Search

Within the context of our anthelmintic discovery program, we recently identified and evaluated a quinoline derivative, called ABX464 or obefazimod, as a nematocidal candidate; synthesised a series of analogues which were assessed for activity against the free-living nematode Caenorhabditis elegans ; and predicted compound-target relationships by thermal proteome profiling (TPP) and in silico docking. Here, we logically extended this work and critically evaluated the anthelmintic activity of ABX464 analogues on Haemonchus contortus (barber's pole worm) – a highly pathogenic nematode of ruminant livestock. First, we tested a series of 44 analogues on H. contortus (larvae and adults) to investigate the nematocidal pharmacophore of ABX464, and identified one compound with greater potency than the parent compound and showed moderate activity against a select number of other parasitic nematodes (including Ancylostoma, Heligmosomoides and Strongyloides species). Using TPP and in silico modelling studies, we predicted protein HCON_00074590 (a predicted aldo-keto reductase) as a target candidate for ABX464 in H. contortus. Future work aims to optimise this compound as a nematocidal candidate and investigate its pharmacokinetic properties. Overall, this study presents a first step toward the development of a new nematocide. [Display omitted] • ABX464, a quinoline molecule, displays anthelmintic activity against H. contortus. • ABX464 and one particular analogue, 36, are also active against several parasitic nematodes. • HCON_00074590, an aldo-keto reductase, is identified as a nematode drug target. • In silico docking predicts ligand interactions with H. contortus protein HCON_00074590. [ABSTRACT FROM AUTHOR]

Clonorchis sinensis (family Opisthorchiidae) is an important foodborne parasite that has a major socioeconomic impact on ~35 million people predominantly in China, Vietnam, Korea and the Russian Far East. In humans, infection with C. sinensis causes clonorchiasis, a complex hepatobiliary disease that can induce cholangiocarcinoma (CCA), a malignant cancer of the bile ducts. Central to understanding the epidemiology of this disease is knowledge of genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species, evidence of karyotypic variation within C. sinensis and cryptic species within a related opisthorchiid fluke ( Opisthorchis viverrini ) emphasise the importance of studying and comparing the genes and genomes of geographically distinct isolates of C. sinensis . Recently, we sequenced, assembled and characterised a draft nuclear genome of a C. sinensis isolate from Korea and compared it with a published draft genome of a Chinese isolate of this species using a bioinformatic workflow established for comparing draft genome assemblies and their gene annotations. We identified that 50.6% and 51.3% of the Korean and Chinese C. sinensis genomic scaffolds were syntenic, respectively. Within aligned syntenic blocks, the genomes had a high level of nucleotide identity (99.1%) and encoded 15 variable proteins likely to be involved in diverse biological processes. Here, we review current technical challenges of using draft genome assemblies to undertake comparative genomic analyses to quantify genetic variation between isolates of the same species. Using a workflow that overcomes these challenges, we report on a high-quality draft genome for C. sinensis from Korea and comparative genomic analyses, as a basis for future investigations of the genetic structures of C. sinensis populations, and discuss the biotechnological implications of these explorations. [ABSTRACT FROM AUTHOR]

Billions of people and animals are infected with parasitic worms (helminths). Many of these worms cause diseases that have a major socioeconomic impact worldwide, and are challenging to control because existing treatment methods are often inadequate. There is, therefore, a need to work toward developing new intervention methods, built on a sound understanding of parasitic worms at molecular level, the relationships that they have with their animal hosts and/or the diseases that they cause. Decoding the genomes and transcriptomes of these parasites brings us a step closer to this goal. The key focus of this article is to critically review and discuss bioinformatic tools used for the assembly and annotation of these genomes and transcriptomes, as well as various post-genomic analyses of transcription profiles, biological pathways, synteny, phylogeny, biogeography and the prediction and prioritisation of drug target candidates. Bioinformatic pipelines implemented and established recently provide practical and efficient tools for the assembly and annotation of genomes of parasitic worms, and will be applicable to a wide range of other parasites and eukaryotic organisms. Future research will need to assess the utility of long-read sequence data sets for enhanced genomic assemblies, and develop improved algorithms for gene prediction and post-genomic analyses, to enable comprehensive systems biology explorations of parasitic organisms. [ABSTRACT FROM AUTHOR]

