The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

DC-conductivity of a suspension of insulating particles with internal rotation

We analyse the consequences of Quincke rotation on the conductivity of a suspension. Quincke rotation refers to the spontaneous rotation of insulating particles dispersed in a slightly conducting liquid and subject to a high DC electric field: above a critical field, each particle rotates continuously around itself with an axis pointing in any direction perpendicular to the DC field. When the suspension is subject to an electric field lower than the threshold one, the presence of insulating particles in the host liquid decreases the bulk conductivity since the particles form obstacles to ion migration. But for electric fields higher than the critical one, the particles rotate and facilitate ion migration: the effective conductivity of the suspension is increased. We provide a theoretical analysis of the impact of Quincke rotation on the apparent conductivity of a suspension and we present experimental results obtained with a suspension of PMMA particles dispersed in weakly conducting liquids

Gene size reduction in the bacterial aphid endosymbiont, Buchnera.

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