Origin of nascent lineages and the mechanisms used to prime second-strand DNA synthesis in the R1 and R2 retrotransposons of Drosophila

Comparative analysis of 12 Drosophila genomes reveals insights into the evolution and mechanism of integration of R1 and R2 retrotransposons

Effects of Anacetrapib in Patients with Atherosclerotic Vascular Disease

BACKGROUND: Patients with atherosclerotic vascular disease remain at high risk for cardiovascular events despite effective statin-based treatment of low-density lipoprotein (LDL) cholesterol levels. The inhibition of cholesteryl ester transfer protein (CETP) by anacetrapib reduces LDL cholesterol levels and increases high-density lipoprotein (HDL) cholesterol levels. However, trials of other CETP inhibitors have shown neutral or adverse effects on cardiovascular outcomes. METHODS: We conducted a randomized, double-blind, placebo-controlled trial involving 30,449 adults with atherosclerotic vascular disease who were receiving intensive atorvastatin therapy and who had a mean LDL cholesterol level of 61 mg per deciliter (1.58 mmol per liter), a mean non-HDL cholesterol level of 92 mg per deciliter (2.38 mmol per liter), and a mean HDL cholesterol level of 40 mg per deciliter (1.03 mmol per liter). The patients were assigned to receive either 100 mg of anacetrapib once daily (15,225 patients) or matching placebo (15,224 patients). The primary outcome was the first major coronary event, a composite of coronary death, myocardial infarction, or coronary revascularization. RESULTS: During the median follow-up period of 4.1 years, the primary outcome occurred in significantly fewer patients in the anacetrapib group than in the placebo group (1640 of 15,225 patients [10.8%] vs. 1803 of 15,224 patients [11.8%]; rate ratio, 0.91; 95% confidence interval, 0.85 to 0.97; P=0.004). The relative difference in risk was similar across multiple prespecified subgroups. At the trial midpoint, the mean level of HDL cholesterol was higher by 43 mg per deciliter (1.12 mmol per liter) in the anacetrapib group than in the placebo group (a relative difference of 104%), and the mean level of non-HDL cholesterol was lower by 17 mg per deciliter (0.44 mmol per liter), a relative difference of -18%. There were no significant between-group differences in the risk of death, cancer, or other serious adverse events. CONCLUSIONS: Among patients with atherosclerotic vascular disease who were receiving intensive statin therapy, the use of anacetrapib resulted in a lower incidence of major coronary events than the use of placebo. (Funded by Merck and others; Current Controlled Trials number, ISRCTN48678192 ; ClinicalTrials.gov number, NCT01252953 ; and EudraCT number, 2010-023467-18 .)

Genomic studies of the ribosomal RNA gene locus and the evolution and retrotransposition mechanisms of its mobile elements

Thesis (Ph. D.)--University of Rochester. Dept. of Biology, 2009.The rDNA locus and the non-LTR retrotransposons R1 and R2 that insert specifically into the 28S genes provide a microcosm to study the interactions between mobile elements and the host genome. While the rRNA genes are not assembled as part of completely sequenced genomes, the explosion in whole genome sequencing projects provided the raw sequencing reads used throughout the research presented in this thesis. These sequence data are used to address three issues: the pattern of nucleotide variation present in rDNA loci, the evolution of R1 and R2, and the mobility mechanisms of these elements. Concerted evolution of the rDNA locus was studied in 11 Drosophila, one Nasonia and nine non-arthropod species. The Drosophila, Nasonia and five of the non-arthropod species contained low levels of sequence variation (less than 0.2%). Four non-arthropod species contained higher levels of variation that suggested the presence of multiple rDNA loci that undergoes separate concerted evolution. The most complete analysis was done in Drosophila where nucleotide variants were generally found to be more numerous in faster evolving regions of the rDNA unit. The one deviation from this pattern was the higher nucleotide variation found in the 18S genes than in the faster evolving 28S genes. The R1 and R2 elements in twelve Drosophila species displayed a spectrum of sequence variation within species suggesting the formation of nascent R1 and R2 lineages, a prerequisite for the evolution of multiple families often seen within species. The Nasonia species contained 11 R1 and R2 families in the three closely related species. The different R1 and R2 families of Nasonia appear to use parts of the retrotransposition machinery of other families, perhaps providing a mechanism to help maintain the many competing element families. While R1 presence is limited to arthropods, a survey of eukaryotes showed R2 elements present in most animal groups except mammals. The common ancestor of bilateria and cnidaria appeared to have two R2 families, suggesting R2 genesis may have occurred over 1 billion years ago. The search for R1 and R2 elements revealed the first examples of non-autonomous SINE-like elements that appeared to use the R1 and R2 machinery for retrotransposition. Non-arthropod R2 elements displayed characteristics not previously observed among the more studied R2 elements in arthropods, most significantly the evolution of new target site preferences. Finally, junction analysis of R1 and R2 elements from 12 Drosophila, three Nasonia and 11 non-arthropod species suggested that during the integration reaction of the elements the DNA strand generated by reverse transcription is positioned to anneal to the upstream target site prior to initiating second strand synthesis. 5’ junctions are precise when the reverse transcribed strand can anneal to the upstream target, otherwise the junctions are variable. Most interesting were the R2 families within non-arthropods with 5’ junctions 1000’s of bp upstream within the rDNA unit of the 3’ junctions. These unusual families encoded three N-terminal zinc fingers, while R2 families with one zinc finger showed no target site evolution. This suggests dramatically different binding sites for the R2 subunit that cleaves the top strand

Evolution of genes and genomes on the Drosophila phylogeny

Comparative analysis of multiple genomes in a phylogenetic framework dramatically improves the precision and sensitivity of evolutionary inference, producing more robust results than single-genome analyses can provide. The genomes of 12 Drosophila species, ten of which are presented here for the first time (sechellia, simulans, yakuba, erecta, ananassae, persimilis, willistoni, mojavensis, virilis and grimshawi), illustrate how rates and patterns of sequence divergence across taxa can illuminate evolutionary processes on a genomic scale. These genome sequences augment the formidable genetic tools that have made Drosophila melanogaster a pre-eminent model for animal genetics, and will further catalyse fundamental research on mechanisms of development, cell biology, genetics, disease, neurobiology, behaviour, physiology and evolution. Despite remarkable similarities among these Drosophila species, we identified many putatively non-neutral changes in protein-coding genes, non-coding RNA genes, and cis-regulatory regions. These may prove to underlie differences in the ecology and behaviour of these diverse species