nGASP – the nematode genome annotation assessment project

Background  

While the C. elegans genome is extensively annotated, relatively little information is available for other Caenorhabditis species. The nematode genome annotation assessment project (nGASP) was launched to objectively assess the accuracy of protein-coding gene prediction software in C. elegans, and to apply this knowledge to the annotation of the genomes of four additional Caenorhabditis species and other nematodes. Seventeen groups worldwide participated in nGASP, and submitted 47 prediction sets across 10 Mb of the C. elegans genome. Predictions were compared to reference gene sets consisting of confirmed or manually curated gene models from WormBase.     

Are filarial nematode Wolbachia obligate mutualist symbionts?

The intracellular symbiotic bacteria of filarial nematodes have inspired new ideas for the control of disease using antibacterial drugs. For effective, long-term control, this requires that the bacteria are essential to their nematode hosts. Two recent studies offer conflicting evidence: long, close coevolution between most filarial nematodes and their symbionts contrasts with many species having naturally lost them. An attempt to transfer symbionts to an uninfected host found that the bacteria did not thrive, suggesting they are adapted to one host.     

How do host immune responses affect nematode infections?

Host immune responses limit, and in some instances eliminate, nematode infections. There is considerable interest in enhancing these natural processes by the use of antinematode vaccines to achieve control of infection or disease. How nematodes are damaged is unclear. Worms might be damaged directly by effector cells and molecules of the immune system. Alternatively, they might be damaged by the physiological stress of their efforts to resist attack. Separating these possibilities could have important implications for approaches to the control of nematode infections and the disease that they cause.     

What causes lymphocyte hyporesponsiveness during filarial nematode infection?

Filarial nematodes persist in the parasitized host by modulating immune responsiveness. A feature of this that has been observed in a multitude of studies dating back several decades is an inability of lymphocytes to respond appropriately to filarial nematode antigens and, in some cases, to other stimuli. The consistency of this observation, allied to the ease of measurement of lymphocyte hyporesponsiveness, has resulted in many attempts to understand its cause.     

Why does a nematode have an invariant cell lineage?

C. elegans is renowned for its invariant embryogenesis and functions as a major paradigm for a mode of development coupled to an invariant lineage. Recent work, however, suggests that the embryogenesis of the nematode is much more flexible than anticipated. The invariant premorphogenetic stage is formed from variable earlier stages through a sorting of cells. Cells do not act as individuals but already early in embryogenesis a regionalization of the embryo occurs. Cells are diversified by a binary specification of 'abstract' blastomere (regional) identities. The determination of tissues may thus be a very late event. It appears that C. elegans, although assigning cell fates in an invariant lineage pattern, uses the same strategies and mechanisms for embryogenesis as organisms with variable lineages.     

Do nematode and macrofauna assemblages provide similar ecological assessment information?

Do nematode and macrofauna assemblages provide similar ecological assessment information? To answer this question, in the summer of 2006, subtidal soft-bottom assemblages were sampled and environmental parameters were measured at seven stations covering the entire salinity gradient of the Mondego estuary. Principal components analysis (PCA) was performed on the environmental parameters, thus establishing different estuarine stretches. The ecological status of each community was determined by applying the Maturity Index and the Index of Trophic Diversity to the nematode data and the Benthic Assessment Tool to the macrofaunal data. Overall, the results indicated that the answer to the initial question is not straightforward. The fact that nematode and macrofauna have provided different responses regarding environmental status may be partially explained by local differentiation in microhabitat conditions, given by distinct sampling locations within each estuarine stretch and by different response-to-stress times of each benthic community. Therefore, our study suggests that both assemblages should be used in marine pollution monitoring programs.     

Transformation: how do nematode sperm become activated and crawl?

