Identification and analysis of single nucleotide polymorphisms (SNPs) in citrus

Most of the cultivated species of citrus have narrow genetic basis. Relationships among species and cultivars are obscured by sexual compatibility, polyembryony, apomixis and a high incidence of somatic mutations. DNA analysis is crucial in genetic studies not only for citrus breeding programs but also for characterization of hybrids and species. In this paper, single nucleotide polymorphisms ( SNPs) were investigated in 58 accessions of Citrus, hybrids and related genera. Genomic sequences of 'Pera IAC' sweet orange ( Citrus sinensis L. Osbeck) were used for primer design and selection of sequence tagged sites (STSs) for identification of SNPs. Analysis of 36 STSs showed identical sequences among 40 of the 41 sweet orange accessions studied. However, these accessions were heterozygous for many SNPs. Ten selected STSs were analyzed in 17 additional accessions from 13 species and hybrids. Comparing to the 'Pera IAC' sweet orange accession, a total of 150 polymorphic nucleotides were identified and most of the alterations were transitions ( 52.7%). The greatest number of SNPs was observed in Poncirus trifoliata ( L.) Raf. and the smallest in 'Ponkan' mandarin ( Citrus reticulata Blanco). At the intra-specific level, 'Bafa Gigante' ( Citrus sinensis L. Osbeck) was the only sweet orange accession with a divergent SNPs genotype, which corroborates the hypothesis of a hybrid origin for this accession. Although the STSs analyzed represent randomly sampled genomic sequences, they provided consistent information about the level of polymorphism and showed the potential of SNPs markers for characterization and phylogenetic studies.

Reliability and validation of a Brazilian version of the Oral Health Impact Profile for assessing edentulous subjects

The aims of this study were to evaluate the reliability and to validate a Brazilian version of Oral Health Impact Profile for assessing edentulous subjects (OHIP-EDENT), an inventory for measuring oral health-related quality of life of edentulous subjects. The sample comprised 65 complete denture wearers (23 men, mean age of 69.1 +/- 10.3 years). The translated OHIP-EDENT was applied on two occasions with a washout period of 3 months. Reliability was assessed by an internal consistency analysis and a test-retest approach. A preliminary validation process was conducted by a qualitative approach/interview. Results of internal consistency showed a Cronbach's alpha of 0.86 or 0.90 for the first or second appointment respectively. Through the test-retest analysis, an intra-class correlation coefficient of 0.57 was found, and individual answers reflected a broad range of agreement. Interviewed volunteers (n = 6) comprehended most questions well. In conclusion, the Brazilian version of OHIP-EDENT is adequate for assessing the oral health-related quality of life for edentulous subjects.

Identification and Analyses of Candidate Genes for Rpp4-Mediated Resistance to Asian Soybean Rust in Soybean

Asian soybean rust is a formidable threat to soybean (Glycine max) production in many areas of the world, including the United States. Only five sources of resistance have been identified (Resistance to Phakopsora pachyrhizi1 [Rpp1], Rpp2, Rpp3, Rpp4, and Rpp5). Rpp4 was previously identified in the resistant genotype PI459025B and mapped within 2 centimorgans of Satt288 on soybean chromosome 18 (linkage group G). Using simple sequence repeat markers, we developed a bacterial artificial chromosome contig for the Rpp4 locus in the susceptible cv Williams82 (Wm82). Sequencing within this region identified three Rpp4 candidate disease resistance genes (Rpp4C1-Rpp4C3 [Wm82]) with greatest similarity to the lettuce (Lactuca sativa) RGC2 family of coiled coil-nucleotide binding site-leucine rich repeat disease resistance genes. Constructs containing regions of the Wm82 Rpp4 candidate genes were used for virus-induced gene silencing experiments to silence resistance in PI459025B, confirming that orthologous genes confer resistance. Using primers developed from conserved sequences in the Wm82 Rpp4 candidate genes, we identified five Rpp4 candidate genes (Rpp4C1-Rpp4C5 [PI459025B]) from the resistant genotype. Additional markers developed from the Wm82 Rpp4 bacterial artificial chromosome contig further defined the region containing Rpp4 and eliminated Rpp4C1 (PI459025B) and Rpp4C3 (PI459025B) as candidate genes. Sequencing of reverse transcription-polymerase chain reaction products revealed that Rpp4C4 (PI459025B) was highly expressed in the resistant genotype, while expression of the other candidate genes was nearly undetectable. These data support Rpp4C4 (PI459025B) as the single candidate gene for Rpp4-mediated resistance to Asian soybean rust.

Development and validation of an UV spectrophotometric method for determination of gatifloxacin in tablets

A simple, sensitive and accurate spectrophotometric method was developed for the assay of gatifloxacin in raw material and tablets. Validation of the method yielded good results concerning range, linearity, precision and accuracy. The absorbance was measured at 287 nm for gatifloxacin tablet solutions. The linearity range was found to be 4.0-14.0 μg/mL for gatifloxacin. It was also found that the excipients in the commercial tablets did not interfere with the method.

