Studies on neuraminidases produced by anaerobic bacteria and their possible role in pathogenicity

These studies were designed to investigate the production of neuraminidase by a wide range of species of strictly anaerobic bacteria and to explore the possibility that the enzyme may play a part in the pathogenic mechanisms of these organisms. A glycoprotein fraction was prepared from pooled human plasma for use as substrate in assays for neuraminidase. Sensitive and reliable procedures were developed for characterisation of neuraminidase production by Clostridium perfrinaens and Bacteroides fragilis, and these studies were extended to a survey of well characterised strains of other species in these genera. There was variation amongst strains of C. oerfrinaens type A; many heatresistant food-poisoning strains did not produce the enzyme whereas most haemolytic, heat-sensitive strains did. The results were consistent for all strains of the other clostridial and bacteroides species examined and it is suggested that tests for neuraminidase production should be a valuable addition to currently used biochemical tests in certain areas of taxonomic studies in both genera. The ability of various Clostridia to produce experimental myonecrosis was tested in guinea pigs. Strains classed as neuraminidase-positive in vitro also produced the enzyme in vivo; neuraminidase-negative strains did not. Pathogenic Clostridia produced extensive myonecrosis and death in 24-48 h; virulence was assessed by the challenge dose required to produce fatal infection or by the severity of local muscle infection in surviving animals. Although a number of pathogenic Clostridia produce neuraminidase, there was no clear-cut correlation between virulence and ability to produce the enzyme. Large amounts of neuraminidase were produced in the tissues by virulent strains of C. oerfrinoens and C. septicum but none by the equally pathogenic but neuraminidasenegative C. novyi: at least one neuraminidase-negative strain of C. perfringens was able to produce fatal infection. Various equine and rabbit antisera were assessed for their ability to protect animals challenged with a virulent strain of C. perfringens: the protective effect was found to correlate with the content of anti-oe-toxin. C. perfringens neuraminidase proved to be a poor antigen and it was difficult to produce sera with high levels of neutralising activity; however, there was no evidence that anti-neuraminidase contributed to the protective effect of the antisera tested. The occurrence and roles of neuraminidase and its substrates are reviewed, and various ways in which neuraminidase produced during infection might contribute to tissue damage are discussed. The pathogenesis of C. perfringens gas gangrene remains incompletely understood and a number of features of the disease are not adequately explained by theories that attribute the major role to oc-toxin. Neuraminidase is one of a collection of digestive enzymes that are thought to be of value to commensal or saprophytic C. perfringens strains and it is probable that it has a similar role during infection; however, there is no evidence that neuraminidase is an important virulence factor for the organism

A first-draft human protein-interaction map

BACKGROUND: Protein-interaction maps are powerful tools for suggesting the cellular functions of genes. Although large-scale protein-interaction maps have been generated for several invertebrate species, projects of a similar scale have not yet been described for any mammal. Because many physical interactions are conserved between species, it should be possible to infer information about human protein interactions (and hence protein function) using model organism protein-interaction datasets. RESULTS: Here we describe a network of over 70,000 predicted physical interactions between around 6,200 human proteins generated using the data from lower eukaryotic protein-interaction maps. The physiological relevance of this network is supported by its ability to preferentially connect human proteins that share the same functional annotations, and we show how the network can be used to successfully predict the functions of human proteins. We find that combining interaction datasets from a single organism (but generated using independent assays) and combining interaction datasets from two organisms (but generated using the same assay) are both very effective ways of further improving the accuracy of protein-interaction maps. CONCLUSIONS: The complete network predicts interactions for a third of human genes, including 448 human disease genes and 1,482 genes of unknown function, and so provides a rich framework for biomedical research

Combinatorial RNA interference in Caenorhabditis elegans reveals that redundancy between gene duplicates can be maintained for more than 80 million years of evolution

