A new method for identification of protein (sub)families in a set of proteins based on hydropathy distribution in proteins

Structural similarity among proteins is reflected in the distribution of hydropathicity along the amino acids in the protein sequence. Similarities in the hydropathy distributions are obvious for homologous proteins within a protein family. They also were observed for proteins with related structures, even when sequence similarities were undetectable. Here we present a novel method that employs the hydropathy distribution in proteins for identification of (sub)families in a set of (homologous) proteins. We represent proteins as points in a generalized hydropathy space, represented by vectors of specifically defined features. The features are derived from hydropathy of the individual amino acids. Projection of this space onto principal axes reveals groups of proteins with related hydropathy distributions. The groups identified correspond well to families of structurally and functionally related proteins. We found that this method accurately identifies protein families in a set of proteins, or subfamilies in a set of homologous proteins. Our results show that protein families can be identified by the analysis of hydropathy distribution, without the need for sequence alignment. (C) 2005 Wiley-Liss, Inc.

Permeability of subcritical hydrocarbons in activated carbon

A new diffusion and flow model is presented to describe the behavior of hydrocarbon vapors in activated carbon. The micro/mesopore size distribution (PSD) is obtained according to Do's method which consists of two sequential processes of pore layering and pore filling. This model uses the micro/meso PSD obtained from each adsorbate equilibrium isotherm, which reflects the dynamics behavior of adsorbing molecules through the solid. The initial rise in total permeability is mainly attributed to adsorbed-phase diffusion (that is, surface diffusion), whereas the decrease over reduced pressure of about 0.9 is attributed to the reduction of pore space available for gas phase diffusion and flow. A functional form of surface diffusivity is proposed and validated with experimental data. This model predicts well the permeability of condensable hydrocarbon vapors in activated carbon. (C) 2005 American Institute of Chemical Engineers.

Living in a potentially toxic environment: comparisons of endofauna in two congeneric sponges from the Great Barrier Reef

The abundance and community composition of the endofauna in 2 species of sponge, Haliclona sp. 1 and Haliclona sp. 2 (phylum Porifera: order Haplosclerida), were examined at different sites on the slope at Heron Island Reef, in the southern Great Barrier Reef, on 2 separate occasions. Both species of Haliclona Occupy Similar habitats on the reef slope and are often found living adjacent to each other, but the major groups of secondary metabolites and the gross external morphology in the 2 species of sponge are different. The 2 species of sponge supported significantly different endofaunal communities, with Haliclona sp. 2 Supporting 3 to 4 times more individuals than Haliclona sp. 1. Fewer demersal zooplankton (copepods), nematodes and some peracarid crustaceans were found in Haliclona sp. I compared with Haliclona sp. 2. There were also differences in the numbers of spionid, nereidid and syllid. polychaetes living in the 2 species of sponge. The only taxon that was more abundant in Haliclona sp. 1 than Haliclona sp. 2 was the spionid Polydorella prolifera, and this difference was only evident on 1. of the 2 occasions. The amount of free space (pores, channels, cavities) for a given weight of sponge was only 19% greater in Haliclona sp. 2 than in Haliclona sp. 1, suggesting other factors, such as the differences in the allelochemicals, may have a role in determining the numbers and types of animals living in these 2 species of sponge.

Dynamic rupture in a 3-D particle-based simulation of a rough planar fault

An appreciation of the physical mechanisms which cause observed seismicity complexity is fundamental to the understanding of the temporal behaviour of faults and single slip events. Numerical simulation of fault slip can provide insights into fault processes by allowing exploration of parameter spaces which influence microscopic and macroscopic physics of processes which may lead towards an answer to those questions. Particle-based models such as the Lattice Solid Model have been used previously for the simulation of stick-slip dynamics of faults, although mainly in two dimensions. Recent increases in the power of computers and the ability to use the power of parallel computer systems have made it possible to extend particle-based fault simulations to three dimensions. In this paper a particle-based numerical model of a rough planar fault embedded between two elastic blocks in three dimensions is presented. A very simple friction law without any rate dependency and no spatial heterogeneity in the intrinsic coefficient of friction is used in the model. To simulate earthquake dynamics the model is sheared in a direction parallel to the fault plane with a constant velocity at the driving edges. Spontaneous slip occurs on the fault when the shear stress is large enough to overcome the frictional forces on the fault. Slip events with a wide range of event sizes are observed. Investigation of the temporal evolution and spatial distribution of slip during each event shows a high degree of variability between the events. In some of the larger events highly complex slip patterns are observed.

