Genome trees constructed using five different approaches suggest new major bacterial clades

Background  

The availability of multiple complete genome sequences from diverse taxa prompts the development of new phylogenetic approaches, which attempt to incorporate information derived from comparative analysis of complete gene sets or large subsets thereof. Such attempts are particularly relevant because of the major role of horizontal gene transfer and lineage-specific gene loss, at least in the evolution of prokaryotes.     

Zooplankton of the Argazi reservoir (Southern Urals, Russia) and its long-term changes

The Argazi reservoir on the Miass River, the oldest reservoir in the Southern Urals, has been investigated. In total 49 species and forms of zooplankton are identified, including new and rare species for the fauna of the Urals. Throughout the reservoir zooplankton has high species diversity and considerable biomass (up to 11 g/m³). Rotifers are the leading group in the plankton of the reservoir. Compared to the early 1960s, the abundance and biomass of zooplankton has increased by 5–10 times. The disappearance of some plankton forms and the emergence of new ones, as well as an increased number of rotifers and some crustaceans by 1–2 orders of magnitude, are noted. The influence of three main factors that could lead to long-term changes in zooplankton—eutrophication, heavy metals pollution, and global warming—are considered. The last factor seems to be the most important.     

Lymphocytic Choriomeningitis Virus RNAs

IT has been proposed that lymphocytic choriomeningitis (LCM) virus and immunologically related viruses should be placed in a new taxonomic group, with LCM virus as the prototype virus^1,2. They were called arenoviruses because they contain, as a unique feature, electron-dense, sand-like or ribo-some-like granules². The LCM virus contains RNA and we have previously reported that this RNA can be separated into three components by density gradient centrifugation³.     

Analysis of donor splice sites in different eukaryotic organisms

We present here a new algorithm for functional site analysis. It is based on four main assumptions: each variation of nucleotide composition makes a different contribution to the overall binding free energy of interaction between a functional site and another molecule; nonfunctioning site-like regions (pseudosites) are absent or rare in genomes; there may be errors in the sample of sites; and nucleotides of different site positions are considered to be mutually dependent. In this algorithm, the site set is divided into subsets, each described by a certain consensus. Donor splice sites of the human protein-coding genes were analyzed. Comparing the results with other methods of donor splice site prediction has demonstrated a more accurate prediction of consensus sequences AG/GU(A,G), G/GUnAG, /GU(A,G)AG, /GU(A,G)nGU, and G/GUA than is achieved by weight matrix and consensus (A,C)AG/GU(A,G)AGU with mismatches. The probability of the first type error, E1, for the obtained consensus set was about 0.05, and the probability of the second type error, E2, was 0.15. The analysis demonstrated that accuracy of the functional site prediction could be improved if one takes into account correlations between the site positions. The accuracy of prediction by using human consensus sequences was tested on sequences from different organisms. Some differences in consensus sequences for the plant Arabidopsis sp., the invertebrate Caenorhabditis sp., and the fungus Aspergillus sp. were revealed. For the yeast Saccharomyces sp. only one conservative consensus, /GUA(U,A,C)G(U,A,C), was revealed (E1 = 0.03, E2 = 0.03). Yeast is a very interesting model to use for analysis of molecular mechanisms of splicing. Received: 14 October 1996 / Accepted: 30 January 1997