The Brugia malayi genome project: expressed sequence tags and gene discovery

To advance and facilitate molecular studies of Brugia malayi, one of the causative agents of human lymphatic filariasis, an expressed sequence tag (EST)-based gene discovery programme has been carried out. Over 22,000 ESTs have been produced and deposited in the public databases by a consortium of laboratories from endemic and non-endemic countries. The ESTs have been analysed using custom informatic tools to reveal patterns of individual gene expression that may point to potential targets for future research on anti-filarial drugs and vaccines. Many genes first discovered as ESTs are now being analysed by researchers for immunodiagnostic, vaccine and drug target potential. Building on the success of the B. malayi EST programme, significant EST datasets are being generated for a number of other major parasites of humans and domesticated animals, and model parasitic species.

Analysis of genes expressed at the infective larval stage validates utility of Litomosoides sigmodontis as a murine model for filarial vaccine development

We used an expressed sequence tag approach to analyze genes expressed by the infective larvae of the rodent filarial parasite Litomosoides sigmodontis. One hundred fifty two new genes were identified, including several proposed as vaccine candidates in studies with human filarial parasites. Our findings have important implications for the use of L. sigmodontis as a model for filarial infection.

The small subunit ribosomal RNA sequence of Strongyloides stercoralis

The published small subunit rRNA (ssrRNA) gene sequences for Strongyloides ratti and Strongyloides stercoralis are remarkably divergent, particularly in the 5' 400 bases of the approximately 1700 base pair (bp) sequences. This level of divergence between species nominally in the same genus was unprecedented. We have redetermined the ssrRNA sequence of S. stercoralis and find that the published sequence is a chimaera of parasite and fungal segments. The true sequence for S. stercoralis ssrRNA is very similar to that of S. ratti.

Genes and genomes of Necator americanus and related hookworms

The human hookworms (Necator americanus and Ancylostoma duodenale) infect over one billion people. The phylogenetic relationships of the human hookworms suggest independent acquisition of the human host. The hookworms probably have a haploid chromosome number n = 6, and an XX-XO sex determination mechanism is likely to be used. Genetic and molecular research on hookworms is in its infancy, but several important genes and gene products have already been identified. Of note are cathepsin genes, a family of secreted proteins known as Ancylostoma activation-associated proteins and a family of anticoagulants. The inception of an expressed sequence tag program on the human hookworm, N. americanus, promises to yield many new genes with novel functions in the biology of these important parasites.

A survey of genes expressed in adults of the human hookworm, Necator americanus

Hookworms are gut-dwelling, blood-feeding nematodes that infect hundreds of millions of people, particularly in the tropics. As part of a program aiming to define novel drug targets and vaccine candidates for human parasitic nematodes, genes expressed in adults of the human hookworm Necator americanus were surveyed by the expressed sequence tag approach. In total 161 new hookworm genes were identified. For the majority of these, a function could be assigned by homology. The dataset includes proteases, protease inhibitors, a lipid binding protein, C-type lectins, an anti-bacterial factor, globins and other genes of interest from a drug or vaccine development viewpoint. Three different classes of small, secreted proteins were identified that may be involved in the host-parasite interaction, including potential potassium channel blocking peptides. One third of the genes were novel. These included highly expressed, secreted (glyco)proteins which may be part of the excretory-secretory products of these important pathogens. Of particular interest are a family of 9 genes with similarity to the immunomodulatory protein, neutrophil inhibitory factor, that may play a role in establishing an immunocompromised niche for this successful parasite.

Caenorhabditis elegans

Transparent, free-living nematode worm. Unsegmented body plan with full set of differentiated tissues (neural, endoderm, ectoderm and muscle). Genome size approximately 97 Mb, as five autosomes and one X sex chromosome. Fully sequenced genome, which comprises approximately 20 000 predicted genes. Defined cell lineage. Has made major contribution to studies of development, cell-to-cell signalling, cell ageing and cell death processes. Large-scale gene deletion, microarray analysis of gene expression and two-hybrid protein interaction analysis projects under way. Comparative studies mainly with C. briggsae, but also with other free-living and parasitic nematodes.

