Global analysis of gene expression reveals mRNA superinduction is required for the inducible immune response to a bacterial pathogen.

The inducible innate immune response to infection requires a concerted process of gene expression that is regulated at multiple levels. Most global analyses of the innate immune response have focused on transcription induced by defined immunostimulatory ligands, such as lipopolysaccharide. However, the response to pathogens involves additional complexity, as pathogens interfere with virtually every step of gene expression. How cells respond to pathogen-mediated disruption of gene expression to nevertheless initiate protective responses remains unclear. We previously discovered that a pathogen-mediated blockade of host protein synthesis provokes the production of specific pro-inflammatory cytokines. It remains unclear how these cytokines are produced despite the global pathogen-induced block of translation. We addressed this question by using parallel RNAseq and ribosome profiling to characterize the response of macrophages to infection with the intracellular bacterial pathogen Legionella pneumophila. Our results reveal that mRNA superinduction is required for the inducible immune response to a bacterial pathogen

PRASCAL: a pataphysical programming language

This paper introduces PRASCAL, a programming language that distorts traditional PASCAL using pataphysical principles. The aim of the language is to stimulate creativity and to embed playfulness in computer systems. A wider aim is to reach towards a less severe, more human, form of logic. Pataphysics was a concept elaborated by the French writer and poet Alfred Jarry (1873–1907) in a series of plays and novels, as well as through his own life. It is defined as the science of imaginary solutions and the science of the laws governing exceptions and contradictions. PRASCAL applies this concept through mechanisms such as patadata and Uboolean logic to arrive at a language which is always exceptional and particular

How to rewire the host cell: A home improvement guide for intracellular bacteria.

Intracellular bacterial pathogens have developed versatile strategies to generate niches inside the eukaryotic cells that allow them to survive and proliferate. Making a home inside the host offers many advantages; however, intracellular bacteria must also overcome many challenges, such as disarming innate immune signaling and accessing host nutrient supplies. Gaining entry into the cell and avoiding degradation is only the beginning of a successful intracellular lifestyle. To establish these replicative niches, intracellular pathogens secrete various virulence proteins, called effectors, to manipulate host cell signaling pathways and subvert host defense mechanisms. Many effectors mimic host enzymes, whereas others perform entirely novel enzymatic functions. A large volume of work has been done to understand how intracellular bacteria manipulate membrane trafficking pathways. In this review, we focus on how intracellular bacterial pathogens target innate immune signaling, the unfolded protein response, autophagy, and cellular metabolism and exploit these pathways to their advantage. We also discuss how bacterial pathogens can alter host gene expression by directly modifying histones or hijacking the ubiquitination machinery to take control of several host signaling pathways

Prenylated isoflavonoids from soya and licorice : analysis, induction and in vitro estrogenicity

Prenylatedisoflavonoids are found in large amountsin soya bean (Glycine max) germinated under stress and in licorice (Glycyrrhiza glabra). Prenylation of isoflavonoids has been associated with modification of theirestrogenic activity. The aims of this thesis were (1) to provide a structural characterisation of isoflavonoids, in particular the prenylated isoflavonoids occurring in soya and licorice, (2) to increase the estrogenic activity of soya beans by a malting treatment in the presence of a food-grade fungus, and (3) to correlate the in vitroagonistic/antagonistic estrogenicity with the presence of prenylated isoflavonoids. A reversed-phase UHPLC-DAD-MSn-based screening method was developed that allowed the tentative identification of all prenylated flavonoids in licorice extracts using neutral losses diagnosticfor prenylation. Moreover, both the chain and pyran ring can be discriminated. This method was also employed on extracts from soya seedlings, which were challenged with the food-grade fungus Rhizopusspp. Besides known prenylated pterocarpans, also novel prenylated isoflavones and coumestans were found in soya. Subsequently, a licorice root extract was fractionated and the fractions were screened for estrogenic activityusing an in vitro yeast ER bioassay.Several fractions were considered estrogenically active on one or both ER-subtypes (α and β). The estrogenic activity of some fractions was associated with the presence of glabrene, a prenylated isoflavene. The predominant phytoestrogen of licorice root, glabridin, did not show any agonistic activity, but was found to bea potent ERα antagonist. Large-scale Rhizopus-challenging of soya seedlings resulted in a 10 to 12 fold increase of the isoflavonoid content, in a diversification of isoflavonoid composition, andin an increase of estrogenic activity. The measured estrogenicity of the extracts on both ERs was lower than the theoretically calculated estrogenicity, indicating the presence of antagonists. This antagonistic activity was hypothesized to be associated with the presence of prenylated isoflavonoids. </p

