The Lantern Vol. 2, No. 1, December 1933

• Petition • Keep it Burning! • Jes\u27 Before Christmas • Noel: Translation from Theophile Gautier • A Young Jew Meets Jesus • Book Review: Little Man, What Now? • Book Review: Thunder and Dawn • Continuity • La Veille de Noel (Reflexions d\u27un Provincial) • Noel Sceptique par Jules LaFargue • Horizon • Winter Night • Linoleum Cutshttps://digitalcommons.ursinus.edu/lantern/1001/thumbnail.jp

GiardiaDB and TrichDB : integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

© 2008 The Authors. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License. The definitive version was published in Nucleic Acids Research 37 (2009): D526-D530, doi:10.1093/nar/gkn631.GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.Federal funds from the National Institute of Allergy and Infectious Diseases; Department of Health and Human Services, National Institutes of Health (HHSN266200400037C). Funding for open access charge: National Institutes of Health (HHSN266200400037C)

SchistoDB: a Schistosoma mansoni genome resource

SchistoDB (http://schistoDB.net/) is a genomic database for the parasitic organism Schistosoma mansoni, one of the major causative agents of schistosomiasis worldwide. It currently incorporates sequences and annotation for S. mansoni in a single user-friendly database. Several genomic scale analyses are available as well as ESTs, oligonucleotides, metabolic pathways and drugs. In this article, we describe the data sets and its analyses, how to query the database and tools available in the website

ToxoDB: an integrated Toxoplasma gondii database resource

ToxoDB (http://ToxoDB.org) is a genome and functional genomic database for the protozoan parasite Toxoplasma gondii. It incorporates the sequence and annotation of the T. gondii ME49 strain, as well as genome sequences for the GT1, VEG and RH (Chr Ia, Chr Ib) strains. Sequence information is integrated with various other genomic-scale data, including community annotation, ESTs, gene expression and proteomics data. ToxoDB has matured significantly since its initial release. Here we outline the numerous updates with respect to the data and increased functionality available on the website

An SNP selection strategy identified IL-22 associating with susceptibility to tuberculosis in Chinese

Recent studies showed that IL-22 plays a protective role in the host defense. However, the contribution of polymorphisms of the IL-22 gene to human TB susceptibility remains untested. We have designed a computational approach to select functional SNPs in the IL-22 gene and genotyped them in a two-stage case-control study in Chinese (479 cases and 358 controls). We found that rs2227473, an SNP in the promoter region of IL-22, is associated with TB susceptibility at both stages of our study. The SNP shows associations with p-values of 0.028 and 0.034 respectively, and a combined p-value of 0.0086, with odds ratio at 0.65 (95% confidence interval 0.45–0.90). We further validated the association with an independent cohort (413 cases and 241 controls in Chinese). Our functional studies showed that patients with A allele have significantly higher IL-22 expression than those without A allele under both non-specific and specific stimulations

Identification of a New Rhoptry Neck Complex RON9/RON10 in the Apicomplexa Parasite Toxoplasma gondii

Apicomplexan parasites secrete and inject into the host cell the content of specialized secretory organelles called rhoptries, which take part into critical processes such as host cell invasion and modulation of the host cell immune response. The rhoptries are structurally and functionally divided into two compartments. The apical duct contains rhoptry neck (RON) proteins that are conserved in Apicomplexa and are involved in formation of the moving junction (MJ) driving parasite invasion. The posterior bulb contains rhoptry proteins (ROPs) unique to an individual genus and, once injected in the host cell act as effector proteins to co-opt host processes and modulate parasite growth and virulence. We describe here two new RON proteins of Toxoplasma gondii, RON9 and RON10, which form a high molecular mass complex. In contrast to the other RONs described to date, this complex was not detected at the MJ during invasion and therefore was not associated to the MJ complex RON2/4/5/8. Disruptions of either RON9 or RON10 gene leads to the retention of the partner in the ER followed by subsequent degradation, suggesting that the RON9/RON10 complex formation is required for proper sorting to the rhoptries. Finally, we show that the absence of RON9/RON10 has no significant impact on the morphology of rhoptry, on the invasion and growth in fibroblasts in vitro or on virulence in vivo. The conservation of RON9 and RON10 in Coccidia and Cryptosporidia suggests a specific relation with development in intestinal epithelial cells

A Kernel for Open Source Drug Discovery in Tropical Diseases

Open source drug discovery, a promising alternative avenue to conventional patent-based drug development, has so far remained elusive with few exceptions. A major stumbling block has been the absence of a critical mass of preexisting work that volunteers can improve through a series of granular contributions. This paper introduces the results from a newly assembled computational pipeline for identifying protein targets for drug discovery in ten organisms that cause tropical diseases. We have also experimentally tested two promising targets for their binding to commercially available drugs, validating one and invalidating the other. The resulting kernel provides a base of drug targets and lead candidates around which an open source community can nucleate. We invite readers to donate their judgment and in silico and in vitro experiments to develop these targets to the point where drug optimization can begin

The TESS science processing operations center

The Transiting Exoplanet Survey Satellite (TESS) will conduct a search for Earth's closest cousins starting in early 2018 and is expected to discover ∼1,000 small planets with R[subscript p] < 4 R[subscript ⊕] and measure the masses of at least 50 of these small worlds. The Science Processing Operations Center (SPOC) is being developed at NASA Ames Research Center based on the Kepler science pipeline and will generate calibrated pixels and light curves on the NASA Advanced Supercomputing Division's Pleiades supercomputer. The SPOC will also search for periodic transit events and generate validation products for the transit-like features in the light curves. All TESS SPOC data products will be archived to the Mikulski Archive for Space Telescopes (MAST)

Phylogenomic analyses of malaria parasites and evolution of their exported proteins

<p>Abstract</p> <p>Background</p> <p><it>Plasmodium falciparum </it>is the most malignant agent of human malaria. It belongs to the taxon Laverania, which includes other ape-infecting <it>Plasmodium </it>species. The origin of the Laverania is still debated. <it>P. falciparum </it>exports pathogenicity-related proteins into the host cell using the <it>Plasmodium </it>export element (PEXEL). Predictions based on the presence of a PEXEL motif suggest that more than 300 proteins are exported by <it>P. falciparum</it>, while there are many fewer exported proteins in non-Laverania.</p> <p>Results</p> <p>A whole-genome approach was applied to resolve the phylogeny of eight <it>Plasmodium </it>species and four outgroup taxa. By using 218 orthologous proteins we received unanimous support for a sister group position of Laverania and avian malaria parasites. This observation was corroborated by the analyses of 28 exported proteins with orthologs present in all <it>Plasmodium </it>species. Most interestingly, several deviations from the <it>P. falciparum </it>PEXEL motif were found to be present in the orthologous sequences of non-Laverania.</p> <p>Conclusion</p> <p>Our phylogenomic analyses strongly support the hypotheses that the Laverania have been founded by a single <it>Plasmodium </it>species switching from birds to African great apes or <it>vice versa</it>. The deviations from the canonical PEXEL motif in orthologs may explain the comparably low number of exported proteins that have been predicted in non-Laverania.</p