Expressed sequence tag survey of gene expression in the scab mite Psoroptes ovis--allergens, proteases and free-radical scavengers

A genomic analysis and transcriptomic atlas of gene expression in Psoroptes ovis reveals feeding- and stage-specific patterns of allergen expression

Background

Psoroptic mange, caused by infestation with the ectoparasitic mite, Psoroptes ovis, is highly contagious, resulting in intense pruritus and represents a major welfare and economic concern for the livestock industry Worldwide. Control relies on injectable endectocides and organophosphate dips, but concerns over residues, environmental contamination, and the development of resistance threaten the sustainability of this approach, highlighting interest in alternative control methods. However, development of vaccines and identification of chemotherapeutic targets is hampered by the lack of P. ovis transcriptomic and genomic resources.

Results

Building on the recent publication of the P. ovis draft genome, here we present a genomic analysis and transcriptomic atlas of gene expression in P. ovis revealing feeding- and stage-specific patterns of gene expression, including novel multigene families and allergens. Network-based clustering revealed 14 gene clusters demonstrating either single- or multi-stage specific gene expression patterns, with 3075 female-specific, 890 male-specific and 112, 217 and 526 transcripts showing larval, protonymph and tritonymph specific-expression, respectively. Detailed analysis of P. ovis allergens revealed stage-specific patterns of allergen gene expression, many of which were also enriched in “fed” mites and tritonymphs, highlighting an important feeding-related allergenicity in this developmental stage. Pair-wise analysis of differential expression between life-cycle stages identified patterns of sex-biased gene expression and also identified novel P. ovis multigene families including known allergens and novel genes with high levels of stage-specific expression.

Conclusions

The genomic and transcriptomic atlas described here represents a unique resource for the acarid-research community, whilst the OrcAE platform makes this freely available, facilitating further community-led curation of the draft P. ovis genome.

The Construction of Full-Length cDNA Library for Otodectes cynotis

BACKGROUND

Otodectes cynotis (Hering, 1838) is the pathogen of otodectic mange distributed worldwide. The mite mainly infests carnivores and, sometimes, humans. However, due to the lack of cDNA library, research on its pathogenesis has been challenging.

METHODS

To solve this problem, the present study first sampled O. cynotis mites from an infested cat from Xi'an, China, for RNA extraction. Then, the full-length cDNA library was constructed using the SMART technique. Finally, positive clones > 500 bp and Hsc70-5 gene fragment specifically amplified from the cDNA library were sequenced and analyzed to verify the library's reliability.

RESULTS

Results showed that RNA extracted from 300 mites had good quality with a concentration of 149 ng/μl and OD260/OD280 of 1.99. The library satisfied the quality standard of a good library with a titer of 5.02 × 10⁵ PFU/ml and a combination rate of 97.61%. In addition, clone 4 and Hsc70-5 showed 98.38% and 99.72% identity with Ef1-α and Hsc70-5 gene sequences of O. cynotis in GenBank, respectively.

CONCLUSION

The cDNA library of O. cynotis constructed here was successful and reliable, creating the basis for research on RNA sequencing and functional genes of O. cynotis.

Characterization of Sarcoptes scabiei Tropomyosin and Paramyosin: Immunoreactive Allergens in Scabies

