2 diagram, the S-micas lie on a smooth line whereas the C-micas from the different facies are separated by distinct chemical gaps reflecting the major or minor chemical overlapping of the facies from the Salto and Cabreúva intrusions.

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.

Development and validation of a Xanthomonas axonopodis pv. citri DNA microarray platform (XACarray) generated from the shotgun libraries previously used in the sequencing of this bacterial genome

Background. From shotgun libraries used for the genomic sequencing of the phytopathogenic bacterium Xanthomonas axonopodis pv. citri (XAC), clones that were representative of the largest possible number of coding sequences (CDSs) were selected to create a DNA microarray platform on glass slides (XACarray). The creation of the XACarray allowed for the establishment of a tool that is capable of providing data for the analysis of global genome expression in this organism. Findings. The inserts from the selected clones were amplified by PCR with the universal oligonucleotide primers M13R and M13F. The obtained products were purified and fixed in duplicate on glass slides specific for use in DNA microarrays. The number of spots on the microarray totaled 6,144 and included 768 positive controls and 624 negative controls per slide. Validation of the platform was performed through hybridization of total DNA probes from XAC labeled with different fluorophores, Cy3 and Cy5. In this validation assay, 86% of all PCR products fixed on the glass slides were confirmed to present a hybridization signal greater than twice the standard deviation of the deviation of the global median signal-to-noise ration. Conclusions. Our validation of the XACArray platform using DNA-DNA hybridization revealed that it can be used to evaluate the expression of 2,365 individual CDSs from all major functional categories, which corresponds to 52.7% of the annotated CDSs of the XAC genome. As a proof of concept, we used this platform in a previously work to verify the absence of genomic regions that could not be detected by sequencing in related strains of Xanthomonas. © 2010 Moreira et al; licensee BioMed Central Ltd.

Two-wavelength whole-field interferometry setup for thermal lens study

In this paper we present a new approach for thermal lens analysis using a two-wavelength DSPI (Digital Speckle Pattern Interferometry) setup for wavefront sensing. The employed geometry enables the sensor to detect wavefronts with small phase differences and inherent aberrations found in induced lenses. The wavefronts was reconstructed by four-stepping fringe evaluation and branch-cut unwrapping from fringes formed onto a diffusive glass. Real-time single-exposure contour interferograms could be obtained in order to get discernible and low-spacial frequency contour fringes and obtain low-noise measurements. In our experiments we studied the thermal lens effect in a 4% Er-doped CaO-Al2O3 glass sample. The diode lasers were tuned to have a contour interval of around 120 μm. The incident pump power was longitudinally and collinearly oriented with the probe beams. Each interferogram described a spherical-like wavefront. Using the ABCD matrix formalism we obtained the induced lens dioptric power from the thermal effect for different values of absorbed pump power. © 2012 Copyright SPIE.

Investigation of Partamona helleri (Apidae, Meliponini) B chromosome origin. An approach by microdissection and whole chromosome painting

The stingless bee Partamona helleri in southeast Brazil shows the regular chromosome number 2n = 34 and a variable number of up to four minute B1 or B2 chromosomes. Previous cytogenetic analyses have indicated morphological similarities between the B1 chromosome and chromosome segments in the regular karyotype. In this study, microdissection and chromosome painting were employed along with C banding, NOR banding, and base-specific fluorochrome staining to investigate the origin of the B1 chromosome in P. helleri. B1-generated probe hybridized exclusively to B1 chromosomes. This result suggests an independent origin from the regular karyotype or, alternatively, that the B chromosome may have suffered substantial genetic alterations along its independent evolution. The absence of higher dosages of these small B chromosomes in this population of P. helleri may be related to the existence of either a genetic or cytogenetic constraint in the establishment of such high numbered karyotypes. © 2012 INRA, DIB and Springer-Verlag, France.