Infection by the castrating parasitic nematode Sphaerularia bombi changes gene expression in Bombus terrestris bumblebee queens.

Parasitism can result in dramatic changes in host phenotype, which are themselves underpinned by genes and their expression. Understanding how hosts respond at the molecular level to parasites can therefore reveal the molecular architecture of an altered host phenotype. The entomoparasitic nematode Sphaerularia bombi is a parasite of bumblebee (Bombus) hosts where it induces complex behavioural changes and host castration. To examine this interaction at the molecular level, we performed genome-wide transcriptional profiling using RNA-Sequencing (RNA-Seq) of S. bombi-infected Bombus terrestris queens at two critical time-points: during and just after overwintering diapause. We found that infection by S. bombi affects the transcription of genes underlying host biological processes associated with energy usage, translation, and circadian rhythm. We also found that the parasite affects the expression of immune genes, including members of the Toll signalling pathway providing evidence for a novel interaction between the parasite and the host immune response. Taken together, our results identify host biological processes and genes affected by an entomoparasitic nematode providing the first steps towards a molecular understanding of this ecologically important host-parasite interaction.

Ultrasequencing of the meiofaunal biosphere: practice, pitfalls and promises.

Biodiversity assessment is the key to understanding the relationship between biodiversity and ecosystem functioning, but there is a well-acknowledged biodiversity identification gap related to eukaryotic meiofaunal organisms. Meiofaunal identification is confounded by the small size of taxa, morphological convergence and intraspecific variation. However, the most important restricting factor in meiofaunal ecological research is the mismatch between diversity and the number of taxonomists that are able to simultaneously identify and catalogue meiofaunal diversity. Accordingly, a molecular operational taxonomic unit (MOTU)-based approach has been advocated for en mass meiofaunal biodiversity assessment, but it has been restricted by the lack of throughput afforded by chain termination sequencing. Contemporary pyrosequencing offers a solution to this problem in the form of environmental metagenetic analyses, but this represents a novel field of biodiversity assessment. Here, we provide an overview of meiofaunal metagenetic analyses, ranging from sample preservation and DNA extraction to PCR, sequencing and the bioinformatic interrogation of multiple, independent samples using 454 Roche sequencing platforms. We report two examples of environmental metagenetic nuclear small subunit 18S (nSSU) analyses of marine and tropical rainforest habitats and provide critical appraisals of the level of putative recombinant DNA molecules (chimeras) in metagenetic data sets. Following stringent quality control measures, environmental metagenetic analyses achieve MOTU formation across the eukaryote domain of life at a fraction of the time and cost of traditional approaches. The effectiveness of Roche 454 sequencing brings substantial advantages to studies aiming to elucidate the molecular genetic richness of not only meiofaunal, but also all complex eukaryotic communities.

Duplication and divergence: the evolution of nematode globins.

In common with many other groups, nematodes express globins with unknown functions. Nematode globin-like genes can be divided into class 1 globins, similar to vertebrate myoglobins, and a wide range of additional classes. Here we show that class 1 nematode globins possess a huge amount of diversity in gene sequence and structure. There is evidence for multiple events of gene duplication, intron insertion and loss between species, and for allelic variation effecting both synonymous and non-synonymous sites within species. We have also examined gene expression patterns in class I globins from a variety of species. The results show variation in the degree of gene expression, but the tissue specificity and temporal specificity of expression may be more conserved in the phylum. Because the structure-function relationships for the binding and transport of oxygen by globins are well understood, the consequences of genetic variation causing amino acid changes are explored. The gene family shows great promise for discovering unique insights into both structure-function relationships of globins and their physiologial roles.

Tetracycline therapy targets intracellular bacteria in the filarial nematode Litomosoides sigmodontis and results in filarial infertility.

