MOTIFATOR: detection and characterization of regulatory motifs using prokaryote transcriptome data

Summary: Unraveling regulatory mechanisms (e.g. identification of motifs in cis-regulatory regions) remains a major challenge in the analysis of transcriptome experiments. Existing applications identify putative motifs from gene lists obtained at rather arbitrary cutoff and require additional manual processing steps. Our standalone application MOTIFATOR identifies the most optimal parameters for motif discovery and creates an interactive visualization of the results. Discovered putative motifs are functionally characterized, thereby providing valuable insight in the biological processes that could be controlled by the motif.

Semiclassical expansion of parametric correlation functions of the quantum time delay

We derive semiclassical periodic orbit expansions for a correlation function of the Wigner time delay. We consider the Fourier transform of the two-point correlation function, the form factor $K(\tau,x,y,M)$, that depends on the number of open channels $M$, a non-symmetry breaking parameter $x$, and a symmetry breaking parameter $y$. Several terms in the Taylor expansion about $\tau=0$, which depend on all parameters, are shown to be identical to those obtained from Random Matrix Theory.Comment: 21 pages, no figure

Mechanism of Transcription Activation at the comG Promoter by the Competence Transcription Factor ComK of Bacillus subtilis

The development of genetic competence in Bacillus subtilis is regulated by a complex signal transduction cascade, which results in the synthesis of the competence transcription factor, encoded by comK. ComK is required for the transcription of the late competence genes that encode the DNA binding and uptake machinery and of genes required for homologous recombination. In vivo and in vitro experiments have shown that ComK is responsible for transcription activation at the comG promoter. In this study, we investigated the mechanism of this transcription activation. The intrinsic binding characteristics of RNA polymerase with and without ComK at the comG promoter were determined, demonstrating that ComK stabilizes the binding of RNA polymerase to the comG promoter. This stabilization probably occurs through interactions with the upstream DNA, since a deletion of the upstream DNA resulted in an almost complete abolishment of stabilization of RNA polymerase binding. Furthermore, a strong requirement for the presence of an extra AT box in addition to the common ComK-binding site was shown. In vitro transcription with B. subtilis RNA polymerase reconstituted with wild-type -subunits and with C-terminal deletion mutants of the -subunits was performed, demonstrating that these deletions do not abolish transcription activation by ComK. This indicates that ComK is not a type I activator. We also show that ComK is not required for open complex formation. A possible mechanism for transcription activation is proposed, implying that the major stimulatory effect of ComK is on binding of RNA polymerase.Peer reviewe

Dynamic sporulation gene co-expression networks for Bacillus subtilis 168 and the food-borne isolate Bacillus amyloliquefaciens:a transcriptomic model

Sporulation is a survival strategy, adapted by bacterial cells in response to harsh environmental adversities. The adaptation potential differs between strains and the variations may arise from differences in gene regulation. Gene networks are a valuable way of studying such regulation processes and establishing associations between genes. We reconstructed and compared sporulation gene co-expression networks (GCNs) of the model laboratory strain Bacillus subtilis 168 and the food-borne industrial isolate Bacillus amyloliquefaciens. Transcriptome data obtained from samples of six stages during the sporulation process were used for network inference. Subsequently, a gene set enrichment analysis was performed to compare the reconstructed GCNs of B. subtilis 168 and B. amyloliquefaciens with respect to biological functions, which showed the enriched modules with coherent functional groups associated with sporulation. On basis of the GCNs and time-evolution of differentially expressed genes, we could identify novel candidate genes strongly associated with sporulation in B. subtilis 168 and B. amyloliquefaciens. The GCNs offer a framework for exploring transcription factors, their targets, and co-expressed genes during sporulation. Furthermore, the methodology described here can conveniently be applied to other species or biological processes

Conceptual spatial representations for indoor mobile robots

We present an approach for creating conceptual representations of human-made indoor environments using mobile robots. The concepts refer to spatial and functional properties of typical indoor environments. Following findings in cognitive psychology, our model is composed of layers representing maps at different levels of abstraction. The complete system is integrated in a mobile robot endowed with laser and vision sensors for place and object recognition. The system also incorporates a linguistic framework that actively supports the map acquisition process, and which is used for situated dialogue. Finally, we discuss the capabilities of the integrated system

Premelting of Thin Wires

Recent work has raised considerable interest on the nature of thin metallic wires. We have investigated the melting behavior of thin cylindrical Pb wires with the axis along a (110) direction, using molecular dynamics and a well-tested many-body potential. We find that---in analogy with cluster melting---the melting temperature $T_m (R)$ of a wire with radius $R$ is lower than that of a bulk solid, $T_m^b$, by $T_m (R) = T_m^b -c/R$. Surface melting effects, with formation of a thin skin of highly diffusive atoms at the wire surface, is observed. The diffusivity is lower where the wire surface has a flat, local (111) orientation, and higher at (110) and (100) rounded areas. The possible relevance to recent results on non-rupturing thin necks between an STM tip and a warm surface is addressed.Comment: 10 pages, 4 postscript figures are appended, RevTeX, SISSA Ref. 131/94/CM/S

A contiuum model for low temperature relaxation of crystal steps

High and low temperature relaxation of crystal steps are described in a unified picture, using a continuum model based on a modified expression of the step free energy. Results are in agreement with experiments and Monte Carlo simulations of step fluctuations and monolayer cluster diffusion and relaxation. In an extended model where mass exchange with neighboring terraces is allowed, step transparency and a low temperature regime for unstable step meandering are found.Comment: Submitted to Phys.Rev.Let

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks

Summary: SpotXplore is a plugin for Cytoscape for extraction and visualization of differentially expressed subnetworks (hotspots) from gene networks. The hotspot-based visualization approach enables interactive exploration of regulatory interactions in differentially expressed gene sets, and it allows a researcher to explore gene expression in direct relation to the affected cellular gene network. The hotspots provide a view beyond the commonly used metabolic pathways and gene ontologies