New tools for self-organised pattern formation

Position-dependent gene expression is a critical aspect of the development and behaviour of multicellular organisms. It requires a complex series of interactions to occur between different cell types in addition to intracellular signalling cascades. We used Escherichia coli to study the properties of an artificial signalling system at the interface between two expanding cell populations. We genetically engineered one population to produce a diffusible acyl-homoserine lactone (AHL) signal, and another population to respond to it. Our experiments demonstrate how such a signal can be used to reproducibly generate simple visible patterns with high accuracy in swimming agar. The producing and responding cassettes of two such signalling systems can be linked to produce a symmetric interface for bidirectional communication that can be used to visualise molecular logic. Intracellular feedback between these two cassettes would then create a framework for self-organised patterning of higher complexity. Adapting the experiments of Basu et al. (Basu et al., 2005) using cell motility, rather than a differential response to AHL concentrations as a way to define zones of response, we noted how the interaction of sender and receiver cell populations on a swimming plate could lead to complex pattern formation. Equipping highly motile strains such as E. coli MC1000 with AHL-mediated auto-inducing systems based on Vibrio fischeri luxI/luxR and Pseudomonas aeruginosa lasI/lasR cassettes would allow the amplification of a response to an AHL signal and its propagation. We designed and synthesised codon-optimised auto-inducing luxI/R and lasI/R cassettes as optimal gene expression is crucial for the generation of robust patterns. We still have to complete and test the entire genetic circuitry, although by modelling the system we were able to demonstrate its feasibility. © 2007 The Institution of Engineering and Technology.

Computer generated hologram with geometric occlusion using GPU-accelerated depth buffer rasterization for three-dimensional display

We present a method of rapidly producing computer-generated holograms that exhibit geometric occlusion in the reconstructed image. Conceptually, a bundle of rays is shot from every hologram sample into the object volume.We use z buffering to find the nearest intersecting object point for every ray and add its complex field contribution to the corresponding hologram sample. Each hologram sample belongs to an independent operation, allowing us to exploit the parallel computing capability of modern programmable graphics processing units (GPUs). Unlike algorithms that use points or planar segments as the basis for constructing the hologram, our algorithm's complexity is dependent on fixed system parameters, such as the number of ray-casting operations, and can therefore handle complicated models more efficiently. The finite number of hologram pixels is, in effect, a windowing function, and from analyzing the Wigner distribution function of windowed free-space transfer function we find an upper limit on the cone angle of the ray bundle. Experimentally, we found that an angular sampling distance of 0:01' for a 2:66' cone angle produces acceptable reconstruction quality. © 2009 Optical Society of America.

Geometric optimization methods for the analysis of gene expression data

DNA microarrays provide such a huge amount of data that unsupervised methods are required to reduce the dimension of the data set and to extract meaningful biological information. This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data. The paper first presents an overview of the most popular algorithms to perform ICA. These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed. This study indicates that ICA significantly outperforms Principal Component Analysis (PCA).

Pattern formation and spatial solitons in bistable liquid-crystal microcavities

We report on spatial pattern formation, and appearances of 'optical bullet holes' in single-mode microcavities that are filled with liquid-crystals, when pumped above the cavity resonance frequency. These phenomena only occur beyond the bistability threshold. ©2002 Optical Society of America.