Heterologous expression screens in Nicotiana benthamiana identify a candidate effector of the wheat Yellow Rust Pathogen that associates with processing bodies

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors

Membrane fission by dynamin: what we know and what we need to know

The large GTPase dynamin is the first protein shown to catalyze membrane fission. Dynamin and its related proteins are essential to many cell functions, from endocytosis to organelle division and fusion, and it plays a critical role in many physiological functions such as synaptic transmission and muscle contraction. Research of the past three decades has focused on understanding how dynamin works. In this review, we present the basis for an emerging consensus on how dynamin functions. Three properties of dynamin are strongly supported by experimental data: first, dynamin oligomerizes into a helical polymer; second, dynamin oligomer constricts in the presence of GTP; and third, dynamin catalyzes membrane fission upon GTP hydrolysis. We present the two current models for fission, essentially diverging in how GTP energy is spent. We further discuss how future research might solve the remaining open questions presently under discussion

Biogenic amines and their metabolites are differentially affected in the Mecp2-deficient mouse brain

International audienceBACKGROUND: Rett syndrome (RTT, MIM #312750) is a severe neurological disorder caused by mutations in the X-linked methyl-CpG binding protein 2 (MECP2) gene. Female patients are affected with an incidence of 1/15000 live births and develop normally from birth to 6-18 months of age before the onset of deficits in autonomic, cognitive, motor functions (stereotypic hand movements, impaired locomotion) and autistic features. Studies on Mecp2 mouse models, and specifically null mice, revealed morphological and functional alterations of neurons. Several functions that are regulated by bioaminergic nuclei or peripheral ganglia are impaired in the absence of Mecp2. RESULTS: Using high performance liquid chromatography, combined with electrochemical detection (HPLC/EC) we found that Mecp2(-/y) mice exhibit an alteration of DA metabolism in the ponto-bulbar region at 5 weeks followed by a more global alteration of monoamines when the disease progresses (8 weeks). Hypothalamic measurements suggest biphasic disturbances of norepinephrine and serotonin at pathology onset (5 weeks) that were found stabilized later on (8 weeks). Interestingly, the postnatal nigrostriatal dopaminergic deficit identified previously does not parallel the reduction of the other neurotransmitters investigated. Finally, dosage in cortical samples do not suggest modification in the monoaminergic content respectively at 5 and 8 weeks of age. CONCLUSIONS: We have identified that the level of catecholamines and serotonin is differentially affected in Mecp2(-/y) brain areas in a time-dependent fashion

The Equilibria of Lipid–K+ Ions in Monolayer at the Air/Water Interface

The effect of K+ ion interaction with monolayers of phosphatidylcholine (lecithin, PC) or cholesterol (Ch) was investigated at the air/water interface. We present surface tension measurements of lipid monolayers obtained using a Langmuir method as a function of K+ ion concentration. Measurements were carried out at 22°C using a Teflon trough and a Nima 9000 tensiometer. Interactions between lecithin and K+ ions or Ch and K+ ions result in significant deviations from the additivity rule. An equilibrium theory to describe the behavior of monolayer components at the air/water interface was developed in order to obtain the stability constants and area occupied by one molecule of lipid–K+ ion complex (LK+). The stability constants for lecithin–K+ ion (PCK+) complex, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K_{{{\text{PCK}}^{ + } }} = { 3}. 2 6\times 10^{ 2} {\text{dm}}^{ 3} \,{\text{mol}}^{ - 1}$$\end{document}, and for cholesterol–K+ ion (ChK+) complex, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$K_{{{\text{ChK}}^{ + } }} = { 1}.00 \times 10^{ 3} {\text{dm}}^{ 3} \,{\text{mol}}^{ - 1}$$\end{document}, were calculated by inserting the experimental data. The value of area occupied by one PCK+ complex is 60 Å2 molecule−1, while the area occupied by one ChK+ complex is 40.9 Å2 molecule−1. The complex formation energy (Gibbs free energy) values for the PCK+ and ChK+ complexes are −14.18 ± 0.71 and −16.92 ± 0.85 kJ mol−1, respectively

Modulation of enhancer looping and differential gene targeting by Epstein-Barr virus transcription factors directs cellular reprogramming