The availability of high-quality genomes and advances in functional genomics have enabled large-scale studies of essential genes in model eukaryotes, including the 'elegant worm' (Caenorhabditis elegans ; Nematoda) and the 'vinegar fly' (Drosophila melanogaster ; Arthropoda). However, this is not the case for other, much less-studied organisms, such as socioeconomically important parasites, for which functional genomic platforms usually do not exist. Thus, there is a need to develop innovative techniques or approaches for the prediction, identification and investigation of essential genes. A key approach that could enable the prediction of such genes is machine learning (ML). Here, we undertake an historical review of experimental and computational approaches employed for the characterisation of essential genes in eukaryotes, with a particular focus on model ecdysozoans (C. elegans and D. melanogaster), and discuss the possible applicability of ML-approaches to organisms such as socioeconomically important parasites. We highlight some recent results showing that high-performance ML, combined with feature engineering, allows a reliable prediction of essential genes from extensive, publicly available 'omic data sets, with major potential to prioritise such genes (with statistical confidence) for subsequent functional genomic validation. These findings could 'open the door' to fundamental and applied research areas. Evidence of some commonality in the essential gene-complement between these two organisms indicates that an ML-engineering approach could find broader applicability to ecdysozoans such as parasitic nematodes or arthropods, provided that suitably large and informative data sets become/are available for proper feature engineering, and for the robust training and validation of algorithms. This area warrants detailed exploration to, for example, facilitate the identification and characterisation of essential molecules as novel targets for drugs and vaccines against parasitic diseases. This focus is particularly important, given the substantial impact that such diseases have worldwide, and the current challenges associated with their prevention and control and with drug resistance in parasite populations. [ABSTRACT FROM AUTHOR]

• Interferon-beta exposure in pregnancy did not increase adverse pregnancy outcomes. • The result remained after stratification by maternal characteristics. • The result also remained, when stratifying by newborn characteristics. • Interferon-beta exposure in pregnancy does not appear to be harmful for the newborn. Previous studies reported no increase in the prevalence of adverse pregnancy outcomes after exposure to interferon-beta (IFN-beta). However, no study has investigated if the prevalence of these outcomes after IFN-beta exposure is modified by maternal and newborn characteristics. Our objective was to describe the stratified prevalence of adverse pregnancy outcomes among women with multiple sclerosis (MS) exposed only to IFN-beta or unexposed to any MS disease modifying drugs (MSDMDs). This population-based cohort study using Finnish (1996-2014) and Swedish (2005-2014) register data included pregnancies of women with MS exposed only to IFN-beta 6 months before or during pregnancy (n=718) or unexposed to MSDMDs (n=1397). The outcome prevalences were described stratified by maternal and newborn characteristics, with 95% confidence intervals (CIs). Confounder-adjusted analyses were performed if the prevalence results indicated modified effect of IFN-beta in specific strata. The stratified analysis indicated that the prevalence of serious (anomaly or stillbirth) and other adverse pregnancy outcomes was similar among the exposed and unexposed, with no statistically significant difference. Among women treated for MS >5 years, serious adverse pregnancy outcomes occurred in 4.3% (95%CI: 1.9-8.3%) of pregnancies exposed only to IFN-beta 6 months before or during pregnancy and in 2.7% (95%CI: 1.2-5.0%) of unexposed pregnancies. The confounder adjusted analyses did not support the hypothesis that MS treatment duration before pregnancy would modify the risk of adverse pregnancy outcomes after exposure to IFN-beta 6 months before or during pregnancy. The prevalence of adverse pregnancy outcomes was not increased after IFN-beta exposure, when pregnancies of women with MS were stratified by maternal and newborn characteristics. The stratified results were similar to the unstratified results in the same population. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • Hc -TGFBR1 is a TGF β type I receptor-like molecule with conserved domains. • Hc-tgfbr1 was transcribed in all developmental stages of Haemonchus contortus. • Hc-tgfbr1 regulates H. contortus development in vitro. • Hc-tgfbr1 might regulate development through the digestive system in H. contortus. • Hc-tgfbr1 failed to rescue the functional deficiency in the Caenorhabditis elegans DR40 strain. Abstract Here we investigated the gene of a transforming growth factor (TGF)-β type I receptor-like molecule in Haemonchus contortus , a highly pathogenic and economically important parasitic nematode of small ruminants. Designated Hc-tgfbr1 , this gene is transcribed in all developmental stages of H. contortus , and the encoded protein has glycine-serine rich and kinase domains characteristic of a TGF-β family type I receptor. Expression of a GFP reporter driven by the putative Hc-tgfbr1 promoter localised to two intestinal rings, the anterior-most intestinal ring (int ring I) and the posterior-most intestinal ring (int ring IX) in Caenorhabditis elegans in vivo. Heterologous genetic complementation using a plasmid construct containing Hc-tgfbr1 genomic DNA failed to rescue the function of Ce-daf-1 (a known TGF-β type I receptor gene) in a daf-1 -deficient mutant strain of C. elegans. In addition, a TGF-β type I receptor inhibitor, galunisertib, and double-stranded RNA interference (RNAi) were employed to assess the function of Hc-tgfbr1 in the transition from exsheathed L3 (xL3) to the L4 of H. contortus in vitro, revealing that both galunisertib and Hc-tgfbr1- specific double-stranded RNA could retard L4 development. Taken together, these results provide evidence that Hc-tgfbr1 is involved in developmental processes in H. contortus in the transition from the free-living to the parasitic stage. [ABSTRACT FROM AUTHOR]