Identification and frequency of transposable elements in Eucalyptus

Transposable elements (TE) are major components of eukaryotic genomes and involved in cell regulation and organism evolution. We have analyzed 123,889 expressed sequence tags of the Eucalyptus Genome Project database and found 124 sequences representing 76 TE in 9 groups, of which copia, MuDR and FAR1 groups were the most abundant. The low amount of sequences of TE may reflect the high efficiency of repression of these elements, a process that is called TE silencing. Frequency of groups of TE in Eucalyptus libraries which were prepared with different tissues or physiologic conditions from seedlings or adult plants indicated that developing plants experience the expression of a much wider spectrum of TE groups than that seen in adult plants. These are preliminary results that identify the most relevant TE groups involved with Eucalyptus development, which is important for industrial wood production. Copyright by the Brazilian Society of Genetics.

Development and validation of HPLC method for quantitative analysis of triamcinolone in biodegradable microparticles

A simple, rapid, selective and specific high performance liquid chromatographic (HPLC) method for quantitative analysis of the triamcinolone in polylactide-co-glycolide acid (PLGA) microparticles was developed. The chromatographic parameters were reversed-phase C18 column, 250mm x 4.6mm, with particle size 5 μm. The column oven was thermostated at 35°C ± 2°C. The mobile phase was methanol/water 45:55 (v/v) and elution was isocratic at a flow-rate of 1 mL.mL-1. The determinations were performed using a UV-Vis detector at 239 nm. The injected sample volume was 10 μL. The standard curve was linear (r2 > 0.999) in the concentration range 100-2500 ng.mL-1. The method showed adequate precision, with a relative standard deviation (RSD) was smaller than 3%. The accuracy was analyzed by adding a standard drug and good recovery values were obtained for all drug concentrations used. The method showed specificity and selectivity with linearity in the working range and good precision and accuracy, making it very suitable for quantitation of triamcinolone in PLGA microparticles.

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.

Identification and filtering of uncharacteristic noise in the CMS hadron calorimeter

Commissioning studies of the CMS hadron calorimeter have identified sporadic uncharacteristic noise and a small number of malfunctioning calorimeter channels. Algorithms have been developed to identify and address these problems in the data. The methods have been tested on cosmic ray muon data, calorimeter noise data, and single beam data collected with CMS in 2008. The noise rejection algorithms can be applied to LHC collision data at the trigger level or in the offline analysis. The application of the algorithms at the trigger level is shown to remove 90% of noise events with fake missing transverse energy above 100 GeV, which is sufficient for the CMS physics trigger operation. © 2010 IOP Publishing Ltd and SISSA.

Development and validation of a microbiological agar assay for determination of orbifloxacin in pharmaceutical preparations

Orbifloxacin is a fluoroquinolone with broad-spectrum antimicrobial activity, and belongs to the third generation of quinolones. Regarding the quality control of medicines, a validated microbiological assay for determination of orbifloxacin in pharmaceutical formulations has not as yet been reported. For this purpose, this paper reports the development and validation of a simple, sensitive, accurate and reproducible agar diffusion method to quantify orbifloxacin in tablet formulations. The assay is based on the inhibitory effect of orbifloxacin upon the strain of Staphylococcus aureus ATCC 25923 used as test microorganism. The results were treated statistically by analysis of variance and were found to be linear (r = 0.9992) in the selected range of 16.0-64.0 μg/mL, precise with relative standard deviation (RSD) of repeatability intraday = 2.88%, intermediate precision RSD = 3.33%, and accurate (100.31%). The results demonstrated the validity of the proposed bioassay, which allows reliable orbifloxacin quantitation in pharmaceutical samples and therefore can be used as a useful alternative methodology for the routine quality control of this medicine. © 2011 by the authors; licensee MDPI, Basel, Switzerland.

Development and validation of a successful microbiological agar assay for determination of ceftriaxone sodium in powder for injectable solution

Ceftriaxone sodium is a cephalosporin with broad-spectrum antimicrobial activity and belongs to the third generation of cephalosporins. Regarding the quality control of medicines, a validated microbiological assay for the determination of ceftriaxone sodium in powder for injectable solution has not been reported yet. This paper reports the development and validation of a simple, accurate and reproducible agar diffusion method to quantify ceftriaxone sodium in powder for injectable solution. The assay is based on the inhibitory effect of ceftriaxone sodium on the strain of Bacillus subtilis ATCC 9371 IAL 1027 used as test microorganism. The results were treated statistically by analysis of variance and were found to be linear (r = 0.999) in the selected range of 15.0-60.0 μg/mL, precise with a relative standard deviation (RSD) of repeatability intraday = 1.40%, accurate (100.46%) and robust with a RSD lower than 1.28%. The results demonstrated the validity of the proposed bioassay, which allows reliable ceftriaxone sodium quantitation in pharmaceutical samples and therefore can be used as a useful alternative methodology for the routine quality control of this medicine. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

Development and validation of a microbiological assay for determination of chlorhexidine digluconate in aqueous solution