Nematode sperm undergo a drastic physiological change during spermiogenesis (sperm activation). Unlike mammalian flagellated sperm, nematode sperm are amoeboid cells and their motility is driven by the dynamics of a cytoskeleton composed of major sperm protein (MSP) rather than actin found in other crawling cells. This review focuses on sperm from Caenorhabditis elegans and Ascaris suum to address the roles of external and internal factors that trigger sperm activation and power sperm motility. Nematode sperm can be activated in vitro by several factors, including Pronase and ionophores, and in vivo through the TRY-5 and SPE-8 pathways. Moreover, protease and protease inhibitors are crucial regulators of sperm maturation. MSP-based sperm motility involves a coupled process of protrusion and retraction, both of which have been reconstituted in vitro. Sperm motility is mediated by phosphorylation signals, as illustrated by identification of several key components (MPOP, MFPs and MPAK) in Ascaris and the characterization of GSP-3/4 in C. elegans.     

A putative nuclear growth factor‐like globular nematode specific protein

Expressed sequence tags (ESTs) are an effective approach for discovery of novel genes. In the current study, approximately 250 ESTs of the cattle parasitic nematode Setaria digitata were examined and a cDNA clone identified whose coding sequence could not be functionally annotated by searching over publicly available genome, protein, EST and STS databases. Here, we report the extensive characterization of this ORF (UP) and its homologues using a bioinformatic approach. Uncharacterized protein (SDUP) of S. digitata consists of 204 amino acids with a predicted molecular weight and isoelectric point of 22.8KDa and 9.94, respectively. A search carried out using SDUP over nucleotide, EST and protein databases at NCBI, NEMBASE3 and Parasite Genome Database (PGD) identified homologous counterparts from the human parasitic nematodes Wuchereria bancrofti (WB), Brugia malayi (BM), Onchocerca volvulus (OV), the mouse filarial worm Litomosoides sigmodontis (LS), swine parasitic nematodes Ascaris suum (AS) and diverged counterparts from the plant parasitic nematode Meloidogyne hapla (MH) and free living nematodes Caenorhabditis elegans (CE) and Caenorhabditis briggsae (CB). Phylogenetic analyses revealed the UPs to be undergoing divergent evolution. A search of the ESTs at PGD showed that UP is expressed in all the stages of BM. Secondary structure analyses of multiply-aligned sequences of homologues using Jpred server indicated UPs to be rich in beta-pleated structures. TMMHH server and beta barrel finder programme indicated, UPs to be neither transmembrane or beta barrels proteins but are likely to be globular proteins. Further, the Motif discovery tool of MEME identified three novel potential motifs for UPS, of which only two are present in CE, CB & MH. Analyses of UPs using Signal IP, TargetP, Psort servers predicted this group of proteins to be devoid of signal peptide cleavage sites, are not mitochondrial targeting peptides but appear to be localized to the nucleus, respectively. Further analyses of the UPs using ScanProsite server for phosphorylation revealed potential sites for cAMP­ and cGMP­dependent protein kinase, Protein kinase C and Casein kinase II. Putative functional analysis using ProtFun 2.1 Server indicated UPs to be nonenzymatic, growth factor like protein. Finally, collating all the information derived from bioinformatic analyses, we conclude that the UPs of nematodes are most likely to be expressed at all stages in the life cycle, localized to the nucleus, regulated by phosphorylation, rich in beta­pleated strands and are growth factor like nematode specific proteins.     

Are we ready to detect nematode diversity by next generation sequencing?

In a Technical Advance article, Porazinska et al. (2009, Molecular Ecology Resources, 9, 1439–1450) assessed next generation sequencing (NGS) as a method for metagenomic analysis of nematode diversity. We agree that NGS has great potential here. However, it is not an easy path to the successful implementation of NGS for environmental DNA analysis of nematodes. Here, we describe the method's limitations and discuss prospective research questions. For instance, only a few direct extraction kits are suitable for nematode DNA extraction from bulk samples without adaptation. They enable the analysis of extracellular nematode DNA. The most crucial and unresolved issue remains the limited availability of suitable primers.     

