Evolutionarily new sequences expressed in tumors

BACKGROUND: Earlier we suggested the concept of the positive evolutionary role of tumors. According to this concept, tumors provide conditions for the expression of evolutionarily new and/or sleeping genes in their cells. Thus, tumors are considered as evolutionary proving ground or reservoir of expression. To support this concept we have previously characterized in silico and experimentally a new class of human tumor-related transcribed sequences. RESULTS: In this article we describe results of further studies of previously described tumor-related sequences. The results of molecular phylogeny studies, Southern hybridization experiments and computational comparison with genomes of other species are presented. CONCLUSION: These results suggest that these previously described tumor-related human transcripts are also relatively evolutionarily new

The structure of microbial community and degradation of diatoms in the deep near-bottom layer of Lake Baikal.

Insight into the role of bacteria in degradation of diatoms is important for understanding the factors and components of silica turnover in aquatic ecosystems. Using microscopic methods, it has been shown that the degree of diatom preservation and the numbers of diatom-associated bacteria in the surface layer of bottom sediments decrease with depth; in the near-bottom water layer, the majority of bacteria are associated with diatom cells, being located either on the cell surface or within the cell. The structure of microbial community in the near-bottom water layer has been characterized by pyrosequencing of the 16S rRNA gene, which has revealed 149 208 unique sequences. According to the results of metagenomic analysis, the community is dominated by representatives of Proteobacteria (41.9%), Actinobacteria (16%); then follow Acidobacteria (6.9%), Cyanobacteria (5%), Bacteroidetes (4.7%), Firmicutes (2.8%), Nitrospira (1.6%), and Verrucomicrobia (1%); other phylotypes account for less than 1% each. For 18.7% of the sequences, taxonomic identification has been possible only to the Bacteria domain level. Many bacteria identified to the genus level have close relatives occurring in other aquatic ecosystems and soils. The metagenome of the bacterial community from the near-bottom water layer also contains 16S rRNA gene sequences found in previously isolated bacterial strains possessing hydrolytic enzyme activity. These data show that potential degraders of diatoms occur among the vast variety of microorganisms in the near-bottom water of Lake Baikal

Diversity of <i>Archaea</i> in Bottom Sediments of the Discharge Areas With Oil- and Gas-Bearing Fluids in Lake Baikal

<p>Using massively parallel sequencing (the Roche 454 platform) we have studied the diversity of archaeal 16S rRNA gene sequences in oxic and anoxic sediments at six sites in Lake Baikal with oil- and gas-bearing fluids discharge. Archaeal communities appeared to be represented mainly by five phyla: <i>Euryarchaeota, Crenarchaeota, Thaumarchaeota, Bathyarchaeota</i> (miscellaneous Crenarchaeotic group), and <i>Woesearchaeota</i> (deep sea hydrothermal vent group 6). Among them we detected sequences of methanogens of the orders <i>Methanomicrobiales, Methanosarsinales, Methanococcales</i>, as well as representatives of the following uncultured archaeal lineages: Group C3, Marine Benthic Group D, and Terrestrial Miscellaneous Group. We have also identified sequences of ammonia-oxidizing archaea of the phyla <i>Crenarchaeota</i> and <i>Thaumarchaeota</i>. Phylogenetic analysis showed the presence ANME-2d-related sequences. However, the analysis of <i>mcr</i>A genes libraries has not revealed typical representatives of ANME groups. Comparison of amplicon libraries 16S rRNA gene fragments from different samples proved the widespread presence of previously detected Baikal archaeal lineages, which are members of the phylum <i>Crenarchaeota</i> and <i>Thaumarchaeota</i> (formerly Group C3 of <i>Crenarchaeota</i>).</p

The structure of bacterial community in the near-bottom water layer of Lake Baikal.

<p>Every taxonomic group presented in the dendrogram accounted for no less than 1% of the total number of sequence reads, with the width of branches being proportional to the number of identified reads. Values at the nodes show the number of OTU_0.03 for a given taxon. The diagram at the bottom shows the proportions of OTU_0.03 assigned to taxa of different ranks.</p

Bacterial isolates associated with the laboratory culture of <i>S. acus.</i>

<p><i> A. johnsonii</i> BW65UT1570 (A, F), <i>M. adhaesivum</i> BW66UT1570 (B), <i>A. tumefaciens</i> BW62UT1570 (D). The degradated siliceous frustules of diatom <i>S. acus</i> in cocultures with <i>B. simplex</i> BW64UT1570 (C), <i>A. johnsonii</i> BW65UT1570 (E). Axenic culture <i>S. acus</i> (G). Epifluorescent microscopy, DAPI staining (A, B); scanning electron microscopy (D, E, F, G). Scale bar: A, B and G, 50 µm; C, 40 µm; D, 10 µm; E, F, 5 µm.</p

Sample coverage, species richness and species diversity indices.

<p>Sample coverage, species richness and species diversity indices.</p

The bacteria from the GenBank database most closely related, according to 16S rRNA gene sequences identified from deep near-bottom layer of Lake Baikal.

<p>The bacteria from the GenBank database most closely related, according to 16S rRNA gene sequences identified from deep near-bottom layer of Lake Baikal.</p

Changes in the degree of preservation of diatom frustules in different layers of Lake Baikal bottom sediments.

<p>(A, B) 0–1 cm. (C, D) 2–3 cm. (E, F) 6–7 cm. Scale bars: (A, C, E) 100 µm; (B, D, F) 10 µm.</p