Histone modifications within the human X centromere region.

Human centromeres are multi-megabase regions of highly ordered arrays of alpha satellite DNA that are separated from chromosome arms by unordered alpha satellite monomers and other repetitive elements. Complexities in assembling such large repetitive regions have limited detailed studies of centromeric chromatin organization. However, a genomic map of the human X centromere has provided new opportunities to explore genomic architecture of a complex locus. We used ChIP to examine the distribution of modified histones within centromere regions of multiple X chromosomes. Methylation of H3 at lysine 4 coincided with DXZ1 higher order alpha satellite, the site of CENP-A localization. Heterochromatic histone modifications were distributed across the 400-500 kb pericentromeric regions. The large arrays of alpha satellite and gamma satellite DNA were enriched for both euchromatic and heterochromatic modifications, implying that some pericentromeric repeats have multiple chromatin characteristics. Partial truncation of the X centromere resulted in reduction in the size of the CENP-A/Cenp-A domain and increased heterochromatic modifications in the flanking pericentromere. Although the deletion removed approximately 1/3 of centromeric DNA, the ratio of CENP-A to alpha satellite array size was maintained in the same proportion, suggesting that a limited, but defined linear region of the centromeric DNA is necessary for kinetochore assembly. Our results indicate that the human X centromere contains multiple types of chromatin, is organized similarly to smaller eukaryotic centromeres, and responds to structural changes by expanding or contracting domains.

Cysteine proteinase-1 and cut protein isoform control dendritic innervation of two distinct sensory fields by a single neuron.

Dendrites often exhibit structural changes in response to local inputs. Although mechanisms that pattern and maintain dendritic arbors are becoming clearer, processes regulating regrowth, during context-dependent plasticity or after injury, remain poorly understood. We found that a class of Drosophila sensory neurons, through complete pruning and regeneration, can elaborate two distinct dendritic trees, innervating independent sensory fields. An expression screen identified Cysteine proteinase-1 (Cp1) as a critical regulator of this process. Unlike known ecdysone effectors, Cp1-mutant ddaC neurons pruned larval dendrites normally but failed to regrow adult dendrites. Cp1 expression was upregulated/concentrated in the nucleus during metamorphosis, controlling production of a truncated Cut homeodomain transcription factor. This truncated Cut, but not the full-length protein, allowed Cp1-mutant ddaC neurons to regenerate higher-order adult dendrites. These results identify a molecular pathway needed for dendrite regrowth after pruning, which allows the same neuron to innervate distinct sensory fields.

Specialized motor-driven dusp1 expression in the song systems of multiple lineages of vocal learning birds.

Mechanisms for the evolution of convergent behavioral traits are largely unknown. Vocal learning is one such trait that evolved multiple times and is necessary in humans for the acquisition of spoken language. Among birds, vocal learning is evolved in songbirds, parrots, and hummingbirds. Each time similar forebrain song nuclei specialized for vocal learning and production have evolved. This finding led to the hypothesis that the behavioral and neuroanatomical convergences for vocal learning could be associated with molecular convergence. We previously found that the neural activity-induced gene dual specificity phosphatase 1 (dusp1) was up-regulated in non-vocal circuits, specifically in sensory-input neurons of the thalamus and telencephalon; however, dusp1 was not up-regulated in higher order sensory neurons or motor circuits. Here we show that song motor nuclei are an exception to this pattern. The song nuclei of species from all known vocal learning avian lineages showed motor-driven up-regulation of dusp1 expression induced by singing. There was no detectable motor-driven dusp1 expression throughout the rest of the forebrain after non-vocal motor performance. This pattern contrasts with expression of the commonly studied activity-induced gene egr1, which shows motor-driven expression in song nuclei induced by singing, but also motor-driven expression in adjacent brain regions after non-vocal motor behaviors. In the vocal non-learning avian species, we found no detectable vocalizing-driven dusp1 expression in the forebrain. These findings suggest that independent evolutions of neural systems for vocal learning were accompanied by selection for specialized motor-driven expression of the dusp1 gene in those circuits. This specialized expression of dusp1 could potentially lead to differential regulation of dusp1-modulated molecular cascades in vocal learning circuits.

The past, present, and future of human centromere genomics.

The centromere is the chromosomal locus essential for chromosome inheritance and genome stability. Human centromeres are located at repetitive alpha satellite DNA arrays that compose approximately 5% of the genome. Contiguous alpha satellite DNA sequence is absent from the assembled reference genome, limiting current understanding of centromere organization and function. Here, we review the progress in centromere genomics spanning the discovery of the sequence to its molecular characterization and the work done during the Human Genome Project era to elucidate alpha satellite structure and sequence variation. We discuss exciting recent advances in alpha satellite sequence assembly that have provided important insight into the abundance and complex organization of this sequence on human chromosomes. In light of these new findings, we offer perspectives for future studies of human centromere assembly and function.