Intracellular bacteria have been described in several species of filarial nematodes, but their relationships with, and effects on, their nematode hosts have not previously been elucidated. In this study, intracellular bacteria were observed in tissues of the rodent parasite Litomosoides sigmodontis by transmission electron microscopy and by immunohistochemistry using antiendobacterial heat shock protein-60 antisera. Molecular phylogenetic analysis of the bacterial 16S ribosomal RNA gene, isolated by PCR, showed a close relationship to the rickettsial Wolbachia endobacteria of arthropods and to other filarial intracellular bacteria. The impact of tetracycline therapy of infected rodents on L. sigmodontis development was analyzed in order to understand the role(s) these bacteria might play in filarial biology. Tetracycline therapy, when initiated with L. sigmodontis infection, eliminated the bacteria and resulted in filarial growth retardation and infertility. If initiated after microfilarial development, treatment reduced filarial fertility. Treatment with antibiotics not affecting rickettsial bacteria did not inhibit filarial development. Acanthocheilonema viteae filariae were shown to lack intracellular bacteria and to be insensitive to tetracycline. These results suggest a mutualistic interaction between the intracellular bacteria and the filarial nematode. Investigation of such a mutualism in endobacteria-containing human filariae is warranted for a potential chemotherapeutic exploitation.

Alimentary fibropapilloma in cattle: a spontaneous tumor, nonpermissive for papillomavirus replication.

Fibropapillomatosis of the upper alimentary canal of cattle is described. The tumors, found in the esophagus, esophageal groove, and rumen, showed involvement of the subepithelial fibroblasts as well as of the squamous epithelial layer. Although the fibropapilloma cells harbored multiple episomal copies of the genome of bovine papillomavirus type 2 (BPV-2) easily detected by hybridization techniques, no mature virus could be isolated from these lesions or seen by electron microscopy, and no viral antigen could be detected by immunohistochemical methods. It would appear, therefore, that within the limitations of the techniques employed the alimentary canal epithelium and the underlying fibroblasts, while allowing BPV-2 DNA replication, are nonpermissive for the expression of the viral vegetative functions and that transformation of the epithelial cells, like transformation of fibroblasts, can take place in the absence of infectious viral progeny.

Sequence, expression and evolution of the globins of the parasitic nematode Nippostrongylus brasiliensis.

The globins of the nematode parasite Nippostrongylus brasiliensis have oxygen affinities 100-fold higher than the rodent host's haemoglobins. Two isoforms are found, one located in the cuticle, and the other in the body of the nematode. Both isoforms have been cloned and analysed for clues as to function and evolution. The body globin isoform is first expressed upon invasion of the mammalian host. The abundant cuticular globin is expressed only by adult nematodes in the gut, and differs significantly from the body globin. Both globins are found as trans-spliced mRNAs: the developmental pattern of expression of the mRNA parallels the protein expression. The pattern of the nematode globin genes is complex. Comparison with other nematode globin sequences suggests that N. brasiliensis is more closely related to Caenorhabditis elegans than to ascarid species. At least two gene duplication events are predicted: gene duplication preceded the radiation of the important vertebrate-parasitic strongylid nematode species. Both N. brasiliensis globins have a central intron the exact position of which suggests that it arose from an independent insertion event in the strongylid-rhabditid line. The globins have been expressed in Escherichia coli as functional holenzymes as a prelude to studies to elucidate the origin of their extraordinary oxygen affinity.

Specific serodiagnosis of visceral leishmaniasis using a Leishmania donovani antigen identified by expression cloning.

A lambda gt11 expression library was constructed using mRNA from the promastigote form of Leishmania donovani (African isolate MHOM/ET/67/HU3). The library was screened with serum obtained from a patient who contracted visceral leishmaniasis in the Sudan. Several cDNA clones which expressed beta-galactosidase/L. donovani antigen fusion proteins were isolated. One of these clones corresponded to a 60 kDa membrane-associated antigen. By a Western blot assay antibodies against the fusion protein were detected universally in the sera of visceral leishmaniasis patients. They were not detected in sera from patients with cutaneous leishmaniasis or other parasitic protozoan infections. The gene coding for this antigen was specific to the genus Leishmania as judged by DNA hybridisation, and its chromosomal location was conserved. A 20 kb mRNA was detected on Northern blots of promastigote RNA.

Differentially expressed, abundant trans-spliced cDNAs from larval Brugia malayi.

