Host cell traversal is important for progression of the malaria parasite through the dermis to the liver

The malaria sporozoite, the parasite stage transmitted by the mosquito, is delivered into the dermis and differentiates in the liver. Motile sporozoites can invade host cells by disrupting their plasma membrane and migrating through them (termed cell traversal), or by forming a parasite-cell junction and settling inside an intracellular vacuole (termed cell infection). Traversal of liver cells, observed for sporozoites in vivo, is thought to activate the sporozoite for infection of a final hepatocyte. Here, using Plasmodium berghei, we show that cell traversal is important in the host dermis for preventing sporozoite destruction by phagocytes and arrest by nonphagocytic cells. We also show that cell infection is a pathway that is masked, rather than activated, by cell traversal. We propose that the cell traversal activity of the sporozoite must be turned on for progression to the liver parenchyma, where it must be switched off for infection of a final hepatocyte.Inst Pasteur, Unite Biol & Genet Paludisme, F-75724 Paris 15, FranceUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilUniv Montpellier 2, CNRS, UMR 5539, F-34095 Montpellier 05, FranceMie Univ, Sch Med, Tsu, Mie 5140001, JapanUniversidade Federal de São Paulo, Dept Bioquim, BR-04044020 São Paulo, BrazilWeb of Scienc

Transcriptional Analysis of Murine Macrophages Infected with Different Toxoplasma Strains Identifies Novel Regulation of Host Signaling Pathways

Most isolates of Toxoplasma from Europe and North America fall into one of three genetically distinct clonal lineages, the type I, II and III lineages. However, in South America these strains are rarely isolated and instead a great variety of other strains are found. T. gondii strains differ widely in a number of phenotypes in mice, such as virulence, persistence, oral infectivity, migratory capacity, induction of cytokine expression and modulation of host gene expression. The outcome of toxoplasmosis in patients is also variable and we hypothesize that, besides host and environmental factors, the genotype of the parasite strain plays a major role. The molecular basis for these differences in pathogenesis, especially in strains other than the clonal lineages, remains largely unexplored. Macrophages play an essential role in the early immune response against T. gondii and are also the cell type preferentially infected in vivo. To determine if non-canonical Toxoplasma strains have unique interactions with the host cell, we infected murine macrophages with 29 different Toxoplasma strains, representing global diversity, and used RNA-sequencing to determine host and parasite transcriptomes. We identified large differences between strains in the expression level of known parasite effectors and large chromosomal structural variation in some strains. We also identified novel strain-specifically regulated host pathways, including the regulation of the type I interferon response by some atypical strains. IFNβ production by infected cells was associated with parasite killing, independent of interferon gamma activation, and dependent on endosomal Toll-like receptors in macrophages and the cytoplasmic receptor retinoic acid-inducible gene 1 (RIG-I) in fibroblasts.National Institutes of Health (U.S.) (R01-AI080621)New England Regional Center of Excellence for Biodefense and Emerging Infectious Diseases (Developmental Grant AIO57159)Pew Charitable Trusts (Biomedical Scholars Program)Robert A. Swanson Career Development awardThe Knights Templar Eye Foundation, Inc.Pre-Doctoral Grant in the Biological Sciences (5-T32-GM007287-33)Cleo and Paul Schimmel Foundatio

Detecting Rhetorical Figures Based on Repetition of Words: Chiasmus, Epanaphora, Epiphora

This thesis deals with the detection of three rhetorical figures based on repetition of words: chiasmus (“Fair is foul, and foul is fair.”), epanaphora (“Poor old European Commission! Poor old European Council.”) and epiphora (“This house is mine. This car is mine. You are mine.”). For a computer, locating all repetitions of words is trivial, but locating just those repetitions that achieve a rhetorical effect is not. How can we make this distinction automatically?  First, we propose a new definition of the problem. We observe that rhetorical figures are a graded phenomenon, with universally accepted prototypical cases, equally clear non-cases, and a broad range of borderline cases in between. This makes it natural to view the problem as a ranking task rather than a binary detection task. We therefore design a model for ranking candidate repetitions in terms of decreasing likelihood of having a rhetorical effect, which allows potential users to decide for themselves where to draw the line with respect to borderline cases.  Second, we address the problem of collecting annotated data to train the ranking model. Thanks to a selective method of annotation, we can reduce by three orders of magnitude the annotation work for chiasmus, and by one order of magnitude the work for epanaphora and epiphora. In this way, we prove that it is feasible to develop a system for detecting the three figures without an unsurmountable amount of human work.  Finally, we propose an evaluation scheme and apply it to our models. The evaluation reveals that, even with a very incompletely annotated corpus, a system for repetitive figure detection can be trained to achieve reasonable accuracy. We investigate the impact of different linguistic features, including length, n-grams, part-of-speech tags, and syntactic roles, and find that different features are useful for different figures. We also apply the system to four different types of text: political discourse, fiction, titles of articles and novels, and quotations. Here the evaluation shows that the system is robust to shifts in genre and that the frequencies of the three rhetorical figures vary with genre.Denna avhandling behandlar tre retoriska figurer som bygger på upprepning av ord, kiasm (“Om inte Muhammed kan komma till berget får berget komma till Muhammed.”), anafor (“Det är inte rimligt. Det är inte hållbart. Det är inte rättvist.”), och epifor (“Den här stugan är min. Den här bilen är min. Du är min.”). En dator kan lätt identifiera upprepningar av ord i en text, men att urskilja enbart de upprepningar som har en retorisk effekt är svårare. Hur kan vi få datorer att göra detta? För det första föreslår vi en ny definition av problemet. Vi noterar att retoriska figurer är ett graderbart fenomen, med prototypiska fall å ena sidan, och klara icke-fall å andra sidan; däremellan finns ett brett spektrum av gränsfall. Detta gör det naturligt att se problemet som en uppgift som gäller rangordning snarare än binär klassificering. Vi skapar därför en modell för att rangordna repetitioner efter sannolikheten att de har en retorisk effekt. Därigenom tillåts  systemets användare att själva avgöra hur gränsfall ska hanteras. För det andra försöker vi undvika tänkbara svårigheter med att samla in annoterade data för att träna modellen för rangordning. Genom att använda en selektiv metod kan vi reducera mängden annoteringsarbete tusenfalt för kiasm och tiofalt för anafor och epifor. Det är alltså möjligt att utveckla ett system för att identifiera de aktuella retoriska figurerna utan en stor mängd manuell annotering. Slutligen föreslår vi en metod för utvärdering och tillämpar den på våra modeller. Utvärderingen visar att vi även med en korpus där få exempel är annoterade kan träna ett system för identifiering av repetitiva figurer med godtagbart resultat. Vi undersöker effekten av olika särdrag som bygger på t.ex. längd, n-gram, ordklasser och syntaktiska roller. En slutsats är att olika särdrag är användbara i olika grad för olika figurer. Vi prövar också systemet på ytterligare texttyper: politisk diskurs, skönlitteratur, titlar på artiklar och romaner, samt citat. Utvärderingen visar att systemet är robust vad gäller genreskillnader. Vi ser även att figurernas frekvens varierar över olika genrer