Experience of using a CFD code for estimating the noise generated by gusts along the sun-roof of a car

The problem to be examined here is the fluctuating pressure distribution along the open cavity of the sun-roof at the top of a car compartment due to gusts passing over the sun-roof. The aim of this test is to investigate the capability of a typical commercial CFD package, PHOENICS, in recognising pressure fluctuations occurring in an important automotive industrial problem. In particular to examine the accuracy of transporting pulsatory gusts traveling along the main flow through the use of finite volume methods with higher order schemes in the numercial solutins of the unsteady compressible Navier-Stokes equations. The Helmholtz equation is used to solve the sound distribution inside the car compartment, resulting from the externally induced fluctuations.

On information rates of time-varying fading channels modeled as finite-state Markov channels

We study information rates of time-varying flat-fading channels (FFC) modeled as finite-state Markov channels (FSMC). FSMCs have two main applications for FFCs: modeling channel error bursts and decoding at the receiver. Our main finding in the first application is that receiver observation noise can more adversely affect higher-order FSMCs than lower-order FSMCs, resulting in lower capacities. This is despite the fact that the underlying higher-order FFC and its corresponding FSMC are more predictable. Numerical analysis shows that at low to medium SNR conditions (SNR lsim 12 dB) and at medium to fast normalized fading rates (0.01 lsim fDT lsim 0.10), FSMC information rates are non-increasing functions of memory order. We conclude that BERs obtained by low-order FSMC modeling can provide optimistic results. To explain the capacity behavior, we present a methodology that enables analytical comparison of FSMC capacities with different memory orders. We establish sufficient conditions that predict higher/lower capacity of a reduced-order FSMC, compared to its original high-order FSMC counterpart. Finally, we investigate the achievable information rates in FSMC-based receivers for FFCs. We observe that high-order FSMC modeling at the receiver side results in a negligible information rate increase for normalized fading rates fDT lsim 0.01.

Shark personalities? Repeatability of social network traits in a widely distributed predatory fish. Behavioral Ecology and Sociobiology, 68, 1995-2003.

Interest in animal personalities has generated a burgeoning literature on repeatability in individual traits such as boldness or exploration through time or across different contexts. Yet, repeatability can be influenced by the interactive social strategies of individuals, for example, consistent inter-individual variation in aggression is well documented. Previous work has largely focused on the social aspects of repeatability in animal behaviour by testing individuals in dyadic pairings. Under natural conditions, individuals interact in a heterogeneous polyadic network. However, the extent to which there is repeatability of social traits at this higher order network level remains unknown. Here, we provide the first empirical evidence of consistent and repeatable animal social networks. Using a model species of shark, a taxonomic group in which repeatability in behaviour has yet to be described, we repeatedly quantified the social networks of ten independent shark groups across different habitats, testing repeatability in individual network position under changing environments. To understand better the mechanisms behind repeatable social behaviour, we also explored the coupling between individual preferences for specific group sizes and social network position. We quantify repeatability in sharks by demonstrating that despite changes in aggregation measured at the group level, the social network position of individuals is consistent across treatments. Group size preferences were found to influence the social network position of individuals in small groups but less so for larger groups suggesting network structure, and thus, repeatability was driven by social preference over aggregation tendency.

Triply differential single ionization cross sections in coplanar and non-coplanar geometry for fast heavy ion-atom collisions

We have performed a kinematically complete experiment and calculations on single ionization in 100 MeV/amu C6+ + He collisions. For electrons ejected into the scattering plane (defined by the initial and final projectile momentum vectors) our first- and higher-order calculations are in good agreement with the data. In the plane perpendicular to the scattering plane and containing the initial projectile axis a strong forward-backward asymmetry is observed. In this plane both the first-order and the higher-order calculations do not provide good agreement neither with the data nor amongst each other.

A novel approach to dynamic modelling of polymer extrusion for improved process control

Polymer extrusion is a complex process and the availability of good dynamic models is key for improved system operation. Previous modelling attempts have failed adequately to capture the non-linearities of the process or prove too complex for control applications. This work presents a novel approach to the problem by the modelling of extrusion viscosity and pressure, adopting a grey box modelling technique that combines mechanistic knowledge with empirical data using a genetic algorithm approach. The models are shown to outperform those of a much higher order generated by a conventional black box technique while providing insight into the underlying processes at work within the extruder.

Green function for the diffusion limit of one-dimensional continuous time random walks

It is shown how the fractional probability density diffusion equation for the diffusion limit of one-dimensional continuous time random walks may be derived from a generalized Markovian Chapman-Kolmogorov equation. The non-Markovian behaviour is incorporated into the Markovian Chapman-Kolmogorov equation by postulating a Levy like distribution of waiting times as a kernel. The Chapman-Kolmogorov equation so generalised then takes on the form of a convolution integral. The dependence on the initial conditions typical of a non-Markovian process is treated by adding a time dependent term involving the survival probability to the convolution integral. In the diffusion limit these two assumptions about the past history of the process are sufficient to reproduce anomalous diffusion and relaxation behaviour of the Cole-Cole type. The Green function in the diffusion limit is calculated using the fact that the characteristic function is the Mittag-Leffler function. Fourier inversion of the characteristic function yields the Green function in terms of a Wright function. The moments of the distribution function are evaluated from the Mittag-Leffler function using the properties of characteristic functions and a relation between the powers of the second moment and higher order even moments is derived. (C) 2004 Elsevier B.V. All rights reserved.