In this study, we explored the molecular alterations in the developmental switch from the L3 to the exsheathed L3 (xL3) and to the L4 stage of Haemonchus contortus in vitro using an integrated transcriptomic, proteomic and bioinformatic approach. Totals of 9,754 mRNAs, 88 microRNAs (miRNAs) and 1,591 proteins were identified, and 6,686 miRNA-mRNA pairs inferred in all larval stages studied. Approximately 16% of transcripts in the combined transcriptome (representing all three larval stages) were expressed as proteins, and there were positive correlations ( r  = 0.39–0.44) between mRNA transcription and protein expression in the three distinct developmental stages of the parasite. Of the predicted targets, 1,019 (27.0%) mRNA transcripts were expressed as proteins, and there was a negative correlation ( r  = −0.60 to −0.50) in the differential mRNA transcription and protein expression between developmental stages upon pairwise comparison. The changes in transcription (mRNA and miRNA) and protein expression from the free-living to the parasitic life cycle phase of H. contortus related to enrichments in biological pathways associated with metabolism (e.g., carbohydrate and lipid degradation, and amino acid metabolism), environmental information processing (e.g., signal transduction, signalling molecules and interactions) and/or genetic information processing (e.g., transcription and translation). Specifically, fatty acid degradation, steroid hormone biosynthesis and the Rap1 signalling pathway were suppressed, whereas transcription, translation and protein processing in the endoplasmic reticulum were upregulated during the transition from the free-living L3 to the parasitic xL3 and L4 stages of the nematode in vitro. Dominant post-transcriptional regulation was inferred to elicit these changes, and particular miRNAs (e.g., hco-miR-34 and hco-miR-252 ) appear to play roles in stress responses and/or environmental adaptations during developmental transitions of H. contortus . Taken together, these integrated results provide a comprehensive insight into the developmental biology of this important parasite at the molecular level in vitro. The approach applied here to H. contortus can be readily applied to other parasitic nematodes. [ABSTRACT FROM AUTHOR]

Roundworms belong to a diverse phylum (Nematoda) which is comprised of many parasitic species including whipworms (genus Trichuris ). These worms have adapted to a biological niche within the host and exhibit unique morphological characteristics compared with other nematodes. Although these adaptations are known, the underlying molecular mechanisms remain elusive. The availability of genomes and transcriptomes of some whipworms now enables detailed studies of their molecular biology. Here, we defined and curated the full complement of an important class of enzymes, the protein kinases (kinomes) of two species of Trichuris , using an advanced and integrated bioinformatic pipeline. We investigated the transcription of Trichuris suis kinase genes across developmental stages, sexes and tissues, and reveal that selectively transcribed genes can be linked to central roles in developmental and reproductive processes. We also classified and functionally annotated the curated kinomes by integrating evidence from structural modelling and pathway analyses, and compared them with other curated kinomes of phylogenetically diverse nematode species. Our findings suggest unique adaptations in signalling processes governing worm morphology and biology, and provide an important resource that should facilitate experimental investigations of kinases and the biology of signalling pathways in nematodes. [ABSTRACT FROM AUTHOR]

Toxocariasis is an important, neglected zoonosis caused mainly by Toxocara canis . Although our knowledge of helminth molecular biology is improving through completed draft genome projects, there is limited detailed information on the molecular biology of Toxocara species. Here, transcriptomic sequencing of male and female adult T. canis and comparative analyses were conducted. For each sex, two-thirds (66–67%) of quality-filtered reads mapped to the gene set of T. canis , and at least five reads mapped to each of 16,196 (87.1%) of all 18,596 genes, and 321 genes were specifically transcribed in female and 1467 in male T. canis . Genes differentially transcribed between the two sexes were identified, enriched biological processes and pathways linked to these genes established, and molecules associated with reproduction and development predicted. In addition, small RNA pathways involved in reproduction were characterized, but there was no evidence for piwi RNA pathways in adult T. canis . The results of this transcriptomic study should provide a useful basis to support investigations of the reproductive biology of T. canis and related nematodes. 2 2 Note: Transcriptomic data can be accessed in the NCBI Gene Expression Omnibus ( http://www.ncbi.nlm.gov/geo ) under accession no. GSE75536. [ABSTRACT FROM AUTHOR]

