TagSNP transferability and relative loss of variability prediction from HapMap to an admixed population

<p>Abstract</p> <p>Background</p> <p>The application of a subset of single nucleotide polymorphisms, the tagSNPs, can be useful in capturing untyped SNPs information in a genomic region. TagSNP transferability from the HapMap dataset to admixed populations is of uncertain value due population structure, admixture, drift and recombination effects. In this work an empirical dataset from a Brazilian admixed sample was evaluated against the HapMap population to measure tagSNP transferability and the relative loss of variability prediction.</p> <p>Methods</p> <p>The transferability study was carried out using SNPs dispersed over four genomic regions: the PTPN22, HMGCR, VDR and CETP genes. Variability coverage and the prediction accuracy for tagSNPs in the selected genomic regions of HapMap phase II were computed using a prediction accuracy algorithm. Transferability of tagSNPs and relative loss of prediction were evaluated according to the difference between the Brazilian sample and the pooled and single HapMap population estimates.</p> <p>Results</p> <p>Each population presented different levels of prediction per gene. On average, the Brazilian (BRA) sample displayed a lower power of prediction when compared to HapMap and the pooled sample. There was a relative loss of prediction for BRA when using single HapMap populations, but a pooled HapMap dataset generated minor loss of variability prediction and lower standard deviations, except at the VDR locus at which loss was minor using CEU tagSNPs.</p> <p>Conclusion</p> <p>Studies that involve tagSNP selection for an admixed population should not be generally correlated with any specific HapMap population and can be better represented with a pooled dataset in most cases.</p

Efeitos do desfolhamento provocado por Brassolis sophorae na produção de frutos de coqueiros.

Publicado também: FRAZÃO, D. A. C.; HOMMA, A. K. O; VIÉGAS, I. de J. M. (Ed.). Contribuição ao desenvolvimento da fruticultura na Amazônia. Belém, PA: Embrapa Amazônia Oriental, 2006. p. 337-343

MA-XRF measurement for corrosion assessment on bronze artefacts

In this study, an innovative portable macro X-Ray Fluorescence (MA-XRF) scanner prototype has been employed in order to gain information on composition and distribution of corrosion products artificially grown on Cu-based coupons. First results have shown the importance of using artificially corroded reference samples before any assessment on archaeological artefacts. Moreover, the prototype used demonstrated to be a powerful tool for understanding complex corrosion processes which might occur on Cu-based alloys. The scanner was able to detect light elements as S and Cl, essential for studying the distribution of specific corrosion compounds. Using imaging techniques, it was possible to observe a gradient in Cu elemental maps intensity caused by the overlapping of a thicker corrosion product layer

Single copy/knock-in models of ALS SOD1 in C. elegans suggest loss and gain of function have different contributions to cholinergic and glutamatergic neurodegeneration

Mutations in Cu/Zn superoxide dismutase 1 (SOD1) lead to Amyotrophic Lateral Sclerosis (ALS), a neurodegenerative disease that disproportionately affects glutamatergic and cholinergic motor neurons. Previous work with SOD1 overexpression models supports a role for SOD1 toxic gain of function in ALS pathogenesis. However, the impact of SOD1 loss of function in ALS cannot be directly examined in overexpression models. In addition, overexpression may obscure the contribution of SOD1 loss of function in the degeneration of different neuronal populations. Here, we report the first single-copy, ALS knock-in models in C. elegans generated by transposon- or CRISPR/Cas9- mediated genome editing of the endogenous sod-1 gene. Introduction of ALS patient amino acid changes A4V, H71Y, L84V, G85R or G93A into the C. elegans sod-1 gene yielded single-copy/knock-in ALS SOD1 models. These differ from previously reported overexpression models in multiple assays. In single-copy/knock-in models, we observed differential impact of sod-1 ALS alleles on glutamatergic and cholinergic neurodegeneration. A4V, H71Y, G85R, and G93A animals showed increased SOD1 protein accumulation and oxidative stress induced degeneration, consistent with a toxic gain of function in cholinergic motor neurons. By contrast, H71Y, L84V, and G85R lead to glutamatergic neuron degeneration due to sod-1 loss of function after oxidative stress. However, dopaminergic and serotonergic neuronal populations were spared in single-copy ALS models, suggesting a neuronal-subtype specificity previously not reported in invertebrate ALS SOD1 models. Combined, these results suggest that knock-in models may reproduce the neurotransmitter-type specificity of ALS and that both SOD1 loss and gain of toxic function differentially contribute to ALS pathogenesis in different neuronal populations.Peer reviewe

MA-XRF measurement for corrosion assessment on bronze artefacts

In this study, an innovative portable macro X-Ray Fluorescence (MA-XRF) scanner prototype has been employed in order to gain information on composition and distribution of corrosion products artificially grown on Cu-based coupons. First results have shown the importance of using artificially corroded reference samples before any assessment on archaeological artefacts. Moreover, the prototype used demonstrated to be a powerful tool for understanding complex corrosion processes which might occur on Cu-based alloys. The scanner was able to detect light elements as S and Cl, essential for studying the distribution of specific corrosion compounds. Using imaging techniques, it was possible to observe a gradient in Cu elemental maps intensity caused by the overlapping of a thicker corrosion product layer

Salinity dependence of the distribution of multicellular magnetotactic prokaryotes in a hypersaline lagoon

Candidatus Magnetoglobus multicellularis is an unusual magnetotactic multicellular microorganism composed of a highly organized assemblage of gram-negative bacterial cells. In this work, the salinity dependence of Ca. M. multicellularis and its abundance in the hypersaline Araruama Lagoon, Brazil were studied. Viability experiments showed that Ca. M. multicellularis died in salinities >55‰ and < 40‰. Low salinities were also observed to modify the cellular assemblage. In microcosms prepared with different salinities, the microorganism grew better at intermediate salinities whereas in high or low salinities, the size of the population did not increase over time. The concentrations of Ca. M. multicellularis in the lagoon were related to salinity; sites with lower and higher salinities than the lagoon average contained less Ca. M. multicellularis. These results demonstrate the influence of salinity on the survival and distribution of Ca. M. multicellularis in the environment. In sediments, the abundance of Ca. M. multicellularis ranged from 0 to 103 microorganisms/ml, which represented 0.001% of the counts of total bacteria. The ability of Ca. M. multicellularis to accumulate iron and sulfur in high numbers of magnetosomes (up to 905 per microorganism) suggests that its impact on the sequestration of these elements (0.1% for biogenic bacterial iron) is not proportional to its abundance in the lagoon. [Int Microbiol 2009; 12(3):193-201