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PubMed2005

RNA interference in Haemonchus contortus: suppression of beta-tubulin gene expression in L3, L4 and adult worms in vitro.

We have used RNAi to target two beta-tubulin genes in the parasitic stages of Haemonchus contortus in vitro. Soaking exsheathed-L3, L4 and adult worms in medium containing dsRNA resulted in a significant decrease (greater than 1000-fold in some cases) in the expression of the specific beta-tubulin transcript, as measured by quantitative PCR. During the initial 24h exposure to the dsRNA, the gene suppression effect was quite specific to the targeted gene. Six days after initial exposure to dsRNA, treated L3 worms were less able to migrate through a filter mesh, indicating decreased motility, and showed less development to the L4 stage than control larvae. The gene suppression effect occurs in exsheathed L3 larvae despite the fact that this life stage does not have functioning mouthparts, indicating that uptake of dsRNA does not depend on its ingestion. Suppression occurred with dsRNA presented in 'naked' or liposome-encapsulated forms, indicating that a liposome formulation was not necessary for uptake to occur. Adult worms also showed significant gene suppression, however, they did not show any reduced motility compared to controls over a 3-day period. Adult worms treated with ivermectin to paralyse their pharynx, still showed significant gene suppression, again suggesting that uptake of dsRNA does not require ingestion. We have shown that soaking in dsRNA is an effective method for RNAi with the parasitic stages of H. contortus, and, hence, may offer significant potential as a tool for studying gene function in this parasite species.

Animals↗
PubMed2004

Molecular cloning of the swine IL-4 receptor alpha and IL-13 receptor 1-chains: effects of experimental Toxoplasma gondii, Ascaris suum and Trichuris suis infections on tissue mRNA levels.

IL-4 and IL-13 are multi-functional cytokines with overlapping roles in the host defense against infection. Equally important in the regulation of IL-4 and IL-13 are their associated receptors. Though, their functional receptor complexes and signaling pathways are intricate and in some cases, share common elements, the specificity of the responses, nonetheless, resides in the structure and binding of the alpha-chain components. This report presents the cloning of the swine receptors IL-4Ralpha and IL-13Ralpha1 and the effects of parasite infection on their transcription. Pairwise alignment of predicted amino acid sequences indicates that the swine IL-13Ralpha1 is 86, 83, and 72% similar to canine, human and mouse sequences, respectively. Amino acid sequence conservation is appreciably lower between the swine IL-4Ralpha sequence and those from equine (72%), human (66%), and mouse (49%); however, noteworthy similarities were observed in their overall predicted secondary structures predominantly among the swine, equine, and human homologues. Relative levels of receptor mRNA in tissues from swine experimentally infected with the protozoan, Toxoplasma gondii (T. gondii) or the nematodes Ascaris suum (A. suum) or Trichuris suis (T. suis), which are known to induce Th1 or Th2 host responses, respectively, were measured by real-time PCR. Results indicated that within 14 days following infection, overall mRNA levels for IL-4Ralpha and IL-13Ralpha1 were elevated in T. gondii-infected animals and reduced in A. suum-infected animals. Levels of swIL-4Ralpha and swIL-13Ralpha1 mRNA in T. suis-infected animals varied coincidentally with the course of the infection and the location of the analyzed tissue.

Amino Acid Sequence↗
PubMed2006

The frataxin-encoding operon of Caenorhabditis elegans shows complex structure and regulation.

The genome of the nematode Caenorhabditis elegans is unusual among eukaryotes, in that it contains operons. Approximately 15% of genes in the worm are clustered into groups of between two and eight genes, which are under the control of shared regulatory sequences. Polycistronic transcripts from such operons are trans-spliced, during transcription, to produce mature monocistronic messengers. The C. elegans frataxin gene, frh-1, is encoded in the operon CEOP2232. This is one of the largest operons identified thus far in the C. elegans genome. Here we describe in detail the structure of all of the coding units within this operon. The operon is composed of eight genes of a diverse nature, organized in a complex structure. We have produced transgenic strains carrying fusions between gfp and a number of genes from the operon. These constructs show complex differential expression patterns that suggest the presence of internal promoters and regulatory sequences in the operon. This organization would permit both coordinated expression and differential expression of the components of the CEOP2232 operon. The heterogeneity of the genes, and their complex expression patterns, suggests that the clustering of CEOP2232 is not due to a need for synchronized expression of genes involved in the same physiological pathway.

Animals↗
PubMed2006

Nematodes of the genus Pristionchus are closely associated with scarab beetles and the Colorado potato beetle in Western Europe.