Quantitative detection of induced systemic resistance genes of potato roots upon ethylene treatment and cyst nematode,Globodera rostochiensis,infection during plant–nematode interactions

Potato cyst nematodes caused by Globodera rostochiensis, are quarantine-restricted pests causing significant yield losses to potato growers. The phytohormone ethylene play significant roles in various plant-pathogen interactions, however, the molecular knowledge of how ethylene influences potato–nematode interaction is still lacking. Precise detection of potato-induced genes is essential for recognizing plant-induced systemic resistance (ISR). Candidate genes or PR- proteins with putative functions in modulating the response to potato cyst nematode stress were selected and functionally characterized. Using real-time polymerase chain reaction (RT-PCR), we measured the quantified expression of four pathogenesis-related (PR) genes, PR2, PR3, peroxidase, and polyphenol oxidase. The activation of these genes is intermediate during the ISR signaling in the root tissues. Using different ethylene concentrations could detect and induce defense genes in infected potato roots compared to the control treatment. The observed differences in the gene expression of treated infected plants are because of different concentrations of ethylene treatment and pathogenicity. Besides, the overexpressed or suppressed of defense- related genes during developmental stages and pathogen infection. We concluded that ethylene treatments positively affected potato defensive genes expression levels against cyst nematode infection. The results emphasize the necessity of studying molecular signaling pathways controlling biotic stress responses. Understanding such mechanisms will be critical for the development of broad-spectrum and stress-tolerant crops in the future.     

Why do fish have so few roundworm (nematode) parasites?

Synopsis Although they are the oldest and most diverse members of the subphylum, the fishes have relatively few nematode parasites in comparison with other vertebrate classes. It is hypothesized that this paucity of parasite species has occurred because nematode parasites first evolved in terrestrial hosts and only a few lines of these parasites were able to transfer to fish after the appearance of heteroxeny (use of intermediate hosts) and paratenesis (use of transport hosts). The inability of nematodes to initiate parasitism in aquatic ecosystems restricted fish parasites mainly to forms first adapted to terrestrial vertebrates and at the same time deprived large groups of aquatic invertebrates such as the crustaceans, annelids and molluscs of a nematode parasite fauna.Invited editorial     

Anthelmintic resistance in nematode parasites of cattle: a global issue?

Acceptable performance of grazing cattle frequently depends on the availability of effective broad-spectrum anthelmintics to remove, or prevent infection with, gastrointestinal nematodes. This control is increasingly threatened by populations of nematodes resistant to the most commonly used anthelmintics. Although this appears to have developed more slowly than in nematodes infecting small ruminants, the number of reports in the literature over the past five years suggests a rapidly escalating problem. This review discusses this literature, several issues unique to cattle parasitism and anthelmintics, and how previous research in small ruminants can improve the management of anthelmintic resistance in cattle.     

Synthesis of N²-modified 7-methylguanosine 5'-monophosphates as nematode translation inhibitors

Preparative scale synthesis of 14 new N(2)-modified mononucleotide 5' mRNA cap analogues was achieved. The key step involved use of an S(N)Ar reaction with protected 2-fluoro inosine and various primary and secondary amines. The derivatives were tested in a parasitic nematode, Ascaris suum, cell-free system as translation inhibitors. The most effective compound with IC(50) ～0.9μM was a N(2)-p-metoxybenzyl-7-methylguanosine-5'-monophosphate 35.     

How effective is pre-release nematode control in farm-reared red-legged partridges Alectoris rufa?

Game bird farming is associated with high parasite levels that reduce farm productivity, reduce survival after releasing, and may pose a health risk for natural populations. The efficacy of albendazole (orally, 20 mg kg(-1) was evaluated in farmed red-legged partridges naturally infected with the nematodes Aonchotheca caudinflata and Heterakis gallinarum. In treated birds body condition improved, nematode egg deposition was reduced and the proportion of gravid A. caudinflata females was reduced, but not the overall worm burdens. Albendazole was found to be 36.8% and 17.1% effective against A. caudinflata and H. gallinarum, respectively. These results indicate that the anthelmintic treatment used normally in Spanish partridge farms is not effective enough to avoid the introduction of parasites into the field after release.     

