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      Activated entomopathogenic nematode infective juveniles release lethal venom proteins

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          Abstract

          Entomopathogenic nematodes (EPNs) are unique parasites due to their symbiosis with entomopathogenic bacteria and their ability to kill insect hosts quickly after infection. It is widely believed that EPNs rely on their bacterial partners for killing hosts. Here we disproved this theory by demonstrating that the in vitro activated infective juveniles (IJs) of Steinernema carpocapsae (a well-studied EPN species) release venom proteins that are lethal to several insects including Drosophila melanogaster. We confirmed that the in vitro activation is a good approximation of the in vivo process by comparing the transcriptomes of individual in vitro and in vivo activated IJs. We further analyzed the transcriptomes of non-activated and activated IJs and revealed a dramatic shift in gene expression during IJ activation. We also analyzed the venom proteome using mass spectrometry. Among the 472 venom proteins, proteases and protease inhibitors are especially abundant, and toxin-related proteins such as Shk domain-containing proteins and fatty acid- and retinol-binding proteins are also detected, which are potential candidates for suppressing the host immune system. Many of the venom proteins have conserved orthologs in vertebrate-parasitic nematodes and are differentially expressed during IJ activation, suggesting conserved functions in nematode parasitism. In summary, our findings strongly support a new model that S. carpocapsae and likely other Steinernema EPNs have a more active role in contributing to the pathogenicity of the nematode-bacterium complex than simply relying on their symbiotic bacteria. Furthermore, we propose that EPNs are a good model system for investigating vertebrate- and human-parasitic nematodes, especially regarding the function of excretory/secretory products.

          Author summary

          Steinernema carpocapsae belongs to a special group of insect-parasitic nematodes known as entomopathogenic nematodes (EPNs). These differ from other insect parasites in at least two ways; first they kill their hosts quickly (within 2–3 days), and second they associate with bacteria to facilitate their parasitic lifestyle. The infective stage of these parasites, the infective juvenile (IJ) stage, is the only free-living stage and these IJs are developmentally arrested and only reinitiate development once they are inside a suitable host. Little is known about the early stages of parasitism and how these parasites initiate the parasitic phase of their life cycle and reinitiate development. Here we characterized the changes that occur to the nematodes' physical morphology, gene expression, and the release of protein molecules that accompany the transition from developmentally arrested IJ to active, developing parasite. We showed that contrary to long-held assumptions, the nematodes are not merely transporting pathogenic bacteria but that the nematodes contribute to parasitism by releasing toxic proteins into the host. Many of the S. carpocapsae toxins are also found in species of human-parasitic nematodes, and S. carpocapsae may serve as a valuable model for understanding the specific function of these toxins.

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          RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

          Background RNA-Seq is revolutionizing the way transcript abundances are measured. A key challenge in transcript quantification from RNA-Seq data is the handling of reads that map to multiple genes or isoforms. This issue is particularly important for quantification with de novo transcriptome assemblies in the absence of sequenced genomes, as it is difficult to determine which transcripts are isoforms of the same gene. A second significant issue is the design of RNA-Seq experiments, in terms of the number of reads, read length, and whether reads come from one or both ends of cDNA fragments. Results We present RSEM, an user-friendly software package for quantifying gene and isoform abundances from single-end or paired-end RNA-Seq data. RSEM outputs abundance estimates, 95% credibility intervals, and visualization files and can also simulate RNA-Seq data. In contrast to other existing tools, the software does not require a reference genome. Thus, in combination with a de novo transcriptome assembler, RSEM enables accurate transcript quantification for species without sequenced genomes. On simulated and real data sets, RSEM has superior or comparable performance to quantification methods that rely on a reference genome. Taking advantage of RSEM's ability to effectively use ambiguously-mapping reads, we show that accurate gene-level abundance estimates are best obtained with large numbers of short single-end reads. On the other hand, estimates of the relative frequencies of isoforms within single genes may be improved through the use of paired-end reads, depending on the number of possible splice forms for each gene. Conclusions RSEM is an accurate and user-friendly software tool for quantifying transcript abundances from RNA-Seq data. As it does not rely on the existence of a reference genome, it is particularly useful for quantification with de novo transcriptome assemblies. In addition, RSEM has enabled valuable guidance for cost-efficient design of quantification experiments with RNA-Seq, which is currently relatively expensive.
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            Entomopathogenic Nematodes

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              A METHOD FOR OBTAINING INFECTIVE NEMATODE LARVAE FROM CULTURES.

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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS Pathog
                PLoS Pathog
                plos
                plospath
                PLoS Pathogens
                Public Library of Science (San Francisco, CA USA )
                1553-7366
                1553-7374
                20 April 2017
                April 2017
                : 13
                : 4
                : e1006302
                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.

                • Conceptualization: DL ARD AM.

                • Data curation: DL MM AM.

                • Formal analysis: DL MM DC AM ARD.

                • Funding acquisition: AM ARD.

                • Investigation: DL MM DC MMB JB AM ARD.

                • Methodology: DL MM JB AM ARD.

                • Project administration: DL JB AM ARD.

                • Resources: DL MM JB AM ARD.

                • Supervision: DL JB AM ARD.

                • Validation: DL MM AM ARD.

                • Visualization: DL MM MMB AM ARD.

                • Writing – original draft: DL MM AM ARD.

                • Writing – review & editing: DL MM DC MMB JB AM ARD.

                Author information
                http://orcid.org/0000-0002-8480-3016
                http://orcid.org/0000-0001-7563-8357
                http://orcid.org/0000-0001-9417-7867
                http://orcid.org/0000-0001-7171-4332
                Article
                PPATHOGENS-D-16-02754
                10.1371/journal.ppat.1006302
                5398726
                28426766
                dc355de3-e001-44ea-b9d7-0abcd22cd8e8
                © 2017 Lu 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
                : 12 December 2016
                : 20 March 2017
                Page count
                Figures: 6, Tables: 1, Pages: 31
                Funding
                Funded by: funder-id http://dx.doi.org/10.13039/100000060, National Institute of Allergy and Infectious Diseases;
                Award ID: AI119155
                Award Recipient :
                Funded by: funder-id http://dx.doi.org/10.13039/100000002, National Institutes of Health;
                Award ID: DP2 GM111100
                Award Recipient :
                This work was supported by a National Institutes of Health K22 award from the National Institute of Allergy and Infectious Diseases (AI119155) to ARD, and by an NIH New Innovator Award to AM (DP2 GM111100) https://www.nih.gov/. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                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
                Nematode Infections
                Medicine and Health Sciences
                Pathology and Laboratory Medicine
                Pathogenesis
                Host-Pathogen Interactions
                Biology and Life Sciences
                Genetics
                Gene Expression
                Biology and Life Sciences
                Developmental Biology
                Life Cycles
                Larvae
                Biology and Life Sciences
                Biochemistry
                Proteins
                Protein Domains
                Medicine and Health Sciences
                Parasitic Diseases
                Biology and Life Sciences
                Computational Biology
                Genome Analysis
                Transcriptome Analysis
                Biology and Life Sciences
                Genetics
                Genomics
                Genome Analysis
                Transcriptome Analysis
                Custom metadata
                All relevant data are within the paper and its Supporting Information files, except the raw secretome mass spectrometry data, which is available in the ProteomeXchange under the accession number PXD005250, and the RNA-seq data, which is available from Gene Expression Omnibus (GEO) under the accession number GSE89961.

                Infectious disease & Microbiology
                Infectious disease & Microbiology

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