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      A core set of venom proteins is released by entomopathogenic nematodes in the genus Steinernema

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          Abstract

          Parasitic helminths release molecular effectors into their hosts and these effectors can directly damage host tissue and modulate host immunity. Excreted/secreted proteins (ESPs) are one category of parasite molecular effectors that are critical to their success within the host. However, most studies of nematode ESPs rely on in vitro stimulation or culture conditions to collect the ESPs, operating under the assumption that in vitro conditions mimic actual in vivo infection. This assumption is rarely if ever validated. Entomopathogenic nematodes (EPNs) are lethal parasites of insects that produce and release toxins into their insect hosts and are a powerful model parasite system. We compared transcriptional profiles of individual Steinernema feltiae nematodes at different time points of activation under in vitro and in vivo conditions and found that some but not all time points during in vitro parasite activation have similar transcriptional profiles with nematodes from in vivo infections. These findings highlight the importance of experimental validation of ESP collection conditions. Additionally, we found that a suite of genes in the neuropeptide pathway were downregulated as nematodes activated and infection progressed in vivo, suggesting that these genes are involved in host-seeking behavior and are less important during active infection. We then characterized the ESPs of activated S. feltiae infective juveniles (IJs) using mass spectrometry and identified 266 proteins that are released by these nematodes. In comparing these ESPs with those previously identified in activated S. carpocapsae IJs, we identified a core set of 52 proteins that are conserved and present in the ESPs of activated IJs of both species. These core venom proteins include both tissue-damaging and immune-modulating proteins, suggesting that the ESPs of these parasites include both a core set of effectors as well as a specialized set, more adapted to the particular hosts they infect.

          Author summary

          In this study we found a core set of 52 venom proteins conserved between two insect-parasitic nematodes Steinernema feltiae and Steinernema carpocapsae, that are released when initially exposed to host tissue. Most of these proteins are conserved in mammalian-parasitic nematodes suggesting that this core set of proteins is important for parasitic nematodes in general. We show that the relevance of in vitro model systems to in vivo model systems needs to be optimized and experimentally measured. Using an in vitro model of parasitic nematode activation, we stimulated protein release from S. feltiae and evaluated its activity in vivo. This activation model was previously developed using S. carpocapsae and we conclude that this method is robust and can be generalized to other EPNs (entomopathogenic nematodes). We found notable characteristics of S. feltiae venom including time-dependent decreases in protein amount and toxicity after exposure to host tissue, which differs from what has been previously reported for other EPNs, illustrating diversity in parasitic strategies among EPNs. Additionally, naïve S. feltiae infective juveniles (IJs) not exposed to host tissue release considerable amounts of protein. These proteins however are not toxic and differ in composition from those of activated IJs.

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          limma powers differential expression analyses for RNA-sequencing and microarray studies

          limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information borrowing to overcome the problem of small sample sizes. Over the past decade, limma has been a popular choice for gene discovery through differential expression analyses of microarray and high-throughput PCR data. The package contains particularly strong facilities for reading, normalizing and exploring such data. Recently, the capabilities of limma have been significantly expanded in two important directions. First, the package can now perform both differential expression and differential splicing analyses of RNA sequencing (RNA-seq) data. All the downstream analysis tools previously restricted to microarray data are now available for RNA-seq as well. These capabilities allow users to analyse both RNA-seq and microarray data with very similar pipelines. Second, the package is now able to go past the traditional gene-wise expression analyses in a variety of ways, analysing expression profiles in terms of co-regulated sets of genes or in terms of higher-order expression signatures. This provides enhanced possibilities for biological interpretation of gene expression differences. This article reviews the philosophy and design of the limma package, summarizing both new and historical features, with an emphasis on recent enhancements and features that have not been previously described.
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            Global numbers of infection and disease burden of soil transmitted helminth infections in 2010

