Chromatin and histones from Giardia lamblia: a new puzzle in primitive eukaryotes

The three deepest eukaryote lineages in small subunit ribosomal RNA phylogenies are the amitochondriate Microsporidia, Metamonada, and Parabasalia. They are followed by either the Euglenozoa (e.g., Euglena and Trypanosoma) or the Percolozoa as the first mitochondria-containing eukaryotes. Considering the great divergence of histone proteins in protozoa we have extended our studies of histones from Trypanosomes (Trypanosoma cruzi, Crithidia fasciculata and Leishmania mexicana) to the Metamonada Giardia lamblia, since Giardia is thought to be one of the most primitive eukaryotes. In the present work, the structure of G. lamblia chromatin and the histone content of the soluble chromatin were investigated and compared with that of higher eukaryotes, represented by calf thymus. The chromatin is present as nucleosome filaments which resemble the calf thymus array in that they show a more regular arrangement than those described for Trypanosoma. SDS-polyacrylamide gel electrophoresis and protein characterization revealed that the four core histones described in Giardia are in the same range of divergence with the histones from other lower eukaryotes. In addition, G. lamblia presented an H1 histone with electrophoretic mobility resembling the H1 of higher eukaryotes, in spite of the fact that H1 has a different molecular mass in calf thymus. Giardia also presents a basic protein which was identified as an HU-like DNA-binding protein usually present in eubacteria, indicating a chimaeric composition for the DNA-binding protein set in this species. Finally, the phylogenetic analysis of selected core histone protein sequences place Giardia divergence before Trypanosoma, despite the fact that Trypanosoma branch shows an acceleration in the evolutionary rate pointing to an unusual evolutionary behavior in this lineage.     

An efficient ligation method in the making of an in vitro virus for in vitro protein evolution

The “in vitro virus” is a molecular construct to perform evolutionary protein engineering. The “virion(=viral particle)”(mRNA-peptide fusion), is made by bonding a nascent protein with its coding mRNA via puromycin in a test tube for in vitro translation. In this work, the puromycin-linker was attached to mRNA using the Y-ligation, which was a method of two single-strands ligation at the end of a double-stranded stem to make a stem-loop structure. This reaction gave a yield of about 95%. We compared the Y-ligation with two other ligation reactions and showed that the Y-ligation gave the best productivity. An efficient amplification of the in vitro virus with this “viral genome” was demonstrated. Published: October 28, 2002     

Preliminary Observations on Specific Adaptations of Exophilic Ixodid Ticks to Forests or Open Country Habitats

Some features of three-host exophilic ticks important for their survival differ at the generic level in relation to the types of their habitat. Ixodes and Haemaphysalis are typical forest genera, Hyalomma is an open country genus, whereas Dermacentor and Rhipicephalus, having some features of forest ticks, are closer to the ticks of open country. Forest ticks encounter rather stable and favorable temperature, humidity and illumination conditions as compared with open country ticks. A few differences determining every-day survival, host-seeking, and reproduction of ticks are considered. (1) Tolerance to desiccation is very low in forest ticks and much greater in ticks of open country. (2) Lack of eyes in forest ticks (having, however, epithelial photoreceptor cells) and formation of eyes as special morphological structures in ticks of open country. (3) Capability of mating and insemination of unfed specimens both on and off hosts in forest ticks (Ixodes) and insemination of partially engorged females only on hosts by fed males in open country ticks. (4) Reciprocal sexual dimorphism where in forest ticks females have a larger body than males and in open country ticks this correlation is opposite. (5) Linear dependence between female weight and number of eggs laid is established in forest ticks after the female weight becomes higher than 50% of mean engorgement weight whereas in open country ticks linear dependence begins to reveal itself much earlier. (6) In forest ticks the compensatory growth occurs only during adult feeding whereas in open country ticks such a growth occurs both during nymphal and adult feeding. The adaptive nature of the above differences and their evolutionary trends have been hypothesized. This revised version was published online in July 2006 with corrections to the Cover Date.     

Selection at linked sites in the partial selfer Caenorhabditis elegans

Natural selection can produce a correlation between local recombination rates and levels of neutral DNA polymorphism as a consequence of genetic hitchhiking and background selection. Theory suggests that selection at linked sites should affect patterns of neutral variation in partially selfing populations more dramatically than in outcrossing populations. However, empirical investigations of selection at linked sites have focused primarily on outcrossing species. To assess the potential role of selection as a determinant of neutral polymorphism in the context of partial self-fertilization, we conducted a multivariate analysis of single-nucleotide polymorphism (SNP) density throughout the genome of the nematode Caenorhabditis elegans. We based the analysis on a published SNP data set and partitioned the genome into windows to calculate SNP densities, recombination rates, and gene densities across all six chromosomes. Our analyses identify a strong, positive correlation between recombination rate and neutral polymorphism (as estimated by noncoding SNP density) across the genome of C. elegans. Furthermore, we find that levels of neutral polymorphism are lower in gene-dense regions than in gene-poor regions in some analyses. Analyses incorporating local estimates of divergence between C. elegans and C. briggsae indicate that a mutational explanation alone is unlikely to explain the observed patterns. Consequently, we interpret these findings as evidence that natural selection shapes genome-wide patterns of neutral polymorphism in C. elegans. Our study provides the first demonstration of such an effect in a partially selfing animal. Explicit models of genetic hitchhiking and background selection can each adequately describe the relationship between recombination rate and SNP density, but only when they incorporate selfing rate. Clarification of the relative roles of genetic hitchhiking and background selection in C. elegans awaits the development of specific theoretical predictions that account for partial self-fertilization and biased sex ratios.     