Scabies is a human skin disease due to the burrowing ectoparasite Sarcoptes scabiei var. hominis resulting in intense itching and inflammation and manifesting as a skin allergy. Because of insufficient mite material and lack of in vitro propagation system for antigen preparation, scabies is a challenging disease to develop serological diagnostics. For allergen characterization, full-length S. scabiei tropomyosin (Sar s 10) was cloned, expressed in pET-15b, and assessed for reactivity with IgE antibodies from human sera. IgE binding was observed to Sar s 10 with sera collected from subjects with ordinary scabies, house dust mite (HDM)-positive and naive subjects and a diagnostic sensitivity of < 30% was observed. S. scabiei paramyosin (Sar s 11) was cloned, and expressed in pET-28a in three overlapping fragments designated Sspara1, Sspara2, and Sspara3. IgE and IgG binding was observed to Sspara2 and Sspara3 antigens with sera collected from ordinary scabies, and HDM-positive subjects, but no binding was observed with sera collected from naive subjects. Sspara2 displayed excellent diagnostic potential with 98% sensitivity and 90% specificity observed for IgE binding and 70% sensitivity for IgG. In contrast, the diagnostic sensitivity of Sspara3 was 84% for IgE binding and 40% for IgG binding. In combination, Sspara2 and Sspara3 provided an IgE sensitivity of 94%. This study shows that IgE binding to Sspara2 and Sspara3 is a highly sensitive method for diagnosis of scabies infestation in clinical practice. The developed enzyme-linked immunosorbent assay helps direct future development of a specific diagnostic tool for scabies.

cDNA library construction of two human Demodexspecies

The research of Demodex, a type of pathogen causing various dermatoses in animals and human beings, is lacking at RNA level. This study aims at extracting RNA and constructing cDNA library for Demodex. First, P. cuniculiand D. farinaewere mixed to establish homogenization method for RNA extraction. Second, D. folliculorumand D. breviswere collected and preserved in Trizol, which were mixed with D. farinaerespectively to extract RNA. Finally, cDNA library was constructed and its quality was assessed. The results indicated that for D. folliculorum& D. farinae, the recombination rate of cDNA library was 90.67% and the library titer was 7.50 × 104 pfu/ml. 17 of the 59 positive clones were predicted to be of D. folliculorum; For D. brevis& D. farinae, the recombination rate was 90.96% and the library titer was 7.85 x104 pfu/ml. 40 of the 59 positive clones were predicted to be of D. brevis. Further detection by specific primers demonstrated that mtDNA cox1, cox3and ATP6 detected from cDNA libraries had 96.52%-99.73% identities with the corresponding sequences in GenBank. In conclusion, the cDNA libraries constructed for Demodexmixed with D. farinaewere successful and could satisfy the requirements for functional genes detection.

Preliminary analysis of Psoroptes ovis transcriptome in different developmental stages

Background

Psoroptic mange is a chronic, refractory, contagious and infectious disease mainly caused by the mange mite Psoroptes ovis, which can infect horses, sheep, buffaloes, rabbits, other domestic animals, deer, wild camels, foxes, minks, lemurs, alpacas, elks and other wild animals. Features of the disease include intense pruritus and dermatitis, depilation and hyperkeratosis, which ultimately result in emaciation or death caused by secondary bacterial infections. The infestation is usually transmitted by close contact between animals. Psoroptic mange is widespread in the world. In this paper, the transcriptome of P. ovis is described following sequencing and analysis of transcripts from samples of larvae (i.e. the Pso_L group) and nymphs and adults (i.e. the Pso_N_A group). The study describes differentially expressed genes (DEGs) and genes encoding allergens, which help understanding the biology of P. ovis and lay foundations for the development of vaccine antigens and drug target screening.

Methods

The transcriptome of P. ovis was assembled and analyzed using bioinformatic tools. The unigenes of P. ovis from each developmental stage and the unigenes differentially between developmental stages were compared with allergen protein sequences contained in the allergen database website to predict potential allergens.

Results

We identified 38,836 unigenes, whose mean length was 825 bp. On the basis of sequence similarity with seven databases, a total of 17,366 unigenes were annotated. A total of 1,316 DEGs were identified, including 496 upregulated and 820 downregulated in the Pso_L group compared with the Pso_N_A group. We predicted 205 allergens genes in the two developmental stages similar to genes from other mites and ticks, of these, 14 were among the upregulated DEGs and 26 among the downregulated DEGs.

