A likelihood method for the detection of selection and recombination using nucleotide sequences

Different regions along nucleotide sequences are often subject to different evolutionary forces. Recombination will result in regions having different evolutionary histories, while selection can cause regions to evolve at different rates. This paper presents a statistical method based on likelihood for detecting such processes by identifying the regions which do not fit with a single phylogenetic topology and nucleotide substitution process along the entire sequence. Subsequent reanalysis of these anomalous regions may then be possible. The method is tested using simulations, and its application is demonstrated using the primate psi eta-globin pseudogene, the V3 region of the envelope gene of HIV-1, and argF sequences from Neisseria bacteria. Reanalysis of anomalous regions is shown to reveal possible immune selection in HIV-1 and recombination in Neisseria. A computer program which implements the method is available.      

Large Scale Identification of Genes Involved in Cell Surface Biosynthesis and Architecture in Saccharomyces Cerevisiae

The sequenced yeast genome offers a unique resource for the analysis of eukaryotic cell function and enables genome-wide screens for genes involved in cellular processes. We have identified genes involved in cell surface assembly by screening transposon-mutagenized cells for altered sensitivity to calcofluor white, followed by supplementary screens to further characterize mutant phenotypes. The mutated genes were directly retrieved from genomic DNA and then matched uniquely to a gene in the yeast genome database. Eighty-two genes with apparent perturbation of the cell surface were identified, with mutations in 65 of them displaying at least one further cell surface phenotype in addition to their modified sensitivity to calcofluor. Fifty of these genes were previously known, 17 encoded proteins whose function could be anticipated through sequence homology or previously recognized phenotypes and 15 genes had no previously known phenotype.     

Selection of polarized growth sites in yeast

The budding yeast Saccharomyces cerevisiae responds to intracellular and extracellular cues to direct cell growth. Genetic analysis has revealed many components that participate in this process and has provided insight into the mechanisms by which these proteins function. Several of these components, such as the septins, pheromone receptors and GTPase proteins, have homologues in multicellular eukaryotes, suggesting that many aspects of polarized cell growth may be conserved throughout evolution. This review discusses our current understanding of the molecular mechanisms of growth-site selection during the different stages of the yeast life cycle.     

Growth and cell wall composition of glucose-limited bean cells (Phaseolus vulgaris L.)

Glucose-limited bean cells (Phaseolus vulgaris L.) were grown in a modified bacterial fermentor at a constant pH of 4.8. The cultures were kept in steady state at different specific growth rates varying from 0.00216 h^–1 to 0.0106 h^–1. Culture conditions are described that are needed to start a continuous culture. First, it was essential to use log-phase cells as starting material. Second, it was important to increase the dilution rate gradually, otherwise cells in the culture aggregated. Cells grown at the highest dilution rate employed contained twice as much protein per gram dry weight as cells grown at the lowest dilution rate. The composition of the cell walls also varied with the dilution rate in contrast to their relatively constant composition when grown in batch culture.     

Benthic ctenophores (Platyctenida: Coeloplanidae) in South Florida: predator–prey interactions

The primary goal of this study was to demonstrate, from field observations and laboratory experiments, some key trophic roles of benthic ctenophores as predators and prey in subtropical communities. We examined individuals of two benthic platyctenid species: Coeloplana waltoni, a minute epibiont on octocorals in exposed, open‐water settings; and Vallicula multiformis, an associate of calm‐water biofouling communities and floating Sargassum spp. Laboratory observations of individuals of both ctenophore species revealed frequent capture and ingestion of diverse zooplankton taxa, especially crustaceans. Laboratory predation trials demonstrated the capture of dolphinfish (Coryphaena hippurus) eggs and larvae by both ctenophore species. Dolphinfish eggs and larvae larger than individuals of C. waltoni were captured but not ingested during 2‐h trial periods. These prey items were sometimes purloined and ingested by polyps of the ctenophore's octocoral host. Ingestion of dolphinfish eggs and larvae by individuals of C. waltoni was observed, however, after longer periods of exposure to prey. In predation trials, dolphinfish eggs and larvae were both captured and ingested by larger individuals of the ctenophore species V. multiformis. Field and laboratory observations revealed diverse invertebrate and fish taxa that prey on both ctenophore species. In the laboratory, the mean daily per capita consumption of individuals of C. waltoni by a pomacanthid fish ranged 0.5–2.8 individuals, and ranged 2.6–3.6 individuals for predation by an ovulid mollusc. Field population densities of these predators ranged 0.1–0.7 individuals per m² for the pomacanthid, and 0.2–1.1 individuals per m² for the mollusc. Laboratory feeding observations demonstrated frequent consumption of individuals of V. multiformis by a sea anemone, and by three species of brachyuran crabs. Field observations revealed eight fishes that probably feed incidentally on individuals of V. multiformis. These findings add to the limited knowledge base of predator–prey dynamics in both C. waltoni and V. multiformis.     

A direct substitution, equation error technique for solving the thermographic tomography problem

A new technique for solving the combined state and parameter estimation problem in thermographic tomography is presented. The technique involves the direct substitution of known skin temperatures into the finite difference form of the bio-heat transfer equation as formulated for solving an initial value problem with a convection boundary condition at the skin surface. These equations are then used to solve the inverse bio-heat transfer problem for the unknown subcutaneous tissue temperatures and physiological parameters. For a small number of nodal points, closed form algebraic solutions are obtained. For larger sets of equations, a hybrid technique is used in which the problem is initially posed as an unconstrained optimization problem in which the model equation error is minimized using the conjugate gradient descent technique to get close to a solution. Then a generalized Newton-Raphson technique was used to solve the equations. A numerical simulation of a one-dimensional problem is investigated both with and without noise superimposed on the input (transient) skin temperature data. The results show that the technique gives very accurate results if the skin temperature data contains little noise. It is also shown that if the physical properties of the tissue and the metabolism are known, that a given set of proper transient skin temperature inputs yields a unique solution for the unknown internal temperatures and blood perfusion rates. However, the similar problem with known blood perfusion rates and unknown metabolisms does not yield a unique solution for the internal temperatures and metabolisms.     

Effects of prostaglandins, calcium, and bradykinin on guanylate cyclase in different organs.

The effects of prostaglandins and bradykinin on the activity of guanylate cyclase in plasma membranes from rat uterus and duodenum have been found strongly dependent on calcium content.     

Structure activity relationship of orally active enkephalin analogues as analgesics.

Substitution of glycine in position 2 of the naturally occurring methionine-enkephalin by D-alanine, methylation of tyrosine and phenylalanine i in position 1 and 4 respectively and conversion of the methionine in position 5 to the corresponding alcohol sulfoxide lead to potent orally active enkephalin analogues with marked analgesic properties.