Epstein-Barr virus (EBV) epigenetically reprogrammes B-lymphocytes to drive immortalization and facilitate viral persistence. Host-cell transcription is perturbed principally through the actions of EBV EBNA 2, 3A, 3B and 3C, with cellular genes deregulated by specific combinations of these EBNAs through unknown mechanisms. Comparing human genome binding by these viral transcription factors, we discovered that 25% of binding sites were shared by EBNA 2 and the EBNA 3s and were located predominantly in enhancers. Moreover, 80% of potential EBNA 3A, 3B or 3C target genes were also targeted by EBNA 2, implicating extensive interplay between EBNA 2 and 3 proteins in cellular reprogramming. Investigating shared enhancer sites neighbouring two new targets (WEE1 and CTBP2) we discovered that EBNA 3 proteins repress transcription by modulating enhancer-promoter loop formation to establish repressive chromatin hubs or prevent assembly of active hubs. Re-ChIP analysis revealed that EBNA 2 and 3 proteins do not bind simultaneously at shared sites but compete for binding thereby modulating enhancer-promoter interactions. At an EBNA 3-only intergenic enhancer site between ADAM28 and ADAMDEC1 EBNA 3C was also able to independently direct epigenetic repression of both genes through enhancer-promoter looping. Significantly, studying shared or unique EBNA 3 binding sites at WEE1, CTBP2, ITGAL (LFA-1 alpha chain), BCL2L11 (Bim) and the ADAMs, we also discovered that different sets of EBNA 3 proteins bind regulatory elements in a gene and cell-type specific manner. Binding profiles correlated with the effects of individual EBNA 3 proteins on the expression of these genes, providing a molecular basis for the targeting of different sets of cellular genes by the EBNA 3s. Our results therefore highlight the influence of the genomic and cellular context in determining the specificity of gene deregulation by EBV and provide a paradigm for host-cell reprogramming through modulation of enhancer-promoter interactions by viral transcription factors

Area deprivation and its association with health in a cross-sectional study: are the results biased by recent migration?

<p>Abstract</p> <p>Background</p> <p>The association between area deprivation and health has mostly been examined in cross-sectional studies or prospective studies with short follow-up. These studies have rarely taken migration into account. This is a possible source of misclassification of exposure, i.e. an unknown number of study participants are attributed an exposure of area deprivation that they may have experienced too short for it to have any influence. The aim of this article was to examine to what extent associations between area deprivation and health outcomes were biased by recent migration.</p> <p>Methods</p> <p>Based on data from the Oslo Health Study, a cross-sectional study conducted in 2000 in Oslo, Norway, we used six health outcomes (self rated health, mental health, coronary heart disease, chronic obstructive pulmonary disease, smoking and exercise) and considered migration nine years prior to the study conduct. Migration into Oslo, between the areas of Oslo, and the changes in area deprivation during the period were taken into account. Associations were investigated by multilevel logistic regression analyses.</p> <p>Results</p> <p>After adjustment for individual socio-demographic variables we found significant associations between area deprivation and all health outcomes. Accounting for migration into Oslo and between areas of Oslo did not change these associations much. However, the people who migrated into Oslo were younger and had lower prevalences of unfavourable health outcomes than those who were already living in Oslo. But since they were evenly distributed across the area deprivation quintiles, they had little influence on the associations between area deprivation and health. Evidence of selective migration within Oslo was weak, as both moving up and down in the deprivation hierarchy was associated with significantly worse health than not moving.</p> <p>Conclusion</p> <p>We have documented significant associations between area deprivation and health outcomes in Oslo after adjustment for socio-demographic variables in a cross-sectional study. These associations were weakly biased by recent migration. From our results it still appears that migration prior to study conduct may be relevant to investigate even within a relatively short period of time, whereas changes in area deprivation during such a period is of limited interest.</p

Adherence to isoniazid preventive therapy in Indonesian children: A quantitative and qualitative investigation

