RNAi Effector Diversity in Nematodes

While RNA interference (RNAi) has been deployed to facilitate gene function studies in diverse helminths, parasitic nematodes appear variably susceptible. To test if this is due to inter-species differences in RNAi effector complements, we performed a primary sequence similarity survey for orthologs of 77 Caenorhabditis elegans RNAi pathway proteins in 13 nematode species for which genomic or transcriptomic datasets were available, with all outputs subjected to domain-structure verification. Our dataset spanned transcriptomes of Ancylostoma caninum and Oesophagostomum dentatum, and genomes of Trichinella spiralis, Ascaris suum, Brugia malayi, Haemonchus contortus, Meloidogyne hapla, Meloidogyne incognita and Pristionchus pacificus, as well as the Caenorhabditis species C. brenneri, C. briggsae, C. japonica and C. remanei, and revealed that: (i) Most of the C. elegans proteins responsible for uptake and spread of exogenously applied double stranded (ds)RNA are absent from parasitic species, including RNAi-competent plant-nematodes; (ii) The Argonautes (AGOs) responsible for gene expression regulation in C. elegans are broadly conserved, unlike those recruited during the induction of RNAi by exogenous dsRNA; (iii) Secondary Argonautes (SAGOs) are poorly conserved, and the nuclear AGO NRDE-3 was not identified in any parasite; (iv) All five Caenorhabditis spp. possess an expanded RNAi effector repertoire relative to the parasitic nematodes, consistent with the propensity for gene loss in nematode parasites; (v) In spite of the quantitative differences in RNAi effector complements across nematode species, all displayed qualitatively similar coverage of functional protein groups. In summary, we could not identify RNAi effector deficiencies that associate with reduced susceptibility in parasitic nematodes. Indeed, similarities in the RNAi effector complements of RNAi refractory and competent nematode parasites support the broad applicability of this research genetic tool in nematodes

Large scale genome-wide association and LDLA mapping study identifies QTLs for boar taint and related sex steroids

<p>Abstract</p> <p>Background</p> <p>Boar taint is observed in a high proportion of uncastrated male pigs and is characterized by an unpleasant odor/flavor in cooked meat, primarily caused by elevated levels of androstenone and skatole. Androstenone is a steroid produced in the testis in parallel with biosynthesis of other sex steroids like testosterone and estrogens. This represents a challenge when performing selection against androstenone in breeding programs, without simultaneously decreasing levels of other steroids. The aim of this study was to use high-density genome wide association (GWA) in combination with linkage disequilibrium-linkage analysis (LDLA) to identify quantitative trait loci (QTL) associated with boar taint compounds and related sex steroids in commercial Landrace (n = 1,251) and Duroc (n = 918) breeds.</p> <p>Results</p> <p>Altogether, 14 genome wide significant (GWS) QTL regions for androstenone in subcutaneous fat were obtained from the LDLA study in Landrace and 14 GWS QTL regions in Duroc. LDLA analysis revealed that 7 of these QTL regions, located on SSC 1, 2, 3, 7 and 15, were obtained in both breeds. All 14 GWS androstenone QTLs in Landrace are also affecting the estrogens at chromosome wise significance (CWS) or GWS levels, while in Duroc, 3 of the 14 QTLs affect androstenone without affecting any of the estrogens. For skatole, 10 and 4 QTLs were GWS in the LDLA analysis for Landrace and Duroc respectively, with 4 of these detected in both breeds. The GWS QTLs for skatole obtained by LDLA are located at SSC 1, 5, 6, 7, 10, 11, 13 and 14.</p> <p>Conclusion</p> <p>This is the first report applying the Porcine 60 K SNP array for simultaneous analysis of boar taint compounds and related sex hormones, using both GWA and LDLA approaches. Several QTLs are involved in regulation of androstenone and skatole, and most of the QTLs for androstenone are also affecting the levels of estrogens. Seven QTLs for androstenone were detected in one breed and confirmed in the other, i.e. in an independent sample, although the majority of QTLs are breed specific. Most QTLs for skatole do not negatively affect other sex hormones and should be easier to implement into the breeding scheme.</p

The <i>Pratylenchus penetrans</i> transcriptome as a source for the development of alternative control strategies:mining for putative genes involved in parasitism and evaluation of <i>in planta</i> RNAi

The root lesion nematode Pratylenchus penetrans is considered one of the most economically important species within the genus. Host range studies have shown that nearly 400 plant species can be parasitized by this species. To obtain insight into the transcriptome of this migratory plant-parasitic nematode, we used Illumina mRNA sequencing analysis of a mixed population, as well as nematode reads detected in infected soybean roots 3 and 7 days after nematode infection. Over 140 million paired end reads were obtained for this species, and de novo assembly resulted in a total of 23,715 transcripts. Homology searches showed significant hit matches to 58% of the total number of transcripts using different protein and EST databases. In general, the transcriptome of P. penetrans follows common features reported for other root lesion nematode species. We also explored the efficacy of RNAi, delivered from the host, as a strategy to control P. penetrans, by targeted knock-down of selected nematode genes. Different comparisons were performed to identify putative nematode genes with a role in parasitism, resulting in the identification of transcripts with similarities to other nematode parasitism genes. Focusing on the predicted nematode secreted proteins found in this transcriptome, we observed specific members to be up-regulated at the early time points of infection. In the present study, we observed an enrichment of predicted secreted proteins along the early time points of parasitism by this species, with a significant number being pioneer candidate genes. A representative set of genes examined using RT-PCR confirms their expression during the host infection. The expression patterns of the different candidate genes raise the possibility that they might be involved in critical steps of P. penetrans parasitism. This analysis sheds light on the transcriptional changes that accompany plant infection by P. penetrans, and will aid in identifying potential gene targets for selection and use to design effective control strategies against root lesion nematodes