Erratum: Cloning and sequencing of the phycocyanin gene from Spirulina maxima and its evolutionary analysis

The genes were cloned for the two apoprotein subunits, and ,of phycocyanin from the cyanobacterium Spirulina maxima = Arthrospiramaxima) strain F3. The - and -subunit gene-coding regionscontain 489 bp and 519 bp, respectively. The -subunit gene is upstreamfrom the -subunit gene, with a 111-bp segment separating them.Similarities between the -subunits of S. maxima and nine othercyanobacteria were between 58% and 99%, as were those between the -subunits. The maximum similarity between the - and -subunits from S. maxima was 27%.     

Fold recognition analysis of glycosyltransferase families: further members of structural superfamilies

Glycosyltransferases (GTs) are diverse enzymes organized into 65 families. X-ray crystallography and in silico studies have shown many of these to belong to two structural superfamilies: GT-A and GT-B. Through application of fold recognition and iterated sequence searches, we demonstrate that families 60, 62, and 64 may also be grouped into the GT-A fold superfamily. Analysis of conserved acidic residues suggests that catalytic sites are better conserved in superfamily GT-B than in GT-A. Although 26% and 29% of GT families may now be confidently placed in superfamilies GT-A and GT-B, respectively, the remaining 45% of families bear no discernible resemblance to either superfamily, which, given the sensitivity of modern fold recognition methods, suggests the existence of novel structural scaffolds associated with GT activity. Furthermore, bioinformatics studies indicate the apparent ease with which mechanism-inverting or retaining-may change during evolution.     

A new class and order of myxozoans to accommodate parasites of bryozoans with ultrastructural observations on Tetracapsula bryosalmonae (PKX organism)

Tetracapsula bryosalmonae, formerly PKX organism, is a myxozoan parasite that causes proliferative kidney disease in salmonid fish. Its primary hosts, in which it undergoes a sexual phase, are phylactolaemate bryozoans. It develops in the bryozoan coelomic cavity as freely floating sacs which contain two types of cells, stellate cells and sporoplasmogenic cells, which become organised as spores. Eight stellate cells differentiate as four capsulogenic cells and four valve cells which surround a single sporoplasmogenic cell. The sporoplasmogenic cell undergoes meiosis and cytoplasmic fission to produce two sporoplasms with haploid nuclei. Sporoplasms contain secondary cells. The unusual development supports previously obtained data from 18S rDNA sequences, indicating that species of Tetracapsula form a clade. It diverged early in the evolution of the Myxozoa, before the radiation that gave rise to the better known genera belonging to the two orders in the single class Myxosporea. The genus Tetracapsula as seen in bryozoans shares some of the characters unique to the myxosporean phase and others typical of the actinosporean phase of genera belonging to the class Myxosporea. However, it exhibits other features which are not found in either phase. A new class Malacosporea and order Malacovalvulida are proposed to accommodate the family Saccosporidae and genus Tetracapsula. Special features of the new class are the sac-like proliferative body, valve cells not covering the exit point of the polar filament, lack of a stopper-like structure sealing the exit, maintenance of valve cell integrity even at spore maturity, absence of hardened spore walls and unique structure of sporoplasmosomes in the sporoplasms.     

Evolutionary ecology of the tropane alkaloids of Datura stramonium L. (Solanaceae)

Abstract.— Although insect herbivory is frequently assumed to be responsible for the maintenance of plant secondary metabolites such as alkaloids, the assumption is controversial and experimental evidence for this assumption is sparse. We examined natural selection on the two major alkaloids present in the leaves of Datura stramonium and found that both alkaloids came under active selection. We found negative directional selection for scopolamine (natural selection acting to reduce scopolamine levels) and stabilizing selection for hyoscyamine (natural selection acting to maintain an intermediate level of hyoscyamine). We also present evidence that insect herbivores act as the agents of selection on these alkaloids. Finally, we show that there were no trade-offs in resistance to different species of insects.     

Mitochondrial DNA phylogeography of the polytypic North American rat snake (Elaphe obsoleta): a critique of the subspecies concept

Subspecies have been considered artificial subdivisions of species, pattern classes, or incipient species. However, with more data and modern phylogenetic techniques, some subspecies may be found to represent true species. Mitochondrial DNA analysis of the polytypic snake, Elaphe obsoleta, yields well-supported clades that do not conform to any of the currently accepted subspecies. Complete nucleotide sequences of the cytochrome b gene and the mitochondrial control region produced robust maximum-parsimony and maximum-likelihood trees that do not differ statistically. Both trees were significantly shorter than a most parsimonious tree in which each subspecies was constrained to be monophyletic. Thus, the subspecies of E. obsoleta do not represent distinct genetic lineages. Instead, the evidence points to three well-supported mitochondrial DNA clades confined to particular geographic areas in the eastern United States. This research underscores the potential problems of recognizing subspecies based on one or a few characters.     

Comparison of life-history traits of the two male morphs of the bulb mite, Rhizoglyphus robini

Two basic male morphs occur in several species of the family Acaridae: heteromorphic fighters, possessing a thickened and sharply terminated third pair of legs, and homeomorphic males with unmodified legs. We compared major life-history traits of the two morphs in the bulb mite, Rhizoglyphus robini. We found no significant differences in development time or virility, but homeomorphic males lived 23% longer than heteromorphs. We discuss the possibility that the trade-off between longevity and adaptation for fighting maintains genetic variation for the male morph in the studied species.