Conclusion

This study provides a reference transcriptome of P. ovis in absence of a reference genome. The analysis of DEGs and putative allergen genes may lay the foundation for studies of functional genomics, immunity and gene expression profiles of this parasitic mite species.

Electronic supplementary material

The online version of this article (doi:10.1186/s13071-016-1856-z) contains supplementary material, which is available to authorized users.

Improvement on the extraction method of RNA in mites and its quality test

To solve the long-existing difficult problems in extracting RNA and constructing a complementary DNA (cDNA) library for trace mites, we conducted a further comparative experiment among three RNA extraction methods (TRIzol method, Omega method, and Azanno method) based on our previous attempts at the construction of cDNA library of mites, with Psoroptes cuniculi still used as the experimental subject. By subsequently decreasing the number of mites, the least number of mites needed for RNA extraction of each method were found by criteria of completeness, concentration, and purity of the extracted RNA. Specific primers were designed according to the allergen Pso c1, Pso c2, and Actin gene sequences of Psoroptes to test the reliability of cDNA library. The results showed that Azanno method needed only 10 mites with sensitivity 204 times higher than previously used TRIzol method and 20 times higher than Omega method; clear RNA band was detected by agarose gel electrophoresis; and ultraviolet spectrophotometer determination showed that RNA concentration, 260/280, and 260/230 were in the range of 102 to 166 ng/μl, 1.83 to 1.99, and 1.49 to 1.72, respectively. Finally, specific primers detection showed that the amplified sequences had 98.33, 98.19, and 99.52% identities with those of P. cuniculi or Psoroptes ovis in GenBank, respectively, indicating that the cDNA library constructed using 10 mites was successful and it could meet the requirements for molecular biology research. Therefore, we concluded that Azanno method was more effective than TRIzol method and Omega method in RNA extraction and cDNA library construction of trace mites.

Constructing and detecting a cDNA library for mites

RNA extraction and construction of complementary DNA (cDNA) library for mites have been quite challenging due to difficulties in acquiring tiny living mites and breaking their hard chitin. The present study is to explore a better method to construct cDNA library for mites that will lay the foundation on transcriptome and molecular pathogenesis research. We selected Psoroptes cuniculi as an experimental subject and took the following steps to construct and verify cDNA library. First, we combined liquid nitrogen grinding with TRIzol for total RNA extraction. Then, switching mechanism at 5' end of the RNA transcript (SMART) technique was used to construct full-length cDNA library. To evaluate the quality of cDNA library, the library titer and recombination rate were calculated. The reliability of cDNA library was detected by sequencing and analyzing positive clones and genes amplified by specific primers. The results showed that the RNA concentration was 836 ng/μl and the absorbance ratio at 260/280 nm was 1.82. The library titer was 5.31 × 10(5) plaque-forming unit (PFU)/ml and the recombination rate was 98.21%, indicating that the library was of good quality. In the 33 expressed sequence tags (ESTs) of P. cuniculi, two clones of 1656 and 1658 bp were almost identical with only three variable sites detected, which had an identity of 99.63% with that of Psoroptes ovis, indicating that the cDNA library was reliable. Further detection by specific primers demonstrated that the 553-bp Pso c II gene sequences of P. cuniculi had an identity of 98.56% with those of P. ovis, confirming that the cDNA library was not only reliable but also feasible.

Group 10 allergens (tropomyosins) from house-dust mites may cause covariation of sensitization to allergens from other invertebrates

Group 10 allergens (tropomyosins) have been assumed to be a major cause of cross-reactivity between house-dust mites (HDMs) and other invertebrates. Despite all of the published data regarding the epidemiology, percent IgE binding and level of sensitization in the population, the role of tropomyosin as a cross-reactive allergen in patients with multiple allergy syndrome still remains to be elucidated. Homology between amino acid sequences reported in allergen databases of selected invertebrate tropomyosins was determined with Der f 10 as the reference allergen. The 66.9 and 54.4% identities were found with selected crustacean and insect species, respectively, whereas only 20.4% identity was seen with mollusks. A similar analysis was performed using reported B-cell IgE-binding epitopes from Met e1 (shrimp allergen) and Bla g7 (cockroach allergen) with other invertebrate tropomyosins. The percent identity in linear sequences was higher than 35% in mites, crustaceans, and cockroaches. The polar and hydrophobic regions in these groups were highly conserved. These findings suggest that tropomyosin may be a major cause of covariation of sensitization between HDMs, crustaceans, and some species of insects and mollusks.