Comparative genomics of the major parasitic worms

Parasitic nematodes (roundworms) and platyhelminths (flatworms) cause debilitating chronic infections of humans and animals, decimate crop production and are a major impediment to socioeconomic development. Here we report a broad comparative study of 81 genomes of parasitic and non-parasitic worms. We have identified gene family births and hundreds of expanded gene families at key nodes in the phylogeny that are relevant to parasitism. Examples include gene families that modulate host immune responses, enable parasite migration though host tissues or allow the parasite to feed. We reveal extensive lineage-specific differences in core metabolism and protein families historically targeted for drug development. From an in silico screen, we have identified and prioritized new potential drug targets and compounds for testing. This comparative genomics resource provides a much-needed boost for the research community to understand and combat parasitic worms

Parution : Scepticisme et religion. Constantes et évolutions, de la philosophie hellénistique à la philosophie médiévale. Études réunies et éditées sous la direction de Anne-Isabelle Bouton-Touboulic et Carlos Lévy

Scepticisme et religion. Constantes et évolutions, de la philosophie hellénistique à la philosophie médiévale. Études réunies et éditées sous la direction de Anne-Isabelle Bouton-Touboulic et Carlos Lévy. « Monothéismes et philosophie » (n° 21) Turnhout, Brepols, 2016. 300 p., 156 x 234 mm, 2016 ISBN: 978-2-503-56545-3 EUR 80,00 Dans le langage commun, le scepticisme apparaît comme l’opposé de la religion. Cette opposition est le produit d’une histoire, d’une relation diachronique aussi tumul..

Planning dam portfolios for low sediment trapping shows limits for sustainable hydropower in the Mekong.

The transboundary Mekong Basin has been dubbed the "Battery of Southeast Asia" for its large hydropower potential. Development of hydropower dams in the six riparian countries proceeds without strategic analyses of dam impacts, e.g., reduced sediment delivery to the lower Mekong. This will impact some of the world's largest freshwater fisheries and endangers the resilience of the delta, which supports 17 million livelihoods, against rising sea levels. To highlight alternatives, we contribute an optimization-based framework for strategic sequencing of dam development. We quantify lost opportunities from past development and identify remaining opportunities for better tradeoffs between sediment and hydropower. We find that limited opportunities remain for less impactful hydropower in the lower basin, where most development is currently planned, while better trade-offs could be reached with dams in the upper Mekong in China. Our results offer a strategic vision for hydropower in the Mekong, introduce a globally applicable framework to optimize dam sequences in space and time, and highlight the importance of strategic planning on multiple scales to minimize hydropower impacts on rivers

Simulation Management Systems Developed by the Northern Gulf Coastal Hazards Collaboratory (NG-CHC): An Overview of Cyberinfrastructure to Support the Coastal Modeling Community in the Gulf of Mexico

Given the significance of natural and built assets of the Gulf of Mexico region, the three states of Alabama, Louisiana, and Mississippi, leveraged their unique partnerships, proximity, and significant prior investments in cyberinfrastructure (CI) to develop the Northern Gulf Coastal Hazards Collaboratory (NG-CHC). This collaboratory was established to catalyze collaborative research via enhanced CI to reduce the regions vulnerability to natural and human disasters by facilitating high performance modeling to test hypotheses focused on engineering design, coastal system response, and risk management of coastal hazards. The objective of the NG-CHC is to advance research and inspire collaboration through highly available innovation-enabling CI, with a particular focus on geosciences and engineering from the watershed to the coast. An integrated CI capable of simulating all relevant interacting processes is needed to implement a system that captures the dynamic nature of coastal surface processes. The NG-CHC has implemented CI to locate appropriate data and computational resources, create necessary workflows associated with different simulation demands, and provide visualization tools for analysis of results. Three simulation management systems, SIMULOCEAN, SULIS, and ASGS, were implemented, each with a defined suite of hypotheses and institutional participants to run collaborator experiments. The NG-CHC focused on developing suites of CI tools centered on handling the functional needs of each simulation management system in a collaborative environment. The NG-CHC also developed curriculum units, computer games and simulations to extend the knowledge of coastal hazards to students from middle school to college. Education and outreach activities were developed to increase public understanding and support for sustainable coastal practices. The elements of the CI tool box within NG-CHC describe generic tools needed to promote a ‘collaborative modeling environment’ in other coastal systems