Isolation and cloning of abundant reverse transcriptase-polymerase chain reaction (RT-PCR) products from the filarial nematode Brugia malayi using the conserved nematode spliced leader sequence and poly A as amplification targets has allowed us to identify abundant, stage specific transcripts from infective and post-infective larvae. The predicted protein products of the most prominent full-length transcripts from mosquito-derived L3 parasites are: (i) Bm-ALT-1, a homologue of a Dirofilaria immitis abundant larval protein: (ii) Bm-CPI-1, a cystatin-type cysteine protease inhibitor; (iii) Bm-ALT-3, a novel predicted 6 kDa glycine/tyrosine-rich protein; and (iv) Bm-TPH-1, a homologue of a mammalian translationally-controlled tumour protein. Some transcripts were not full-length but had mis-primed at A-rich stretches of coding sequence: the most abundant of these was Bm-col-3, a which encodes a collagen homologous to Bp-COL-1 of Brugia pahangi. Similar analysis of abundant spliced leader (SL)/oligo-dT products from fourth-stage larvae 9 days post-infection yielded two dominant transcripts: (i) Bm-cdd-1, which encodes a protein with homology to cytidine deaminase, differing at only one amino acid position from its homologue described in Brugia pahangi; and (ii) the same truncated form of Bm-col-3 found in L3 preparations. Expression of the major transcripts was assessed by PCR amplification of cDNA libraries derived from each stage of the life cycle. alt1, alt-3 and cpi-1 were all found to be specific to the L3 stage, while cdd-1 was found only in the L4 cDNA library. Expression of these larval-specific transcripts was not detected in either microfilarial or adult libraries.

Characterisation of an immunodominant glycoprotein antigen of Onchocerca volvulus with homologues in other filarial nematodes and Caenorhabditis elegans.

The full-length cDNA corresponding to an Onchocerca volvulus antigen, OvMBP/11, which had been selected as a serodiagnostic tool was isolated, sequenced, and the native antigen encoded by the cDNA characterised. The cDNA encodes a protein of 20.5 kDa (termed Ov 20) containing a putative signal peptide. Southern blot analysis indicates that there is only a single O. volvulus gene corresponding to Ov 20 but it has significant sequence similarity to genes corresponding to two 20.5-kDa predicted proteins of Caenorhabditis elegans. Homologues of the Ov 20 gene were detected at high stringency by Southern blot in the other Onchocerca species O. gibsoni, and O. gutturosa and at lower stringency in the related filarial nematodes Brugia malayi and Acanthocheilonema viteae. The Ov 20 native antigen has two molecular mass forms, 20 and 22 kDa, in all the life cycle stages studied. These isoforms have different levels of N-linked glycosylation on a peptide backbone of 17.5 kDa. Immunolocalisation and in situ hybridisation studies demonstrated that Ov 20 is transcribed and translated in the body wall of adult females and also in microfilariae, third and fourth stage larvae. Antigen was detected in the supernatant of in vitro cultured adult female nematodes. The B. malayi and A. viteae homologues are antigenically cross-reactive to Ov 20, share the same size peptide backbone but differ in their degree of glycosylation.

Genes expressed in Brugia malayi infective third stage larvae.

We have used a tag sequencing approach to survey genes expressed in the third stage infective larvae of the human filarial nematode parasite Brugia malayi. RNA was isolated from late vector-stage L3 larvae after days 9 or 10 of infection in mosquitos, and converted to cDNA by reverse transcriptase. Double-stranded cDNA was produced by either conventional methods (non-SL cDNA library) or by PCR using the nematode spliced leader (SLI) and oligo(dT) primers (SL cDNA library). Two clone libraries (one from SL and one from non-SL cDNAs) were constructed in lambda ZapII. A set of these full-length clones was selected and 596 inserts were sequenced from the 5' end. We have identified 364 B. malayi genes (the majority of which are new) that encode housekeeping proteins, structural proteins, proteins of immediate immunological or drug-discovery interest as well as a large class of novel sequences which may prove to have significant involvement in host invasion. Extensive, genome-wide approaches to the analysis of larval gene expression are now possible for B. malayi. We present several examples of this approach.

Phylogeny of Wolbachia in filarial nematodes.

