Biomolecules at phase boundaries

Experimental and theoretical studies of biomolecules at water surfaces and metal surfaces are presented. We studied lecithin molecules (monolayers) and phospholipase A₂ at a water surface with molecular dynamics (MD) simulations. Results were compared with those obtained for a pure water surface. We also studied amino acids at a TiO₂ surface with thermal desorption spectroscopy in the presence and absence of water.     

Swimming in circles: motion of bacteria near solid boundaries

Near a solid boundary, Escherichia coli swims in clockwise circular motion. We provide a hydrodynamic model for this behavior. We show that circular trajectories are natural consequences of force-free and torque-free swimming and the hydrodynamic interactions with the boundary, which also leads to a hydrodynamic trapping of the cells close to the surface. We compare the results of the model with experimental data and obtain reasonable agreement. In particular, the radius of curvature of the trajectory is observed to increase with the length of the bacterium body.     

Biological computation of image motion from flows over boundaries.

A theory of early motion processing in the human and primate visual system is presented which is based on the idea that spatio-temporal retinal image data is represented in primary visual cortex by a truncated 3D Taylor expansion that we refer to as a jet vector. This representation allows all the concepts of differential geometry to be applied to the analysis of visual information processing. We show in particular how the generalised Stokes theorem can be used to move from the calculation of derivatives of image brightness at a point to the calculation of image brightness differences on the boundary of a volume in space-time and how this can be generalised to apply to integrals of products of derivatives. We also provide novel interpretations of the roles of direction selective, bi-directional and pan-directional cells and of type I and type II cells in V5/MT.     

Structure-from-motion based on information at surface boundaries

Existing computational models of structurefrom-motion — the appearance of three-dimensional motion generated by moving two-dimensional patterns — are all based on variations of optical flow or feature point correspondence within the interior of single objects. Three separate phenomena provide strong evidence that in human vision, structure-from-motion is significantly affected by surface boundary cues. In the first, a rotating cylinder is seen, though no variation in optical flow exists across the apparent cylinder. In the second, the shape of the bounding contour of a moving pattern dominates the actual differential motion within the pattern. In the third, the appearance of independently moving objects changes significantly when the boundary between them becomes indistinct. We describe a simple computational model sufficient to account for these effects. The model is based on qualitative constraints relating possible object motions to patterns of flow, together with an understanding of the patterns of flow that can be discriminated in practice.     

Electrostatic forces at helix-coil boundaries in DNA

The Tm of internal loop-forming (dA.dT)N domains in pBR322 DNA has been measured over a tenfold range of [Na+]. The slopes SN = dTm/d log [Na+] are linear and decrease in magnitude with decreasing loop size N, signaling a reduction in Na+ released during the transition of these domains to the coil state. Values of SN decrease linearly with increasing N-1 in accordance with the expectation of a simple model for the occurrence of a gradient of long-range electrostatic forces at helix-coil boundaries, and extrapolate almost precisely to the value of S infinity observed for (dA.dT) infinity. These results indicate (1) less counterion is released per phosphate residue from the finite loop than from the infinite-sized loop, and (2) the difference in binding is constant for each boundary formed and independent of the size of the loop within the range examined: approximately 350 base pair (bp) greater than N greater than 71 bp. The slope of the dependence of SN on N-1 indicates the region of higher charge density at the boundary extends at least 18 A into the coil and probably 40-50 A before dropping to a value characteristic of the unperturbed coil. The free energy for excess counterion binding at boundaries can be expressed by -delta G/RT = 10.47 log[Na+] + 5.234 When the loop entropy function in a statistical mechanical algorithm for the dissociation of DNA is weighted by this quantity, calculated Tm are seen to vary by only +/- 0.09 degrees C from observed.     

Reduced junctional permeability at interrhombomeric boundaries.

Intercellular communication is considered to have a role during pattern specification processes in early embryonic development. This report analyzes the changing gap junctional communication properties of chick neuroepithelial cells depending on their position relative to the segmental partitions of the rhombencephalon. Intercellular electrical coupling and dye transfer were studied with microelectrode techniques. Neuroepithelial cells were electrically coupled irrespective of their location relative to interneuromeric boundaries. Iontophoretic injection of biocytin or Lucifer Yellow into single cells inside the rhombomeres was followed by transjunctional diffusion to the surrounding cells. In contrast, dye transfer was strictly limited when the diffusion zone contacted the cells forming the interneuromeric limits. Label injected into the boundary cells did not spread to other cells at all. Avian interrhombomeric boundaries are thus sites of reduced junctional permeability during early morphogenesis.     