Evolutionary developmental biology examines how changes in developmental programmes give rise to developmental and, ultimately, morphological novelty. To this end, comparisons of related but distinct organisms have to be performed. The diplogastrid nematode Pristionchus pacificus has been developed as a satellite system for a detailed comparison of various developmental processes to the model organism Caenorhabditis elegans, a rhabditid nematode. In addition to developmental and genetic studies, a genomic platform has been established to analyse the biology of this organism. However, only little is known about where and how Pristionchus pacificus and its relatives live in the wild. Here we show that nematodes of the genus Pristionchus live in close association with scarabaeoid beetles and the Colorado potato beetle. In total, we generated 371 isogenic female lines from 4242 beetles collected at 25 sampling sites all over Europe. Isogenic female lines were subjected to sequence analysis and mating experiments for species determination. The 371 isolates fell into six species. Two hermaphroditic species account for about 60% of the collected nematodes. We found Pristionchus maupasi almost exclusively on cockchafers and Pristionchus entomophagus predominantly on dung beetles. Colorado potato beetles carried the gonochoristic species Pristionchus uniformis, which was only rarely observed on scarabaeoid beetles. We describe the initial evidence for the association of Pristionchus nematodes with beetles and provide a phylogeny based on sequence analysis of the small subunit ribosomal RNA gene.

Animals↗
PubMed2002

The minimal tRNA: unique structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) having a short T arm and lacking the entire D arm.

The tertiary structure of Ascaris suum mitochondrial tRNA(Ser)(UCU) was examined by nuclear magnetic resonance analysis using its transcript, since tRNA(Ser)(UCU), lacking the D arm and possessing a truncated T arm, is the shortest of all the known tRNAs. Most basepairs in the proposed secondary structure of tRNA(Ser)(UCU) were shown to exist, but the connector region comprising the truncated D loop and the extra loop was flexible. This flexibility, would enable adjustment of the mutual distance between the 3'-terminus and the anticodon consistent with that of usual tRNAs. Thus, tRNA(Ser)UCU appears to function in a similar way to that of usual tRNAs in the ribosome.

Animals↗
PubMed1998

Non-monophyly of the monogeneans?

There is currently no congruence between phylogenies based on morphology, in which the Monogenea are considered a monophylum, and molecular phylogenies based on 18S or 28S rDNA, in which the Monogenea are never considered monophyletic. However, all analyses based on morphology and sperm characters or molecular data found constantly the two subgroups composing the Monogenea, namely the Monopisthocotylea and Polyopisthocotylea (or Polyonchoinea and Oligonchoinea) to be independently monophyletic. This conflict concerns not only monophyly of the Monogenea, but also the relationships of the Monopisthocotylea and Polyopisthocotylea with the Trematoda (Digenea and Aspidogastrea) and Cestoda, and therefore the phylogeny of the parasitic Platyhelminthes as a whole. It is concluded that a reappraisal of morphological synapomorphies should be undertaken.

Animals↗
PubMed1999

ITS2 sequences of Dictyocaulus species from cattle, roe deer and moose in Sweden: molecular evidence for a new species.

Total DNA was isolated from adult lungworms of the genus Dictyocaulus, collected from cattle, moose (Alces alces) and roe deer (Capreolus capreolus) in Sweden. The second ribosomal internal transcribed spacer was amplified with PCR, and DNA sequences were determined from nine individual worms that all came from different hosts in order to avoid analysis of siblings. The sequence data obtained were aligned and compared with similar data derived from German lungworm isolates from cattle and fallow deer (Cervus dama). These analyses clearly showed that specimens of the cattle lungworm, Dictyocaulus viviparus, were almost identical irrespective of their geographical origin. However, when the second internal transcribed spacer sequence of D. viviparus was compared with that of lungworms from moose and roe deer, major differences were noticed. Although lungworms collected from these cervids had identical second internal transcribed spacer sequences, they proved to be genetically different from Dictyocaulus eckerti of German fallow deer, displaying a 66.5% similarity. In an evolutionary tree, inferred by maximum likelihood analysis, the Dictyocaulus species from cattle and wild cervids clustered as compared with Dictyocaulus filaria from sheep. The study has thus demonstrated that A. alces and C. capreolus in Sweden are parasitised with a Dictyocaulus species that is different from D. viviparus and D. eckerti, indicating that we are dealing with a new species in moose and roe deer.

Animals↗
PubMed1999

Up-regulation of extracellular copper/zinc superoxide dismutase mRNA after transmission of the filarial parasite Acanthocheilonema viteae in the vertebrate host Meriones unguiculatus.