Sheep psoroptic mange: an update

Psoroptic mange is one of the most severe skin conditions of sheep. This highly contagious disease is responsible for huge economical losses in many sheep-raising countries. It is also a significant welfare concern. Our understanding of the biology of Psoroptes ovis and of the host-parasite relationship during psoroptic mange made remarkable progress during the last decade. These data combined with the availability of powerful molecular tools have opened new avenues of research. Clearly, there is still a long way to go before a vaccine becomes a reality. Additionally, other diagnostic tools and control methods should be further investigated such as breeding for genetic resistance and the use of biocontrol agents.

Generation, analysis and functional annotation of expressed sequence tags from the ectoparasitic mite Psoroptes ovis

Background

Sheep scab is caused by Psoroptes ovis and is arguably the most important ectoparasitic disease affecting sheep in the UK. The disease is highly contagious and causes and considerable pruritis and irritation and is therefore a major welfare concern. Current methods of treatment are unsustainable and in order to elucidate novel methods of disease control a more comprehensive understanding of the parasite is required. To date, no full genomic DNA sequence or large scale transcript datasets are available and prior to this study only 484 P. ovis expressed sequence tags (ESTs) were accessible in public databases.

Results

In order to further expand upon the transcriptomic coverage of P. ovis thus facilitating novel insights into the mite biology we undertook a larger scale EST approach, incorporating newly generated and previously described P. ovis transcript data and representing the largest collection of P. ovis ESTs to date. We sequenced 1,574 ESTs and assembled these along with 484 previously generated P. ovis ESTs, which resulted in the identification of 1,545 unique P. ovis sequences. BLASTX searches identified 961 ESTs with significant hits (E-value < 1E-04) and 584 novel P. ovis ESTs. Gene Ontology (GO) analysis allowed the functional annotation of 880 ESTs and included predictions of signal peptide and transmembrane domains; allowing the identification of potential P. ovis excreted/secreted factors, and mapping of metabolic pathways.

Conclusions

This dataset currently represents the largest collection of P. ovis ESTs, all of which are publicly available in the GenBank EST database (dbEST) (accession numbers FR748230 - FR749648). Functional analysis of this dataset identified important homologues, including house dust mite allergens and tick salivary factors. These findings offer new insights into the underlying biology of P. ovis, facilitating further investigations into mite biology and the identification of novel methods of intervention.