Rhetorical Figure Detection: Chiasmus, Epanaphora, Epiphora

Rhetorical figures are valuable linguistic data for literary analysis. In this article, we target the detection of three rhetorical figures that belong to the family of repetitive figures: chiasmus (I go where I please, and I please where I go.), epanaphora also called anaphora (“Poor old European Commission! Poor old European Council.”) and epiphora (“This house is mine. This car is mine. You are mine.”). Detecting repetition of words is easy for a computer but detecting only the ones provoking a rhetorical effect is difficult because of many accidental and irrelevant repetitions. For all figures, we train a log-linear classifier on a corpus of political debates. The corpus is only very partially annotated, but we nevertheless obtain good results, with more than 50% precision for all figures. We then apply our models to totally different genres and perform a comparative analysis, by comparing corpora of fiction, science and quotes. Thanks to the automatic detection of rhetorical figures, we discover that chiasmus is more likely to appear in the scientific context whereas epanaphora and epiphora are more common in fiction

Inverted topology of the Toxoplasma gondii ROP5 rhoptry protein provides new insights into the association of the ROP2 protein family with the parasitophorous vacuole membrane.

International audienceToxoplasma gondii, as many intracellular parasites, is separated from the cytosol of its host cell by a parasitophorous vacuole membrane (PVM). This vacuole forms during host cell invasion and parasite apical organelles named rhoptries discharge proteins that associate with its membrane during this process. We report here the characterization of the rhoptry protein ROP5, which is a new member of the ROP2 family. Contrasting with what is known for other ROP2 family proteins, ROP5 is not processed during trafficking to rhoptries. We show here that ROP5 is secreted during invasion and associates with the PVM. Using differential permeabilization of infected cells, we have shown that ROP5 exposes its C-terminus towards the host cell cytoplasm, which corresponds to a reverse topology compared with ROP2 and ROP4. Taken together with recent modelling data suggesting that the C-terminal hydrophobic domain hitherto described as transmembrane may correspond to a hydrophobic helix buried in the catalytic domain of kinase-related proteins, these findings call for a reappraisal of the current view of ROP2 family proteins association with the PVM

Mic1-3 knockout of Toxoplasma gondii is a successful vaccine against chronic and congenital toxoplasmosis in mice

International audienc

Functional domains of the Toxoplasma GRA2 protein in the formation of the membranous nanotubular network of the parasitophorous vacuole.

Amphipathic alpha-helices have been proposed as the general means used by soluble proteins to induce membrane tubulation. Previous studies had shown that the GRA2 dense granule protein of Toxoplasma gondii would be a crucial protein for the formation of the intravacuolar membranous nanotubular network (MNN) and that one of the functions of the MNN is to organise the parasites within the parasitophorous vacuole. GRA2 is a small protein (185 amino acids), predicted to contain three amphipathic alpha-helices (alpha1: 70-92; alpha2: 95-110 and alpha3: 119-139) when using the standard programs of secondary structure prediction. To investigate the respective contribution of each alpha-helix in the GRA2 functions, we used DeltaGRA2-HXGPRT knock-out complementation: eight truncated forms of GRA2 were expressed in the deleted recipient and the phenotypes of these mutants were analysed. This study showed that: (i) alpha3, when associated with the N-terminal region (NT) and the C-terminal region (CT), is sufficient to target the protein to the parasite posterior end and to induce formation of membranous vesicles within the vacuole. However, when associated only with CT, alpha3 is not sufficient to provide the hydrophobicity required for membrane association; (ii) the alpha1alpha2 region is alone not sufficient to induce membrane tubulation within the PV; and (iii) only one mutant, NT-alpha1alpha2alpha3, restores most of the biochemical and functional properties of GRA2, including traffic to the dense granules, secretion into the vacuole, association with vacuolar membranes, induction of the MNN formation and organisation of the parasites within the vacuole