Caenorhabditis elegans

Transparent, free-living nematode worm. Unsegmented body plan with full set of differentiated tissues (neural, endoderm, ectoderm and muscle). Genome size approximately 97 Mb, as five autosomes and one X sex chromosome. Fully sequenced genome, which comprises approximately 20 000 predicted genes. Defined cell lineage. Has made major contribution to studies of development, cell-to-cell signalling, cell ageing and cell death processes. Large-scale gene deletion, microarray analysis of gene expression and two-hybrid protein interaction analysis projects under way. Comparative studies mainly with C. briggsae, but also with other free-living and parasitic nematodes.

Patterns and processes in the evolution of animal parasitic nematodes

Abstract

The parasitic Nematoda have traditionally been classified distinct from free-living species, and animal parasites treated separately from plant parasites. In classical concepts of phylogenetic relationships within the phylum, parasitic groups are usually afforded ordinal status and their origins are often obscure. We have been using molecular phylogenetics to examine the interrelationships of animal parasites with free-living and plant-parasitic groups, and find that a new view of the origins and radiation of animal parasites is warranted. Using sequence from the nuclear small subunit ribosomal RNA gene, we have constructed an alignment that allows robust phylogenetic inference. With this dataset, we place the Strongylida as a monophyletic clade nested within the Rhabditina. The Ascaridida, Oxyurida and Spirurida are closely related, but currently have no clear closest free-living sister taxon. Strongyloides spp. are rooted in a radiation of cephalobid/tylenchid species. Where available, other sequences in general confirm these relationships. Les Nematoda parasites ont été traditionnellement classifiés séparément des espèces libres, les parasites d’animaux étant traités séparément des parasites de plantes. Suivant les concepts classiques des relations phylogénétiques à l’intérieur du phylum, les groupes parasites sont habituellement traités au niveau ordinal et leurs origines sont souvent inconnues. Utilisant la phylogénie moléculaire, les interrelations des parasites animaux avec les groupes d’espèces libres et parasites de plantes ont été étudiées conduisant à la conclusion qu’une nouvelle approche des origines et de l’évolution des parasites animaux est nécessaire. Sur la base de la petite sous-unité nucléaire du gène de l’ARN ribosomal, un alignement est proposé qui permet une inférence phylogénétique solide. Avec cet ensemble de données, les Strongylida sont considérés comme un clade monophylétique emboîté au sein des Rhabditina. Les Ascaridida, Oxyurida et Spirurida sont étroitement reliés, mais jusqu’à présent sans relation étroite claire avec des taxons de nématode libre. Les Strongyloides spp. ont évolué à partir des cephalobides/tylenchides. Lorsqu’elles sont disponibles, les données issues d’autres séquences confirment le plus souvent ces relations.

Reports from the cutting edge of parasitic genome analysis

This new feature in Parasitology Today will host reports from the laboratories involved in genomics of parasites, be that sequencing, mapping or 'functional genomics' - the mining and analysis of the sequence datasets, and the development of postgenomics tools to examine gene expression, response to drugs and population variability. It will publicize new technology to wider audiences, let communities of researchers know about novel resources (particularly those available through the World Wide Web) and highlight significant advances in the understanding of parasitic genomes through functional genomics.

Parasitic helminth genomics. Filarial Genome Project

The initiation of genome projects on helminths of medical importance promises to yield new drug targets and vaccine candidates in unprecedented numbers. In order to exploit this emerging data it is essential that the user community is aware of the scope and quality of data available, and that the genome projects provide analyses of the raw data to highlight potential genes of interest. Core bioinformatics support for the parasite genome projects has promoted these approaches. In the Brugia genome project, a combination of expressed sequence tag sequencing from multiple cDNA libraries representing the complete filarial nematode lifecycle, and comparative analysis of the sequence dataset, particularly using the complete genome sequence of the model nematode C. elegans, has proved very effective in gene discovery.