Identification of an abundant allergen from the sheep louse, Bovicola ovis

Infestation of sheep with the louse Bovicola ovis is common worldwide and leads to an allergic dermatitis referred to as 'scatter cockle'. IgE from an infested lamb was used in immunoaffinity chromatography to purify allergens from crude preparations of whole B. ovis and its faeces. SDS-PAGE of the affinity-purified eluates from both preparations showed a dominant band with M(r) of 28.5 kDa. Spleen cells from a mouse immunised with B. ovis faecal antigens were used to produce hybridomas which were screened by ELISA to identify those producing monoclonal antibodies (mAb) to the allergens purified by IgE immunoaffinity chromatography. Western blotting demonstrated that all of the mAbs examined recognised the 28.5 kDa allergen. The allergen, purified using immunoaffinity columns constructed with one of the specific mAbs, was shown to cause immediate and late-phase responses on intradermal skin testing in B. ovis-infested but not in naïve lambs. Levels of serum IgE specific for the purified allergen were significantly higher in infested than in naïve lambs (P < or = 0.0025). N-terminal and internal amino acid (aa) sequences obtained from the purified 28.5 kDa allergen were used to design primers to amplify a partial cDNA probe from B. ovis cDNA by PCR. The amplified probe was radiolabeled and used to screen a B. ovis cDNA library. The complete nucleotide sequence of the allergen was determined from the sequences of the positive clones from the library. The full-length cDNA encodes a 255 aa protein including a secretory leader sequence of 26 aas and a mature protein of 229 aas. The encoded protein showed strong homology to several hypothetical proteins of unknown function from diverse species and weak homology with lipid-binding proteins of Xenopus tropicalis and Galleria mellonella. This is the first allergen to be identified from a louse and it has been designated Bov o 1 in accordance with the criteria of the World Health Organization/International Union of Immunological Societies Allergen Nomenclature Subcommittee.

Feeding-associated gene expression in sheep scab mites (Psoroptes ovis)

The mite Psoroptes ovis is the causative agent of sheep scab. Although not usually fatal, the disease can spread rapidly and is a serious animal welfare concern. Vaccine development against ectoparasites has primarily focussed on two sources of candidate vaccine antigens – “exposed” antigens that are secreted in saliva during feeding on a host and “concealed” antigens that are usually expressed in the parasite gut and may be involved in digestion. Here, we sought to identify genes encoding proteins important for mite feeding and digestion by a subtractive suppressive hybridisation approach comparing mRNA transcript abundance in “fed” and “starved” mites. The study identified a variety of genes which are up-regulated by feeding mites. These included group 1, 5, 7 and 13 allergens including the previously described cysteine protease Pso o 1. In addition, numerous novel genes were identified here including some encoding potential salivary gland proteins and others encoding proteins which may facilitate feeding such as a serum opacity factor. An olfactory receptor-like protein was identified in the starved mite population which may help the mite to identify a host.

Ovine IgE and its role in immunological protection and disease

The importance of internal and external parasites in limiting productivity and compromising the welfare of sheep has provided the impetus for extensive research on ovine IgE with the objectives of better understanding protective immunological responses and developing novel methods of control; particularly vaccination. The molecular structures of ovine IgE and its high affinity receptor have been determined and the former information has assisted the development of monoclonal antibodies (mAb) to ovine IgE by 2 of 3 groups who have produced these reagents. The availability of these mAbs has enabled the description of IgE responses following infections with a wide variety of parasites in sheep and in an ovine model of atopic asthma. While IgE responses are consistently associated with parasitic diseases of sheep, it has not been proven that this antibody isotype is involved in protection. The foundation of present knowledge and reagents, together with new emerging technologies, should allow the role of IgE in parasitic diseases of sheep to be determined.

Molecular characterization, expression and localization of a peroxiredoxin from the sheep scab mite,Psoroptes ovis

The sheep scab mite,Psoroptes ovis, induces an intensely pruritic exudative dermatitis which is responsible for restlessness, loss of appetite and weight loss. Within the first 24 h of infection, there is a rapid inflammatory influx of eosinophils and apoptosis of the keratinocytes at the site of infection. The former cell type is capable of a sustained respiratory burst, toxic products of which may directly damage the mite and also contribute to lesion formation. Analysis of aP. ovisexpressed sequence tag (EST) database identified a number of antioxidant enzyme-encoding sequences, including peroxiredoxin (thioredoxin peroxidase EC 1.11.1.15), all of which may help the mite endure the potentially toxic skin environment. A full length sequence encodingPo-TPx, a protein of 206 amino acids which showed high homology to a peroxiredoxin from the salivary gland of the tickIxodes scapularis, was amplified fromP. oviscDNA. RecombinantPo-TPx was expressed in bacteria and antiserum to this protein was used to localize nativePo-TPx in mite sections. Peroxiredoxin was localized, amongst other sites, to a subpharyngeal region in mite sections. The recombinant protein was recognized by sera from sheep infested with the mite suggesting that it may be secreted or excreted by the mite and interact with the host immune response.

