Transcript profiles of long- and short-lived adults implicate protein synthesis in evolved differences in ageing in the nematode Strongyloides ratti

Strongyloides questions-a research agenda for the future

The Strongyloides genus of parasitic nematodes have a fascinating life cycle and biology, but are also important pathogens of people and a World Health Organization-defined neglected tropical disease. Here, a community of Strongyloides researchers have posed thirteen major questions about Strongyloides biology and infection that sets a Strongyloides research agenda for the future. This article is part of the Theo Murphy meeting issue 'Strongyloides: omics to worm-free populations'.

Insulin-like growth factor-1 signaling in cardiac aging

Cardiovascular disease (CVD) is the leading cause of death in most developed countries. Aging is associated with enhanced risk of CVD. Insulin-like growth factor-1 (IGF-1) binds to its cognate receptor, IGF-1 receptor (IGF-1R), and exerts pleiotropic effects on cell growth, differentiation, development, and tissue repair. Importantly, IGF-1/IGF-1R signaling is implicated in cardiac aging and longevity. Cardiac aging is an intrinsic process that results in cardiac dysfunction, accompanied by molecular and cellular changes. In this review, we summarize the current state of knowledge regarding the link between the IGF-1/IGF-1R system and cardiac aging. The biological effects of IGF-1R and insulin receptor will be discussed and compared. Furthermore, we describe data regarding how deletion of IGF-1R in cardiomyocytes of aged knockout mice may delay the development of senescence-associated myocardial pathologies. This article is part of a Special issue entitled Cardiac adaptations to obesity, diabetes and insulin resistance, edited by Professors Jan F.C. Glatz, Jason R.B. Dyck and Christine Des Rosiers.

Transgenesis in Strongyloides and related parasitic nematodes: historical perspectives, current functional genomic applications and progress towards gene disruption and editing

Transgenesis for Strongyloides and Parastrongyloides was accomplished in 2006 and is based on techniques derived for Caenorhabditis elegans over two decades earlier. Adaptation of these techniques has been possible because Strongyloides and related parasite genera carry out at least one generation of free-living development, with adult males and females residing in soil contaminated by feces from an infected host. Transgenesis in this group of parasites is accomplished by microinjecting DNA constructs into the syncytia of the distal gonads of free-living females. In Strongyloides stercoralis, plasmid-encoded transgenes are expressed in promoter-regulated fashion in the F1 generation following gene transfer but are silenced subsequently. Stable inheritance and expression of transgenes in S. stercoralis requires their integration into the genome, and stable lines have been derived from integrants created using the piggyBac transposon system. More direct investigations of gene function involving expression of mutant transgene constructs designed to alter intracellular trafficking and developmental regulation have shed light on the function of the insulin-regulated transcription factor Ss-DAF-16. Transgenesis in Strongyloides and Parastrongyloides opens the possibility of powerful new methods for genome editing and transcriptional manipulation in this group of parasites. Proof of principle for one of these, CRISPR/Cas9, is presented in this review.

Genetics: modes of reproduction and genetic analysis

Classical and reverse genetics remain invaluable tools for the scientific investigation of model organisms. Genetic analysis of endoparasites is generally difficult because the sexual adults required for crossing and other manipulations are usually hidden within their host. Strongyloides spp. and Parastrongyloides spp. are notable exceptions to this and their free-living adults offer unique opportunities to manipulate these parasites experimentally. Here I review the modes of inheritance in the two generations of Strongyloides/Parastrongyloides and I discuss the opportunities and the limitations of the currently available methodology for the genetic analysis of these two genera.

Strongyloides ratti and S. venezuelensis - rodent models of Strongyloides infection

Strongyloides spp. are common parasites of vertebrates and two species, S. ratti and S. venezuelensis, parasitize rats; there are no known species that naturally infect mice. Strongyloides ratti and S. venezuelensis overlap in their geographical range and in these regions co-infections appear to be common. These species have been widely used as tractable laboratory systems in rats as well as mice. The core biology of these two species is similar, but there are clear differences in aspects of their within-host biology as well as in their free-living generation. Phylogenetic evidence suggests that S. ratti and S. venezuelensis are the result of two independent evolutionary transitions to parasitism of rats, which therefore presents an ideal opportunity to begin to investigate the basis of host specificity in Strongyloides spp.

