treegraph: automated drawing of complex tree figures using an extensible tree description format

treegraph assists in producing complex ready‐to‐publish figures of phylogenetic trees. The TGF format used by the program automates formatting of several different statistical support value types (confidence estimates) per tree node. Moreover, internal text and graphical labels are automatically arranged at the nodes as are annotations for clades or groups of terminals. treegraph imports nexus trees and related file formats. Beyond common tree edit operations, simultaneous pruning of subtrees (simplification of the tree to higher order clades) and saving of subtrees is possible. treegraph exports to the standard vector graphics formats Scalable Vector Graphics and PostScript.     

Structure of hydroxylated galactocerebrosides from myelin at the air-water interface.

Hydroxy-galactocerebrosides (mixed chain length, constituent of myelin membranes) from bovine brain are investigated as monolayers at the air-water interface with isotherms, fluorescence microscopy, x-ray reflectivity and grazing incidence diffraction. With grazing incidence diffraction a monoclinic tilted chain lattice is found in the condensed phase. According to x-ray reflectivity, the longest chains protrude above the chain lattice and roughen the lipid/air interface. On compressing the chain lattice, the correlation length increases by approximately 65%; obviously, the sugar headgroups are flexible enough to allow for lattice deformation. With fluorescence experiments, small coexisting fluid and ordered domains are observed, and there is lipid dissolution into the subphase as well. The dissolved hydroxy-galactocerebroside molecules reenter on monolayer expansion. The electron density profiles derived from x-ray reflectometry (coherent superposition) show that the chain-ordering transition causes the molecules to grow into the subphase.     

Developmental stability in brown trout: are there any effects of heterozygosity or environmental stress?

We studied the developmental stability of brown trout, Salmo trutta L., in 10 populations (five acidified, five control) in Norway, measured as fluctuating asymmetry (FA) and departure from the morphological norm. We measured four meristic and four morphometric characters, and scored the level of biochemical heterozygosity at 49 loci (20 polymorphic). We reared eggs of a single population in a hatchery using four different water qualities (three replicates of each treatment) to test the effect of acidification stress on developmental instability. There were no significant differences in the level of FA, in departure from the morphological norm between brown trout sampled from lakes with acidified or control water qualities, or in brown trout hatched at different water qualities. There was no correlation between level of heterozygosity and FA or departure from the morphological norm, either when tested within populations or among populations. There were no single-locus effects on developmental stability tested for 11 loci. We conclude that measures of developmental stability or morphological variability are not useful for detecting acidification stress in brown trout. Furthermore, we conclude that developmental stability in our material varies independently of heterozygosity.     

Toward an International Standard for PCR-Based Detection of Food-Borne Thermotolerant Campylobacters: Assay Development and Analytical Validation

As part of a European research project (FOOD-PCR), we developed a standardized and robust PCR detection assay specific for the three most frequently reported food-borne pathogenic Campylobacter species, C. jejuni, C. coli, and C. lari. Fifteen published and unpublished PCR primers targeting the 16S rRNA gene were tested in all possible pairwise combinations, as well as two published primers targeting the 23S rRNA gene. A panel of 150 strains including target and nontarget strains was used in an in-house validation. Only one primer pair, OT1559 plus 18-1, was found to be selective. The inclusivity and exclusivity were 100 and 97%, respectively. In an attempt to find a thermostable DNA polymerase more resistant than Taq to PCR inhibitors present in chicken samples, three DNA polymerases were evaluated. The DNA polymerase Tth was not inhibited at a concentration of 2% (vol/vol) chicken carcass rinse, unlike both Taq DNA polymerase and DyNAzyme. Based on these results, Tth was selected as the most suitable enzyme for the assay. The standardized PCR test described shows potential for use in large-scale screening programs for food-borne Campylobacter species under the assay conditions specified.     

