Mechanisms of Action of Rabbit CAP18 on Monolayers and Liposomes Made from Endotoxins or Phospholipids

We have investigated the mechanism of action of the cationic antimicrobial protein (18 kDa) CAP18 on liposomes and monolayers made from phospholipids and enterobacterial lipopolysaccharides (LPS). CAP18 intercalates into lipid matrices composed of LPS from sensitive strains, weaker into those made of LPS from a resistant strain (Proteus mirabilis strain R45) or negatively charged phospholipids, but not into those composed of neutral phosphatidylcholine. From the combination of data obtained with fluorescence resonance energy transfer and Fourier-transform infrared spectroscopy and film balance measurements, it can be concluded that structural differences in the LPS determine the depth of intercalation of CAP18 into the respective lipid matrices. Thus, we identified the L-Arap4N linked to the first Kdo of the LPS of P. mirabilis strain R45 to be responsible for the CAP18 resistance of this strain. These data provide insight into CAP18-mediated effects on the integrity of the outer membrane of Gram-negative bacteria and led to an improved model for rabbit CAP18 membrane interaction. Received: 14 January 2000/Revised: 20 April 2000     

A survey of flagellate diversity at four deep-sea hydrothermal vents in the Eastern Pacific Ocean using structural and molecular approaches

Eighteen strains of flagellated protists representing nine species were isolated and cultured from four deep-sea hydrothermal vents: Juan de Fuca Ridge (2,200 m), Guaymas Basin (2,000 m), 21 degrees N (2,550 m) and 9 degrees N (2,000 m). Light and electron microscopy were used to identify flagellates to genus and, when possible, species. The small subunit ribosomal RNA genes of each vent species and related strains from shallow-waters and the American Type Culture Collection were sequenced then used for comparative analysis with database sequences to place taxa in an rDNA tree. The hydrothermal vent flagellates belonged to six different taxonomic orders: the Ancyromonadida, Bicosoecida, Cercomonadida, Choanoflagellida, Chrysomonadida, and Kinetoplastida. Comparative analysis of vent isolate and database sequences resolved systematic placement of some well-known species with previously uncertain taxonomic affinities, such as Ancyromonas sigmoides, Caecitellus parvulus, and Massisteria marina. Many of these vent isolates are ubiquitous members of marine, freshwater, and terrestrial ecosystems worldwide, suggesting a global distribution of these flagellate species.     

Nucleolar Organizing Regions, 18S and 5S rDNA in Astyanax Scabripinnis (Pisces, Characidae): Populations Distribution and Functional Diversity

Astyanax scabripinnis specimens from four distinct populations in Brazil were studied with respect to their karyotype macrostructure, nucleolar organizer regions, and 18S and 5S rRNA genes. The four populations showed a 2n = 50 chromosomes (3 M + 11 SM + 5 ST + 6 A pairs) and 1–2 B chromosomes. No chromosomal differentiations were observed between sexes. Although a karyotypic diversity has been characterized in this fish group, the populations now analyzed presented the same macrokaryotypic pattern. Chromosome mapping of 5S rDNA showed a total of eight sites located in four distinct chromosomal pairs, with no apparent differences among populations. A comparative study on 18S rDNA locations and Ag-NORs showed some secondary NOR sites that are not usually expressed in karyotypes and a probable differential NOR activity among populations. Correlations between these data, environmental conditions and B chromosomes are discussed. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenetic Relationships of Acanthocephala Based on Analysis of 18S Ribosomal RNA Gene Sequences

Acanthocephala (thorny-headed worms) is a phylum of endoparasites of vertebrates and arthropods, included among the most phylogenetically basal tripoblastic pseudocoelomates. The phylum is divided into three classes: Archiacanthocephala, Palaeacanthocephala, and Eoacanthocephala. These classes are distinguished by morphological characters such as location of lacunar canals, persistence of ligament sacs in females, number and type of cement glands in males, number and size of proboscis hooks, host taxonomy, and ecology. To understand better the phylogenetic relationships within Acanthocephala, and between Acanthocephala and Rotifera, we sequenced the nearly complete 18S rRNA genes of nine species from the three classes of Acanthocephala and four species of Rotifera from the classes Bdelloidea and Monogononta. Phylogenetic relationships were inferred by maximum-likelihood analyses of these new sequences and others previously determined. The analyses showed that Acanthocephala is the sister group to a clade including Eoacanthocephala and Palaeacanthocephala. Archiacanthocephala exhibited a slower rate of evolution at the nucleotide level, as evidenced by shorter branch lengths for the group. We found statistically significant support for the monophyly of Rotifera, represented in our analysis by species from the clade Eurotatoria, which includes the classes Bdelloidea and Monogononta. Eurotatoria also appears as the sister group to Acanthocephala. Received: 12 October 1999 / Accepted: 8 February 2000     