Chemiluminescent detection of sequential DNA hybridizations to high-density, filter-arrayed cDNA libraries: a subtraction method for novel gene discovery

A chemiluminescent approach for sequential DNA hybridizations to high-density filter arrays of cDNAs, using a biotin-based random priming method followed by a streptavidin/alkaline phosphatase/CDP-Star detection protocol, is presented. The method has been applied to the Brugia malayi genome project, wherein cDNA libraries, cosmid and bacterial artificial chromosome (BAC) libraries have been gridded at high density onto nylon filters for subsequent analysis by hybridization. Individual probes and pools of rRNA probes, ribosomal protein probes and expressed sequence tag probes show correct specificity and high signal-to-noise ratios even after ten rounds of hybridization, detection, stripping of the probes from the membranes and rehybridization with additional probe sets. This approach provides a subtraction method that leads to a reduction in redundant DNA sequencing, thus increasing the rate of novel gene discovery. The method is also applicable for detecting target sequences, which are present in one or only a few copies per cell; it has proven useful for physical mapping of BAC and cosmid high-density filter arrays, wherein multiple probes have been hybridized at one time (multiplexed) and subsequently "deplexed" into individual components for specific probe localizations.

Phylogeny of Bursaphelenchus species derived from analysis of ribosomal internal transcribed spacer DNA sequences

Abstract

Bursaphelenchus species can cause serious economic damage to pine forestry, and are widely distributed across the globe. The genetic structure of the B. mucronatus-B. xylophilus species group was investigated using sequences of the internal transcribed spacers of the ribosomal RNA gene repeat as a marker. Analysis of the ITS from 11 Bursaphelenchus isolates, using Aphelenchoides rhytium as an outgroup, supports the perception that the two species are distinct genetic entities. Significant divergence was however found within each species. ITS sequence analysis does not support a separation of European and Japanese B. mucronatus into distinct species-level taxa. Phylogenie des especes de Bursaphelenchus issue d'une analyse des sequences du DNA ribosomique de l'espaceur interne transcrit - Les especes de Bursaphelenchus peuvent provoquer de serieux degats aux cultures de pins et sont largement reparties dans le monde. La structure genetique des especes du groupe B.mucronatus-B. xylophilus a ete etudiee en utilisant comme marqueur des sequences repetees de l'espaceur interne transcrit du gene de l'ARN ribosomique. L'analyse des ITS de 11 isolats de Bursaphelenchus, en utilisant Aphelenchoides rhytium comme un extra-groupe, conforte l'idee que les deux especes sont des entites genetiques distinctes. Une divergence significative a cependant ete trouvee a l'interieur de chaque especes. L'analyse des sequences des ITS n'accredite pas la separation des B. mucronatus europeen et japonais en deux especes distinctes.

Caenorhabditis elegans is a nematode

Caenorhabditis elegans is a rhabditid nematode. What relevance does this have for the interpretation of the complete genome sequence, and how will it affect the exploitation of the sequence for scientific and social ends? Nematodes are only distantly related to humans and other animal groups; will this limit the universality of the C. elegans story? Many nematodes are parasites; can knowledge of the C. elegans sequence aid in the prevention and treatment of disease?

Structural, functional, and genetic characterization of Gastrophilus hemoglobin

Hemoglobin of Gastrophilus intestinalis (Insecta, Diptera), was purified and characterized. At least two isoforms have been identified by isoelectrofocusing, mass spectrometry, and genomic Southern blotting. Functional studies show a high oxygen affinity due to a low ligand dissociation rate (koff = 2.4 s-1) and a relatively high autoxidation rate (t1/2 = 1.6/h). The globins were separated under denaturing conditions, and the sequence of Hb1 (Mr = 17,965 +/- 2) was determined at the protein and DNA level. The open reading frame codes for a polypeptide of 150 amino acids. Although the globin is distantly related to globins from other species, it has a low penalty score against globin templates. Freshly isolated hemoglobin was crystallized from polyethylene glycol. Crystals contain two hemoglobin molecules per asymmetric unit. Solution of the three-dimensional structure by molecular replacement could not be achieved, possibly due to the presence of three protein isoforms in the crystals. In order to determine its three-dimensional structure, G. intestinalis Hb1 was overexpressed in Escherichia coli, resulting in a fully functional molecule as confirmed by ligand binding affinity. The globin gene contains two introns at positions D7.0 and G7.0. The D7.0 intron is unprecedented, suggesting that globin gene evolution is much more complex than originally thought.