<p>Abstract</p> <p>Background</p> <p>It is recommended that young child contacts of sputum smear positive tuberculosis cases receive isoniazid preventive therapy (IPT) but reported adherence is low and risk factors for poor adherence in children are largely unknown.</p> <p>Methods</p> <p>We prospectively determined rates of IPT adherence in children < 5 yrs in an Indonesian lung clinic. Possible risk factors for poor adherence, defined as ≤3 months prescription collection, were calculated using logistic regression. To further investigate adherence barriers in-depth interviews were conducted with caregivers of children with good and poor adherence.</p> <p>Results</p> <p>Eighty-two children eligible for IPT were included, 61 (74.4%) of which had poor adherence. High transport costs (OR 3.3, 95% CI 1.1-10.2) and medication costs (OR 20.0, 95% CI 2.7-414.5) were significantly associated with poor adherence in univariate analysis. Access, medication barriers, disease and health service experience and caregiver TB and IPT knowledge and beliefs were found to be important determinants of adherence in qualitative analysis.</p> <p>Conclusion</p> <p>Adherence to IPT in this setting in Indonesia is extremely low and may result from a combination of financial, knowledge, health service and medication related barriers. Successful reduction of childhood TB urgently requires evidence-based interventions that address poor adherence to IPT.</p

The impact of regional and neighbourhood deprivation on physical health in Germany: a multilevel study

Voigtländer S, Berger U, Razum O. The impact of regional and neighbourhood deprivation on physical health in Germany: a multilevel study. BMC Public Health. 2010;10(1): 403.Background There is increasing evidence that individual health is at least partly determined by neighbourhood and regional factors. Mechanisms, however, remain poorly understood, and evidence from Germany is scant. This study explores whether regional as well as neighbourhood deprivation are associated with physical health and to what extent this association can be explained by specific neighbourhood exposures. Methods Using 2004 data from the German Socio-Economic Panel Study (SOEP) merged with regional and neighbourhood characteristics, we fitted multilevel linear regression models with subjective physical health, as measured by the SF-12, as the dependent variable. The models include regional and neighbourhood proxies of deprivation (i.e. regional unemployment quota, average purchasing power of the street section) as well as specific neighbourhood exposures (i.e. perceived air pollution). Individual characteristics including socioeconomic status and health behaviour have been controlled for. Results This study finds a significant association between area deprivation and physical health which is independent of compositional factors and consistent across different spatial scales. Furthermore the association between neighbourhood deprivation and physical health can be partly explained by specific features of the neighbourhood environment. Among these perceived air pollution shows the strongest association with physical health (-2.4 points for very strong and -1.5 points for strong disturbance by air pollution, standard error (SE) = 0.8 and 0.4, respectively). Beta coefficients for perceived air pollution, perceived noise and the perceived distance to recreational resources do not diminish when including individual health behaviour in the models. Conclusions This study highlights the difference regional and in particular neighbourhood deprivation make to the physical health of individuals in Germany. The results support the argument that specific neighbourhood exposures serve as an intermediary step between deprivation and health. As people with a low socioeconomic status were more likely to be exposed to unfavourable neighbourhood characteristics these conditions plausibly contribute towards generating health inequalities

Combining Experiments and Simulations Using the Maximum Entropy Principle

A key component of computational biology is to compare the results of computer modelling with experimental measurements. Despite substantial progress in the models and algorithms used in many areas of computational biology, such comparisons sometimes reveal that the computations are not in quantitative agreement with experimental data. The principle of maximum entropy is a general procedure for constructing probability distributions in the light of new data, making it a natural tool in cases when an initial model provides results that are at odds with experiments. The number of maximum entropy applications in our field has grown steadily in recent years, in areas as diverse as sequence analysis, structural modelling, and neurobiology. In this Perspectives article, we give a broad introduction to the method, in an attempt to encourage its further adoption. The general procedure is explained in the context of a simple example, after which we proceed with a real-world application in the field of molecular simulations, where the maximum entropy procedure has recently provided new insight. Given the limited accuracy of force fields, macromolecular simulations sometimes produce results that are at not in complete and quantitative accordance with experiments. A common solution to this problem is to explicitly ensure agreement between the two by perturbing the potential energy function towards the experimental data. So far, a general consensus for how such perturbations should be implemented has been lacking. Three very recent papers have explored this problem using the maximum entropy approach, providing both new theoretical and practical insights to the problem. We highlight each of these contributions in turn and conclude with a discussion on remaining challenges