Analysis of the multi-copy gene family FAM90A as a copy number variant in different ethnic backgrounds

Copy number variants contribute extensively to inter-individual genomic differences, but little is known about their inter-population variability and diversity. In a previous study (Bosch et al., 2007; 16:2572-2582), we reported that the primate-specific gene family FAM90A, which accounts for as many as 25 members in the human reference assembly, has expanded the number of FAM90A clusters across the hominoid lineage. Here we examined the copy number variability of FAM90A genes in 260 HapMap samples of European, African, and Asian ancestry, and showed significant inter-population differences (p<0.0001). Based on the recent study of Stranger et al. (2007; 315:848-853), we also explored the correlation between copy number variability and expression levels of the FAM90A gene family. Despite the high genomic variability, we found a low correlation between FAM90A copy number and expression levels, which could be due to the action of independent trans-acting factors. Our results show that FAM90A is highly variable in copy number between individuals and between populations. However, this variability has little impact on gene expression levels, thus highlighting the importance of genomic variability for genes located in regions containing segmental duplications.     

Probe-specific mixed-model approach to detect copy number differences using multiplex ligation-dependent probe amplification (MLPA)

Background  

MLPA method is a potentially useful semi-quantitative method to detect copy number alterations in targeted regions. In this paper, we propose a method for the normalization procedure based on a non-linear mixed-model, as well as a new approach for determining the statistical significance of altered probes based on linear mixed-model. This method establishes a threshold by using different tolerance intervals that accommodates the specific random error variability observed in each test sample.     

Effect of reserpine on the differentiation of the external granular layer of the cerebellum in the chick embryo

In this work we analyse the effect produced by reserpine on the development of thickness and cell number in the external granular layer in the cerebellum of chick embryo. A striking 48-hour histogenetic delay is observed in the treated embryos relative to controls, as show by greater thickness and cell density of this layer in the former, as well as by retarded appearance of a typical radial morphological organization of the external granular layer.     

Characterization of adaptability components of Brazilian isolates of Macrophomina pseudophaseolina

Macrophomina pseudophaseolina is a new Macrophomina species reported on different crop and weed species in Brazil, India and Senegal, but to date there are no studies about its adaptability components. In this work, a collection of 62 M. pseudophaseolina isolates obtained from roots of the weed species Trianthema portulacastrum and Boerhavia diffusa collected in Northeastern Brazil, was used to: (a) study the effect of temperature and salinity on mycelial growth, (b) to determine their sensitivity to the fungicide carbendazim and (c) to assess their aggressiveness on melon and watermelon seedlings. Results showed variability among M. pseudophaseolina isolates. The optimum temperature for mycelial growth ranged between 26.4 and 38.1ºC. NaCl reduced the in vitro growth of all isolates, which were also highly sensitive to the fungicide carbendazim, exhibiting EC₅₀ values ranging from 0.013 to 0.089 mg/L a.i. Disease severity values on melon and watermelon seedlings showed that M. pseudophaseolina isolates were more aggressive in melon than in watermelon. Information about adaptability components of M. pseudophaseolina obtained in this study could be incorporated on breeding programs for melon and watermelon crops.     

Mosaic Uniparental Disomies and Aneuploidies as Large Structural Variants of the Human Genome

Mosaicism is defined as the coexistence of cells with different genetic composition within an individual, caused by postzygotic somatic mutation. Although somatic mosaicism for chromosomal abnormalities is a well-established cause of developmental and somatic disorders and has also been detected in different tissues, its frequency and extent in the adult normal population are still unknown. We provide here a genome-wide survey of mosaic genomic variation obtained by analyzing Illumina 1M SNP array data from blood or buccal DNA samples of 1991 adult individuals from the Spanish Bladder Cancer/EPICURO genome-wide association study. We found mosaic abnormalities in autosomes in 1.7% of samples, including 23 segmental uniparental disomies, 8 complete trisomies, and 11 large (1.5–37 Mb) copy-number variants. Alterations were observed across the different autosomes with recurrent events in chromosomes 9 and 20. No case-control differences were found in the frequency of events or the percentage of cells affected, thus indicating that most rearrangements found are not central to the development of bladder cancer. However, five out of six events tested were detected in both blood and bladder tissue from the same individual, indicating an early developmental origin. The high cellular frequency of the anomalies detected and their presence in normal adult individuals suggest that this type of mosaicism is a widespread phenomenon in the human genome. Somatic mosaicism should be considered in the expanding repertoire of inter- and intraindividual genetic variation, some of which may cause somatic human diseases but also contribute to modifying inherited disorders and/or late-onset multifactorial traits.     

Occurrence of Monosporascus cannonballus in Watermelon Fields in Tunisia and Factors Associated with Ascospore Density in Soil

Surveys of 11 watermelon fields throughout production areas of this crop in southern and central regions in Tunisia were conducted in 2007 to determine the aetiology and distribution of watermelon vine decline. Monosporascus cannonballus was isolated from diseased roots in all surveyed fields. All the isolates were identified according to morphological features and confirmed by amplification of a fragment of the ITS region with specific primers. Ascospores of M. cannonballus were recovered from soil in all watermelon fields surveyed and the average population densities ranged from 3.65 to 10.14 ascospores per g of soil. Multiple linear regression analysis revealed that only four of the crop and soil factors evaluated had a significant correlation with ascospore density at the end of the growing season: vertisol vs. other soils, disease incidence, percentage of clay and pH. The pH of the soil showed a strong significant negative linear relationship with ascospore density, while the other three factors correlated positively.