Drug target prediction and prioritization: using orthology to predict essentiality in parasite genomes

<p>Abstract</p> <p>Background</p> <p>New drug targets are urgently needed for parasites of socio-economic importance. Genes that are essential for parasite survival are highly desirable targets, but information on these genes is lacking, as gene knockouts or knockdowns are difficult to perform in many species of parasites. We examined the applicability of large-scale essentiality information from four model eukaryotes, <it>Caenorhabditis elegans, Drosophila melanogaster, Mus musculus </it>and <it>Saccharomyces cerevisiae</it>, to discover essential genes in each of their genomes. Parasite genes that lack orthologues in their host are desirable as selective targets, so we also examined prediction of essential genes within this subset.</p> <p>Results</p> <p>Cross-species analyses showed that the evolutionary conservation of genes and the presence of essential orthologues are each strong predictors of essentiality in eukaryotes. Absence of paralogues was also found to be a general predictor of increased relative essentiality. By combining several orthology and essentiality criteria one can select gene sets with up to a five-fold enrichment in essential genes compared with a random selection. We show how quantitative application of such criteria can be used to predict a ranked list of potential drug targets from <it>Ancylostoma caninum </it>and <it>Haemonchus contortus </it>- two blood-feeding strongylid nematodes, for which there are presently limited sequence data but no functional genomic tools.</p> <p>Conclusions</p> <p>The present study demonstrates the utility of using orthology information from multiple, diverse eukaryotes to predict essential genes. The data also emphasize the challenge of identifying essential genes among those in a parasite that are absent from its host.</p

Kdo Hydrolase Is Required for Francisella tularensis Virulence and Evasion of TLR2-Mediated Innate Immunity

ABSTRACT The highly virulent Francisella tularensis subsp. tularensis has been classified as a category A bioterrorism agent. A live vaccine strain (LVS) has been developed but remains unlicensed in the United States because of an incomplete understanding of its attenuation. Lipopolysaccharide (LPS) modification is a common strategy employed by bacterial pathogens to avoid innate immunity. A novel modification enzyme has recently been identified in F. tularensis and Helicobacter pylori. This enzyme, a two-component Kdo (3-deoxy-d-manno-octulosonic acid) hydrolase, catalyzes the removal of a side chain Kdo sugar from LPS precursors. The biological significance of this modification has not yet been studied. To address the role of the two-component Kdo hydrolase KdhAB in F. tularensis pathogenesis, a ΔkdhAB deletion mutant was constructed from the LVS strain. In intranasal infection of mice, the ΔkdhAB mutant strain had a 50% lethal dose (LD50) 2 log10 units higher than that of the parental LVS strain. The levels of the proinflammatory cytokines tumor necrosis factor alpha (TNF-α) and interleukin-1β (IL-1β) in bronchoalveolar lavage fluid were significantly higher (2-fold) in mice infected with the ΔkdhAB mutant than in mice infected with LVS. In vitro stimulation of bone marrow-derived macrophages with the ΔkdhAB mutant induced higher levels of TNF-α and IL-1β in a TLR2-dependent manner. In addition, TLR2−/− mice were more susceptible than wild-type mice to ΔkdhAB bacterial infection. Finally, immunization of mice with ΔkdhAB bacteria elicited a high level of protection against the highly virulent F. tularensis subsp. tularensis strain Schu S4. These findings suggest an important role for the Francisella Kdo hydrolase system in virulence and offer a novel mutant as a candidate vaccine

Differences in transcription between free-living and CO_2-activated third-stage larvae of Haemonchus contortus