Strongyloides stercoralis and relatives: recent advances in general and molecular biology

Human strongyloidiasis is a threat to global health, presenting significant challenges in diagnosis and clinical management. The imperative to incorporate strongyoidiasis more fully into control programs for soil-transmitted helminths is increasingly recognized. The unique life cycles of S. stercoralis and congeneric species contain both free-living and parasitic generations, and transcriptomic methods have recently identified genes of potential importance to parasitism in these parasites. Proteomics recently revealed stage-specific secreted proteins that appear crucial to the host-parasite interaction. A comprehensive genome sequencing project for Strongyloides spp. is now nearing completion. Recent technical advances in transgenesis for S. stercoralis and S. ratti, including the first establishment of stable transgenic lines, promise to advance functional evaluations of genes expressed in conjunction with crucial life cycle events. Studies employing these methods recently bolstered the hypothesis that S. stercoralis uses cellular signaling pathways homologous to three that regulate dauer larval development in Caenorhabditis elegans to regulate morphogenesis and development of its infective third-stage larva. The free-living generation of Strongyloides makes classical genetics formally possible. Recent advances, such as a genetic map of S. ratti and a molecular genetic and karyotypic analysis of sex determination in S. papillosus, will greatly facilitate this approach. Advanced methods for study of chemosensation in C. elegans were recently applied to discover numerous host attractant molecules that mediate host finding and contact by infective third-stage larvae of Strongyloides spp. Finally, nucleic acid-based diagnostic methods have recently come to the fore as alternatives to parasitological and immunodiagnostic techniques.

Transcriptome analysis of a long-lived natural Drosophila variant: a prominent role of stress- and reproduction-genes in lifespan extension

Background

While studying long-lived mutants has advanced our understanding of the processes involved in ageing, the mechanisms underlying natural variation in lifespan and ageing rate remain largely unknown. Here, we characterise genome-wide expression patterns of a long-lived, natural variant of Drosophila melanogaster resulting from selection for starvation resistance (SR) and compare it with normal-lived control flies (C). We do this at two time points representing middle age (90% survival) and old age (10% survival) respectively, in three adult diets (malnutrition, optimal food, and overfeeding).

Results

We found profound differences between Drosophila lines in their age-related expression. Most of the age-associated changes in normal-lived flies were abrogated in long-lived Drosophila. The stress-related genes, including those involved in proteolysis and cytochrome P450, were generally higher expressed in SR flies and showed a smaller increase in expression with age compared to C flies. The genes involved in reproduction showed a lower expression in middle-aged SR than in C flies and, unlike C flies, a lack of their downregulation with age. Further, we found that malnutrition strongly affected age-associated transcript patterns overriding the differences between the lines. However, under less stressful dietary conditions, line and diet affected age-dependent expression similarly. Finally, we present lists of candidate markers of ageing and lifespan extension.

Conclusions

Our study unveils transcriptional changes associated with lifespan extension in SR Drosophila. The results suggest that natural genetic variation for SR and lifespan can operate through similar transcriptional mechanisms as those of dietary restriction and life-extending mutations.

Characterization of genes with a putative key role in the parasitic lifestyle of the nematode Strongyloides ratti

Parasitic nematodes are significant pathogens of humans and other animals. The molecular and genetic basis of animal parasitism is not yet fully understood. Strongyloides spp. are a genus of gastrointestinal nematodes of which species infect approximately 100–200 million people worldwide. S. ratti is a natural parasite of the rat, and a useful and amenable laboratory model. Previous EST and microarray analyses of the S. ratti life cycle have identified genes whose expression was specific, or biased, to the parasitic adult stage, suggesting that they may play a key role in parasitism in this species. Here we have further investigated the expression of these genes (by RT-PCR) throughout the S. ratti life-cycle. We produced recombinant proteins in vitro for a subset of these genes, which were used in Western blot analyses to investigate the distribution of the gene products among different stages of the S. ratti life cycle. We tested the efficacy of these recombinant proteins as anti-S. ratti vaccines. One of the proteins was detected in the excretory/secretory products of the parasitic stages.

In silico secretome analysis approach for next generation sequencing transcriptomic data

BACKGROUND

Excretory/secretory proteins (ESPs) play a major role in parasitic infection as they are present at the host-parasite interface and regulate host immune system. In case of parasitic helminths, transcriptomics has been used extensively to understand the molecular basis of parasitism and for developing novel therapeutic strategies against parasitic infections. However, none of transcriptomic studies have extensively covered ES protein prediction for identifying novel therapeutic targets, especially as parasites adopt non-classical secretion pathways.

RESULTS

We developed a semi-automated computational approach for prediction and annotation of ES proteins using transcriptomic data from next generation sequencing platforms. For the prediction of non-classically secreted proteins, we have used an improved computational strategy, together with homology matching to a dataset of experimentally determined parasitic helminth ES proteins. We applied this protocol to analyse 454 short reads of parasitic nematode, Strongyloides ratti. From 296231 reads, we derived 28901 contigs, which were translated into 20877 proteins. Based on our improved ES protein prediction pipeline, we identified 2572 ES proteins, of which 407 (1.9%) proteins have classical N-terminal signal peptides, 923 (4.4%) were computationally identified as non-classically secreted while 1516 (7.26%) were identified by homology to experimentally identified parasitic helminth ES proteins. Out of 2572 ES proteins, 2310 (89.8%) ES proteins had homologues in the free-living nematode Caenorhabditis elegans and 2220 (86.3%) in parasitic nematodes. We could functionally annotate 1591 (61.8%) ES proteins with protein families and domains and establish pathway associations for 691 (26.8%) proteins. In addition, we have identified 19 representative ES proteins, which have no homologues in the host organism but homologous to lethal RNAi phenotypes in C. elegans, as potential therapeutic targets.