The gene encoding the cytoplasmic copper/zinc superoxide dismutase (AVSOD1) from the filarial parasite Acanthocheilonema viteae was isolated from a genomic DNA library using a degenerate oligonucleotide probe. Additionally, cDNAs of the AVSOD1 and the secreted extracellular SOD (AVSOD2) were both cloned by RT-PCR, and the AVSOD2 was expressed at high levels in E. coli. The amino acid sequence of the AVSOD1 is 89.5 and 87.5% identical to that of the corresponding enzymes of Brugia pahangi and Onchocerca volvulus, respectively. In contrast, the AVSOD2 shows a lower degree of identity to the other filarial SODs and is extensively glycosylated. RT-PCR studies demonstrate the expression of both SOD subtypes in all developmental stages of A. viteae and indicate up-regulation of the AVSOD2 expression after transmission from the vector to the definitive host. This suggests an enhanced requirement for SOD activity in post-infective larval stages and adults of A. viteae. ELISAs performed with purified recombinant AVSOD2 show that the AVSOD2 is not a major target for the immune system in naturally infected jirds.

Amino Acid Sequence↗
PubMed1999

Secondary structure model for the ITS-2 precursor rRNA of strongyloid nematodes of equids: implications for phylogenetic inference.

In order to maximise the positional homology in the primary sequence alignment of the second internal transcribed spacer for 30 species of equine strongyloid nematodes, the secondary structures of the precursor ribosomal RNA were predicted using an approach combining an energy minimisation method and comparative sequence analysis. The results indicated that a common secondary structure model of the second internal transcribed spacer of these nematodes was maintained despite significant interspecific differences (2-56%) in primary sequences. The secondary structure model was then used to refine the primary second internal transcribed spacer sequence alignment. The 'manual' and 'structure' alignments were both subjected to phylogenetic analysis to compare the effect of using different sequence alignments on phylogenetic inference. The topologies of the phylogenetic trees inferred from the manual second internal transcribed spacer alignment were usually different to those derived from the structure second internal transcribed spacer alignment. The results suggested that the positional homology in the second internal transcribed spacer primary sequence alignment was maximised when the secondary structure model was taken into consideration.

Animals↗
PubMed1999

Mut-7 of C. elegans, required for transposon silencing and RNA interference, is a homolog of Werner syndrome helicase and RNaseD.

While all known natural isolates of C. elegans contain multiple copies of the Tc1 transposon, which are active in the soma, Tc1 transposition is fully silenced in the germline of many strains. We mutagenized one such silenced strain and isolated mutants in which Tc1 had been activated in the germline ("mutators"). Interestingly, many other transposons of unrelated sequence had also become active. Most of these mutants are resistant to RNA interference (RNAi). We found one of the mutated genes, mut-7, to encode a protein with homology to RNaseD. This provides support for the notion that RNAi works by dsRNA-directed, enzymatic RNA degradation. We propose a model in which MUT-7, guided by transposon-derived dsRNA, represses transposition by degrading transposon-specific messengers, thus preventing transposase production and transposition.

Amino Acid Sequence↗
PubMed2000

Isolation and characterisation of sex-specific transcripts from Oesophagostomum dentatum by RNA arbitrarily-primed PCR.

In light of the lack of molecular data on the sexual differentiation, maturation and interaction of parasitic nematodes of livestock, the present study investigated sex-specific gene expression in the nodule worm, Oesophagostomum dentatum (Strongylida). Using the technique of RNA arbitrarily-primed polymerase chain reaction (RAP-PCR), 31 expressed sequence tags (ESTs) differentially-displayed between the sexes were cloned. Northern blot analysis proved ten ESTs to be expressed exclusively in males (adults and fourth-stage larvae), while two were expressed solely in female stages. None of the ESTs were expressed in infective third-stage larvae. Sequence analysis and subsequent database searches revealed two male-specific ESTs to have significant similarity to Caenorhabditis elegans (predicted) proteins, a protein containing an EGF-like cysteine motif and a serine/threonine phosphatase. Another two male-specific ESTs had similarity to non-nematode sequences. The two female-specific ESTs had similarity to vitellogenin-5 and endonuclease III (predicted) from C. elegans. The remaining ESTs had no similarity to any nucleic acid or protein sequences contained in the databases. The isolation and characterisation of sex-specific ESTs from O. dentatum provides a unique opportunity for studying the reproductive biology of parasitic nematodes at the molecular level, with a view toward novel approaches for parasite control.

Animals↗
PubMed2000

Identification of a stress-responsive Onchocerca volvulus glutathione S-transferase (Ov-GST-3) by RT-PCR differential display.

