EARLY FLOWERING4 recruitment of EARLY FLOWERING3 in the nucleus sustains the Arabidopsis circadian clock

The plant circadian clock is proposed to be a network of several interconnected feedback loops, and loss of any component leads to changes in oscillator speed. We previously reported that Arabidopsis thaliana EARLY FLOWERING4 (ELF4) is required to sustain this oscillator and that the elf4 mutant is arrhythmic. This phenotype is shared with both elf3 and lux. Here, we show that overexpression of either ELF3 or LUX ARRHYTHMO (LUX) complements the elf4 mutant phenotype. Furthermore, ELF4 causes ELF3 to form foci in the nucleus. We used expression data to direct a mathematical position of ELF3 in the clock network. This revealed direct effects on the morning clock gene PRR9, and we determined association of ELF3 to a conserved region of the PRR9 promoter. A cis-element in this region was suggestive of ELF3 recruitment by the transcription factor LUX, consistent with both ELF3 and LUX acting genetically downstream of ELF4. Taken together, using integrated approaches, we identified ELF4/ELF3 together with LUX to be pivotal for sustenance of plant circadian rhythms. © 2012 American Society of Plant Biologists.

Investigation of the poro-elastic response of seabed to solitary

A numerical model is established and validated to study the behavior of porous seabed under solitary wave propagation. Using Biot's poro-elastic theory, the problem is formulated as a two dimensional plane strain problem, and it is modelled using the Finite Element Method. The responses due to the solitary wave are compared with those of linear waves of the same height. It is found that regardless of the wave period, stresses due to solitary waves are generally larger. This indicates a higher potential for shear failure at the seabed under solitary waves. Implications on liquefaction need further investigation. Copyright © 2012 by the International Society of Offshore and Polar Engineers (ISOPE).

Numerical investigation of the active role of the actin cytoskeleton in the compression resistance of cells.

Numerous in-vitro studies have established that cells react to their physical environment and to applied mechanical loading. However, the mechanisms underlying such phenomena are poorly understood. Previous modelling of cell compression considered the cell as a passive homogenous material, requiring an artificial increase in the stiffness of spread cells to replicate experimentally measured forces. In this study, we implement a fully 3D active constitutive formulation that predicts the distribution, remodelling, and contractile behaviour of the cytoskeleton. Simulations reveal that polarised and axisymmetric spread cells contain stress fibres which form dominant bundles that are stretched during compression. These dominant fibres exert tension; causing an increase in computed compression forces compared to round cells. In contrast, fewer stress fibres are computed for round cells and a lower resistance to compression is predicted. The effect of different levels of cellular contractility associated with different cell phenotypes is also investigated. Highly contractile cells form more dominant circumferential stress fibres and hence provide greater resistance to compression. Computed predictions correlate strongly with published experimentally observed trends of compression resistance as a function of cellular contractility and offer an insight into the link between cell geometry, stress fibre distribution and contractility, and cell deformability. Importantly, it is possible to capture the behaviour of both round and spread cells using a given, unchanged set of material parameters for each cell type. Finally, it is demonstrated that stress distributions in the cell cytoplasm and nucleus computed using the active formulation differ significantly from those computed using passive material models.

Vowel normalisation: Time-domain processing of the internal dynamics of speech

Human listeners can identify vowels regardless of speaker size, although the sound waves for an adult and a child speaking the ’same’ vowel would differ enormously. The differences are mainly due to the differences in vocal tract length (VTL) and glottal pulse rate (GPR) which are both related to body size. Automatic speech recognition machines are notoriously bad at understanding children if they have been trained on the speech of an adult. In this paper, we propose that the auditory system adapts its analysis of speech sounds, dynamically and automatically to the GPR and VTL of the speaker on a syllable-to-syllable basis. We illustrate how this rapid adaptation might be performed with the aid of a computational version of the auditory image model, and we propose that an auditory preprocessor of this form would improve the robustness of speech recognisers.

Cellular contractility and substrate elasticity: A numerical investigation of the actin cytoskeleton and cell adhesion

Numerous experimental studies have established that cells can sense the stiffness of underlying substrates and have quantified the effect of substrate stiffness on stress fibre formation, focal adhesion area, cell traction, and cell shape. In order to capture such behaviour, the current study couples a mixed mode thermodynamic and mechanical framework that predicts focal adhesion formation and growth with a material model that predicts stress fibre formation, contractility, and dissociation in a fully 3D implementation. Simulations reveal that SF contractility plays a critical role in the substrate-dependent response of cells. Compliant substrates do not provide sufficient tension for stress fibre persistence, causing dissociation of stress fibres and lower focal adhesion formation. In contrast, cells on stiffer substrates are predicted to contain large amounts of dominant stress fibres. Different levels of cellular contractility representative of different cell phenotypes are found to alter the range of substrate stiffness that cause the most significant changes in stress fibre and focal adhesion formation. Furthermore, stress fibre and focal adhesion formation evolve as a cell spreads on a substrate and leading to the formation of bands of fibres leading from the cell periphery over the nucleus. Inhibiting the formation of FAs during cell spreading is found to limit stress fibre formation. The predictions of this mutually dependent material-interface framework are strongly supported by experimental observations of cells adhered to elastic substrates and offer insight into the inter-dependent biomechanical processes regulating stress fibre and focal adhesion formation. © 2013 Springer-Verlag Berlin Heidelberg.