CONCLUSION

We report a comprehensive approach using freely available computational tools for the secretome analysis of NGS data. This approach has been applied to S. ratti 454 transcriptomic data for in silico excretory/secretory proteins prediction and analysis, providing a foundation for developing new therapeutic solutions for parasitic infections.

Transgenesis in the parasitic nematode Strongyloides ratti

Strongyloides and related genera are advantageous subjects for transgenesis in parasitic nematodes, primarily by gonadal microinjection as has been used with Caenorhabditis elegans. Transgenesis has been achieved in Strongyloides stercoralis and in Parastrongyloides trichosuri, but both of these lack well-adapted, conventional laboratory hosts in which to derive transgenic lines. By contrast, Strongyloides ratti develops in laboratory rats with high efficiency and offers the added advantages of robust genomic and transcriptomic databases and substantial volumes of genetic, developmental and immunological data. Therefore, we evaluated methodology for transgenesis in S. stercoralis as a means of transforming S. ratti. S. stercoralis-based GFP reporter constructs were expressed in a proportion of F1 transgenic S. ratti following gonadal microinjection into parental free-living females. Frequencies of transgene expression in S. ratti, ranged from 3.7% for pAJ09 to 6.8% for pAJ20; respective frequencies for these constructs in S. stercoralis were 5.6% and 33.5%. Anatomical patterns of transgene expression were virtually identical in S. ratti and S. stercoralis. This is the first report of transgenesis in S. ratti, an important model organism for biological investigations of parasitic nematodes. Availability of the rat as a well-adapted laboratory host will facilitate derivation of transgenic lines of this parasite.

Microarray-based analysis of differential gene expression between infective and noninfective larvae of Strongyloides stercoralis

BACKGROUND

Differences between noninfective first-stage (L1) and infective third-stage (L3i) larvae of parasitic nematode Strongyloides stercoralis at the molecular level are relatively uncharacterized. DNA microarrays were developed and utilized for this purpose.

METHODS AND FINDINGS

Oligonucleotide hybridization probes for the array were designed to bind 3,571 putative mRNA transcripts predicted by analysis of 11,335 expressed sequence tags (ESTs) obtained as part of the Nematode EST project. RNA obtained from S. stercoralis L3i and L1 was co-hybridized to each array after labeling the individual samples with different fluorescent tags. Bioinformatic predictions of gene function were developed using a novel cDNA Annotation System software. We identified 935 differentially expressed genes (469 L3i-biased; 466 L1-biased) having two-fold expression differences or greater and microarray signals with a p value<0.01. Based on a functional analysis, L1 larvae have a larger number of genes putatively involved in transcription (p = 0.004), and L3i larvae have biased expression of putative heat shock proteins (such as hsp-90). Genes with products known to be immunoreactive in S. stercoralis-infected humans (such as SsIR and NIE) had L3i biased expression. Abundantly expressed L3i contigs of interest included S. stercoralis orthologs of cytochrome oxidase ucr 2.1 and hsp-90, which may be potential chemotherapeutic targets. The S. stercoralis ortholog of fatty acid and retinol binding protein-1, successfully used in a vaccine against Ancylostoma ceylanicum, was identified among the 25 most highly expressed L3i genes. The sperm-containing glycoprotein domain, utilized in a vaccine against the nematode Cooperia punctata, was exclusively found in L3i biased genes and may be a valuable S. stercoralis target of interest.

CONCLUSIONS

A new DNA microarray tool for the examination of S. stercoralis biology has been developed and provides new and valuable insights regarding differences between infective and noninfective S. stercoralis larvae. Potential therapeutic and vaccine targets were identified for further study.

A genetic map of the animal-parasitic nematode Strongyloides ratti

Classical genetic approaches are rarely used with metazoan endo-parasites, largely because the adult stages are usually hidden within hosts, making controlled crosses difficult. The nematode Strongyloides ratti is a parasite of the small intestine of rats, and is a relative of the parasite of humans S. stercoralis. The life-cycle of Strongyloides spp. has a facultative free-living adult generation. Here we describe procedures for genetic mapping, and a genetic map, for S. ratti. This is, as far as we are aware, the first genetic map of an animal parasitic nematode. This significantly improves the usefulness of S. ratti as experimentally tractable system for parasitological investigations and for comparative studies with the model nematode Caenorhabditis elegans.