Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gazave, Elodie et al.Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages.Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.Financial support was provided by a Beatriu de Pinos postdoctoral Grant to E.G., the Spanish Ministry of Science and Innovation (Grant BFU2009-13409-02-02toA.N.),and the Spanish National Institute for Bioinformatics (INB, www.inab.org).Peer reviewe

Determination of total strontium in uruguayan rice by inductively coupled plasma optical emission spectrometry (ICP-OES)

Strontium (Sr) is found naturally as a non-radioactive element and has 16 known isotopes. Naturally occurring Sr is found as four stable isotopes: Sr-84, -86, -87, and -88. Twelve other isotopes are radioactive. Sr-90 is the most important radioactive isotope in the environment, discovered mostly after the nuclear experiments conducted in the 1950s and 1960s. In the present work, 86 rice samples (Oryza sativa L.) and 7 rice husk samples were digested by dry ashing for the purpose of determining the total Sr levels by ICP-OES. The mean concentrations found were: 0.281 µg g–1 for milled, 0.287 µg g–1 for parboiled milled, 0.564 µg g–1 for brown, 0.73 µg g–1 for parboiled brown, and 1.16 µg g–1 for paddy rice, and 3.44 µg g–1 for the rice husks. Validation of the method was conducted with a certified reference material, NIST CRM 8418 Wheat Gluten, and the recovery obtained ranged from 89–98%. As the outer layers (aleurone, pericarp) of the grain are removed, the Sr concentration decreases. It can then be assumed that most of the Sr is stored in these layers. Although no extensive data exist for Sr levels in rice, the values obtained are in good agreement with the results reported for Sr in brown rice from Japan (0.25–0.72 µg g–1) and with non-contaminated foodstuffs from other parts of the world. Thus, the Uruguayan rice has Sr levels that match non-contaminated samples and its consumption presents no health threat

Concentrations of As, Ca, Cd, Co, Cr, Cu, Fe, Hg, K, Mg, Mn, Mo, Na, Ni, Pb, and Zn in uruguayan rice determined by atomic absorption spectrometry

The United Nations General Assembly declared the year 2004 the International Year of Rice and the concept Rice is Life. The largest nutritional problems occurring globally are proteinenergy malnutrition, and Ca, Fe, I, Zn, and vitamin A deficiency. In this report, 49 rice samples (Oryza sativa L.) were digested by dry ashing in order to determine As, Cd, Cr, and Pb by ETAAA

Bioavailability, ecotoxicity, and geological characteristics of trace lead in sediments from two sites on Negro River, Uruguay, South America

Bioassays of two sites along the Rio Negro in Uruguay indicate ecotoxicity, which could be attributable to trace concentrations of lead in river sediments. Monthly samples at two sites at Baygorria and Bonete locations were analyzed for both particle size and lead. Lead was determined by atomic spectrometry in river water and sediment and particle size by sieving and sedimentation. Data showed that Baygorria 0s sediments have greater percentage of clay than Bonete 0s (20.4 and 5.8%, respectively). Lead was measurable in Baygorria 0s sediments, meanwhile in Bonete 0s, it was always below the detection limit. In water samples, lead was below detection limit at both sites. Bioassays using sublethal growth and survival test with Hyalella curvispina amphipod, screening with bioluminescent bacteria Photobacterium leiognathi,and acute toxicity bioassay with Pimephales promelas fish indicated toxicity at Baygorria, with much less effect at Bonete. Even though no lethal effects could be demonstrated, higher sublethal toxicity was found in samples from Baygorria site, showing a possible concentration of the contaminant in the clay fraction

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans