Genetic relationships within and among Iberian fescues (Festuca L.) based on PCR-amplified markers

The genus Festuca comprises approximately 450 species and is widely distributed around the world. The Iberian Penninsula, with more than 100 taxa colonizing very diverse habitats, is one of its main centers of diversification. This study was conducted to assess molecular genetic variation and genetic relatedness among 91 populations of 31 taxa of Iberian fescues, based on several molecular markers (random amplified polymorphic DNA, amplified fragment length polymorphisms, and trnL sequences). The analyses showed the paraphyletic origin of the broad-leaved (subgenus Festuca, sections Scariosae and Subbulbosae, and subgenus Schedonorus) and the fine-leaved fescues (subgenus Festuca, sections Aulaxyper, Eskia, and Festuca). Schedonorus showed a weak relationship with Lolium rigidum and appeared to be the most recent of the broad-leaved clade. Section Eskia was the most ancient and Festuca the most recent of the fine-leaved clade. Festuca and Aulaxyper were the most related sections, in concordance with their taxonomic affinities. All taxa grouped into their sections, except F. ampla and F. capillifolia (section Festuca), which appeared to be more closely related to Aulaxyper and to a new independent section, respectively. Most populations clustered at the species level, but some subspecies and varieties mixed their populations. This study demonstrated the value in combining different molecular markers to uncover hidden genetic relationships between populations of Festuca

Quasispecies in wild-type tula hantavirus populations.

Tula virus (TUL) is a recently detected hantavirus carried by European common voles. Reverse transcriptase PCR cloning was used to study TUL S segment/N protein quasispecies. Both the distribution and character of mutations observed in three mutant spectra indicated limited selection at the protein level. At least 8% of the mutations were neutral or well tolerated; fixation of such mutations may play a role in TUL evolution in its natural host

HGVbase: a human sequence variation database emphasizing data quality and a broad spectrum of data sources

HGVbase (Human Genome Variation database; http://hgvbase.cgb.ki.se, formerly known as HGBASE) is an academic effort to provide a high quality and non-redundant database of available genomic variation data of all types, mostly comprising single nucleotide polymorphisms (SNPs). Records include neutral polymorphisms as well as disease-related mutations. Online search tools facilitate data interrogation by sequence similarity and keyword queries, and searching by genome coordinates is now being implemented. Downloads are freely available in XML, Fasta, SRS, SQL and tagged-text file formats. Each entry is presented in the context of its surrounding sequence and many records are related to neighboring human genes and affected features therein. Population allele frequencies are included wherever available. Thorough semi-automated data checking ensures internal consistency and addresses common errors in the source information. To keep pace with recent growth in the field, we have developed tools for fully automated annotation. All variants have been uniquely mapped to the draft genome sequence and are referenced to positions in EMBL/GenBank files. Data utility is enhanced by provision of genotyping assays and functional predictions. Recent data structure extensions allow the capture of haplotype and genotype information, and a new initiative (along with BiSC and HUGO-MDI) aims to create a central repository for the broad collection of clinical mutations and associated disease phenotypes of interest

Gene fusions to lacZ reveal new expression patterns of chimeric genes in transgenic plants.

The lacZ gene of Escherichia coli, coding for beta-galactosidase, is a widely used reporter gene for gene expression studies in microbial and animal systems. To demonstrate that it is also a powerful reporter gene in plants, lacZ was fused to 5' regulatory elements of several genes known to be functional in plant cells. By measuring LacZ activities in transgenic plants containing these gene constructs, we showed that the reporter is correctly monitoring the regulatory properties of the well-characterized promoters fused to lacZ. beta-Galactosidase was assayed directly in plant extracts when they contained high levels of LacZ or, when LacZ was expressed at low level, by separating the endogenous and LacZ activities electrophoretically and detecting the enzymes with a fluorogenic substrate. The most outstanding property of the marker is its amenability to histochemical detection. Due to its stability, LacZ can be fixed in the tissue with glutaraldehyde without loss of activity and detected with high resolution by using XGal. We could reveal expression patterns unnoticed earlier for many of the regulatory elements studied. The chlorophyll a/b binding protein gene, expressed at very high levels in green tissues, is also expressed at a low level in the vascular cylinder of the root. The Agrobacterium T-DNA gene encoding octopine synthase is especially active in the epidermis of the root tip and the TR2' gene was shown to be root specific in the intact plant and stimulated by wounding in the leaf tissue. The TR1' gene, fused to nptII, shows similar characteristics suggesting co-regulation of this tightly linked dual promoter

HGVbase: a curated resource describing human DNA variation and phenotype relationships

The Human Genome Variation Database (HGVbase; http://hgvbase.cgb.ki.se) has provided a curated summary of human DNA variation for more than 5 years, thus facilitating research into DNA sequence variation and human phenotypes. The database has undergone many changes and improvements to accommodate increasing volumes and new types of data. The focus of HGVbase has recently shifted towards information on haplotypes and phenotypes, relationships between phenotypes and DNA variation, and collaborative efforts to provide a global resource for genome–phenome data. Open sharing and precise phenotype definitions are necessary to advance the current understanding of common diseases that are typified by complex aetiologies, small genetic effect sizes and multiple confounding factors that obscure positive study results. Association data will increasingly be collected as part of this new project thrust. This report describes the evolving features of HGVbase, and covers in detail the technological choices we have made to enable efficient storage and data mining of increasingly large and complex data sets

Tula virus: a newly detected hantavirus carried by European common voles.

A novel hantavirus has been discovered in European common voles, Microtus arvalis and Microtus rossiaemeridionalis. According to sequencing data for the genomic RNA S segment and nucleocapsid protein and data obtained by immunoblotting with a panel of monoclonal antibodies, the virus, designated Tula virus, is a distinct novel member of the genus Hantavirus. Phylogenetic analyses of Tula virus indicate that it is most closely related to Prospect Hill, Puumala, and Muerto Canyon viruses. The results support the view that the evolution of hantaviruses follows that of their primary carriers. Comparison of strains circulating within a local rodent population revealed a genetic drift via accumulation of base substitutions and deletions or insertions. The Tula virus population from individual animals is represented by quasispecies, indicating the potential for rapid evolution of the agent