Two models of the recognition and detection of texture-defined letters compared

We quantified texture segregation by measuring psychophysically the percentage correct detection scores for each of a set of 10 texture-defined (TD) letters using the temporal two-alternative forced choice method, and at the same time quantified spatial discrimination of the TD form of measuring psychophysically the percentage correct letter recognition scores for the 10 letters. Ten levels of task difficulty were created by adding noise dots to the texture patterns. The resulting psychophysical data were used to test and compare models of the detection and recognition of texture-defined letters. Each model comprised a sequence of physiologically plausible stages in early visual processing. Each had the same first, second and third stages, namely linear orientation-tuned spatial filters followed by rectification and smoothing. Model 1 had only one non-linear stage. Model 2 had two non-linear stages. In model 2 the second non-linear stage was cross-orientation inhibition. This second non-linear stage enhanced the texture borders by, in effect, comparing textures at different locations in the texture pattern. In both models, the last stage modelled either letter detection or letter recognition. Letter recognition was modelled as follows. We passed a given letter stimulus through the first several stages of a model and, in 10 separate calculations, cross-correlated the output with a template of each of the 10 letters. From these 10 correlations we obtained a predicted percentage correct letter recognition score for the given letter stimulus. The predicted recognition scores closely agreed with the experimental data at all 10 levels of task difficulty for model 2, but not for model 1. We conclude that a borderenhancing algorithm is necessary to model letter recognition. The letter-detection algorithm modelled detection of part of a letter (a single letter stroke) in terms of the signal-to-noise ratio of a letter-segment detector. The predicted letter detection scores fitted the data closely for both models.     

Regulating mechanical tension at compartment boundaries in Drosophila

During animal development, cells with similar function and fate often stay together and sort out from cells with different fates. In Drosophila wing imaginal discs, cells of anterior and posterior fates are separated by a straight compartment boundary. Separation of anterior and posterior cells requires the homeodomain-containing protein Engrailed, which is expressed in posterior cells. Engrailed induces the expression of the short-range signaling molecule Hedgehog in posterior cells and confines Hedgehog signal transduction to anterior cells. Transduction of the Hedgehog signal in anterior cells is required for the separation of anterior and posterior cells. Previous work showed that this separation of cells involves a local increase in mechanical tension at cell junctions along the compartment boundary. However, how mechanical tension was locally increased along the compartment boundary remained unknown. A recent paper now shows that the difference in Hedgehog signal transduction between anterior and posterior cells is necessary and sufficient to increase mechanical tension. The local increase in mechanical tension biases junctional rearrangements during cell intercalations to maintain the straight shape of the compartment boundary. These data highlight how developmental signals can generate patterns of mechanical tension important for tissue organization.     

Partitioning of lipids at domain boundaries in model membranes

Line-active molecules (“linactants”) that bind to the boundary interface between different fluid lipid domains in membranes have a strong potential as regulators of the lateral heterogeneity that is important for many biological processes. Here, we use molecular dynamics simulations in combination with a coarse-grain model that retains near-atomic resolution to identify lipid species that can act as linactants in a model membrane that is segregated into two lipid domains of different fluidity. Our simulations predict that certain hybrid saturated/unsaturated chain lipids can bind to the interface and lower the line tension, whereas cone-shaped lysolipids have a less pronounced effect.     

Stopped at the border: boundaries and insulators.

Boundaries in chromatin are often marked by the presence of insulator elements. New results in Drosophila have identified an insulator with a proven boundary function essential for development. Other studies suggest a connection between the activity of some insulators and Drosophila trithorax-Group and Polycomb-Group genes. Several examples of vertebrate insulators have now been found; their locations suggest important boundary functions. Enhancer-blocking studies in oocytes and position-effect studies in transformed cells shed new light on insulator mechanisms.     

Compartment boundaries: at the edge of development.

Compartment boundaries have fascinated biologists for more than 25 years. We now know that these boundaries play important roles in pattern formation, yet how these boundaries are established during development remained a mystery. Here, we describe the exciting progress that has been made recently towards elucidating the mechanisms of boundary formation.     

Assortative mating by white-crowned sparrows at song dialect boundaries

We tested the hypothesis that female Nuttall's white-crowned sparrows (Zonotrichia leucophrys nuttalli) mate assortatively with males from the same dialect population. Young birds of both sexes learn their natal dialect during an early sensitive period, and for females, this early experience may be the basis of future mate choice. A total of 32 female sparrows were mist-netted for three experiments at or near dialect boundaries just inside the Limantour, Drake and Clear dialect populations in Marin Co., California. The mates of all captured females sang the home dialect. All females were implanted with testosterone and maintained in captivity. Of the females which began to sing, 25 sang recognizable white-crowned sparrow songs. Of those 25 females, 24 had mated assortatively, thus supporting the assortative mating hypothesis.     

Mapping space by NMR using susceptibility changes at phase boundaries

A technique for differentiating high-resolution NMR signals from different regions of small objects is outlined and some initial results on model systems are given. This method uses inorganic paramagnetic or diamagnetic ions to create magnetic field gradients at phase boundaries.