Searching for convergence in phylogenetic Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a metachain to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely. [Bayesian phylogenetic inference; heating parameter; Markov chain Monte Carlo; replicated chains.]

Three classes of starch granule swelling: Influence of surface proteins and lipids

The role of non-carbohydrate surface components of granular starch in determining gelatinisation behaviour has been tested by treatment of native starches with a range of extractants. Resulting washed starches were analysed for (bio)chemical, calorimetric and theological properties. Sodium dodecyl sulphate (SDS) was the most efficient extractant tested, and resulted in major changes to the subsequent theological properties of wheat and maize starches but not other starches. Three classes of starch granule swelling behaviour are identified: (i) rapid swelling (e.g. waxy maize, potato), (ii) slow swelling that can be converted to rapid swelling by extraction of surface proteins and lipids (e.g. wheat, maize), and (iii) limited swelling not affected by protein/lipid extraction (e.g. high amylose maize/potato). Comparison of a range of extractants suggests that all of protein, lipid and amylose are involved in restriction of swelling for wheat or maize starches. Treatment of starches with SDS leads to a residue at comparable (low) levels of SDS for all starches. C-13 NMR analysis shows that this SDS is present as a glucan inclusion complex, even for waxy maize starch. We infer that under the conditions used, glucan inclusion complexation of SDS is equally likely with amylopectin as with amylose. (c) 2006 Elsevier Ltd. All rights reserved.

TCR{alpha} Genes Direct MHC Restriction in the Potent Human T Cell Response to a Class I-Bound Viral Epitope

The underlying generic properties of {alpha}β TCRs that control MHC restriction remain largely unresolved. To investigate MHC restriction, we have examined the CTL response to a viral epitope that binds promiscuously to two human leukocyte Ags (HLAs) that differ by a single amino acid at position 156. Individuals expressing either HLA-B*3501 (156Leucine) or HLA-B*3508 (156Arginine) showed a potent CTL response to the 407HPVGEADYFEY417 epitope from EBV. Interestingly, the response was characterized by highly restricted TCR β-chain usage in both HLA-B*3501+ and HLA-B*3508+ individuals; however, this conserved TRBV9+ β-chain was associated with distinct TCR {alpha}-chains depending upon the HLA-B*35 allele expressed by the virus-exposed host. Functional assays confirmed that TCR {alpha}-chain usage determined the HLA restriction of the CTLs. Structural studies revealed significant differences in the mobility of the peptide when bound to HLA-B*3501 or HLA-B*3508. In HLA-B*3501, the bulged section of the peptide was disordered, whereas in HLA-B*3508 the bulged epitope adopted an ordered conformation. Collectively, these data demonstrate not only that mobile MHC-bound peptides can be highly immunogenic but can also stimulate an extremely biased TCR repertoire. In addition, TCR {alpha}-chain usage is shown to play a critical role in controlling MHC restriction between closely related allomorphs.

Spatially localized distortions of event time

A fundamental question about the perception of time is whether the neural mechanisms underlying temporal judgements are universal and centralized in the brain or modality specific and distributed []. Time perception has traditionally been thought to be entirely dissociated from spatial vision. Here we show that the apparent duration of a dynamic stimulus can be manipulated in a local region of visual space by adapting to oscillatory motion or flicker. This implicates spatially localized temporal mechanisms in duration perception. We do not see concomitant changes in the time of onset or offset of the test patterns, demonstrating a direct local effect on duration perception rather than an indirect effect on the time course of neural processing. The effects of adaptation on duration perception can also be dissociated from motion or flicker perception per se. Although 20 Hz adaptation reduces both the apparent temporal frequency and duration of a 10 Hz test stimulus, 5 Hz adaptation increases apparent temporal frequency but has little effect on duration perception. We conclude that there is a peripheral, spatially localized, essentially visual component involved in sensing the duration of visual events.