Phylogenomic analysis of EST datasets

To date the genomes of over 600 organisms have been generated of which 100 are from eukaryotes. Together with partial genome data for an additional 700 eukaryotic organisms, these exceptional sequence resources offer new opportunities to explore phylogenetic relationships and species diversity. The identification of highly diverse sequences specific to an EST-based sequence dataset offers insights into the extent of genetic novelty within that dataset. Sequences that are only shared with other related species from the same taxon might represent genes associated with taxon-specific innovations. On the other hand, sequences that are highly conserved across many other species offer valuable resources for performing more in-depth phylogenetic analyses. In the following chapter, we guide the reader through the process of examining their sequence datasets in the context of phylogenetic relationships. Performed across large-scale datasets, such analyses are termed Phylogenomics. Two complementary approaches are described, both based on the use of BLAST similarity metrics. The first uses an established Java tool - SimiTri - to visualize sequence similarity relationships between the EST dataset and three user-defined datasets. The second focuses on the use of phylogenetic profiles to identify groups of taxonomically related sequences.

Expressed sequence tags: an overview

Expressed sequence tags (ESTs) are fragments of mRNA sequences derived through single sequencing reactions performed on randomly selected clones from cDNA libraries. To date, over 45 million ESTs have been generated from over 1400 different species of eukaryotes. For the most part, EST projects are used to either complement existing genome projects or serve as low-cost alternatives for purposes of gene discovery. However, with improvements in accuracy and coverage, they are beginning to find application in fields such as phylogenetics, transcript profiling and proteomics. This volume provides practical details on the generation and analysis of ESTs. Chapters are presented which cover creation of cDNA libraries; generation and processing of sequence data; bioinformatics analysis of ESTs; and their application to phylogenetics and transcript profiling.

The global landscape of sequence diversity

BACKGROUND

Systematic comparisons between genomic sequence datasets have revealed a wide spectrum of sequence specificity from sequences that are highly conserved to those that are specific to individual species. Due to the limited number of fully sequenced eukaryotic genomes, analyses of this spectrum have largely focused on prokaryotes. Combining existing genomic datasets with the partial genomes of 193 eukaryotes derived from collections of expressed sequence tags, we performed a quantitative analysis of the sequence specificity spectrum to provide a global view of the origins and extent of sequence diversity across the three domains of life.

RESULTS

Comparisons with prokaryotic datasets reveal a greater genetic diversity within eukaryotes that may be related to differences in modes of genetic inheritance. Mapping this diversity within a phylogenetic framework revealed that the majority of sequences are either highly conserved or specific to the species or taxon from which they derive. Between these two extremes, several evolutionary landmarks consisting of large numbers of sequences conserved within specific taxonomic groups were identified. For example, 8% of sequences derived from metazoan species are specific and conserved within the metazoan lineage. Many of these sequences likely mediate metazoan specific functions, such as cell-cell communication and differentiation.

CONCLUSION

Through the use of partial genome datasets, this study provides a unique perspective of sequence conservation across the three domains of life. The provision of taxon restricted sequences should prove valuable for future computational and biochemical analyses aimed at understanding evolutionary and functional relationships.

Eukaryotic expression of recombinant Pso o 1, an allergen fromPsoroptes ovis, and its localization in the mite

A cDNA encoding the immunogen Pso o 1 fromPsoroptes oviswas obtained by polymerase chain reaction (PCR) amplification. The amplicon contained the entire coding sequence for the prepro-enzyme in an open reading frame (ORF) of 966 bp. This gene encoded a predicted protein of 322 amino acids (aa) with 64% aa identity (80% similarity) to the major house dust mite faecal allergen Der f 1. The pro-enzyme form of Pso o 1 was expressed as a recombinant protein in thePichia pastoris-eukaryotic expression system. Maturation of the recombinant pro-enzyme by autocatalytic activation was not observed, and such maturation could not be achieved using a number of techniques known to activate recombinant Der p 1 and Der f 1 expressed in the same system. Serum raised against recombinant Pso o 1 cross-reacted with mature Der p 1 and allowed Pso o 1 to be immunolocalized to the gut ofP. ovis.

