Turing Instability in the Solid State: Void Lattices in Irradiated Metals.

Turing (or double-diffusive) instabilities describe pattern formation in reaction-diffusion systems, and were proposed in 1952 as a potential mechanism behind pattern formation in nature, such as leopard spots and zebra stripes. Because the mechanism requires the reacting species to have significantly different diffusion rates, only a few liquid phase chemical reaction systems exhibiting the phenomenon have been discovered. In solids the situation is markedly different, since species such as impurities or other defects typically have mobilities ∝exp(-E/k_{B}T), where E is the migration barrier and T is the temperature. This often leads to mobilities differing by several orders of magnitude. Here, we use a simple, minimal model to show that an important class of emergent patterns in solids, namely void superlattices in irradiated metals, could also be explained by the Turing mechanism. Analytical results are confirmed by phase field simulations. The model (Cahn-Hilliard equations for interstitial and vacancy concentrations, coupled by generation and annihilation terms) is generic, and the mechanism could also be responsible for the patterns and structure observed in many solid state systems.

Effects of trawling on the diets of common demersal fish by-catch of a tropical prawn trawl fishery.

The ecological effect of prawn trawling on the benthos of the Gulf of Carpentaria, northern Australia, was investigated by examining stomach contents of common demersal fishes incidentally caught as by-catch in the fishery. Fishes were collected from high and low fishing intensity sites in three regions based on vessel monitoring system data. The diets of eight species of benthic fish predators were compared between regions and fishing intensities. A regional effect on diet was evident for seven species. Only one generalist species had no significant difference in diet among the three regions. For the comparisons within each region, five predator species had significantly different diet between high and low fishing intensities in at least one region. Across the three regions, high fishing intensity sites had predators that consumed a greater biomass of crustaceans, molluscs and echinoderms. At low fishing intensity sites, predators had diets comprising a greater biomass of cnidarians and teleosts, and a different assemblage of molluscs, crustaceans and fishes. These changes in diet suggest that there may have been a shift in the structure of the benthic community following intensive fishing. Analysis of predator diets is a useful tool to help identify changes in the benthic community composition after exposure to fishing. This study also provided valuable diet information on a range of abundant generalist benthic predators to improve the ecosystem modelling tools needed to support ecosystem-based fisheries management.

Fluorescent Amplified Fragment Length Polymorphism Analysis of Norwegian Bacillus cereus and Bacillus thuringiensis Soil Isolates.

We examined 154 Norwegian B. cereus and B. thuringiensis soil isolates (collected from five different locations), 8 B. cereus and 2 B. thuringiensis reference strains, and 2 Bacillus anthracis strains by using fluorescent amplified fragment length polymorphism (AFLP). We employed a novel fragment identification approach based on a hierarchical agglomerative clustering routine that identifies fragments in an automated fashion. No method is free of error, and we identified the major sources so that experiments can be designed to minimize its effect. Phylogenetic analysis of the fluorescent AFLP results reveals five genetic groups in these group 1 bacilli. The ATCC reference strains were restricted to two of the genetic groups, clearly not representative of the diversity in these bacteria. Both B. anthracis strains analyzed were closely related and affiliated with a B. cereus milk isolate (ATCC 4342) and a B. cereus human pathogenic strain (periodontitis). Across the entire study, pathogenic strains, including B. anthracis, were more closely related to one another than to the environmental isolates. Eight strains representing the five distinct phylogenetic clusters were further analyzed by comparison of their 16S rRNA gene sequences to confirm the phylogenetic status of these groups. This analysis was consistent with the AFLP analysis, although of much lower resolution. The innovation of automated genotype analysis by using a replicated and statistical approach to fragment identification will allow very large sample analyses in the future.

Induction of antigen-specific class I-restricted cytotoxic T cells by soluble proteins in vivo.

Cytotoxic T lymphocytes (CTL) are induced specifically against viral and tumor antigens presented by major histocompatibility complex class I molecules on the surface of infected or transformed cells. Intracellular synthesized antigens are processed and associated with class I antigens within cells before presentation on the cell surface. Because of this special requirement for CTL induction, exogenous soluble antigens do not, in general, induce specific CTL responses. To overcome this problem, various laboratories have resorted to the use of vaccinia virus and other replicating expression vectors for intracellular antigen delivery leading to the stimulation of humoral and cell-mediated immunity to specific proteins. However, for human use it is safer to use purified and defined antigens for inducing immune responses. Using soluble ovalbumin and human immunodeficiency virus glycoprotein gp120, we have explored the possibility of using an antigen formulation consisting of squalane and Tween 80 to elicit antigen-specific CTL responses in mice. We have demonstrated that this antigen formulation is a potent inducer of CD8+, class I-restricted, antigen-specific CTLs. The CTL priming induced by soluble antigen in squalane/Tween 80 resembles the reported response to the vaccinia recombinant containing human immunodeficiency virus envelope protein and by splenocytes cytoplasmically loaded with soluble ovalbumin. The ramifications of these findings for vaccine development are discussed.

Analysis of murine lymphocyte subpopulations by dual-color flow cytometry: technical considerations and specificities of monoclonal antibodies directed against surface markers.

We performed detailed phenotypic analysis of murine lymphocytes from thymus, spleen, lymph node, and peripheral blood using commercially available monoclonal antibodies, each with specificities for membrane surface markers and dual-color flow cytometry. Erythrocyte lysis techniques were utilized for lymphocyte preparation so that inherent difficulties with gradient techniques would be avoided, such as the potential for loss of abnormally sized cells. These studies demonstrated that the specificities of each monoclonal must be carefully determined; for example, the Lyt-1 monoclonal, frequently utilized to identify helper/inducer T cells, also reacts with suppressor/cytotoxic (Lyt-2+) cells; helper/inducer cells are better studied with a more recently available monoclonal, L3T4. Cells from different tissues may differ greatly not only in the presence of surface markers, but also in the surface density of each marker; this density can be studied and quantitated using appropriate analytic software. We also show that larger and more granular lymphocytes appear to be enriched for surface Ia antigen, indicating that these cells may be activated or regulatory subsets; these large, Ia+ T-cells will be lost from analysis if standard, narrow gate settings are used for analyzing forward and side-scatter characteristics or for cell sorting.

Changes in the nuclear pore complexes of the dentate granule cells in aged rats.

In 3-, 9-, 24-, and 30-month-old male rats (Fischer 344), the nuclear perimeter and the density and diameter of nuclear pore complexes in the granule cells of the dentate fascia were studied. Whereas the nuclear perimeter and the diameter of nuclear pore complexes did not change as a function of age, there was a significant loss of them at 24 months (20%), compared with the third month. This change suggests that the nucleocytoplasmic communication may be impaired with age which would adversely affect protein synthesis, and could explain the loss of the postsynaptic sites of the dentate fascia of aged rats.