Fascioloides magna (Bassi, 1875) in feral swine from southern Texas.

Between 1971 and 1975, Fascioloides magna was found in 46 of 67 (69%) feral swine (Sus scrofa) in southern Texas. Flukes were recovered from swine in areas where F. magna commonly has been recovered from white-tailed deer and cattle. One to 12 flukes were recovered from each infected animal. Their presence was indicated by black hematin pigment on the liver and various other internal organs. Eggs were not detected in the gallbladder or feces of infected animals although mature flukes and eggs were recovered in the livers suggesting that, like cattle, feral swine can be infected but are aberrant hosts for the parasite and do not disseminate eggs.     

Auxin signaling and transport promote susceptibility to the root-infecting fungal pathogen Fusarium oxysporum in Arabidopsis

Fusarium oxysporum is a root-infecting fungal pathogen that causes wilt disease on a broad range of plant species, including the model plant Arabidopsis thaliana. Currently, very little is known about the molecular or physiological processes that are activated in the host during infection and the roles these processes play in resistance and susceptibility to F. oxysporum. In this study, we analyzed global gene expression profiles of F. oxysporum-infected Arabidopsis plants. Genes involved in jasmonate biosynthesis as well as jasmonate-dependent defense were coordinately induced by F. oxysporum. Similarly, tryptophan pathway genes, including those involved in both indole-glucosinolate and auxin biosynthesis, were upregulated in both the leaves and the roots of inoculated plants. Analysis of plants expressing the DR5:GUS construct suggested that root auxin homeostasis was altered during F. oxysporum infection. However, Arabidopsis mutants with altered auxin and tryptophan-derived metabolites such as indole-glucosinolates and camalexin did not show an altered resistance to this pathogen. In contrast, several auxin-signaling mutants were more resistant to F. oxysporum. Chemical or genetic alteration of polar auxin transport also conferred increased pathogen resistance. Our results suggest that, similarly to many other pathogenic and nonpathogenic or beneficial soil organisms, F. oxysporum requires components of auxin signaling and transport to colonize the plant more effectively. Potential mechanisms of auxin signaling and transport-mediated F. oxysporum susceptibility are discussed.     

Systematic identification of proteins that elicit drug side effects

Side effect similarities of drugs have recently been employed to predict new drug targets, and networks of side effects and targets have been used to better understand the mechanism of action of drugs. Here, we report a large‐scale analysis to systematically predict and characterize proteins that cause drug side effects. We integrated phenotypic data obtained during clinical trials with known drug–target relations to identify overrepresented protein–side effect combinations. Using independent data, we confirm that most of these overrepresentations point to proteins which, when perturbed, cause side effects. Of 1428 side effects studied, 732 were predicted to be predominantly caused by individual proteins, at least 137 of them backed by existing pharmacological or phenotypic data. We prove this concept in vivo by confirming our prediction that activation of the serotonin 7 receptor (HTR7) is responsible for hyperesthesia in mice, which, in turn, can be prevented by a drug that selectively inhibits HTR7. Taken together, we show that a large fraction of complex drug side effects are mediated by individual proteins and create a reference for such relations.     

Analyses of dryland biological soil crusts highlight lichens as an important regulator of microbial communities

Biological soil crusts (BSCs) provide important ecosystem services in dryland regions, including erosion control and contribution to nitrogen and CO₂ fixation. As soil microorganisms are still rarely studied within the context of biodiversity planning, we describe, as a contribution to the Soil Crust International project, an approach that addresses this gap in biodiversity assessments. The purpose of the present study was a characterization of prokaryotic communities of BSCs formed by two species of lichenized fungi, Psora decipiens and Toninia sedifolia, in relation to surrounding BSCs and the below-crust soil layer from Tabernas basin (Almería, Spain). Microbial community profiles were determined using 454 pyrosequencing targeting the V4 hypervariable region of the bacterial and archaeal 16S rRNA gene. The majority of the 65,497 sequences obtained belonged to Proteobacteria (mainly Alphaproteobacteria), Actinobacteria, Bacteroidetes and Cyanobacteria. Cyanobacteria were more abundant at the soil surface but rare in below-crust soils, whilst below-crust soils harbored significantly more Acidobacteria, Verrucomicrobia, Gemmatimonadetes, Planctomycetes and Armatimonadetes. Additionally, terricolous lichens were investigated using fluorescence in situ hybridization in conjunction with confocal laser scanning microscopy, the objective being to illustrate bacterial niches in BSC-forming lichens. Bacteria were mainly present at the upper cortex of the squamules and attachment organs. Our findings indicate that the composition of soil prokaryotes varies at a small scale not only in adjacent soil layers but also in BSC-forming lichen species. Furthermore, bacteria were shown to be attached to fungal structures, probably representing a case of fungal-bacterial interaction.     

Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age

Recently duplicated genes are believed to often overlap in function and expression. A priori, they are thus less likely to be essential. Although this was indeed observed in yeast, mouse singletons and duplicates were reported to be equally often essential. This contradiction can only partly be explained by experimental biases. We herein show that older genes (i.e., genes with earlier phyletic origin) are more likely to be essential, regardless of their duplication status. At a given phyletic gene age, duplicates are always less likely to be essential compared with singletons. The "paradoxical" high essentiality among mouse gene duplicates is then caused by different age profiles of singletons and duplicates, with the latter tending to be derived from older genes.     

The Potential for pathogenicity was present in the ancestor of the Ascomycete subphylum Pezizomycotina

Background  

Previous studies in Ascomycetes have shown that the function of gene families of which the size is considerably larger in extant pathogens than in non-pathogens could be related to pathogenicity traits. However, by only comparing gene inventories in extant species, no insights can be gained into the evolutionary process that gave rise to these larger family sizes in pathogens. Moreover, most studies which consider gene families in extant species only tend to explain observed differences in gene family sizes by gains rather than by losses, hereby largely underestimating the impact of gene loss during genome evolution.     

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks

SUMMARY: Network motifs in integrated molecular networks represent functional relationships between distinct data types. They aggregate to form dense topological structures corresponding to functional modules which cannot be detected by traditional graph clustering algorithms. We developed CyClus3D, a Cytoscape plugin for clustering composite three-node network motifs using a 3D spectral clustering algorithm. AVAILABILITY: Via the Cytoscape plugin manager or http://bioinformatics.psb.ugent.be/software/details/CyClus3D.