Conspiracy in bacterial genomes

The rank ordered distribution of the codon usage frequencies for 123 bacteriae is best fitted by a three parameters function that is the sum of a constant, an exponential and a linear term in the rank n. The parameters depend (two parabolically) from the total GC content. The rank ordered distribution of the amino acids is fitted by a straight line. The Shannon entropy computed over all the codons is well fitted by a parabola in the GC content, while the partial entropies computed over subsets of the codons show peculiar different behavior, exhibiting therefore a first conspiracy effect. Moreover the sum of the codon usage frequencies over particular sets, e.g. with C and A (respectively G and U) as i-th nucleotide, shows a clear linear dependence from the GC content, exhibiting another conspiracy effect.Comment: revised version: introduction and conclusion enhanced, references added, figures added, some tables remove

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

A Gibbs approach to Chargaff's second parity rule

Chargaff's second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is currently no explanation for its presence in DNA strands. Here we argue that CSPR is a probabilistic consequence of the reverse complementarity between paired strands, because the Gibbs distribution associated with the chemical energy between the bonds satisfies CSPR. We develop a statistical test to study the validity of CSPR under the Gibbsian assumption and we apply it to a large set of bacterial genomes taken from the GenBank repository.Comment: 16 page

Electron and positron scattering from 1,1-C₂H₂F₂

1,1-difluoroethylene (1,1-C₂H₂F₂) molecules have been studied for the first time experimentally and theoretically by electron and positron impact. 0.4-1000 eV electron and 0.2-1000 eV positron impact total cross sections (TCSs) were measured using a retarding potential time-of-flight apparatus. In order to probe the resonances observed in the electron TCSs, a crossed-beam method was used to investigate vibrational excitation cross sections over the energy range of 1.3-49 eV and scattering angles 90 degrees and 120 degrees for the two loss energies 0.115 and 0.381 eV corresponding to the dominant C-H (ν₂ and ν₉) stretching and the combined C-F (ν₃) stretching and CH₂ (ν₁₁) rocking vibrations, respectively. Electron impact elastic integral cross sections are also reported for calculations carried out using the Schwinger multichannel method with pseudopotentials for the energy range from 0.5 to 50 eV in the static-exchange approximation and from 0.5 to 20 eV in the static-exchange plus polarization approximation. Resonance peaks observed centered at about 2.3, 6.5, and 16 eV in the TCSs have been shown to be mainly due to the vibrational and elastic channels, and assigned to the B₂, B₁, and A₁ symmetries, respectively. The pi* resonance peak at 1.8 eV in C₂H₄ is observed shifted to 2.3 eV in 1,1-C₂H₂F₂ and to 2.5 eV in C₂F₄; a phenomenon attributed to the decreasing C=C bond length from C₂H₄ to C₂F₄. For positron impact a conspicuous peak is observed below the positronium formation threshold at about 1 eV, and other less pronounced ones centered at about 5 and 20 eV.The work was supported in part by a Grant-in-Aid, the Ministry of Education, Science, Technology, Sport and Culture, Japan, the Japan Society for the Promotion of Science JSPS, and the Japan Atomic Energy Research Institute JAERI. One of the authors C.M. is also grateful to the JSPS for financial support under Grant No. P04064. Another author H.T. acknowledges Dr. T. Ozeki of the JAERI for his encouragement and support during this work. This work was also done under the International Atomic Energy Agency IAEA project for three of the authors C.M., M.H., and H.T.. Two of the authors M.H.F.B. and M.A.P.L. acknowledge support from the Brazilian agency Conselho Nacional de Desenvolvimento Científico e Tecnológico CNPq. MHFB also acknowledges support from the Paraná state agency Fundação Araucária and from FINEP ( under Project No. CT-Infra 1)

Contact-Induced Nonlinearity in Oscillating Belts and Webs

This study is motivated by issues in belt dynamics and paper forming where the oscillatory motion of the contact point between the belt and pulley or the web and roll is important. The objective is to evaluate the influence of the nonlinear contact boundary conditions on the dynamics of the belt or web. To accomplish this objective, two models are analyzed using perturbation methods. The first model represents a string on an elastic foundation (an approximation of the paper forming process) and the second model represents a tensioned beam (accessory drive belt). The first correction to the fundamental natural frequency and the dynamic belt/web length are determined as a function of the governing parameters. For both models, the change in belt length is found to be proportional to the radius of the pulley/roll and the initial belt/web energy.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/69021/2/10.1177_107754639500100404.pd

Does codon bias have an evolutionary origin?