The apicoplast (ap) is a unique, non-photosynthetic organelle found in most apicomplexan parasites. Due to the essential roles that this organelle has, it has been widely considered as target for drugs against diseases caused by apicomplexans. Exploring the ap genomes of such parasites would provide a better understanding of their systematics and their basic molecular biology for therapeutics. However, there is limited information available on the ap genomes of apicomplexan parasites. In the present study, the ap genomes of two operational taxonomic units of Babesia (known as Babesia sp. Lintan [ Bl ] and Babesia sp. Xinjiang [ Bx ]) from sheep were sequenced, assembled and annotated using a massive parallel sequencing-based approach. Then, the gene content and gene order in these ap genomes (∼30.7 kb in size) were defined and compared, and the genetic differences were assessed. In addition, a phylogenetic analysis of ap genomic data sets was carried out to assess the relationships of these taxonomic units with other apicomplexan parasites for which complete ap genomic data sets were publicly available. The results showed that the ap genomes of Bl and Bx encode 59 and 57 genes, respectively, including 2 ribosomal RNA genes, 25 transfer RNA genes and 30–32 protein-encoding genes, being similar in content to those of Babesia bovis and B. orientalis . Ap gene regions that might serve as markers for future epidemiological and population genetic studies of Babesia species were identified. Using sequence data for a subset of six protein-encoding genes, a close relationship of Bl and Bx with Babesia bovis from cattle and B. orientalis from water buffalo was inferred. Although the focus of the present study was on Babesia , we propose that the present sequencing-bioinformatic approach should be applicable to organellar genomes of a wide range of apicomplexans of veterinary importance. [ABSTRACT FROM AUTHOR]

Here, we sequenced, assembled and annotated the mitochondrial (mt) genomes of two operational taxonomic units of Babesia from sheep from China using a deep sequencing-coupled approach. Then, we defined and compared the gene order of these mt genomes (~ 5.8 to 6.2 kb in size), assessed sequence differences in mt genes among Babesia taxa and evaluated genetic relationships among these taxa and related apicomplexans ( Theileria ) for which mt genomic data sets were available. We also identified mt genetic regions that might be useful as markers for future population genetic and molecular epidemiological studies of Babesia from small ruminants. We propose that the sequencing-bioinformatic approach used here should be applicable to a wide range of protists of veterinary importance. [ABSTRACT FROM AUTHOR]

The blow fly, Lucilia cuprina (Wiedemann, 1830) is a parasitic insect of major global economic importance. Maggots of this fly parasitize the skin of animal hosts, feed on excretions and tissues, and cause severe disease (flystrike or myiasis). Although there has been considerable research on L. cuprina over the years, little is understood about the molecular biology, biochemistry and genetics of this parasitic fly, as well as its relationship with its hosts and the disease that it causes. This situation might change with the recent report of the draft genome and transcriptome of this blow fly, which has given new and global insights into its biology, interactions with the host animal and aspects of insecticide resistance at the molecular level. This genomic resource will likely enable many fundamental and applied research areas in the future. The present article gives a background on L. cuprina and myiasis, a brief account of past and current treatment, prevention and control approaches, and provides a perspective on the impact that the L. cuprina genome should have on future research of this and related parasitic flies, and the design of new and improved interventions for myiasis. [ABSTRACT FROM AUTHOR]

Objective The Women's Health Initiative (WHI) study clarified the indications and contraindications for postmenopausal hormone therapy (HT). We studied the impact of the WHI results on the risk of fatal stroke in HT users in Finland. Study design Retrospective analysis setting : Nationwide registers on postmenopausal HT use and causes of death between 1995 and 2009. Population Women ≥40 years ( n = 290,272) using systemic estradiol-based postmenopausal HT. Methods Follow-up started from the first HT purchase during the pre-WHI era (1995–2001) and post-WHI era (2002–2009). Main outcome measures Stroke deaths in HT users were compared with that in the age-matched background population and expressed as standardized mortality ratio (SMR) with 95% confidence intervals. Results Overall, 311 HT users died due to stroke. The exposure to HT ≤1 year was associated with a similarly reduced 22% (0.67–0.91) risk of stroke death in the pre-WHI era and in the post-WHI era 27% (0.55–0.94). The risk reductions for HT exposure of 1–8 years in the pre-WHI era (47%, 0.42–0.65) did not differ from that in the post-WHI era (32%, 0.48–0.94). The discontinuation of HT was accompanied by a significant 33% (1.02–1.72) increase in stroke death risk in the pre-WHI era and a non-significant 32% (0.84–1.99) increase in the post-WHI era within the first post-treatment year, but no longer after 1–8 years. Conclusions The change in prescribing policy after the WHI study did not affect the risk of fatal stroke in Finnish HT users. [ABSTRACT FROM AUTHOR]