Molecular characterization, expression and localization of tropomyosin and paramyosin immunodominant allergens from sheep scab mites (Psoroptes ovis)

cDNAs encoding the immunodominant allergens tropomyosin and paramyosin were amplified from RNA extracted from the sheep scab mite Psoroptes ovis. The tropomyosin cDNA contained an open reading frame (ORF) of 852 bp which encoded a predicted protein with 98% and 97% identity to the house dust mite allergens Der f 10 and Der p 10 respectively. The complete paramyosin ORF generated by RT-PCR was 2625 bp in length and encoded an 875aa predicted protein of 102.6 kDa with 97%, 95% and 89% identity to the paramyosins of Dermatophagoides pteronyssinus (Der p 11), Sarcoptes scabiei and Blomia tropicalis (Blo t 11) respectively. Full length tropomyosin and truncated and full-length paramyosin were expressed as recombinant proteins. IgG and IgE in sera from sheep with a 6-week duration primary infestation of P. ovis did not detect either full-length or truncated recombinant paramyosin. IgG in both infested and naïve sheep sera detected recombinant tropomyosin, suggesting cross-reactivity to tropomyosin and to other invertebrate species to which the sheep may have been exposed. Staining with antibodies directed against tropomyosin and paramyosin was observed throughout sections of P. ovis. Staining was especially prevalent in the anterior sections of the mites, possibly associated with locomotory muscles in this region.

Progress and opportunities in the development of vaccines against mites, fleas and myiasis-causing flies of veterinary importance

Despite the potential benefits offered by vaccination against ectoparasites, there have been few commercial successes with this strategy, in spite of sustained efforts using increasingly sophisticated techniques. This review outlines the progress and challenges offered by recent research into vaccination against some of the major ectoparasites of veterinary importance, and provides an insight into the opportunities arising from our increased understanding of the immunology of host-parasite relationships and the potential for exploitation of this knowledge and that arising from new genomic data provided by expressed sequence tag projects.

Invertebrate Muscles: Muscle Specific Genes and Proteins

This is the first of a projected series of canonic reviews covering all invertebrate muscle literature prior to 2005 and covers muscle genes and proteins except those involved in excitation-contraction coupling (e.g., the ryanodine receptor) and those forming ligand- and voltage-dependent channels. Two themes are of primary importance. The first is the evolutionary antiquity of muscle proteins. Actin, myosin, and tropomyosin (at least, the presence of other muscle proteins in these organisms has not been examined) exist in muscle-like cells in Radiata, and almost all muscle proteins are present across Bilateria, implying that the first Bilaterian had a complete, or near-complete, complement of present-day muscle proteins. The second is the extraordinary diversity of protein isoforms and genetic mechanisms for producing them. This rich diversity suggests that studying invertebrate muscle proteins and genes can be usefully applied to resolve phylogenetic relationships and to understand protein assembly coevolution. Fully achieving these goals, however, will require examination of a much broader range of species than has been heretofore performed.