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Development and validation of a D-loop mtDNA SNP assay for the screening of specimens in forensic casework

Mitochondrial DNA (mtDNA) analysis is usually a last resort in routine forensic DNA casework. However, it has become a powerful tool for the analysis of highly degraded samples or samples containing too little or no nuclear DNA, such as old bones and hair shafts. The gold standard methodology still constitutes the direct sequencing of polymerase chain reaction (PCR) products or cloned amplicons from the HVS-1 and HVS-2 (hypervariable segment) control region segments. Identifications using mtDNA are time consuming, expensive and can be very complex, depending on the amount and nature of the material being tested. The main goal of this work is to develop a less labour-intensive and less expensive screening method for mtDNA analysis, in order to aid in the exclusion of non-matching samples and as a presumptive test prior to final confirmatory DNA sequencing. We have selected 14 highly discriminatory single nucleotide polymorphisms (SNPs) based on simulations performed by Salas and Amigo (2010) [1] to be typed using SNaPShotTM (Applied Biosystems, Foster City, CA, USA). The assay was validated by typing more than 100 HVS-1/HVS-2 sequenced samples. No differences were observed between the SNP typing and DNA sequencing when results were compared, with the exception of allelic dropouts observed in a few haplotypes. Haplotype diversity simulations were performed using 172 mtDNA sequences representative of the Brazilian population and a score of 0.9794 was obtained when the 14 SNPs were used, showing that the theoretical prediction approach for the selection of highly discriminatory SNPs suggested by Salas and Amigo (2010) [1] was confirmed in the population studied. As the main goal of the work is to develop a screening assay to skip the sequencing of all samples in a particular case, a pair-wise comparison of the sequences was done using the selected SNPs. When both HVS-1/HVS-2 SNPs were used for simulations, at least two differences were observed in 93.2% of the comparisons performed. The assay was validated with casework samples. Results show that the method is straightforward and can be used for exclusionary purposes, saving time and laboratory resources. The assay confirms the theoretic prediction suggested by Salas and Amigo (2010) [1]. All forensic advantages, such as high sensitivity and power of discrimination, as also the disadvantages, such as the occurrence of allele dropouts, are discussed throughout the article. © 2013 Elsevier B.V.

Guía para la identificación y formulación de proyectos de salud = Guidelines for the identification and formulation of health projects

Incluye Bibliografía

Construction and validation of an instrument to assess the reading comprehension of students from the third to the fifth grades of elementary school

Objetivo:Este estudo teve como objetivo construir e validar um instrumento de avaliação da compreensão de leitura a fim de caracterizar o perfil de leitura e detectar dificuldades de compreensão em escolares do terceiro ao quinto ano do Ensino Fundamental.Métodos:Participaram 378 escolares divididos em trés grupos para avaliação da compreensão de proposições literais e inferenciais de micro e macroestruturas de dois textos expositivos e dois textos narrativos por meio de questões de múltipla escolha.Resultados:Os dados analisados estatisticamente indicaram valores do teste alfa de Cronbach apresentando consisténcia interna nos quatros textos aplicados para os trés grupos.Conclusão:Foi possível constatar que os escolares apresentaram menor número de erros com o aumento da escolarização e que cada tipo de texto apresentou uma dificuldade específica para os escolares.

Translation, cultural adaptation to Brazil and validation of the venous leg ulcer quality of life questionnaire (VLU-QoL-Br)

Objetivo:traduzir o instrumento Venous legulcer quality of life questionnaire (VLU-QoL), adaptá-lo culturalmente para o português do Brasil e validá-lo com pacientes do Hospital das Clínicas da Faculdade de Medicina de Botucatu (FMB) da Universidade Estadual Paulista (Unesp). Métodos:o questionário foi traduzido por um tradutor profissional e por dois dermatologistas especialistas na área de úlceras venosas (UV), sendo reformulado em reunião com os três tradutores. O constructo (VLU-QoL-Br) foi submetido a pré-entrevista com 10 portadores de UV para a adaptação da linguagem. Posteriormente, foi aplicado em pacientes do HC-Unesp, e como teste-reteste para verificação de sua reprodutibilidade. Resultados:foram avaliados 82 pacientes, sendo 56 (68%) do sexo feminino. A idade média foi de 67,3 anos. O questionário foi traduzido, adaptado e aplicado aos pacientes. O constructo apresentou alta consistência interna (alfa= 0,94) e adequada correlação item-total. Quando avaliados os 32 retestes, observou-se correlação intraclasse para concordância de 0,78 (p < 0,01), indicando boa reprodutibilidade do constructo. A análise fatorial confirmatória corroborou as dimensões do questionário original: atividades, psicológico e sintomas. Escores do VLU-QoL-Br se associaram, independentemente, à área total das úlceras e a menor escolaridade dos sujeitos (p < 0,01). Conclusão:a tradução, a adaptação e a validação do questionário VLU-Qol-Br demonstrou boa performance psicométrica, permitindo seu uso clínico no Brasil. É importante avaliar seu desempenho em outras regiões e em diferentes amostras de indivíduos.