Training selective use of a complex categorisation strategy

The present study aims to encourage selective use of a complex categorisation strategy. More specifically, participants will be trained to use a two dimensional strategy in one region of category space and a more complex three-dimensional strategy in another region of category space. In the 2–3 conditions, participants will be presented with stimuli requiring the two-dimensional strategy in the first phase of training and the three-dimensional strategy in the second phase of training. In the 3-2 conditions, participants will be presented with stimuli requiring the three-dimensional strategy in the first phase of training and the two-dimensional strategy in the second phase of training. The main dependent measure will be performance on exceptions to the two-dimensional strategy. If participants learn to selectively use the three-dimensional strategy, then we expect them to correctly classify novel exceptions that occur in the three-dimensional region of the category space and incorrectly classify novel exceptions that occur in the two-dimensional region of the category space.

Danger zones and hot spots: Traversing Canadian and Australian narratives of urban multiculturalism

The ethnicity of urban space has long been an element in the burgeoning discourse of national multiculturalisms; so much so that spatial theorist Edward Soja uses the term “ethni-city” to speak of so-called postmodern or postcolonial urban geographies (239). In our focus on the urban, we point to both the conceptual and material thresholds of multiculturalism within the borders of the city, as well as the internal urban/suburban borders that delineate belonging. These are often as strongly patrolled as larger national borders. In taking up Sneja Gunew’s call in Haunted Nations for comparative and critical work on multiculturalisms, this paper offers preliminary and exploratory avenues and points of departure, and aims to particularise the multicultural as an encounter and experience that is regulated spatially and corporeally.

Investigating ontogenetic space with developmental cell lineages

Development plays a significant role in biological evolution, and is likely to prove an effective route to overcoming the limitations of direct genotype-phenotype mappings in artificial evolution. Nonetheless, the relationship between development and evolution is complex and still poorly understood. One question of current interest concerns the possible role that developmental processes may play in orienting evolution. A first step towards exploring this issue from a theoretical perspective is understanding the structure of ontogenetic space: the space of possible genotype-phenotype mappings. Using a quantitative model of development that enables ontogenetic space to be characterised in terms of complexity, we show that ontogenetic landscapes have a characteristic structure that varies with genotypic properties.

A rough cluster analysis of shopping orientation data

This paper describes the application of a new technique, rough clustering, to the problem of market segmentation. Rough clustering produces different solutions to k-means analysis because of the possibility of multiple cluster membership of objects. Traditional clustering methods generate extensional descriptions of groups, that show which objects are members of each cluster. Clustering techniques based on rough sets theory generate intensional descriptions, which outline the main characteristics of each cluster. In this study, a rough cluster analysis was conducted on a sample of 437 responses from a larger study of the relationship between shopping orientation (the general predisposition of consumers toward the act of shopping) and intention to purchase products via the Internet. The cluster analysis was based on five measures of shopping orientation: enjoyment, personalization, convenience, loyalty, and price. The rough clusters obtained provide interpretations of different shopping orientations present in the data without the restriction of attempting to fit each object into only one segment. Such descriptions can be an aid to marketers attempting to identify potential segments of consumers.