Intracellular bacteria have been observed in various species of filarial nematodes (family Onchocercidae). The intracellular bacterium of the canine filaria Dirofilaria immitis has been shown to be closely related to Wolbachia, a rickettsia-like micro-organism that is widespread among arthropods. However, the relationships between endosymbionts of different filariae, and between these and the arthropod wolbachiae, appear not to have been studied. To address these issues we have examined ten species of filarial nematodes for the presence of Wolbachia. For nine species, all samples examined were PCR positive using primers specific for the ftsZ gene of Wolbachia. For one species, the examined samples were PCR negative. Sequences of the amplified ftsZ gene fragments of filarial wolbachiae fall into two clusters (C and D), which are distinct from the A and B clusters recognized for arthropod wolbachiae. These four lineages (A-D) are related in a star-like phylogeny, with higher nucleotide divergence observed between C and D wolbachiae than that observed between A and B wolbachiae. In addition, within each of the two lineages of filarial wolbachiae, the phylogeny of the symbionts is consistent with the host phylogeny. Thus, there is no evidence for recent Wolbachia transmission between arthropods and nematodes. Endosymbiont 16S ribosomal DNA sequences from a subset of filarial species support these findings.

Caenorhabditis elegans as a model for parasitic nematodes.

Caenorhabditis elegans has become a popular model system for genetic and molecular research, since it is easy to maintain and has a very fast life-cycle. Its genome is small and a virtually complete physical map in the form of cosmids and YAC clones exists. Thus it was chosen as a model system by the Genome Project for sequencing, and it is expected that by 1998 the complete sequence (100 million bp) will be available. The accumulated wealth of information about C. elegans should be a boon for nematode parasitologists, as many aspects of gene regulation and function can be studied in this simple model system. A large array of techniques is available to study many aspects of C. elegans biology. In combination with genome projects for parasitic nematodes, conserved genes can be identified rapidly. We expect many new areas of fertile research that will lead to new insights in helminth parasitology, which are based not only on the information gained from C. elegans per se, but also from its use as a heterologous system to study parasitic genes.

The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi.

The Filarial Genome Project (FGP) was initiated in 1994 under the auspices of the World Health Organisation. Brugia malayi was chosen as the model organism due to the availability of all life cycle stages for the construction of cDNA libraries. To date, over 20000 cDNA clones have been partially sequenced and submitted to the EST database (dbEST). These ESTs define approximately 7000 new Brugia genes. Analysis of the EST dataset provides useful information on the expression pattern of the most abundantly expressed Brugia genes. Some highly expressed genes have been identified that are expressed in all stages of the parasite's life cycle, while other highly expressed genes appear to be stage-specific. To elucidate the structure of the Brugia genome and to provide a basis for comparison to the Caenorhabditis elegans genome, the FGP is also constructing a physical map of the Brugia chromosomes and is sequencing genomic BAC clones. In addition to the nuclear genome, B. malayi possesses two other genomes: the mitochondrial genome and the genome of a bacterial endosymbiont. Eighty percent of the mitochondrial genome of B. malayi has been sequenced and is being compared to mitochondrial sequences of other nematodes. The bacterial endosymbiont genome found in B. malayi is closely related to the Wolbachia group of rickettsia-like bacteria that infects many insect species. A set of overlapping BAC clones is being assembled to cover the entire bacterial genome. Currently, half of the bacterial genome has been assembled into four contigs. A consortium has been established to sequence the entire genome of the Brugia endosymbiont. The sequence and mapping data provided by the FGP is being utilised by the nematode research community to develop a better understanding of the biology of filarial parasites and to identify new vaccine candidates and drug targets to aid the elimination of human filariasis.

Cuticular proteins of Brugia filarial parasites.

Surface-labelling techniques have been used to delineate a number of constituent molecules of the cuticle in adult stage Brugia malayi and Brugia pahangi. These molecules can be separated by virtue of their physical properties, and localised either by sequential solubilisation of intact cuticles or immunoelectron microscopy with relevant antisera. The major structural components of the cuticular matrix consist of a set of collagenous proteins of diverse molecular weight ranging from 36 to 160 kDa, cross-linked by disulphide bonds and confined to the basal and inner cortical layers. Each stage of the parasite has a distinctive set of between 12 to 25 collagenous proteins whose synthesis is regulated temporally with respect to moulting. As in other nematodes, the outer cortex and epicuticle is composed of a cross-linked insoluble proteinaceous structure. Two non-structural and water-soluble proteins are also resolved by Iodogen-mediated labelling; a 15 kDa peptide which shows no evidence of glycosylation, and a major 29 kDa glycoprotein, which carries at least two N-linked oligosaccharide chains and which we have termed Gp29. The former protein can be detected in L3, L4 and adult B. malayi by surface labelling, whereas Gp29 appears to be restricted to L4 and adult worms. The possible significance of cuticular proteins as targets of immunity or causative agents of pathology is discussed.