Despite right open reading frame kinases (RIOKs) being essential for life, their functions, substrates and cellular pathways remain enigmatic. In the present study, gene structures were characterised for 26 RIOKs from draft genomes of parasitic and free-living nematodes. RNA-seq transcription profiles of riok genes were investigated for selected parasitic nematodes and showed that these kinases are transcribed in developmental stages that infect their mammalian host. Three-dimensional structural models of Caenorhabditis elegans RIOKs were predicted, and elucidated functional domains and conserved regions in nematode homologs. These findings provide prospects for functional studies of riok genes in C. elegans , and an opportunity for the design and validation of nematode-specific inhibitors of these enzymes in socioeconomic parasitic worms. [ABSTRACT FROM AUTHOR]

Abstract: Compounded by a massive global food shortage, many parasitic diseases have a devastating, long-term impact on animal and human health and welfare worldwide. Parasitic helminths (worms) affect the health of billions of animals. Unlocking the systems biology of these neglected pathogens will underpin the design of new and improved interventions against them. Currently, the functional annotation of genomic and transcriptomic sequence data for socio-economically important parasitic worms relies almost exclusively on comparative bioinformatic analyses using model organism- and other databases. However, many genes and gene products of parasitic helminths (often >50%) cannot be annotated using this approach, because they are specific to parasites and/or do not have identifiable homologs in other organisms for which sequence data are available. This inability to fully annotate transcriptomes and predicted proteomes is a major challenge and constrains our understanding of the biology of parasites, interactions with their hosts and of parasitism and the pathogenesis of disease on a molecular level. In the present article, we compiled transcriptomic data sets of key, socioeconomically important parasitic helminths, and constructed and validated a curated database, called HelmDB (www.helmdb.org). We demonstrate how this database can be used effectively for the improvement of functional annotation by employing data integration and clustering. Importantly, HelmDB provides a practical and user-friendly toolkit for sequence browsing and comparative analyses among divergent helminth groups (including nematodes and trematodes), and should be readily adaptable and applicable to a wide range of other organisms. This web-based, integrative database should assist ‘systems biology’ studies of parasitic helminths, and the discovery and prioritization of novel drug and vaccine targets. This focus provides a pathway toward developing new and improved approaches for the treatment and control of parasitic diseases, with the potential for important biotechnological outcomes. [Copyright &y& Elsevier]

[Display omitted] Global challenges with treatment failures and/or widespread resistance in parasitic worms against commercially available anthelmintics lend impetus to the development of new anthelmintics with novel mechanism(s) of action. The free-living nematode Caenorhabditis elegans is an important model organism used for drug discovery, including the screening and structure-activity investigation of new compounds, and target deconvolution. Previously, we conducted a whole-organism phenotypic screen of the ' Pandemic Response Box ' (from Medicines for Malaria Venture, MMV) and identified a hit compound, called ABX464, with activity against C. elegans and a related, parasitic nematode, Haemonchus contortus. Here, we tested a series of 44 synthesized analogues to explore the pharmacophore of activity on C. elegans and revealed five compounds whose potency was similar or greater than that of ABX464, but which were not toxic to human hepatoma (HepG2) cells. Subsequently, we employed thermal proteome profiling (TPP), protein structure prediction and an in silico- docking algorithm to predict ABX464-target candidates. Taken together, the findings from this study contribute significantly to the early-stage drug discovery of a new nematocide based on ABX464. Future work is aimed at validating the ABX464-protein interactions identified here, and at assessing ABX464 and associated analogues against a panel of parasitic nematodes, towards developing a new anthelmintic with a mechanism of action that is distinct from any of the compounds currently-available commercially. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • First large-scale somatic proteomic investigation of the barber's pole worm. • Identified and quantitated 2487 unique proteins with high confidence. • Established protein profiles in free-living and parasitic stages. • Possible roles of selected protein groups in adaptive processes in the host are discussed. Abstract Currently, there is a dearth of proteomic data to underpin fundamental investigations of parasites and parasitism at the molecular level. Here, using a high throughput LC–MS/MS-based approach, we undertook the first reported comprehensive, large-scale proteomic investigation of the barber's pole worm (Haemonchus contortus) – one of the most important parasitic nematodes of livestock animals worldwide. In total, 2487 unique H. contortus proteins representing different developmental stages/sexes (i.e. eggs, L3s and L4s, female (Af) and male (Am) adults) were identified and quantified with high confidence. Bioinformatic analyses of this proteome revealed substantial alterations in protein profiles during the life cycle, particularly in the transition from the free-living to the parasitic phase, and key groups of proteins involved specifically in feeding, digestion, metabolism, development, parasite-host interactions (including immunomodulation), structural remodelling of the body wall and adaptive processes during parasitism. This proteomic data set will facilitate future molecular, biochemical and physiological investigations of H. contortus and related nematodes, and the discovery of novel intervention targets against haemonchosis. [ABSTRACT FROM AUTHOR]