Comparative studies in the morphology of Crenias weddelliana and Maferria indica with reference to Sphaerothylax abyssinica (Podostemaceae: Podostemoideae)

The scope of morphological plasticity of vegetative structures among Podostemoideae (Podostemaceae) is documented for Crenias weddelliana, a neotropical species, Maferria indica, a palaeotropical species, and Sphaerothylax abyssinica, from Kenya, and compared with related taxa. The study highlights intrinsic characters of the widely enigmatic plant body of many species of the subfamily Podostemoideae. These include dorsiventrality of shoots occurring irrespective of gravity, incurvate distichy and one‐sided spirodistichy correlated with shoot dorsiventrality, asymmetric leaves, and several types of positioning of the two prophylls and inflorescence structures. The homogeneity of hairs of the ‘Zeylanidium olivaceum type’ established on the subulate leaves of some Indian species is of taxonomic value. The latter also applies to the stipella (not stipule) on the asymmetric compound leaf in New World species. The morphological data represent a framework of features consistent for the subfamily. © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society, 138 , 63–84.     

Aquatic invertebrates in riverine landscapes

1. Riverine systems consist of a mosaic of patches and habitats linked by diverse processes and supporting highly complex communities. Invertebrates show a high taxonomic and functional diversity in riverine systems and are in several ways important components of these systems. Their distribution patterns, movements and effects on ecological flows, testify to their importance in various landscape ecological processes. This paper reviews the invertebrate literature with respect to patterns and processes in the riverine landscape. 2. The distribution of invertebrates in riverine habitats is governed by a number of factors that typically act at different scales. Hence, the local community structure can be seen as the result of a continuous sorting process through environmental filters ranging from regional or catchment‐wide processes, involving speciation, geological history and climate, to the small‐scale characteristics of individual patches, such as local predation risk, substratum porosity and current velocity. 3. Dispersal is an important process driving invertebrate distribution, linking different ecological systems across boundaries. Dispersal occurs within the aquatic habitat as well as into the terrestrial surrounding, and also over land to other waterbodies. New genetic techniques have contributed significantly to the understanding of aquatic invertebrate dispersal and revealed the importance of factors such as physical barriers, synchrony of emergence and taxonomic affiliation. 4. Invertebrates affect the cycling of nutrients and carbon by being a crucial intermediate link between primary producers, detritus pools or primary consumers, and predators higher up in the trophic hierarchy. Suspension feeders increase the retention of carbon. The subsidies of aquatic invertebrates to the terrestrial ecosystem have been shown to be important, as are reciprocal processes such as the supply of terrestrial invertebrates that fall into the water. 5. Future studies are needed both to advance theoretical aspects of landscape ecology pertaining to the invertebrates in riverine systems and to intensify the experimental testing of hypotheses, for example with respect to the scaling of processes and to linkages between the terrestrial and aquatic systems. Another promising avenue is to take advantage of naturally steep environmental gradients, and of systems disturbed by humans, such as regulated rivers. By comparison with unimpaired reference sites, the mechanisms involved might be identified. The use of `natural' experiments, especially where environmental gradients are steep, is another technique with great potential.     

Effect of heparin modification on its activity in enhancing the inhibition of thrombin by antithrombin III

Studies were conducted to determine the effect of modifying specific functional groups of heparin on its antithrombin III-enhancing activity. The derivatives employed were heparin methyl ester, heparinylglycine and N-desulfated heparin. The carboxyl-modified derivatives increase the rate of inhibition of thrombin by antithrombin III, although not to the same extent as heparin. N-Desulfated heparin is devoid of any activity. Heparin methyl ester is more potent than heparinylglycine in activating antithrombin III, as exhibited by its immediate effect on the thrombin-fibrinogen reaction. However, heparinylglycine is the more effective of the two, in increasing the rate of thrombin deactivation by antithrombin III. The results indicate that although free carboxyl groups of heparin are not crucial for its binding to antithrombin III, they are important for the combination of the latter with thromobin. In contrast, N-sulfates are critical for the interaction of heparin with antithrombin III.