Lobe growth in foliose lichen thalli

The margins of foliose lichen thalli comprise individual lobes which grow radially and divide. This results in a complex marginal structure in which lobes differing in morphology, state of division, and growth pattern are crowded together. Various aspects of the biology of these lobes are reviewed including their carbohydrate supply, morphology, pattern of division and branching, the effect of lobe overcrowding and interactions between neighbouring lobes. As the thalus grows, lobes become increasingly crowded together and this restricts further lateral growth. Restriction of lobe width may be reponsible for the changes in radial growth rate (RGR) with size observed in foliose species. Various aspects of lobe biology may be responsible for lobe growth variation including the physical independence of lobes from their neighbours, the genetic origin of the lobes, and the pattern of lobe branching. Overall symmetry of a thallus is maintained by a fluctuating pattern of growth of individual lobes in successive months together with competition for space at the margin

Pragmatic approach to the development of robust real-time protocols

This research is concerned with the development of distributed real-time systems, in which software is used for the control of concurrent physical processes. These distributed control systems are required to periodically coordinate the operation of several autonomous physical processes, with the property of an atomic action. The implementation of this coordination must be fault-tolerant if the integrity of the system is to be maintained in the presence of processor or communication failures. Commit protocols have been widely used to provide this type of atomicity and ensure consistency in distributed computer systems. The objective of this research is the development of a class of robust commit protocols, applicable to the coordination of distributed real-time control systems. Extended forms of the standard two phase commit protocol, that provides fault-tolerant and real-time behaviour, were developed. Petri nets are used for the design of the distributed controllers, and to embed the commit protocol models within these controller designs. This composition of controller and protocol model allows the analysis of the complete system in a unified manner. A common problem for Petri net based techniques is that of state space explosion, a modular approach to both the design and analysis would help cope with this problem. Although extensions to Petri nets that allow module construction exist, generally the modularisation is restricted to the specification, and analysis must be performed on the (flat) detailed net. The Petri net designs for the type of distributed systems considered in this research are both large and complex. The top down, bottom up and hybrid synthesis techniques that are used to model large systems in Petri nets are considered. A hybrid approach to Petri net design for a restricted class of communicating processes is developed. Designs produced using this hybrid approach are modular and allow re-use of verified modules. In order to use this form of modular analysis, it is necessary to project an equivalent but reduced behaviour on the modules used. These projections conceal events local to modules that are not essential for the purpose of analysis. To generate the external behaviour, each firing sequence of the subnet is replaced by an atomic transition internal to the module, and the firing of these transitions transforms the input and output markings of the module. Thus local events are concealed through the projection of the external behaviour of modules. This hybrid design approach preserves properties of interest, such as boundedness and liveness, while the systematic concealment of local events allows the management of state space. The approach presented in this research is particularly suited to distributed systems, as the underlying communication model is used as the basis for the interconnection of modules in the design procedure. This hybrid approach is applied to Petri net based design and analysis of distributed controllers for two industrial applications that incorporate the robust, real-time commit protocols developed. Temporal Petri nets, which combine Petri nets and temporal logic, are used to capture and verify causal and temporal aspects of the designs in a unified manner.

Factors associated with degeneration of the thallus centre in foliose lichens

Degeneration of the older parts of foliose lichen thalli often lead to the formation of a space or 'window' in the centre of the colonies. The percentage of thalli of different size which exhibited 'windows' was studied in twenty saxicolous lichen populations in south Gwynedd, Wales. The proportion of thalli with 'windows' increased with thallus size. The size class at which 50% and 100% of thalli exhibited 'windows' varied between populations. Differences between populations were not correlated with distance from the sea, aspect, slope or porosity of the substrate or the total number of lichen species present. However, a higher percentage of smaller thalli had 'windows' on rock surfaces with a greater lichen cover. There were no significant differences in the levels of Ca, Mg, Cu or Zn in large (>4 cm) and small (<2 cm) Parmelia conspersa (Ehrh. ex Ach.) Ach. thalli or in the centres and marginal lobes of these thalli. The concentration of ribitol, arabitol and mannitol was significantly reduced in the centre of large thalli compared with the margin of large thalli and the centre of small thalli. However, carbohydrate levels were similar in the centre of large thalli and the margin of small thalli. The data suggest that loss of the thallus centre is a degenerative process related to thallus size. In the field, the formation of 'windows' may be related to the intensity of competition on a substrate. Central degeneration was not associated with a deficiency or an accumulation of Ca, Mg, Cu and Zn in the thallus centre. However, degeneration may be associated with a reduction in carbohydrates in the centre compared with the marginal lobes.