Graphical abstract Highlights • The first global lipidome for a parasitic nematode – Haemonchus contortus. • More than 500 lipid species (in 18 classes) were characterised with statistical confidence. • Significant differences in lipid abundance in developmental transitions of H. contortus. Abstract Lipids play crucial roles in the biology of organisms, particularly relating to cellular membranes, energy storage, and intra- or inter-cellular signalling. Despite the recent expansion of the lipidomics field, very little is known about the biology of lipids in metzoan pathogens, and, to date, there has been no global lipidomic study of a parasitic nematode. Using Haemonchus contortus (barber's pole worm) as a model, we describe the first known global lipidome for a parasitic nematode via high throughput LC–MS/MS-based lipidomics. We identified a total of 554 lipid species across four lipid categories, and 18 lipid classes exhibited alterations among six developmental stages (eggs; L3 and exsheathed L3 (xL3) and L4 larval stages; female and male adults) of H. contortus. The lipid composition and abundance of H. contortus changed significantly during the transition from free-living (egg, L3 and xL3) to parasitic (L4 and adult) stages. The three main changes observed were: (i) decreased synthesis of triradylglycerols; (ii) increased glycerophospholipids (predominantly glycerophosphoethanolamines and glycerophosphocholines); and (iii) a 'cooperative' modulation of ether-linked lipids and saturated fatty acids. These changes suggest specific adaptations, in terms of nutrient acquisition, metabolism and development, as the nematode makes its transition to the parasitic stage inside the host animal. This lipidomic data set serves as a stimulus for studies to understand lipid biology in parasitic worms, and their roles in parasite–host interactions and disease processes. [ABSTRACT FROM AUTHOR]

Clonorchiasis is a neglected tropical disease that affects > 35 million people mainly in China, Vietnam, South Korea and some parts of Russia. The disease-causing agent, Clonorchis sinensis , is a liver fluke of humans and other piscivorous animals, and has a complex aquatic life cycle involving snails and fish intermediate hosts. Chronic infection in humans causes liver disease and associated complications including malignant bile duct cancer. Central to control and to understanding the epidemiology of this disease is knowledge of the specific identity of the causative agent as well as genetic variation within and among populations of this parasite. Although most published molecular studies seem to suggest that C. sinensis represents a single species and that genetic variation within the species is limited, karyotypic variation within C. sinensis among China, Korea (2n = 56) and Russian Far East (2n = 14) suggests that this taxon might contain sibling species. Here, we assessed and applied a deep sequencing-bioinformatic approach to sequence and define a reference mitochondrial (mt) genome for a particular isolate of C. sinensis from Korea ( Cs -k2), to confirm its specific identity, and compared this mt genome with homologous data sets available for this species. Comparative analyses revealed consistency in the number and structure of genes as well as in the lengths of protein-coding genes, and limited genetic variation among isolates of C. sinensis. Phylogenetic analyses of amino acid sequences predicted from mt genes showed that representatives of C. sinensis clustered together, with absolute nodal support, to the exclusion of other liver fluke representatives, but sub-structuring within C. sinensis was not well supported. The plan now is to proceed with the sequencing, assembly and annotation of a high quality draft nuclear genome of this defined isolate ( Cs -k2) as a basis for a detailed investigation of molecular variation within C. sinensis from disparate geographical locations in parts of Asia and to prospect for cryptic species. [ABSTRACT FROM AUTHOR]