            Background Quantifying the burden of parasitic diseases in relation to other diseases and injuries requires reliable estimates of prevalence for each disease and an analytic framework within which to estimate attributable morbidity and mortality. Here we use data included in the Global Atlas of Helminth Infection to derive new global estimates of numbers infected with intestinal nematodes (soil-transmitted helminths, STH: Ascaris lumbricoides, Trichuris trichiura and the hookworms) and use disability-adjusted life years (DALYs) to estimate disease burden. Methods Prevalence data for 6,091 locations in 118 countries were sourced and used to estimate age-stratified mean prevalence for sub-national administrative units via a combination of model-based geostatistics (for sub-Saharan Africa) and empirical approaches (for all other regions). Geographical variation in infection prevalence within these units was approximated using modelled logit-normal distributions, and numbers of individuals with infection intensities above given thresholds estimated for each species using negative binomial distributions and age-specific worm/egg burden thresholds. Finally, age-stratified prevalence estimates for each level of infection intensity were incorporated into the Global Burden of Disease Study 2010 analytic framework to estimate the global burden of morbidity and mortality associated with each STH infection. Results Globally, an estimated 438.9 million people (95% Credible Interval (CI), 406.3 - 480.2 million) were infected with hookworm in 2010, 819.0 million (95% CI, 771.7 – 891.6 million) with A. lumbricoides and 464.6 million (95% CI, 429.6 – 508.0 million) with T. trichiura. Of the 4.98 million years lived with disability (YLDs) attributable to STH, 65% were attributable to hookworm, 22% to A. lumbricoides and the remaining 13% to T. trichiura. The vast majority of STH infections (67%) and YLDs (68%) occurred in Asia. When considering YLDs relative to total populations at risk however, the burden distribution varied more considerably within major global regions than between them. Conclusion Improvements in the cartography of helminth infection, combined with mathematical modelling approaches, have resulted in the most comprehensive contemporary estimates for the public health burden of STH. These numbers form an important benchmark upon which to evaluate future scale-up of major control efforts.
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              Entomopathogenic Nematodes

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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Writing – original draft
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: ConceptualizationRole: Data curationRole: Formal analysisRole: Funding acquisitionRole: InvestigationRole: MethodologyRole: Project administrationRole: SupervisionRole: Writing – original draftRole: Writing – review & editing
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                1 May 2019
                May 2019
                : 15
                : 5
                : e1007626
                Affiliations
                [1 ] Department of Nematology, University of California, Riverside, California, United States of America
                [2 ] Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, California, United States of America
                University of Pennsylvania, UNITED STATES
                Author notes

                The authors have declared that no competing interests exist.

                Author information
                http://orcid.org/0000-0002-8480-3016
                http://orcid.org/0000-0002-4259-6362
                http://orcid.org/0000-0001-7171-4332
                Article
                PPATHOGENS-D-18-01936
                10.1371/journal.ppat.1007626
                6513111
                31042778
                58c3fb8b-8072-45c4-bc76-fc120411f465
                © 2019 Chang et al

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 2 October 2018
                : 7 February 2019
                Page count
                Figures: 5, Tables: 0, Pages: 29
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100005825, National Institute of Food and Agriculture;
                Award ID: GRANT12448467
                Award Recipient :
                This work was supported by funding from the USDA NIFA (GRANT12448467) to ARD. The funders had no role in the study design, data collection, and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Medicine and Health Sciences
                Parasitic Diseases
                Nematode Infections
                Biology and Life Sciences
                Biochemistry
                Enzymology
                Enzymes
                Proteases
                Biology and Life Sciences
                Biochemistry
                Proteins
                Enzymes
                Proteases
                Biology and Life Sciences
                Toxicology
                Toxic Agents
                Toxins
                Venoms
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Toxicology
                Toxic Agents
                Toxins
                Venoms
                Medicine and Health Sciences
                Parasitic Diseases
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Organisms
                Eukaryota
                Animals
                Invertebrates
                Arthropoda
                Insects
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Domains
                Biology and Life Sciences
                Toxicology
                Toxicity
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Toxicology
                Toxicity
                Custom metadata
                vor-update-to-uncorrected-proof
                2019-05-13
                All relevant data are within the paper and its Supporting Information files, except the raw secretome mass spectrometry data, which is available at the ProteomeXchange using these links: ftp://massive.ucsd.edu/MSV000082993 and ftp://massive.ucsd.edu/MSV000082997, and the RNA-seq data, which is available from Gene Expression Omnibus (GEO) under the accession number GSE119223.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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