SSU rDNA phylogeny of cladoniiform lichens

To examine phylogenetic relationships among the "cladoniiform" lichenized fungi, i.e., the families Cladoniaceae, Baeomycetaceae, Icmadophilaceae, Stereocaulaceae, and Siphulaceae, and to provide evidence for the anticipated independent origins of podetia and pseudopodetia, we conducted phylogenetic analyses of SSU (small subunit) rDNA sequences from 39 lichen-forming fungi. These fungi represent all of the major growth forms of lichen associations, fruticose (including "cladoniiform"), foliose, and crustose. Our analysis suggests that lichen-forming fungi with a "cladoniiform" morphology arose multiple times within the ascomycetes. Additionally, each of the other thallus growth forms, crustose, foliose, and fruticose, have originated multiple times. It also seems to be clear that neither all podetiate nor all pseudopodetiate taxa form a monophyletic group. Therefore the term "podetium" should be restricted to homologous structures that are most probably limited to the genera Cladonia, Cladina, Pycnothelia, and allies. The "pseudopodetia" of Stereocaulon (Stereocaulaceae) and Cladia (Cladiaceae) may represent different states of the same homologous character. Our phylogenetic hypothesis supports the monophyletic origin of the order Lecanorales sensu stricto, including representatives of five suborders Cladoniineae, Lecanorineae, Teloschistineae, Agyriineae and Peltigerineae, but excluding representatives of the suborders Acarosporineae (Acarospora schleicheri and Megaspora verrucosa), Pertusariineae (Pertusaria trachythallina), and Umbilicarineae. The suborder Cladoniineae and the family Cladoniaceae both appear to be polyphyletic assemblages.     

Flatworm phylogeny from partial 18S rDNA sequences

Partial 18S rDNA sequences from 29 flatworms and 2 outgroup taxa were used in a cladistic analysis of the Platyhelminthes. Support for the clades in the resulting single most parsimonious tree was estimated through bootstrap analysis, jack-knife analysis and decay indices. The Acoelomorpha (Acoela and Nemertodermatida) were absent from the most parsimonious tree. The Acoela and the Fecampiidae form a strongly supported clade, the sister group of which may be the Tricladida. There is some support for monophyly of the rhabdocoel taxon Dalyellioida, previously regarded as paraphyletic. The sister group of the Neodermata remains unresolved. This revised version was published online in July 2006 with corrections to the Cover Date.     

Water use by woody plants on contrasting soils in a savanna parkland: assessment with δ2H and δ18O

In savanna parklands of southern Texas, patches of grassland and discrete clusters of small trees and shrubs occur on sandy loam surface soils underlain by an argillic horizon (claypan) at 40 cm. Large trees and shrubs in groves occur on deep (2 m) sandy loam soils without an argillic horizon. 2H and 18O of rainfall, groundwater, and soil and plant water were measured to: (1) determine if coexistence in woody patches occurs via vertical stratification of soil water uptake; (2) document differences in plant water acquisition on contrasting soil types; and (3) evaluate recharge and evaporative losses of soil moisture from grassland vs. wooded landscape elements. Groundwater was isotopically similar to weighted rainfall, suggesting local recharge at this site. Linear regressions of soil water 2H on 18O yielded slopes less than the meteoric water line, indicating significant evaporative losses of soil moisture in all landscape elements. Interspecific differences in root density distribution were significant; some woody species had roots well below 1.6 m, while others had few roots below 0.8 m. 2H and 18O values of stem water from all plants in groves were lower than those of soil water in the upper 1.5 m of the profile, suggesting all species obtained their water from depths >1.5 m. Deep roots of trees and shrubs at this savanna parkland site thus appeared to have a functional significance that was not revealed by biomass or density determinations. Root densities of species in discrete clusters (claypan present) were typically greater than those of the same species in groves (claypan absent), especially in the upper 80 cm of the soil profile. Consistent with rooting profiles, 2H and 18O values of plant water indicated that trees and shrubs in discrete clusters with fine- textured subsoils obtained most of their water at depths <1.5 m. As with groves, there was no indication of water resource partitioning between species. In summary, we saw no isotopic evidence that co- occurring woody plants at this savanna parkland site were partitioning soil moisture vertically during late summer/early fall, despite marked differences in their root density distributions. This supports other lines of evidence which indicate that species interactions in tree/shrub clumps are competitive, and that species composition is therefore unstable in those landscape elements.     

Limitations of Metazoan 18S rRNA Sequence Data: Implications for Reconstructing a Phylogeny of the Animal Kingdom and Inferring the Reality of the Cambrian Explosion

We document the phylogenetic behavior of the 18S rRNA molecule in 67 taxa from 28 metazoan phyla and assess the effects of among-site rate variation on reconstructing phylogenies of the animal kingdom. This empirical assessment was undertaken to clarify further the limits of resolution of the 18S rRNA gene as a phylogenetic marker and to address the question of whether 18S rRNA phylogenies can be used as a source of evidence to infer the reality of a Cambrian explosion. A notable degree of among-site rate variation exists between different regions of the 18S rRNA molecule, as well as within all classes of secondary structure. There is a significant negative correlation between inferred number of nucleotide substitutions and phylogenetic information, as well as with the degree of substitutional saturation within the molecule. Base compositional differences both within and between taxa exist and, in certain lineages, may be associated with long branches and phylogenetic position. Importantly, excluding sites with different degrees of nucleotide substitution significantly influences the topology and degree of resolution of maximum-parsimony phylogenies as well as neighbor-joining phylogenies (corrected and uncorrected for among-site rate variation) reconstructed at the metazoan scale. Together, these data indicate that the 18S rRNA molecule is an unsuitable candidate for reconstructing the evolutionary history of all metazoan phyla, and that the polytomies, i.e., unresolved nodes within 18S rRNA phylogenies, cannot be used as a single or reliable source of evidence to support the hypothesis of a Cambrian explosion. Received: 9 December 1997 / Accepted: 23 March 1998