Although substantial research has been focused on the ‘hidden antigen’ H11 of Haemonchus contortus as a vaccine against haemonchosis in small ruminants, little is know about this and related aminopeptidases. In the present article, we reviewed genomic and transcriptomic data sets to define, for the first time, the complement of aminopeptidases (designated Hc- AP-1 to Hc- AP-13) of the family M1 with homologues in Caenorhabditis elegans , characterised by zinc-binding (HEXXH) and exo-peptidase (GAMEN) motifs. The three previously published H11 isoforms (accession nos. X94187 , FJ481146 and AJ249941 ) had most sequence similarity to Hc- AP-2 and Hc- AP-8, whereas unpublished isoforms (accession nos. AJ249942 and AJ311316 ) were both most similar to Hc- AP-3. The aminopeptidases characterised here had homologues in C. elegans . Hc- AP-1 to Hc- AP-8 were most similar in amino acid sequence (28–41%) to C. elegans T07F10.1; Hc- AP-9 and Hc- AP-10 to C. elegans PAM-1 (isoform b) (53–54% similar); Hc- AP-11 and Hc- AP-12 to C. elegans AC3.5 and Y67D8C.9 (26% and 50% similar, respectively); and Hc- AP-13 to C. elegans C42C1.11 and ZC416.6 (50–58% similar). Comparative analysis suggested that Hc- AP-1 to Hc- AP-8 play roles in digestion, metabolite excretion, neuropeptide processing and/or osmotic regulation, with Hc- AP-4 and Hc- AP-7 having male-specific functional roles. The analysis also indicated that Hc- AP-9 and Hc- AP-10 might be involved in the degradation of cyclin (B3) and required to complete meiosis. Hc- AP-11 represents a leucyl/cystinyl aminopeptidase, predicted to have metallopeptidase and zinc ion binding activity, whereas Hc- AP-12 likely encodes an aminopeptidase Q homologue also with these activities and a possible role in gonad function. Finally, Hc- AP-13 is predicted to encode an aminopeptidase AP-1 homologue of C. elegans with hydrolase activity, suggested to operate, possibly synergistically with a PEPT-1 ortholog, as an oligopeptide transporter in the gut for protein uptake and normal development and/or reproduction of the worm. An appraisal of structure-based amino acid sequence alignments revealed that all conceptually translated Hc -AP proteins, with the exception of Hc -AP-12, adopt a topology similar to those observed for the two subgroups of mammalian M1 aminopeptidases, which possess either three (I, II and IV) or four (I–IV) domains. In contrast, Hc -AP-12 lacks the N-terminal domain (I), but possesses a substantially expanded domain III. Although further work needs to be done to assess amino acid sequence conservation of the different aminopeptidases among individual worms within and among H. contortus populations, we hope that these insights will support future localisation, structural and functional studies of these molecules in H. contortus as well as facilitate future assessments of a recombinant subunit or cocktail vaccine against haemonchosis. [ABSTRACT FROM AUTHOR]

Parasitic worm proteins that belong to the cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 (CAP) superfamily are proposed to play key roles in the infection process and the modulation of immune responses in host animals. However, there is limited information on these proteins for most socio-economically important worms. Here, we review the CAP protein superfamily of Haemonchus contortus (barber's pole worm), a highly significant parasitic roundworm (order Strongylida) of small ruminants. To do this, we mined genome and transcriptomic datasets, predicted and curated full-length amino acid sequences (n = 45), undertook systematic phylogenetic analyses of these data and investigated transcription throughout the life cycle of H. contortus . We inferred functions for selected Caenorhabditis elegans orthologs (including vap-1 , vap-2 , scl-5 and lon-1 ) based on genetic networking and by integrating data and published information, and were able to infer that a subset of orthologs and their interaction partners play pivotal roles in growth and development via the insulin-like and/or the TGF-beta signalling pathways. The identification of the important and conserved growth regulator LON-1 led us to appraise the three-dimensional structure of this CAP protein by comparative modelling. This model revealed the presence of different topological moieties on the canonical fold of the CAP domain, which coincide with an overall charge separation as indicated by the electrostatic surface potential map. These observations suggest the existence of separate sites for effector binding and receptor interactions, and thus support the proposal that these worm molecules act in similar ways as venoms act as ligands for chemokine receptors or G protein-coupled receptor effectors. In conclusion, this review should guide future molecular studies of these molecules, and could support the development of novel interventions against haemonchosis. [ABSTRACT FROM AUTHOR]

Due to major problems with drug resistance in parasitic nematodes of animals, there is a substantial need and excellent opportunities to develop new anthelmintics via genomic-guided and/or repurposing approaches. In the present study, we established a practical and cost-effective whole-organism assay for the in vitro-screening of compounds for activity against parasitic stages of the nematode Haemonchus contortus (barber’s pole worm). The assay is based on the use of exsheathed L3 (xL3) and L4 stages of H. contortus of small ruminants (sheep and goats). Using this assay, we screened a panel of 522 well-curated kinase inhibitors (GlaxoSmithKline, USA; code: PKIS2) for activity against H. contortus by measuring the inhibition of larval motility using an automated image analysis system. We identified two chemicals within the compound classes biphenyl amides and pyrazolo[1,5-α]pyridines, which reproducibly inhibit both xL3 and L4 motility and development, with IC 50 s of 14–47 μM. Given that these inhibitors were designed as anti-inflammatory drugs for use in humans and fit the Lipinski rule-of-five (including bioavailability), they show promise for hit-to-lead optimisation and repurposing for use against parasitic nematodes. The screening assay established here has significant advantages over conventional methods, particularly in terms of ease of use, throughput, time and cost. Although not yet fully automated, the current assay is readily suited to the screening of hundreds to thousands of compounds for subsequent hit-to-lead optimisation. The current assay is highly adaptable to many parasites of socioeconomic importance, including those causing neglected tropical diseases. This aspect is of major relevance, given the urgent need to deliver the goals of the London Declaration ( http://unitingtocombatntds.org/resource/london-declaration ) through the rapid and efficient repurposing of compounds in public–private partnerships. [ABSTRACT FROM AUTHOR]