Background: The disease caused by Haemonchus contortus, a blood-feeding nematode of small ruminants, is of major economic importance worldwide. The infective third-stage larva (L3) of this gastric nematode is enclosed in a cuticle (sheath) and, once ingested with herbage by the host, undergoes an exsheathment process that marks the transition from the free-living (L3) to the parasitic (xL3) stage. This study explored changes in gene transcription associated with this transition and predicted, based on comparative analysis, functional roles for key transcripts in the metabolic pathways linked to larval development. Results: Totals of 101,305 (L3) and 105,553 (xL3) expressed sequence tags (ESTs) were determined using 454 sequencing technology, and then assembled and annotated; the most abundant transcripts encoded transthyretin-like, calcium-binding EF-hand, NAD(P)-binding and nucleotide-binding proteins as well as homologues of Ancylostoma-secreted proteins (ASPs). Using an in silico-subtractive analysis, 560 and 685 sequences were shown to be uniquely represented in the L3 and xL3 stages, respectively; the transcripts encoded ribosomal proteins, collagens and elongation factors (in L3), and mainly peptidases and other enzymes of amino acid catabolism (in xL3). Caenorhabditis elegans orthologues of transcripts that were uniquely transcribed in each L3 and xL3 were predicted to interact with a total of 535 other genes, all of which were involved in embryonic development. Conclusion: The present study indicated that some key transcriptional alterations taking place during the transition from the L3 to the xL3 stage of H. contortus involve genes predicted to be linked to the development of neuronal tissue (L3 and xL3), formation of the cuticle (L3) and digestion of host haemoglobin (xL3). Future efforts using next-generation sequencing and bioinformatic technologies should provide the efficiency and depth of coverage required for the determination of the complete transcriptomes of different developmental stages and/or tissues of H. contortus as well as the genome of this important parasitic nematode. Such advances should lead to a significantly improved understanding of the molecular biology of H. contortus and, from an applied perspective, to novel methods of intervention

Phytoplankton spatial distribution patterns along the western Antarctic Peninsula (Southern Ocean)

This paper describes spatial distribution patterns of the phytoplankton community (composition, cell abundance and biomass concentration) in relation to local environmental conditions in the Southern Ocean. Sampling was performed during summer 1997 off the coast of the western Antarctic Peninsula between Anvers Island and Marguerite Bay. Phytoplankton was characterized by relatively low biomass throughout most of the study area and was dominated by nanoalgae (<20 μm). Phytoplankton varied along an on-offshore gradient, with decreasing total cell abundance, chlorophyll a (chl a) concentration and carbon biomass toward the open ocean. Chl a concentration showed surface or subsurface maxima in coastal and middle-shelf waters, and deep maxima between ∼40 and 100 m in oceanic waters. Across-shelf variability in phytoplankton correlated with vertical stability in the water column, which appears to be the major parameter affecting phytoplankton community structure in the area. We hypothesize that the deep chl a maximum offshore may be associated with iron limitation in near-surface waters and higher iron concentration in 'winter waters' (subsurface remnant of Antarctic Surface Waters). On a smaller spatial scale, a cluster analysis showed great regional variability in phytoplankton assemblages. The area was divided into 4 main regions based on differences in the phytoplankton composition and concentration. Three peaks in phytoplankton abundance were found on a north-to-south gradient in near-shore waters: a Cryptomonas spp. bloom near Anvers Island, a small unidentified phytoflagellate bloom in Grandidier Channel, and a diatom bloom in Marguerite Bay. These assemblages resemble different stages of the phytoplankton seasonal succession, and may be related to the progressive sea-ice retreat, which might have regulated the timing of the onset of the phytoplankton seasonal succession in a north-south gradient. Biological environmental factors, such as seeding of the water column by epontic algae and selective zooplankton herbivory, are hypothesized to affect community composition in coastal regions. We conclude that large-scale variability in phytoplankton community structure is related to water column physical conditions and possibly iron availability, while mesoscale variability, as seen in coastal waters, is more likely due to seasonal succession of different algae groups.Facultad de Ciencias Naturales y Muse

The vertebrate fauna of the Upper Permian of Niger. IV. Nigerpeton ricqlesi (Temnospondyli: Cochleosauridae), and the Edopoid Colonization of Gondwana

We describe the edopoid temnospondyl Nigerpeton ricqlesi from the Upper Permian Moradi Formation of northern Niger on the basis of two partial skulls and tentatively associated postcranial material. This crocodile-like taxon displays several edopoid characters states such as a long prenarial region with enlarged premaxillae, elongated vomers, large, posteriorly tapering choanae, and a jugal that broadens anteriorly. Nigerpeton possesses a unique carnivorous dentition. It is autapomorphic in its possession of an extremely elongate snout bearing a maxillary bulge that accommodates three hypertrophied caniniform teeth, inner premaxillary tusks, and anterior paired fenestrae, which pierce the skull roof. In addition, both the maxilla and dentary tooth rows show the sporadic appearance of ‘doubled’ tooth positions. The lateral-line system is present at the adult stage, which suggests an aquatic habitat for this taxon. A phylogenetic analysis of Edopoidea and its relatives places Nigerpeton as the sister taxon to the Permo-Carboniferous genus Chenoprosopus from the U.S.A. As with other members of the Moradi tetrapod fauna, the discovery of Nigerpeton strengthens support for the hypothesis that West Africa hosted an endemic fauna at the close of the Paleozoic Era. Biogeographically, we propose that Late Carboniferous and Permian edopoids were geographically widespread and that they twice crossed the Central Pangean mountain chain (between Laurussia and Gondwana) during their evolution. This distribution was later fragmented with the onset of Late Permian climatic warming