PartiGeneDB--collating partial genomes

Owing to the high costs involved, only 28 eukaryotic genomes have been fully sequenced to date. On the other hand, an increasing number of projects have been initiated to generate survey sequence data for a large number of other eukaryotic organisms. For the most part, these data are poorly organized and difficult to analyse. Here, we present PartiGeneDB (http://www.partigenedb.org), a publicly available database resource, which collates and processes these sequence datasets on a species-specific basis to form non-redundant sets of gene objects—which we term partial genomes. Users may query the database to identify particular genes of interest either on the basis of sequence similarity or via the use of simple text searches for specific patterns of BLAST annotation. Alternatively, users can examine entire partial genome datasets on the basis of relative expression of gene objects or by the use of an interactive Java-based tool (SimiTri), which displays sequence similarity relationships for a large number of sequence objects in a single graphic. PartiGeneDB facilitates regular incremental updates of new sequence datasets associated with both new and exisitng species. PartiGeneDB currently contains the assembled partial genomes derived from 1.83 million sequences associated with 247 different eukaryotes.

Identification of tropomyosin, paramyosin and apolipophorin/vitellogenin as three major allergens of the sheep scab mite, Psoroptes ovis

Analysis by one-dimensional (1-D) SDS-PAGE/Western blotting of whole mite extract (larval and adult stages) with sheep sera taken 0-84 days after infection with the sheep scab mite, Psoroptes ovis revealed a progressive IgE antibody response, with a dominant high molecular weight allergen (MW 180 kDa) detected early during infection. Further analysis by two-dimensional (2-D) SDS-PAGE/Western blotting with post-infection sera, revealed a more complex picture with numerous (> 20) IgE reactive spots. Trypsin digest and Maldi-ToF analyses of these spots identified two house dust mite allergen homologues, namely tropomyosin (Der p 10) and paramyosin (Der p 11), and analysis of a third spot indicated an apolipoprotein-like IgE reactive protein (Der p 14). Further 1-D and 2-D SDS/Western blotting, with specific antibodies to the house dust mite allergens Der p 10, 11, and to the IgE reactive peptide of the high molecular weight house dust mite allergen, Der p 14 (vitellogenin/apolipophorin), provided firm evidence for the presence of these three allergens in extracts of the Psoroptes mite. These studies show for the first time that homologues of the house dust mite 10, 11 and 14 group allergens are represented as immunodominant allergens of the sheep scab mite, and may represent important vaccine candidates.

Technological advances and genomics in metazoan parasites

Molecular biology has provided the means to identify parasite proteins, to define their function, patterns of expression and the means to produce them in quantity for subsequent functional analyses. Whole genome and expressed sequence tag programmes, and the parallel development of powerful bioinformatics tools, allow the execution of genome-wide between stage or species comparisons and meaningful gene-expression profiling. The latter can be undertaken with several new technologies such as DNA microarray and serial analysis of gene expression. Proteome analysis has come to the fore in recent years providing a crucial link between the gene and its protein product. RNA interference and ballistic gene transfer are exciting developments which can provide the means to precisely define the function of individual genes and, of importance in devising novel parasite control strategies, the effect that gene knockdown will have on parasite survival.

Scabies: New Future for a Neglected Disease

Scabies is a disease of global proportions in both human and animal populations, resulting from infestation of the skin with the "itch" mite Sarcoptes scabiei. Despite the availability of effective chemotherapy the intensely itching lesions engender significant morbidity primarily due to secondary sepsis and post-infective complications. Some patients experience an extreme form of the disease, crusted scabies, in which many hundreds of mites may infest the skin causin severe crusting and hyperkeratosis. Overcrowded living conditions and poverty have been identified as significant confounding factors in transmission of the mite in humans. Control is hindered by difficulties with diagnosis, the cost of treatment, evidence for emerging resistance and lack of effective vaccines. Historically research on scabies has been extremely limited because of the difficulty in obtaining sufficient quantities of the organism. Recent molecular approaches have enabled considerable advances in the study of population genetics and transmission dynamics of S. scabiei. However, the most exciting and promising development is the potential exploitation of newly available data from S. scabiei cDNA libraries and EST projects. Ultimately this knowledge may aid early identification of disease, novel forms of chemotherapy, vaccine development and new treatment possibilities for this important but neglected parasite.