Virus-derived variation in diverse human genomes

Acquisition of genetic material from viruses by their hosts can generate inter-host structural genome variation. We developed computational tools enabling us to study virus-derived structural variants (SVs) in population-scale whole genome sequencing (WGS) datasets and applied them to 3,332 humans. Although SVs had already been cataloged in these subjects, we found previously-overlooked virus-derived SVs. We detected non-germline SVs derived from squirrel monkey retrovirus (SMRV), human immunodeficiency virus 1 (HIV-1), and human T lymphotropic virus (HTLV-1); these variants are attributable to infection of the sequenced lymphoblastoid cell lines (LCLs) or their progenitor cells and may impact gene expression results and the biosafety of experiments using these cells. In addition, we detected new heritable SVs derived from human herpesvirus 6 (HHV-6) and human endogenous retrovirus-K (HERV-K). We report the first solo-direct repeat (DR) HHV-6 likely to reflect DR rearrangement of a known full-length endogenous HHV-6. We used linkage disequilibrium between single nucleotide variants (SNVs) and variants in reads that align to HERV-K, which often cannot be mapped uniquely using conventional short-read sequencing analysis methods, to locate previously-unknown polymorphic HERV-K loci. Some of these loci are tightly linked to trait-associated SNVs, some are in complex genome regions inaccessible by prior methods, and some contain novel HERV-K haplotypes likely derived from gene conversion from an unknown source or introgression. These tools and results broaden our perspective on the coevolution between viruses and humans, including ongoing virus-to-human gene transfer contributing to genetic variation between humans.     

A rapid procedure for eliminating chromatofocusing buffer and concentrating minor active subforms of mitochondrial malate dehydrogenase

Mitochondrial malate dehydrogenase from several sources contains different molecular forms whose origin is still under discussion. Separation of these subforms has been achieved by chromatofocusing. A simple and rapid method, based on 5' AMP Sepharose chromatography, has been developed to concentrate mitochondrial malate dehydrogenase subforms and simultaneously remove chromatofocusing buffer.     

Ciliated Protozoan communities in a fluvial ecosystem

The ciliated protozoan communities in the Llobregat River (Barcelona, Spain) were studied for one year. Samples were taken from 11 different stations. The physical-chemical factors of the water as well as the qualitative and quantitative nature of the ciliate populations were considered. 105 species of ciliates, grouped in 13 orders, were found.The species which constantly appeared at all 11 stations (although not every month) were Litonotus fasciola, Trithigmostoma cucullulus, Cyclidium glaucoma, Glaucoma scintillans, Vorticella microstoma, Oxytricha sp., Stylonychia mytilus, Aspidisca costata and Aspidisca lynceus. The index of diversity at the different stations, and the affinity between the most abundant species, were also determined.