Oligomerization of the vesicular stomatitis virus phosphoprotein is dispensable for mRNA synthesis but facilitates RNA replication

Nonsegmented negative-strand (NNS) RNA viruses possess a ribonucleoprotein template in which the genomic RNA is sequestered within a homopolymer of nucleocapsid protein (N). The viral RNA-dependent RNA polymerase (RdRP) resides within an approximately 250-kDa large protein (L), along with unconventional mRNA capping enzymes: a GDP:polyribonucleotidyltransferase (PRNT) and a dual-specificity mRNA cap methylase (MT). To gain access to the N-RNA template and orchestrate the

Mixed valency in cerium oxide crystallographic phases: Determination of valence of the different cerium sites by the bond valence method

We have applied the bond valence method to cerium oxides to determine the oxidation states of the Ce ion at the various site symmetries of the crystals. The crystals studied include cerium dioxide and the two sesquioxides along with some selected intermediate phases which are crystallographically well characterized. Our results indicate that cerium dioxide has a mixed-valence ground state with an f-electron population on the Ce site of 0.27 while both the A- and C-sesquioxides have a nearly pure f^1 configuration. The Ce sites in most of the intermediate oxides have non-integral valences. Furthermore, many of these valences are different from the values predicted from a naive consideration of the stoichiometric valence of the compound

Maternal urinary iodine concentration in pregnancy and children's cognition: Results from a population-based birth cohort in an iodine-sufficient area

OBJECTIVE: Reports from populations with an insufficient iodine intake suggest that children of mothers with mild iodine deficiency during pregnancy are at risk for cognitive impairments. However, it is unknown whether, even in iodine-sufficient areas, low levels of iodine intake occur that influence cognitive development in the offspring. This study investigated the association between maternal low urinary iodine concentration (UIC) in pregnancy and children's cognition in a population-based sample from a country with an optimal iodine status (the Netherlands). SETTING AND PARTICIPANTS: In 1525 mother–child pairs in a Dutch multiethnic birth cohort, we investigated the relation between maternal UIC<150 μg/g creatinine, assessed <18 weeks gestation and children's cognition. OUTCOMES MEASURES: Non-verbal IQ and language comprehension were assessed during a visit to the research centre using Dutch test batteries when the children were 6 years. RESULTS: In total, 188 (12.3%) pregnant women had UIC<150 μg/g creatinine, with a median UIC equal to 119.3 μg/g creatinine. The median UIC in the group with UIC>150 μg/g creatinine was 322.9 μg/g and in the whole sample 296.5 μg/g creatinine. There was a univariate association between maternal low UIC and children's suboptimum non-verbal IQ (unadjusted OR=1.44, 95% CI 1.02 to 2.02). However, after adjustment for confounders, maternal low UIC was not associated with children's non-verbal IQ (adjusted OR=1.33, 95% CI 0.92 to 1.93). There was no relation between maternal UIC in early pregnancy and children's language comprehension at 6 years. CONCLUSIONS: The lack of a clear association between maternal low UIC and children's cognition probably reflects that low levels of iodine were not frequent and severe enough to affect neurodevelopment. This may result from the Dutch iodine fortification policy, which allows iodised salt to be added to almost all processed food and emphasises the monitoring of iodine intake in the population

Instantons and the Ground State of the Massive Schwinger Model

We study the massive Schwinger model, quantum electrodynamics of massive, Dirac fermions, in 1+1 dimensions; with space compactified to a circle. In the limit that transitions to fermion--anti-fermion pairs can be neglected, we study the full ground state. We focus on the effect of instantons which mediate tunnelling transitions in the induced potential for the dynamical degree of freedom in the gauge field.Comment: 17 pages, plain te