Gene structure, activity and localization of a catalase from intracellular bacteria in Onchocerca volvulus

Within the context of studies on the antioxidant enzymes in Onchocerca volvulus, DNA clones encoding catalase (CAT) were isolated from an O. volvulus adult lambda zapII cDNA library. Analysis of their nucleotide and encoded amino acid sequences revealed that they derive from intracellular bacteria, rather than the O. volvulus nuclear genome. The endobacterial CAT gene was found to lie in a gene cluster, followed by a ferritin gene and an excinuclease gene. The endobacterial CAT gene encodes a functional enzyme capable of detoxifying H2O2, demonstrated by producing an active recombinant protein in an E. coli expression system. The purified 54 kDa protein has CAT activity over a broad pH range, with a specific activity of 103,000 +/- 3000 U mg(-1). The optical spectrum of the endobacterial CAT shows that it is a ferric haem-containing protein with a Soret band at 405 nm. To investigate the phylogeny of the intracellular bacterium in O. volvulus, a segment of the 16S rRNA gene was amplified from total genomic DNA by a polymerase chain reaction using universal eubacterial primers. A phylogenetic analysis of the O. volvulus-derived 16S rRNA sequence revealed that the endobacterium belongs to a distinct Wolbachia clade of the order Rickettsiales. Onchocercomata and biopsies containing different onchocercal species were immunohistochemically stained using polyclonal antibodies raised against the recombinant endobacterial CAT. CAT was detected in the endobacteria in the hypodermis of adult male and female O. volvulus, O. ochengi, O. gibsoni and O. fasciata. The endobacterial enzyme was also detected in onchocercal oocytes and all embryonic stages including intrauterine microfilariae as well as skin microfilariae. O. volvulus thus harbours Wolbachia-like endosymbionts which are transovarially transmitted and show particular affinity for the hypodermal tissues of the lateral chords.

Whose fault is it? People's own conceptions of the reasons for health inequalities

How do people themselves think about inequalities in health? The topic has rarely been investigated, and oblique evidence has to be drawn from research on general lay ideas about health and the causes of illness. Data from a large British survey are combined with a review of the extensive body of, more usually, qualitative research on attitudes to health in Western industrialised societies. One tentative conclusion is that social inequality in health is not a topic which is very prominent in lay presentations, and paradoxically this is especially true among those who are most likely to be exposed to disadvantaging environments. Possible explanations are offered in terms of the effects of widespread "health promotion" activities, and the way in which lay theorising incorporates relationships between the group and the individual. The methods used in asking people to talk about health are also relevant: accounts of health and illness are accounts of social identity, and it is unreasonable to expect people to devalue that identity by labelling their own "inequality".

Nematode spliced leaders--ubiquity, evolution and utility

Most nematode messenger RNAs (mRNAs) have at their 5' end a common 22 nucleotide leader sequence, the trans-spliced leader or SL1. The presence of this leader on some but not all mRNAs raises several questions: What is the role of the spliced leader in mRNA maturation, stability and translation? Why do some genes have a spliced leader and others not? What is the evolutionary origin of this trans-splicing mechanism? Recently, additional trans-spliced leaders (SL2, 3, 4, 5) have been described. What role do these variants play in nematode gene expression? While definitive answers to these questions remain elusive, it is clear that the spliced leader will significantly facilitate the cloning and sequence analysis of most nematode mRNAs.