BACKGROUND: Systematic analyses of loss-of-function phenotypes have been carried out for most genes in Saccharomyces cerevisiae, Caenorhabditis elegans, and Drosophila melanogaster. Although such studies vastly expand our knowledge of single gene function, they do not address redundancy in genetic networks. Developing tools for the systematic mapping of genetic interactions is thus a key step in exploring the relationship between genotype and phenotype. RESULTS: We established conditions for RNA interference (RNAi) in C. elegans to target multiple genes simultaneously in a high-throughput setting. Using this approach, we can detect the great majority of previously known synthetic genetic interactions. We used this assay to examine the redundancy of duplicated genes in the genome of C. elegans that correspond to single orthologs in S. cerevisiae or D. melanogaster and identified 16 pairs of duplicated genes that have redundant functions. Remarkably, 14 of these redundant gene pairs were duplicated before the divergence of C. elegans and C. briggsae 80-110 million years ago, suggesting that there has been selective pressure to maintain the overlap in function between some gene duplicates. CONCLUSION: We established a high throughput method for examining genetic interactions using combinatorial RNAi in C. elegans. Using this technique, we demonstrated that many duplicated genes can retain redundant functions for more than 80 million years of evolution. This provides strong support for evolutionary models that predict that genetic redundancy between duplicated genes can be actively maintained by natural selection and is not just a transient side effect of recent gene duplication events

Systematic analysis of off-target effects in an RNAi screen reveals microRNAs affecting sensitivity to TRAIL-induced apoptosis.

BACKGROUND: RNA inhibition by siRNAs is a frequently used approach to identify genes required for specific biological processes. However RNAi screening using siRNAs is hampered by non-specific or off target effects of the siRNAs, making it difficult to separate genuine hits from false positives. It is thought that many of the off-target effects seen in RNAi experiments are due to siRNAs acting as microRNAs (miRNAs), causing a reduction in gene expression of unintended targets via matches to the 6 or 7 nt 'seed' sequence. We have conducted a careful examination of off-target effects during an siRNA screen for novel regulators of the TRAIL apoptosis induction pathway(s). RESULTS: We identified 3 hexamers and 3 heptamer seed sequences that appeared multiple times in the top twenty siRNAs in the TRAIL apoptosis screen. Using a novel statistical enrichment approach, we systematically identified a further 17 hexamer and 13 heptamer seed sequences enriched in high scoring siRNAs. The presence of one of these seeds sequences (which could explain 6 of 8 confirmed off-target effects) is sufficient to elicit a phenotype. Three of these seed sequences appear in the human miRNAs miR-26a, miR-145 and miR-384. Transfection of mimics of these miRNAs protects several cell types from TRAIL-induced cell death. CONCLUSIONS: We have demonstrated a role for miR-26a, miR-145 and miR-26a in TRAIL-induced apoptosis. Further these results show that RNAi screening enriches for siRNAs with relevant off-target effects. Some of these effects can be identified by the over-representation of certain seed sequences in high-scoring siRNAs and we demonstrate the usefulness of such systematic analysis of enriched seed sequences

Climate Science, Development Practice, and Policy Interactions in Dryland Agroecological Systems

The literature on drought, livelihoods, and poverty suggests that dryland residents are especially vulnerable to climate change. However, assessing this vulnerability and sharing lessons between dryland communities on how to reduce vulnerability has proven difficult because of multiple definitions of vulnerability, complexities in quantification, and the temporal and spatial variability inherent in dryland agroecological systems. In this closing editorial, we review how we have addressed these challenges through a series of structured, multiscale, and interdisciplinary vulnerability assessment case studies from drylands in West Africa, southern Africa, Mediterranean Europe, Asia, and Latin America. These case studies adopt a common vulnerability framework but employ different approaches to measuring and assessing vulnerability. By comparing methods and results across these cases, we draw out the following key lessons: (1) Our studies show the utility of using consistent conceptual frameworks for vulnerability assessments even when quite different methodological approaches are taken; (2) Utilizing narratives and scenarios to capture the dynamics of dryland agroecological systems shows that vulnerability to climate change may depend more on access to financial, political, and institutional assets than to exposure to environmental change; (3) Our analysis shows that although the results of quantitative models seem authoritative, they may be treated too literally as predictions of the future by policy makers looking for evidence to support different strategies. In conclusion, we acknowledge there is a healthy tension between bottom-up/ qualitative/place-based approaches and top-down/quantitative/generalizable approaches, and we encourage researchers from different disciplines with different disciplinary languages, to talk, collaborate, and engage effectively with each other and with stakeholders at all levels

High resolution transcriptome maps for wild-type and nonsense-mediated decay-defective Caenorhabditis elegans

The high-resolution transcriptome of wild-type and nonsense-mediated decay (NMD) defective C. elegans during development reveals insights into the NMD pathway and it’s role in development