Biochemical Analysis of Caenorhabditis elegans Surface Mutants.

A collection of Caenorhabditis elegans mutants that show ectopic surface lectin binding (Srf mutants) was analyzed to determine the biochemical basis for this phenotype. This analysis involved selective removal or labeling of surface components, specific labeling of surface glycans, and fractionation of total protein with subsequent detection of wheat germ agglutinin (WGA) binding proteins. Wild-type and mutant nematodes showed no differences in their profiles of extractable surface glycoproteins or total WGA-binding proteins, suggesting that the ectopic lectin binding does not result from the novel expression of surface glycans. Instead, these results support a model in which ectopic lectin binding results from an unmasking of glycosylated components present in the insoluble cuticle matrix of wild-type animals. To explain the multiple internal defects found in some surface mutants, we propose that these mutants have a basic defect in protein processing. This defect would interfere with the expression of the postulated masking protein(s), as well as other proteins required for normal development.

An expressed sequence tag survey of gene expression in the pond snail Lymnaea stagnalis, an intermediate vector of trematodes [corrected].

The pond snail Lymnaea stagnalis is an intermediate vector for the liver fluke Fasciola hepatica, a common parasite of ruminants and humans. Yet, despite being a disease of medical and economic importance, as well as a potentially useful comparative tool, the genetics of the relationship between Lymnaea and Fasciola has barely been investigated. As a complement to forthcoming F. hepatica expressed sequence tags (ESTs), we generated 1320 ESTs from L. stagnalis central nervous system (CNS) libraries. We estimate that these sequences derive from 771 different genes, of which 374 showed significant similarity to proteins in public databases, and 169 were similar to ESTs from the snail vector Biomphalaria glabrata. These L. stagnalis ESTs will provide insight into the function of the snail CNS, as well as the molecular components of behaviour and response to parasitism. In the future, the comparative analysis of Lymnaea/Fasciola with Biomphalaria/Schistosoma will help to understand both conserved and divergent aspects of the host-parasite relationship. The L. stagnalis ESTs will also assist gene prediction in the forthcoming B. glabrata genome sequence. The dataset is available for searching on the world-wide web at http://zeldia.cap.ed.ac.uk/mollusca.html.

Cuticle surface proteins of wild type and mutant Caenorhabditis elegans.

The molecular components of the surface of the free-living nematode Caenorhabditis elegans have been identified by surface-specific radioiodination. Four compartments were defined by fractionation of labeled wild type (N2 strain) adult hermaphrodites. Organic solvents extracted cuticular lipids. Homogenization in detergents released a single, non-collagenous, hydrophobic protein. This is not glycosylated and is a heterodimer of 6.5- and 12-kDa subunits. The third compartment, proteins solubilized by reducing agents, included both the cuticular collagens and the heterodimer. Residual material corresponds to the cuticlin fraction. Larval stages showed a similar pattern, except that the dauer larva had an additional 37-kDa detergent-soluble protein. Other species of rhabditid nematodes displayed similar profiles, and comparison with parasitic species suggests that this simple pattern may be primitive in the Nematoda. A C. elegans strain mutant in cuticular collagen (rol-6) had a pattern identical to that of wild type, but another morphological mutant (dpy-3) [corrected] and several mutants that differ in surface reactivity to antibody and lectins (srf mutants) also had striking differences in surface labeling patterns.

Nemoglobins: divergent nematode globins.

Globins are proteins commonly associated with oxygen transport in vertebrate blood, but the invertebrate phyla display a wide variety of globin types that reflect their disparate life styles and evolutionary history. It has been known for over 100 years that parasitic nematodes contain globins, but recent molecular investigations are only now beginning to shed some light on their curious properties. Mark Blaxter here describes the diversity of the different globins found in nematodes, and reviews emerging data on their evolution and function.