The colour evolution of the process q q -> q q g

We calculate the soft anomalous dimension matrix for a five-parton process, qq -> qqg. Considering different bases we unveil some interesting properties of this matrix.Comment: 11 pages; calculation extended to general 5-parton kinematic

Ingrowth by photoreceptor axons induces transcription of a retrotransposon in the developing Drosophila brain

The development of the lamina, the first optic ganglion of the fly visual system, depends on inductive cues from the innervating photoreceptor axons. lacZ expression from a P-element insertion, A72, occurs in the anlage of the lamina coincident with axon ingrowth from the eye imaginal disc. In eyeless mutants lacking photoreceptor axons, lacZ expression did not occur. The P-element was found to have inserted within the 3′ long terminal repeat (LTR) of a ‘17.6′ type retrotransposon. The expression pattern of 17.6 transcripts in the brain in wild-type and eyeless mutants paralleled the expression of the lacZ reporter. Analysis of 17.6 cis-regulatory sequences indicates that the lamina-specific expression is due to the combined action of an enhancer element in the LTR and a repressor element within the internal body of the retrotransposon. The regulation of the 17.6 retrotransposon provides a model for the study of innervation-dependent gene expression in postsynaptic cells during neurogenesis

Evidence for chaotic behaviour in pulsar spin-down rates

We present evidence for chaotic dynamics within the spin-down rates of 17 pulsars originally presented by Lyne et al. Using techniques that allow us to re-sample the original measurements without losing structural information, we have searched for evidence of a strange attractor in the time series of frequency derivatives for each of the 17 pulsars. We demonstrate the effectiveness of our methods by applying them to a component of the Lorenz and R\"ossler attractors that were sampled with similar cadence to the pulsar time series. Our measurements of correlation dimension and Lyapunov exponent show that the underlying behaviour appears to be driven by a strange attractor with approximately three governing non-linear differential equations. This is particularly apparent in the case of PSR B1828$-$11 where a correlation dimension of 2.06\pm0.03 and a Lyapunov exponent of $(4.0\pm0.3)\times10^{-4}$ inverse days were measured. These results provide an additional diagnostic for testing future models of this behaviour.Comment: 15 pages, 18 figures, 2 tables, Accepted to MNRA

Using large-scale perturbations in gene network reconstruction

Background: Recent analysis of the yeast gene network shows that most genes have few inputs, indicating that enumerative gene reconstruction methods are both useful and computationally feasible. A simple enumerative reconstruction method based on a discrete dynamical system model is used to study how microarray experiments involving modulated global perturbations can be designed to obtain reasonably accurate reconstructions. The method is tested on artificial gene networks with biologically realistic in/out degree characteristics.Results: It was found that a relatively small number of perturbations significantly improve inference accuracy, particularly for low-order inputs of one or two genes. The perturbations themselves should alter the expression level of approximately 50-60% of the genes in the network.Conclusions: Time-series obtained from perturbations are a common form of expression data. This study illustrates how gene networks can be significantly reconstructed from such time-series while requiring only a relatively small number of calibrated perturbations, even for large networks, thus reducing experimental costs

Symmetry of anomalous dimension matrices explained

In a previous paper, one of us pointed out that the anomalous dimension matrices for all physical processes that have been calculated to date are complex symmetric, if stated in an orthonormal basis. In this paper we prove this fact and show that it is only true in a subset of all possible orthonormal bases, but that this subset is the natural one to use for physical calculations.Comment: 4 page

Breakdown of QCD coherence ?

We reconsider the calculation of a non-global QCD observable and find the possible breakdown of QCD coherence. This breakdown arises as a result of wide angle soft gluon emission developing a sensitivity to emission at small angles and it leads to the appearance of super-leading logarithms. We use the `gaps between jets' cross-section as a concrete example and illustrate that the new logarithms are intimately connected with the presence of Coulomb gluon contributions. Numerical estimates of their potential phenomenological significance are presented.Comment: 7 pages, 3 figures; proceedings of Workshop on Diffraction in High-Energy Physics - DIFFRACTION 2006, Sep. 5-10 2006, Adamantas, Milos island, Greec

Under-dominance constrains the evolution of negative autoregulation in diploids

Regulatory networks have evolved to allow gene expression to rapidly track changes in the environment as well as to buffer perturbations and maintain cellular homeostasis in the absence of change. Theoretical work and empirical investigation in Escherichia coli have shown that negative autoregulation confers both rapid response times and reduced intrinsic noise, which is reflected in the fact that almost half of Escherichia coli transcription factors are negatively autoregulated. However, negative autoregulation is rare amongst the transcription factors of Saccharomyces cerevisiae. This difference is surprising because E. coli and S. cerevisiae otherwise have similar profiles of network motifs. In this study we investigate regulatory interactions amongst the transcription factors of Drosophila melanogaster and humans, and show that they have a similar dearth of negative autoregulation to that seen in S. cerevisiae. We then present a model demonstrating that this stiking difference in the noise reduction strategies used amongst species can be explained by constraints on the evolution of negative autoregulation in diploids. We show that regulatory interactions between pairs of homologous genes within the same cell can lead to under-dominance - mutations which result in stronger autoregulation, and decrease noise in homozygotes, paradoxically can cause increased noise in heterozygotes. This severely limits a diploid's ability to evolve negative autoregulation as a noise reduction mechanism. Our work offers a simple and general explanation for a previously unexplained difference between the regulatory architectures of E. coli and yeast, Drosophila and humans. It also demonstrates that the effects of diploidy in gene networks can have counter-intuitive consequences that may profoundly influence the course of evolution

The Predicted Binding Site and Dynamics of Peptide Inhibitors to the Methuselah GPCR from Drosophila melanogaster

Peptide inhibitors of Methuselah (Mth), a G protein-coupled receptor (GPCR), were reported that can extend the life span of Drosophila melanogaster. Mth is a class B GPCR, which is characterized by a large, N-terminal ectodomain that is often involved with ligand recognition. The crystal structure of the Mth ectodomain, which binds to the peptide inhibitors with high affinity, was previously determined. Here we report the predicted structures for RWR motif peptides in complex with the Mth ectodomain. We studied representatives of both Pro-class and Arg-class RWR motif peptides and identified ectodomain residues Asp139, Phe130, Asp127, and Asp78 as critical in ligand binding. To validate these structures, we predicted the effects of various ligand mutations on the structure and binding to Mth. The binding of five mutant peptides to Mth was characterized experimentally by surface plasmon resonance, revealing measured affinities that are consistent with predictions. The electron density map calculated from our MD structure compares well with the experimental map of a previously determined peptide/Mth crystal structure and could be useful in refining the current low-resolution data. The elucidation of the ligand binding site may be useful in analyzing likely binding sites in other class B GPCRs

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