Integration of biological networks and gene expression data using Cytoscape

Cytoscape is a free software package for visualizing, modeling and analyzing molecular and genetic interaction networks. This protocol explains how to use Cytoscape to analyze the results of mRNA expression profiling, and other functional genomics and proteomics experiments, in the context of an interaction network obtained for genes of interest. Five major steps are described: (i) obtaining a gene or protein network, (ii) displaying the network using layout algorithms, (iii) integrating with gene expression and other functional attributes, (iv) identifying putative complexes and functional modules and (v) identifying enriched Gene Ontology annotations in the network. These steps provide a broad sample of the types of analyses performed by Cytoscape.     

Backbone and sidechain 1H, 13C and 15N resonance assignments of the RGS domain from human RGS14

We have assigned ¹H, ¹⁵N and ¹³C resonances of the RGS domain from the human RGS14 protein, a multi-domain member of the RGS (Regulators of G-protein signalling) family of proteins, important in the down-regulation of specific G-protein signalling pathways.     

Initiating Change: Negotiations of Subjectivity in a Danish Activation Programme for Young Adults with Psychosocial Problems and Common Mental Disorders

Culture, Medicine, and Psychiatry - An increasing number of young adults in Denmark experience difficulties in completing their education and holding down a job. Many of these young adults have...     

Preliminary survey on putative insect vectors for Rubus stunt phytoplasmas

Phytoplasmas are cell wall‐less phytopathogenic bacteria which are associated with a disease in Rubus species known as Rubus stunt. Symptoms range from stunting, witches’ broom, small leaves, short internodes, enlarged sepals, phyllody and flower proliferation to fruit malformations. Phytoplasmas can be spread by vegetative propagation and by phloem‐feeding insect vectors. However, little is known about the spectrum and distribution of putative Rubus stunt insect vectors. In this study, a screening of putative insect vectors of Rubus stunt in raspberry plantations in southern and northern Germany was carried out during two successive years (2014 and 2015) with multiple sampling dates throughout the growing seasons. A total of 2,891 hemipteran insects were sorted, identified to family, genus or species level when possible, and a subset of 319 DNA samples containing a sum of 932 selected individuals representing all identified species, sampling locations and sampling dates were tested for phytoplasma DNA using qPCR. Altogether, eight DNA samples were positive for phytoplasma DNA, among them species from the genera Euscelidius, Macrosteles, Euscelis, Anaceratagalliaand Psammotettix. These data will form the basis for choosing and timing appropriate control measures against Rubus stunt and also for potential insect vector transmission experiments.     

Acceptability of Drosophila suzukii as prey for common predators occurring in cherries and berries

The invasive cherry vinegar fly, Drosophila suzukii, has been identified in Europe as a destructive fruit pest since its arrival in 2008. In the present laboratory study, three predatory insects (Orius majusculus, Chrysoperla carnea, and Forficula auricularia) naturally occurring on fruit crops in Europe were investigated for their ability to attack and feed on D. suzukii within and outside fruits. The predators were provided with various D. suzukii life stages (eggs, larvae, pupae or adults) exposed or within infested cherries. The anthocorid bug O. majusculus fed on eggs and larvae, but was not able to attack pupae. Larvae of the lacewing C. carnea preyed upon D. suzukii eggs, larvae and pupae and also captured adult flies. The European earwig F. auricularia was the most voracious predator of these three tested species. Although the earwigs were not able to catch adult flies, they readily preyed upon every other developmental stage. Adult O. majusculus or third instar larvae of C. carnea significantly reduced the offspring of D. suzukii from infested cherries, when these contained the egg stage of the pest. None of the predators were able to attack early larval stages inside the cherries. But pupae that protruded from the fruit epicarp or that had pupated outside the fruit were accessible to lacewing larvae and earwigs and significantly reduced by them. Orius bugs, lacewing larvae and earwigs were able, under laboratory conditions, to capture and prey upon various life stages of the invasive pest, if not completely concealed inside the fruit. Our findings suggest that these generalist predators may have some control capacity on infested fruit in cultivated fruit crops and also in non‐crop habitats.     

Endosomal escape of delivered mRNA from endosomal recycling tubules visualized at the nanoscale

Delivery of exogenous mRNA using lipid nanoparticles (LNPs) is a promising strategy for therapeutics. However, a bottleneck remains in the poor understanding of the parameters that correlate with endosomal escape versus cytotoxicity. To address this problem, we compared the endosomal distribution of six LNP-mRNA formulations of diverse chemical composition and efficacy, similar to those used in mRNA-based vaccines, in primary human adipocytes, fibroblasts, and HeLa cells. Surprisingly, we found that total uptake is not a sufficient predictor of delivery, and different LNPs vary considerably in endosomal distributions. Prolonged uptake impaired endosomal acidification, a sign of cytotoxicity, and caused mRNA to accumulate in compartments defective in cargo transport and unproductive for delivery. In contrast, early endocytic/recycling compartments have the highest probability for mRNA escape. By using super-resolution microscopy, we could resolve a single LNP-mRNA within subendosomal compartments and capture events of mRNA escape from endosomal recycling tubules. Our results change the view of the mechanisms of endosomal escape and define quantitative parameters to guide the development of mRNA formulations toward higher efficacy and lower cytotoxicity.