In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella . The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites. [ABSTRACT FROM AUTHOR]

Highlights: [•] A Haemonchus contortus gene (Hc-daf-2) and its inferred product (Hc-DAF-2) were identified and characterised. [•] Hc-DAF-2 contains conserved structural domains of insulin receptor. [•] The Hc-daf-2 gene was transcribed in all life stages of Haemonchus contortus, with significant up-regulation in infective L3s. [•] Hc-DAF-2 is expressed in amphidial neurons of Caenorabditis elegans transformed with the Hc-daf-2 promoter region. [•] Heterologous genetic complementation in a daf-2-deficient strain of C. elegans showed partial rescue of function by Hc-daf-2. [Copyright &y& Elsevier]

Highlights: [•] Dictyocaulus filaria and Dictyocaulus viviparus transcriptomes were compared. [•] Some enriched molecules were linked to host interactions. [•] Prospects for new interventions. [Copyright &y& Elsevier]

Abstract: Angiostrongylus vasorum is a metastrongyloid nematode of dogs and other canids of major clinical importance in many countries. In order to gain first insights into the molecular biology of this worm, we conducted the first large-scale exploration of its transcriptome, and predicted essential molecules linked to metabolic and biological processes as well as host immune responses. We also predicted and prioritized drug targets and drug candidates. Following Illumina sequencing (RNA-seq), 52.3million sequence reads representing adult A. vasorum were assembled and annotated. The assembly yielded 20,033 contigs, which encoded proteins with 11,505 homologues in Caenorhabditis elegans, and additional 2252 homologues in various other parasitic helminths for which curated data sets were publicly available. Functional annotation was achieved for 11,752 (58.6%) proteins predicted for A. vasorum, including peptidases (4.5%) and peptidase inhibitors (1.6%), protein kinases (1.7%), G protein-coupled receptors (GPCRs) (1.5%) and phosphatases (1.2%). Contigs encoding excretory/secretory and immuno-modulatory proteins represented some of the most highly transcribed molecules, and encoded enzymes that digest haemoglobin were conserved between A. vasorum and other blood-feeding nematodes. Using an essentiality-based approach, drug targets, including neurotransmitter receptors, an important chemosensory ion channel and cysteine proteinase-3 were predicted in A. vasorum, as were associated small molecular inhibitors/activators. Future transcriptomic analyses of all developmental stages of A. vasorum should facilitate deep explorations of the molecular biology of this important parasitic nematode and support the sequencing of its genome. These advances will provide a foundation for exploring immuno-molecular aspects of angiostrongylosis and have the potential to underpin the discovery of new methods of intervention. [Copyright &y& Elsevier]

Advances in nucleic acid sequencing, mass spectrometry and computational biology have facilitated the identification, annotation and analysis of genes, transcripts, proteins and metabolites in model nematodes (Caenorhabditis elegans and Pristionchus pacificus) and socioeconomically important parasitic nematodes (Clades I, III, IV and V). Significant progress has been made in genomics and transcriptomics as well as in the proteomics and lipidomics of Haemonchus contortus (the barber's pole worm) – one of the most pathogenic representatives of the order Strongylida. Here, we review salient aspects of genomics, transcriptomics, proteomics, lipidomics, glycomics and functional genomics, and discuss the rise of integrative 'omics of this economically important parasite. Although our knowledge of the molecular biology, genetics and biochemistry of H. contortus and related species has progressed significantly, much remains to be explored, particularly in areas such as drug resistance, unique/unknown genes, host-parasite interactions, parasitism and the pathogenesis of disease, by integrating the use of multiple 'omics methods. This approach should lead to a better understanding of H. contortus and its relatives at a 'systems biology' level, and should assist in developing new interventions against these parasites. • Comprehensive review of 'omics of Haemonchus contortus. • Discuss the application of integrative 'omics to this and related parasitic nematodes. • Perspective on future research avenues. [ABSTRACT FROM AUTHOR]