The effects of oxidative insult on gene transcript levels in the filarial nematode Onchocerca volvulus were investigated using differential display RT-PCR. Oxidative stress was applied with the reagents paraquat, plumbagin and xanthine-xanthine oxidase. In all three cases, a cDNA fragment encoding a novel glutathione S-transferase (GST) resembling members of the theta-class was identified as upregulated (PQ29, PG112, XOD26). The subsequently isolated full-length cDNA harbors a 753-bp open reading frame encoding a GST with 268 amino acid residues and a predicted molecular mass of 31 kDa. This stress-responsive GST (Ov-GST-3) possesses only 14 and 21% sequence identity with the other O. volvulus GSTs (Ov-GST-1 and Ov-GST-2, respectively). Interestingly, Ov-GST-3 shares higher sequence identity with GSTs that are upregulated due to environmental stress. In order to confirm the specific upregulation of the Ov-GST-3 transcripts identified by differential display and to analyze the mRNA levels of the other Ov-GSTs (Ov-GST-1 and Ov-GST-2) under elevated stress conditions, a semi-quantitative polymerase chain reaction-enzyme-linked immunosorbent assay was performed. The Ov-GST-3 gene transcript level increased dramatically in response to xanthine-xanthine oxidase and to a lesser extent with paraquat and plumbagin. In contrast, Ov-GST-1 and Ov-GST-2 did not show any significant alterations in their steady-state mRNA levels in response to oxidative stress when examining the same mRNA samples. The present study clearly demonstrates that Ov-GST-3 is a critical enzyme in the defense against oxidative stress.

Amino Acid Sequence↗
PubMed2002

Full-length-enriched cDNA libraries from Echinococcus granulosus contain separate populations of oligo-capped and trans-spliced transcripts and a high level of predicted signal peptide sequences.

The tissue-dwelling larval stages of the cestode Echinococcus granulosus are intimately associated with the host, implying that a range of molecular mediators may be secreted by the parasite into the host environment. These mediators are being sought through a transcriptome-based analysis, using recombinant cDNA libraries. Conventional cDNA libraries of E. granulosus contain high levels of mitochondrial transcripts, as well as host (bovine) genomic DNA. In particular, 60% of a conventional protoscolex stage cDNA library corresponds to the large subunit (LSU) of mitochondrial rRNA. We attribute the presence of LSU rRNA copies to its polyadenylation in E. granulosus. To circumvent this problem, we adapted the 5' Rapid Amplification of cDNA Ends (RNA-ligase mediated RACE) technique that excludes all polynucleotides missing the 7-methyl-guanosine (7MG) cap specific to the 5' end of full-length mRNA. By ligating a specific oligonucleotide (oligo-cap) to 7MG-bearing mRNA, three cDNA libraries were made by PCR from oligo-cap and oligo-dT primers. Analysis of these libraries showed that mitochondrial RNA contaminants had been excluded. Moreover, no bovine genomic sequences were detected. In parallel, we constructed three cDNA libraries using the newly described trans-spliced leader (SL) from Echinococcus. Although these represent a smaller subset of parasite genes, mitochondrial and genomic contributions were again excluded. In both cases, a majority of cDNAs (61-92%) were judged to contain the initiation ATG codon, and 11-27% of inserts included potential N-terminal signal sequences. The 5' UTR tracts of most oligo-capped cDNAs were <100 nt, although approximately 8% were longer than this. Among the trans-spliced cDNAs, 43% potentially utilise the AUG donated by the SL, and in only 6% was the SL separated from an endogenous putative start site by >60 nt. Sequence analysis of randomly selected clones shows virtually no overlap between the oligo-capped and SL libraries, indicating that trans-spliced E. granulosus mRNAs appear to be insensitive to the enzymatic treatments used to 'oligo-cap' unspliced mRNAs. The oligo-capped and SL strategies represent efficient and complementary pathways to isolate full-length cDNA clones from this cestode parasite and, possibly, from related parasitic flatworms.

5' Untranslated Regions↗
PubMed2003

Molecular analysis of repetitive DNA elements from Entamoeba histolytica, which encode small RNAs and contain matrix/scaffold attachment recognition sequences.

We have isolated two DNA elements-Eh MRS1 and Eh MRS2-from Entamoeba histolytica, which contain the eukaryotic consensus Scaffold/Matrix Attachment Region (S/MAR) bipartite recognition sequences. Both these sequences bind to high salt extractable nuclear proteins and insoluble nuclear matrix proteins in E. histolytica HM1:IMSS, suggesting that the predicted S/MAR recognition sequences may indeed function as scaffold attachment regions in E. histolytica. Sequence analysis shows that Eh MRS1 and Eh MRS2 contain internal tandem repeats ranging from units of 8-11bp and are themselves present as independent arrays of tandemly repeating units of approximately 1100bp each. Eh MRS1 and Eh MRS2 are localised on different chromosomes in E. histolytica HM1:IMSS. Both Eh MRS1 and Eh MRS2 also code for small molecular weight RNAs of unknown function. Thus, two unique sequences-Eh MRS1 and Eh MRS2-demonstrate very similar properties, suggesting that they belong to a superfamily of genomic elements, which may function as scaffold or matrix attachment sites in Entamoeba.

Animals↗