Global variation in copy number in the human genome

Copy number variation (CNV) of DNA sequences is functionally significant but has yet to be fully ascertained. We have constructed a first-generation CNV map of the human genome through the study of 270 individuals from four populations with ancestry in Europe, Africa or Asia (the HapMap collection). DNA from these individuals was screened for CNV using two complementary technologies: single-nucleotide polymorphism (SNP) genotyping arrays, and clone-based comparative genomic hybridization. A total of 1,447 copy number variable regions (CNVRs), which can encompass overlapping or adjacent gains or losses, covering 360 megabases (12% of the genome) were identified in these populations. These CNVRs contained hundreds of genes, disease loci, functional elements and segmental duplications. Notably, the CNVRs encompassed more nucleotide content per genome than SNPs, underscoring the importance of CNV in genetic diversity and evolution. The data obtained delineate linkage disequilibrium patterns for many CNVs, and reveal marked variation in copy number among populations. We also demonstrate the utility of this resource for genetic disease studies.     

Capybaras (Rodentia: Cavidae) in highlands: environmental variables related to distribution,and herbivory effects on a common plant species

The capybara Hydrochoerus hydrochaeris is one of the largest and most widely distributed herbivores in the Neotropical lowlands. However, as yet, there are no records of its occurrence in highland environments. Our aim was to evaluate the environmental variables related to the capybara’s distribution and monitor the effects of its herbivory on the individuals and on the reproductive phenology of A. polyanthus, a common and important plant species of the high-altitude grasslands. Our results show that capybaras frequently occur in the high-altitude grasslands along the Campo Belo River, but they avoid waterlogged areas, occurring more frequently on the dry rocky areas. Capybara herbivory affected the number of A. polyanthus rosettes in flower, leading to the presence of inflorescence formation anomalies. High-altitude grasslands apparently provide capybaras with the three main components (food, shelter and water) required for their occurrence. However, although they seem to present a seasonal feeding strategy, which also happens in lowlands, their avoidance of the waterlogged areas suggests that in highlands the species may present different environmental preferences from those presented in lowlands. In addition, the impact of capybaras’ herbivory on A. polyanthus individuals indicates the potential impact that capybaras can represent on the plant community of the high-altitude grasslands. This appears to be a great opportunity to study the effect of the arrival of a large herbivore in a new environment and possible impacts on plant assemblages.     

Nitrogen saturation and net ecosystem production

Magnani et al. found that net carbon (C) sequestration of temperate and boreal forests is clearly driven by nitrogen (N) deposition. From the positive relationship between average net ecosystem production (NEP) and wet N deposition, the authors further conclude that "no signs of N saturation were apparent" in the studied forests and that this is "casting doubts on the risk of widespread ecosystem nitrogen saturation". Nitrogen additions can clearly alter net ecosystem production, but net ecosystem production cannot be used as an indicator of N saturation.     

A genome-wide association study for celiac disease identifies risk variants in the region harboring IL2 and IL21

We tested 310,605 SNPs for association in 778 individuals with celiac disease and 1,422 controls. Outside the HLA region, the most significant finding (rs13119723; P = 2.0 x 10(-7)) was in the KIAA1109-TENR-IL2-IL21 linkage disequilibrium block. We independently confirmed association in two further collections (strongest association at rs6822844, 24 kb 5' of IL21; meta-analysis P = 1.3 x 10(-14), odds ratio = 0.63), suggesting that genetic variation in this region predisposes to celiac disease.     

Mutations in LMF1 cause combined lipase deficiency and severe hypertriglyceridemia

Hypertriglyceridemia is a hallmark of many disorders, including metabolic syndrome, diabetes, atherosclerosis and obesity. A well-known cause is the deficiency of lipoprotein lipase (LPL), a key enzyme in plasma triglyceride hydrolysis. Mice carrying the combined lipase deficiency (cld) mutation show severe hypertriglyceridemia owing to a decrease in the activity of LPL and a related enzyme, hepatic lipase (HL), caused by impaired maturation of nascent LPL and hepatic lipase polypeptides in the endoplasmic reticulum (ER). Here we identify the gene containing the cld mutation as Tmem112 and rename it Lmf1 (Lipase maturation factor 1). Lmf1 encodes a transmembrane protein with an evolutionarily conserved domain of unknown function that localizes to the ER. A human subject homozygous for a deleterious mutation in LMF1 also shows combined lipase deficiency with concomitant hypertriglyceridemia and associated disorders. Thus, through its profound effect on lipase activity, LMF1 emerges as an important candidate gene in hypertriglyceridemia.