The pathobiology of the septin gene family.

Septins are an evolutionarily conserved group of GTP-binding and filament-forming proteins that belong to the large superclass of P-loop GTPases. While originally discovered in yeast as cell division cycle mutants with cytokinesis defects, they are now known to have diverse cellular roles which include polarity determination, cytoskeletal reorganization, membrane dynamics, vesicle trafficking, and exocytosis. Septin proteins form homo- and hetero-oligomeric polymers which can assemble into higher-order filaments. They are also known to interact with components of the cytoskeleton, ie actin and tubulin. The precise role of GTP binding is not clear but a current model suggests that it is associated with conformational changes which alter binding to other proteins. There are at least 12 human septin genes, and although information on expression patterns is limited, most undergo complex alternative splicing with some degree of tissue specificity. Nevertheless, an increasing body of data implicates the septin family in the pathogenesis of diverse disease states including neoplasia, neurodegenerative conditions, and infections. Here the known biochemical properties of mammalian septins are reviewed in the light of the data from yeast and other model organisms. The data implicating septins in human disease are considered and a model linking these data is proposed. It is posited that septins can act as regulatable scaffolds where the stoichiometry of septin associations, modifications, GTP status, and the interactions with other proteins allow the regulation of key cellular processes including polarity determination. Derangements of such septin scaffolds thus explain the role of septins in disease states. Copyright © 2004 Pathological Society of Great Britain and Ireland.

Nonlinear excitations in electron-positron-ion plasmas in accretion disks of active galactic nuclei

The propagation of acoustic nonlinear excitations in an electron-positron-ion (e-p-i) plasma composed of warm electrons and positrons, as well as hot ions, has been investigated by adopting a two-dimensional cylindrical geometry. The electrons and positrons are modeled by hydrodynamic fluid equations, while the ions are assumed to follow a temperature-parametrized Boltzmann distribution (the fixed ion model is recovered in the appropriate limit). This situation applies in the accretion disk near a black hole in active galactic nuclei, where the ion temperature may be as high as 3 to 300 times that of the electrons. Using a reductive perturbation technique, a cylindrical Kadomtsev-Petviashvili equation is derived and its exact soliton solutions are presented. Furthermore, real situations in which the strength of the nonlinearity may be weak are considered, so that higher-order nonlinearity plays an important role. Accordingly, an extended cylindrical Kadomtsev-Petviashvili equation is derived, which admits both soliton and double-layer solutions. The characteristics of the nonlinear excitations obtained are investigated in detail

Simple and accurate analytical model of planar grids and high-impedance surfaces, comprising metal strips or patches

Simple analytical formulas are introduced for the grid impedance of electrically dense arrays of square patches and for the surface impedance of high-impedance surfaces based on the dense arrays of metal strips or square patches over ground planes. Emphasis is on the oblique-incidence excitation. The approach is based on the known analytical models for strip grids combined with the approximate Babinet principle for planar grids located at a dielectric interface. Analytical expressions for the surface impedance and reflection coefficient resulting from our analysis are thoroughly verified by full-wave simulations and compared with available data in open literature for particular cases. The results can be used in the design of various antennas and microwave or millimeter wave devices which use artificial impedance surfaces and artificial magnetic conductors (reflect-array antennas, tunable phase shifters, etc.), as well as for the derivation of accurate higher-order impedance boundary conditions for artificial (high-) impedance surfaces. As an example, the propagation properties of surface waves along the high-impedance surfaces are studied.

Adaptability in organisms and artifacts: A multi level perspective on adaptive processes

Abstract Adaptability to changing circumstances is a key feature of living creatures. Understanding such adaptive processes is central to developing successful autonomous artifacts. In this paper two perspectives are brought to bear on the issue of adaptability. The first is a short term perspective which looks at adaptability in terms of the interactions between the agent and the environment. The second perspective involves a hierarchical evolutionary model which seeks to identify higher-order forms of adaptability based on the concept of adaptive meta-constructs. Task orientated and agent-centered models of adaptive processes in artifacts are considered from these two perspectives. The former isrepresented by the fitness function approach found in evolutionary learning, and the latter in terms of the concepts of empowerment and homeokinesis found in models derived from the self-organizing systems approach. A meta-construct approach to adaptability based on the identification of higher level meta-metrics is also outlined. 2009 Published by Elsevier B.V.

Inter- and intrapersonal processes underlying authoritarianism: The role of social conformity and personal need for structure

Several personality constructs have been theorised to underlie right-wing authoritarianism (RWA). In samples from New Zealand and Germany (Ns = 218, 259), we tested whether these constructs can account for specific variance in RWA. In both samples, social conformity and personal need for structure were independent predictors of RWA. In Sample 2, where also openness to experience was measured, social conformity and personal need for structure fully mediated the impact of the higher-order factor of openness on RWA. Our results contribute to the integration of current approaches to the personality basis of authoritarianism. and suggest that two distinct personality processes contribute to RWA: An interpersonal process related to social conformity and an intrapersonal process related to rigid cognitive style. Copyright (C) 2009 John Wiley & Sons, Ltd.