<p>Abstract</p> <p>Background</p> <p>There is a 3-fold redundancy in the Genetic Code; most amino acids are encoded by more than one codon. These synonymous codons are not used equally; there is a Codon Usage Bias (CUB). This article will provide novel information about the origin and evolution of this bias.</p> <p>Results</p> <p>Codon Usage Bias (CUB, defined here as deviation from equal usage of synonymous codons) was studied in 113 species. The average CUB was 29.3 ± 1.1% (S.E.M, n = 113) of the theoretical maximum and declined progressively with evolution and increasing genome complexity. A Pan-Genomic Codon Usage Frequency (CUF) Table was constructed to describe genome-wide relationships among codons. Significant correlations were found between the number of synonymous codons and (i) the frequency of the respective amino acids (ii) the size of CUB. Numerous, statistically highly significant, internal correlations were found among codons and the nucleic acids they comprise. These strong correlations made it possible to predict missing synonymous codons (wobble bases) reliably from the remaining codons or codon residues.</p> <p>Conclusion</p> <p>The results put the concept of "codon bias" into a novel perspective. The internal connectivity of codons indicates that all synonymous codons might be integrated parts of the Genetic Code with equal importance in maintaining its functional integrity.</p

An observation of spin-valve effects in a semiconductor field effect transistor: a novel spintronic device

We present the first spintronic semiconductor field effect transistor. The injector and collector contacts of this device were made from magnetic permalloy thin films with different coercive fields so that they could be magnetized either parallel or antiparallel to each other in different applied magnetic fields. The conducting medium was a two dimensional electron gas (2DEG) formed in an AlSb/InAs quantum well. Data from this device suggest that its resistance is controlled by two different types of spin-valve effect: the first occurring at the ferromagnet-2DEG interfaces; and the second occuring in direct propagation between contacts.Comment: 4 pages, 2 figure

Pressures in Archaeal Protein Coding Genes: A Comparative Study

Our studies on the bases of codons from 11 completely sequenced archaeal genomes show that, as we move from GC-rich to AT-rich protein-coding gene-containing species, the differences between G and C and between A and T, the purine load (AG content), and also the overall persistence (i.e. the tendency of a base to be followed by the same base) within codons, all increase almost simultaneously, although the extent of increase is different over the three positions within codons. These findings suggest that the deviations from the second parity rule (through the increasing differences between complementary base contents) and the increasing purine load hinder the chance of formation of the intra-strand Watson–Crick base-paired secondary structures in mRNAs (synonymous with the protein-coding genes we dealt with), thereby increasing the translational efficiency. We hypothesize that the ATrich protein-coding gene-containing archaeal species might have better translational efficiency than their GC-rich counterparts

DNA Asymmetric Strand Bias Affects the Amino Acid Composition of Mitochondrial Proteins

Variations in GC content between genomes have been extensively documented. Genomes with comparable GC contents can, however, still differ in the apportionment of the G and C nucleotides between the two DNA strands. This asymmetric strand bias is known as GC skew. Here, we have investigated the impact of differences in nucleotide skew on the amino acid composition of the encoded proteins. We compared orthologous genes between animal mitochondrial genomes that show large differences in GC and AT skews. Specifically, we compared the mitochondrial genomes of mammals, which are characterized by a negative GC skew and a positive AT skew, to those of flatworms, which show the opposite skews for both GC and AT base pairs. We found that the mammalian proteins are highly enriched in amino acids encoded by CA-rich codons (as predicted by their negative GC and positive AT skews), whereas their flatworm orthologs were enriched in amino acids encoded by GT-rich codons (also as predicted from their skews). We found that these differences in mitochondrial strand asymmetry (measured as GC and AT skews) can have very large, predictable effects on the composition of the encoded proteins