Evolutionary loss of parasitism by nematodes? Discovery of a free-living filaroid nematode

A cattle-drinking pool in nature reserve "Zwin" on the Belgian coast contained free-living third-stage infective filaroid juveniles. These juveniles clearly differ morphologically from all known nematodes. Morphological and molecular analyses indicate a position within the Filaroidea. The aberrant biology of this nematode, namely, a free-living stage in an aquatic environment, is unknown within this superfamily, and the evolution of the parasitic phenotype to a free-living state is generally thought to be unlikely. However, the obtained placement in the small subunit molecular phylogenetic tree suggests that this free-living stage is most likely a secondary adaptation. It is reasonable to assert that nematodes with complex life cycles still have the genetic potential for a reversion from parasitism to a (partial) free-living stage.     

Immune-mediated pathology of nematode infection in sheep--is immunity beneficial to the animal?

Nematode parasitism is a severe impediment to sustainable and profitable sheep production in many countries in the world. Parasite resistance to anthelmintic treatment and consumer demand for organic agricultural products has led to much research into harnessing natural immunity as a long-term control measure. However, there is evidence that many of the clinical signs of nematode infection in sheep are due to immune-mediated pathology rather than direct effects of the parasite. Therefore, the desirability of promoting a strong natural immunity in sheep has been questioned. This review attempts to clarify some of the arguments for and against promoting strong natural immunity, particularly through selective breeding of parasite-resistant animals. It is concluded that the detrimental effects of immune-mediated pathology are outweighed by epidemiological and welfare benefits. Thus, control of nematode parasites through selection of naturally resistant sheep is a sustainable and desirable objective.     

A thiabendazole sulfonamide shows potent inhibitory activity against mammalian and nematode α-carbonic anhydrases

A sulfonamide derivative of the antihelmintic drug thiabendazole was prepared and investigated for inhibition of the zinc enzyme carbonic anhydrase CA (EC 4.2.1.1). Mammalian isoforms CA I–XIV and the nematode enzyme of Caenorhabditis elegans CAH-4b were included in this study. Thiabendazole-5-sulfonamide was a very effective inhibitor of CAH-4b and CA IX (K_Is of 6.4–9.5 nm) and also inhibited effectively isozymes CA I, II, IV–VII, and XII, with K_Is in the range of 17.8–73.2 nM. The high resolution X-ray crystal structure of its adduct with isozyme II evidenced the structural elements responsible for this potent inhibitory activity.     

A role for α-adducin (ADD-1) in nematode and human memory

Identifying molecular mechanisms that underlie learning and memory is one of the major challenges in neuroscience. Taken the advantages of the nematode Caenorhabditis elegans, we investigated α-adducin (add-1) in aversive olfactory associative learning and memory. Loss of add-1 function selectively impaired short- and long-term memory without causing acquisition, sensory, or motor deficits. We showed that α-adducin is required for consolidation of synaptic plasticity, for sustained synaptic increase of AMPA-type glutamate receptor (GLR-1) content and altered GLR-1 turnover dynamics. ADD-1, in a splice-form- and tissue-specific manner, controlled the storage of memories presumably through actin-capping activity. In support of the C. elegans results, genetic variability of the human ADD1 gene was significantly associated with episodic memory performance in healthy young subjects. Finally, human ADD1 expression in nematodes restored loss of C. elegans add-1 gene function. Taken together, our findings support a role for α-adducin in memory from nematodes to humans. Studying the molecular and genetic underpinnings of memory across distinct species may be helpful in the development of novel strategies to treat memory-related diseases.