A role for eosinophils in the intestinal immunity against infective Ascaris suum larvae

The aim of this study was to explore the mechanisms of resistance against invading Ascaris suum larvae in pigs. Pigs received a low dose of 100 A. suum eggs daily for 14 weeks. This resulted in a .99% reduction in the number of larvae that could migrate through the host after a challenge infection of 5000 A. suum eggs, compared to naı¨ve pigs. Histological analysis at the site of parasite entry, i.e. the caecum, identified eosinophilia, mastocytosis and goblet cell hyperplasia. Increased local transcription levels of genes for IL5, IL13, eosinophil peroxidase and eotaxin further supported the observed eosinophil influx. Further analysis showed that eosinophils degranulated in vitro in response to contact with infective Ascaris larvae in the presence of serum from both immune and naı¨ve animals. This effect was diminished with heat-inactivated serum, indicating a complement dependent mechanism. Furthermore, eosinophils were efficient in killing the larvae in vitro when incubated together with serum from immune animals, suggesting that A. suum specific antibodies are required for efficient elimination of the larvae. Together, these results indicate an important role for eosinophils in the intestinal defense against invading A. suum larvae

PheNetic : network-based interpretation of molecular profiling data

Molecular profiling experiments have become standard in current wet-lab practices. Classically, enrichment analysis has been used to identify biological functions related to these experimental results. Combining molecular profiling results with the wealth of currently available interactomics data, however, offers the opportunity to identify the molecular mechanism behind an observed molecular phenotype. In this paper, we therefore introduce 'PheNetic', a userfriendly web server for inferring a sub-network based on probabilistic logical querying. PheNetic extracts from an interactome, the sub-network that best explains genes prioritized through a molecular profiling experiment. Depending on its run mode, PheNetic searches either for a regulatorymechanism that gave explains to the observed molecular phenotype or for the pathways (in) activated in the molecular phenotype. The web server provides access to a large number of interactomes, making sub-network inference readily applicable to a wide variety of organisms. The inferred sub-networks can be interactively visualized in the browser. PheNetic's method and use are illustrated using an example analysis of differential expression results of ampicillin treated Escherichia coli cells. The PheNetic web service is available at http://bioinformatics.intec.ugent.be/phenetic/

Combining Stochastic Constraint Optimization and Probabilistic Programming

Algorithms and the Foundations of Software technolog

Reconciling biodiversity and carbon stock conservation in an Afrotropical forest landscape

Protecting aboveground carbon stocks in tropical forests is essential for mitigating global climate change and is assumed to simultaneously conserve biodiversity. Although the relationship between tree diversity and carbon stocks is generally positive, the relationship remains unclear for consumers or decomposers. We assessed this relationship for multiple trophic levels across the tree of life (10 organismal groups, 3 kingdoms) in lowland rainforests of the Congo Basin. Comparisons across regrowth and old-growth forests evinced the expected positive relationship for trees, but not for other organismal groups. Moreover, differences in species composition between forests increased with difference in carbon stock. These variable associations across the tree of life contradict the implicit assumption that maximum co-benefits to biodiversity are associated with conservation of forests with the highest carbon storage. Initiatives targeting climate change mitigation and biodiversity conservation should include both old-growth and regenerating forests to optimally benefit biodiversity and carbon storage

Shallow-depth sequencing of cell-free DNA for Hodgkin and diffuse large B-cell lymphoma (differential) diagnosis: a standardized approach with underappreciated potential

Shallow-depth sequencing of cell-free DNA, an inexpensive and standardized approach to obtain molecular information on tumors non-invasively, has been insufficiently explored for the diagnosis of lymphoma and disease follow-up. This study collected 318 samples, including longitudinal liquid and paired solid biopsies, from a prospectively- recruited cohort of 38 Hodgkin lymphoma (HL) and 85 aggressive B-cell non-HL patients, represented by 81 diffuse large B-cell lymphoma (DLBCL) cases. Following sequencing, copy number alterations and viral read fractions were derived and analyzed. At diagnosis, liquid biopsies showed detectable copy number alterations in 84.2% of HL patients (88.6% for classical HL) and 74.1% of DLBCL patients. Of the DLBCL patients, copy number profiles between liquid-solid pairs were highly concordant (r=0.815±0.043); and, compared to tissue, HL liquid biopsies had abnormalities with higher amplitudes (P=0.010). This implies that tumor DNA is more abundant in plasma. Additionally, 39.5% of HL and 13.6% of DLBCL cases had a significantly elevated number of plasma Epstein-Barr virus DNA fragments, achieving a sensitivity of 100% compared to the current standard. A longitudinal analysis determined that, when detectable, copy number patterns were similar across (re)staging moments in refractory or relapsed patients. Further, the overall profile anomaly correlated highly with the total metabolic tumor volume (P<0.001). To conclude, as a proof of principle, we demonstrate that liquid biopsy-derived copy numbers can aid diagnosis: e.g., by differentiating HL from DLBCL, random forest modeling is represented by an area under the receiver operating characteristic curve of 0.967. This application is potentially useful when tissue is difficult to obtain or when biopsies are small and inconclusive

The intestinal expulsion of the roundworm Ascaris suum is associated with eosinophils, intra-epithelial T cells and decreased intestinal transit time

Ascaris lumbricoides remains the most common endoparasite in humans, yet there is still very little information available about the immunological principles of protection, especially those directed against larval stages. Due to the natural host-parasite relationship, pigs infected with A. suum make an excellent model to study the mechanisms of protection against this nematode. In pigs, a self-cure reaction eliminates most larvae from the small intestine between 14 and 21 days post infection. In this study, we investigated the mucosal immune response leading to the expulsion of A. suum and the contribution of the hepato-tracheal migration. Self-cure was independent of previous passage through the liver or lungs, as infection with lung stage larvae did not impair self-cure. When animals were infected with 14-day-old intestinal larvae, the larvae were being driven distally in the small intestine around 7 days post infection but by 18 days post infection they re-inhabited the proximal part of the small intestine, indicating that more developed larvae can counter the expulsion mechanism. Self-cure was consistently associated with eosinophilia and intra-epithelial T cells in the jejunum. Furthermore, we identified increased gut movement as a possible mechanism of self-cure as the small intestinal transit time was markedly decreased at the time of expulsion of the worms. Taken together, these results shed new light on the mechanisms of self-cure that occur during A. suum infections

Cryptophaea, a new genus of byssoid Arthoniaceae (lichenized Ascomycota) and its phylogenetic position

Abstract: Cryptophaea, a new corticolous lichen genus, is described from the Congo basin as belonging to the cryptothecioid Arthoniaceae. It is characterized by (1) maculiform, tomentose, brownish ascomata lacking a distinct exciple, (2) the absence of a distinct hamathecium of paraphysoids, (3) a byssoid crustose thallus with a trentepohlioid photobiont, (4) greyish to brown (sub) muriform ascospores and (5) the presence of parietin, an anthraquinone, absent in the other cryptothecioid Arthoniaceae. At this moment the new genus is represented by only one species, Cryptophaea phaeospora sp. nov. A phylogenetic analysis of mtSSU and RPB2 sequences shows Cryptophaea as sister genus to Glomerulophoron in the cryptothecioid Arthoniaceae