Marked variability in the extent of protein disorder within and between viral families.

Intrinsically disordered regions in eukaryotic proteomes contain key signaling and regulatory modules and mediate interactions with many proteins. Many viral proteomes encode disordered proteins and modulate host factors through the use of short linear motifs (SLiMs) embedded within disordered regions. However, the degree of viral protein disorder across different viruses is not well understood, so we set out to establish the constraints acting on viruses, in terms of their use of disordered protein regions.

Meta-analysis to test the association of HIV-1 nef amino acid differences and deletions with disease progression.

Previous relatively small studies have associated particular amino acid replacements and deletions in the HIV-1 nef gene with differences in the rate of HIV disease progression. We tested more rigorously whether particular nef amino acid differences and deletions are associated with HIV disease progression. Amino acid replacements and deletions in patients' consensus sequences were investigated for 153 progressor (P), 615 long-term nonprogressor (LTNP), and 2,311 unknown progressor sequences from 582 subtype B HIV-infected patients.

Comparison of prokaryotic diversity at offshore oceanic locations reveals a different microbiota in the Mediterranean Sea.

The bacterial and archaeal assemblages at two offshore sites located in polar (Greenland Sea; depth: 50 and 2000 m) and Mediterranean (Ionian Sea; depth 50 and 3000 m) waters were studied by PCR amplification and sequencing of the last 450-500 bp of the 16S rRNA gene. A total of 1621 sequences, together with alignable 16S rRNA gene fragments from the Sargasso Sea metagenome database, were analysed to ascertain variations associated with geographical location and depth. The Ionian 50 m sample appeared to be the most diverse and also had remarkable differences in terms of the prokaryotic groups retrieved; surprisingly, however, many similarities were found at the level of large-scale diversity between the Sargasso database fragments and the Greenland 50 m sample.

The Neolithic revolution of bacterial genomes.

Current human activities undoubtedly impact natural ecosystems. However, the influence of Homo sapiens on living organisms must have also occurred in the past. Certain genomic characteristics of prokaryotes can be used to study the impact of ancient human activities on microorganisms.

IWoCS: analyzing ribosomal intergenic transcribed spacers configuration and taxonomic relationships.

Motivation: Lately the use of 16S-23S Intergenic Transcribed Spacer (ITS) sequences for bacterial typing purposes has increased. The presence of conserved regions like tRNA genes or boxes together with hypervariable regions allows performing intraspecific discrimination of very close bacterial strains. On the other hand this mosaic of variability makes the ITS a sequence difficult to analyze and compare.

Micro-Mar: a database for dynamic representation of marine microbial biodiversity.

Background: The cataloging of marine prokaryotic DNA sequences is a fundamental aspect for bioprospecting and also for the development of evolutionary and speciation models. However, large amount of DNA sequences used to quantify prokaryotic biodiversity requires proper tools for storing, managing and analyzing these data for research purposes.

Description: The Micro-Mar database has been created to collect DNA diversity information from marine prokaryotes for biogeographical and ecological analyses.

The silencing of pseudogenes.

Pseudogenes are nonfunctional DNA sequences that can accumulate in the genomes of some bacterial species, especially those undergoing processes like niche change, host specialization, or weak selection strength. They may last for long evolutionary periods, opening the question of how the genome prevents expression of these degenerated or disrupted genes that would presumably give rise to malfunctioning proteins. We have investigated ribosomal binding strength at Shine-Dalgarno sequences and the prevalence of sigma70 promoter regions in pseudogenes across bacteria.

Evolutionary relationships of Fusobacterium nucleatum based on phylogenetic analysis and comparative genomics.

Background: The phylogenetic position and evolutionary relationships of Fusobacteria remain uncertain. Especially intriguing is their relatedness to low G+C Gram positive bacteria (Firmicutes) by ribosomal molecular phylogenies, but their possession of a typical gram negative outer membrane. Taking advantage of the recent completion of the Fusobacterium nucleatum genome sequence we have examined the evolutionary relationships of Fusobacterium genes by phylogenetic analysis and comparative genomics tools.

Comparative genomics of gene-family size in closely related bacteria.

Background: The wealth of genomic data in bacteria is helping microbiologists understand the factors involved in gene innovation. Among these, the expansion and reduction of gene families appears to have a fundamental role in this, but the factors influencing gene family size are unclear.

Results: The relative content of paralogous genes in bacterial genomes increases with genome size, largely due to the expansion of gene family size in large genomes.