Modulation of dendritic cell maturation by ribotoxic and oxidative stress

Dendritic cells (DC) are known to be vital to the immune response, priming naive T cells to antigen specific proliferation. Dendritic cells in their immature state have a unique capacity to ingest large numbers of antigens via macopinocytosis. After receiving an appropriate signal they mature to an antigen presenting and T cell stimulatory state, displaying antigens bound to MHC molecules and up-regulating expression of co-stimulatory molecules. It is now well established that DC are matured by recognition of conserved molecular pattern on pathogenic organisms, often referred to as PAMPs (pathogen associated molecular patterns). In addition DC can mature in response to inflammatory cytokines such as TNF-a and IL-1 p. In this thesis an alternative DC maturation pathway is proposed, in which DC mature in response to interference with the ribosomal machinery, particularly 28S rRNA. The stress kinases are also proposed to signal any changes in 28S rRNA status within the DC. To test this hypothesis DC are incubated with ribotoxic compounds and maturation is measured by phenotype analysis, T cell stimulation and cytokine release. The results show that ribotoxic compounds can at low doses cause partial activation of DC. The proposal is then made that this route of DC activation may signal viral infection of DC, leading to maturation in response. In addition low level redox stress is shown to act in synergy with LPS to enhance T cell proliferation and cytokine release. Finally necrotic lymphocyte treated DC are shown to enhance T cell proliferation. Therefore the conclusion is made that stress per se acts as an auxiliary mechanism of enhancing immune responses, acting in synergy with receptor driven immune activation. The 28S rRNA pathway however is proposed as a major route of viral activation of DC

Ligand control of in vivo interaction between ecdysteroid receptor and Ultraspiracle ligand binding domain

Ecdysteroids (Ecs) enhance the formation of Ec receptor-ultraspiracle protein (EcR-USP) heterodimers which regulate gene transcription. To study EcR-USP heterodimerization, fusion proteins were constructed from the LBDs (ligand-binding domains) of Drosophila EcR or USP and the activation or DNA-binding region of GAL4 respectively. Reporter gene ( lacZ ) activation was fully dependent on the co-expression of the two fusion proteins and thus constitutes a reliable measure for the interaction in vivo between the two LBDs in the yeast cell. To identify structures involved in heterodimerization, a total of 27 point mutations were generated in the EcR and USP LBDs at selected sites. Heterodimerization and its inducibility by ligand were mainly affected by mutations in the dimerization interface and in the ligand-binding pocket of EcR respectively. However, also mutations not located in these structures or even in the LBD of USP influenced ligand-dependent heterodimerization. Together with previously reported ligand-binding studies, the existence of such local, intra- and inter-molecular mutation effects suggest that ligand-induced dimerization results from a synergistic interaction between ligand-binding and heterodimerization functions in EcR LBD, and that it depends on global features of the LBDs of EcR and USP and on their mutual surface compatibility

Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks

The sirtuin Sirt6 is a NAD-dependent histone deacetylase that is implicated in gene regulation and lifespan control. Sirt6 can interact with the stress-responsive transcription factor NF-κB and regulate some NF-κB target genes, but the full scope of Sirt6 target genes as well as dynamics of Sirt6 occupancy on chromatin are not known. Here we map Sirt6 occupancy on mouse promoters genome-wide and show that Sirt6 occupancy is highly dynamic in response to TNF-α. More than half of Sirt6 target genes are only revealed upon stress-signaling. The majority of genes bound by NF-κB subunit RelA recruit Sirt6, and dynamic Sirt6 relocalization is largely driven in a RelA-dependent manner. Integrative analysis with global gene expression patterns in wild-type, Sirt6−/−, and double Sirt6−/− RelA−/− cells reveals the epistatic relationships between Sirt6 and RelA in shaping diverse temporal patterns of gene expression. Genes under the direct joint control of Sirt6 and RelA include several with prominent roles in cell senescence and organismal aging. These data suggest dynamic chromatin relocalization of Sirt6 as a key output of NF-κB signaling in stress response and aging