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

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

Optical limiting in solid-core photonic crystal fibers

Optical limiting in solid-core photonic crystal fibers filled with reverse-saturable absorbers has been observed. A sharp change in limiting threshold was found for materials in the fiber holes with refractive indices near n = 1.44

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

Spin-dependent transport in metal/semiconductor tunnel junctions

This paper describes a model as well as experiments on spin-polarized tunnelling with the aid of optical spin orientation. This involves tunnel junctions between a magnetic material and gallium arsenide (GaAs), where the latter is optically excited with circularly polarized light in order to generate spin-polarized carriers. A transport model is presented that takes account of carrier capture in the semiconductor surface states, and describes the semiconductor surface in terms of a spin-dependent energy distribution function. The so-called surface spin-splitting can be calculated from the balance of the polarized electron and hole flow in the semiconductor subsurface region, the polarized tunnelling current across the tunnel barrier between the magnetic material and the semiconductor surface, and the spin relaxation at the semiconductor surface. Measurements are presented of the circular-polarization-dependent photocurrent (the so-called helicity asymmetry) in thin-film tunnel junctions of Co/Al2O3/GaAs. In the absence of a tunnel barrier, the helicity asymmetry is caused by magneto-optical effects (magnetic circular dichroism). In the case where a tunnel barrier is present, the data cannot be explained by magneto-optical effects alone; the deviations provide evidence that spin-polarized tunnelling due to optical spin orientation occurs. In Co/τ-MnAl/AlAs/GaAs junctions no deviations from the magneto-optical effects are observed, most probably due to the weak spin polarization of τ-MnAl along the tunnelling direction; the latter is corroborated by bandstructure calculations. Finally, the application of photoexcited GaAs for spin-polarized tunnelling in a scanning tunnelling microscope is discussed.

Deregulated expression of hnRNP A/B proteins in human non-small cell lung cancer: parallel assessment of protein and mRNA levels in paired tumour/non-tumour tissues

<p>Abstract</p> <p>Background</p> <p>Heterogeneous nuclear ribonucleoproteins (hnRNPs) of the A/B type (hnRNP A1, A2/B1, A3) are highly related multifunctional proteins participating in alternative splicing by antagonising other splicing factors, notably ASF/SF2. The altered expression pattern of hnRNP A2/B1 and/or splicing variant B1 alone in human lung cancer and their potential to serve as molecular markers for early diagnosis remain issues of intense investigation. The main objective of the present study was to use paired tumour/non-tumour biopsies from patients with non-small cell lung cancer (NSCLC) to investigate the expression profiles of hnRNP A1, A2/B1 and A3 in conjunction with ASF/SF2.</p> <p>Methods</p> <p>We combined western blotting of tissue homogenates with immunohistochemical examination of fixed tissue sections and quantification of mRNA expression levels in tumour versus adjacent normal-looking areas of the lung in the same patient.</p> <p>Results</p> <p>Our study, in addition to clear evidence of mostly uncoupled deregulation of hnRNPs A/B, has revealed hnRNP A1 to be the most deregulated protein with a high frequency of over-expression (76%), followed by A3 (52%) and A2/B1 (43%). Moreover, direct comparison of protein/mRNA levels showed a lack of correlation in the case of hnRNP A1 (as well as of ASF/SF2), but not of A2/B1, suggesting that different mechanisms underlie their deregulation.</p> <p>Conclusion</p> <p>Our results provide strong evidence for the up-regulation of hnRNP A/B in NSCLC, and they support the existence of distinct mechanisms responsible for their deregulated expression.</p

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches

Protein sequence database search programs may be evaluated both for their retrieval accuracy—the ability to separate meaningful from chance similarities—and for the accuracy of their statistical assessments of reported alignments. However, methods for improving statistical accuracy can degrade retrieval accuracy by discarding compositional evidence of sequence relatedness. This evidence may be preserved by combining essentially independent measures of alignment and compositional similarity into a unified measure of sequence similarity. A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set

Mutationism and the Dual Causation of Evolutionary Change

The rediscovery of Mendel's laws a century ago launched the science that William Bateson called "genetics," and led to a new view of evolution combining selection, particulate inheritance, and the newly characterized phenomenon of "mutation." This "mutationist" view clashed with the earlier view of Darwin, and the later "Modern Synthesis," by allowing discontinuity, and by recognizing mutation (or more properly, mutation-and-altered-development) as a source of creativity, direction, and initiative. By the mid-20th century, the opposing Modern Synthesis view was a prevailing orthodoxy: under its influence, "evolution" was redefined as "shifting gene frequencies," that is, the sorting out of pre-existing variation without new mutations; and the notion that mutation-and-altered-development can exert a predictable influence on the course of evolutionary change was seen as heretical. Nevertheless, mutationist ideas re-surfaced: the notion of mutational determinants of directionality emerged in molecular evolution by 1962, followed in the 1980s by an interest among evolutionary developmental biologists in a shaping or creative role of developmental propensities of variation, and more recently, a recognition by theoretical evolutionary geneticists of the importance of discontinuity and of new mutations in adaptive dynamics. The synthetic challenge presented by these innovations is to integrate mutation-and-altered-development into a new understanding of the dual causation of evolutionary change--a broader and more predictive understanding that already can lay claim to important empirical and theoretical results--and to develop a research program appropriately emphasizing the emergence of variation as a cause of propensities of evolutionary change