FLASH: ultra-fast protocol to identify RNA-protein interactions in cells

Determination of the in vivo binding sites of RNA-binding proteins (RBPs) is paramount to understanding their function and how they affect different aspects of gene regulation. With hundreds of RNA-binding proteins identified in human cells, a flexible, high-resolution, high-throughput, highly multiplexible and radioactivity-free method to determine their binding sites has not been described to date. Here we report FLASH (Fast Ligation of RNA after some sort of Affinity Purification for High-throughput Sequencing), which uses a special adapter design and an optimized protocol to determine protein-RNA interactions in living cells. The entire FLASH protocol, starting from cells on plates to a sequencing library, takes 1.5 days. We demonstrate the flexibility, speed and versatility of FLASH by using it to determine RNA targets of both tagged and endogenously expressed proteins under diverse conditions in vivo

Skyrmion morphology in ultrathin magnetic films

Nitrogen-vacancy magnetic microscopy is employed in quenching mode as a non-invasive, high resolution tool to investigate the morphology of isolated skyrmions in ultrathin magnetic films. The skyrmion size and shape are found to be strongly affected by local pinning effects and magnetic field history. Micromagnetic simulations including static disorder, based on a physical model of grain-to-grain thickness variations, reproduce all experimental observations and reveal the key role of disorder and magnetic history in the stabilization of skyrmions in ultrathin magnetic films. This work opens the way to an in-depth understanding of skyrmion dynamics in real, disordered media.Comment: 9 pages, 8 figures, including supplementary information

EFFECTS OF LOCAL GAMETOCYTE AND LIVACOX VACCINES ON LIVE BODY WEIGHT GAIN AND LYMPHOID ORGANS IN CHICKENS

Organ to body weight ratio in chickens is considered to be an important parameter to study the immune status due to any infection or vaccination. The present paper reports the effects of local gametocyte and Livacox vaccines on live weight gains and lymphoid organs in chickens. The mean body weight gains in chickens with local gametocytes vaccine were significantly better (P<0.05) than in chickens with Livacox vaccine. Higher organ to body weight ratio was recorded in vaccinated chickens compared to control, although difference was non significant. Organ to body weight ratio of the lymphoid organs had higher values in chickens vaccinated with Livacox compared to local gametocyte vaccinated group, the difference was also found to be non significant. It was concluded that local gametocyte vaccine significantly increased the body weights of chickens compared to Livacox and control groups

Del Pezzo surfaces with 1/3(1,1) points

We classify del Pezzo surfaces with 1/3(1,1) points in 29 qG-deformation families grouped into six unprojection cascades (this overlaps with work of Fujita and Yasutake), we tabulate their biregular invariants, we give good model constructions for surfaces in all families as degeneracy loci in rep quotient varieties and we prove that precisely 26 families admit qG-degenerations to toric surfaces. This work is part of a program to study mirror symmetry for orbifold del Pezzo surfaces.Comment: 42 pages. v2: model construction added of last remaining surface, minor corrections, minor changes to presentation, references adde

Psychiatric disorders among young male adult prisoners: a cross sectional study in a Malaysian prison

Introduction: In recent years there has been an increase in the number of young people in prison. This study is the firstto look at the proportion of psychiatric disorders among young adultprisoners. Objective: The main objective is to determine the percentage of psychiatric disorders among young adult male prisoners. Method: A cross sectional study of young adult male prisoners, with ages ranged between 18 and 21 years old, was conducted between September and December, 2008 at the Kajang Prison. A total of 225 inmates participated in the study which used the Mini International Neuropsychiatric Interview (MINI) as its instrument. Results: The percentage of psychiatric disorders was 60.0%. Alcohol and substance related disorders had the highest prevalence at 50.2%, followed by Major Depressive Disorders and Dysthymia at 16.9%. About 39.6% were observed to have antisocial personality disordet Psychiatric disorders were found to have significant differences (p<O.05) in connection with parental marriage and recidivism. Conclusion: This study shows that the percentage of psychiatric disorders, especially substance related disorders, is high among young male adult prisoners. It highlights the urgent need for early intervention for this group of young people

Testing message framing to increase physical activity among British South Asians

Objective: British South Asians (BSAs) experience a higher incidence of coronary heart disease (CHD) which is not declining in line with the UK national average. Low physical activity levels are likely to contribute to this elevated risk. This study investigated the effectiveness of message framing, cultural sensitivity and their interaction on promoting physical activity among BSAs. Design: One hundred and seventy-nine participants (70 males and 109 females) were randomly allocated to watch one of four films in a 2 (loss vs. gain) × 2 (culturally sensitive vs. non-culturally sensitive) design. Main outcome measures: Measures of self-reported physical activity and behavioural intention were completed at baseline and two-month follow-up. Results: The analysis revealed no main effects for message framing, cultural sensitivity or for the interaction between these factors for self-reported physical activity and behavioural intention. Conclusions: Healthy BSAs appear not to respond to health promotion messages which have been manipulated by message framing or cultural sensitivity. Possible explanations are that despite an increased risk of developing CHD, healthy BSAs may be unwilling to engage in immediate action for a potential future health problem and cultural sensitivity may be irrelevant to a ‘Westernised’ sample. Nevertheless, future research ought to investigate variations of the current intervention by using a larger sample size, targeting a more sedentary population, varying the length and exposure to the intervention in less assimilated groups, clinically symptomatic populations or those at high risk of CHD

Religious citizenship: The case of the globalised Khoja

The African Khōjā are an Indic Muslim caste, which began migrating from Sindh and Gujarat to East Africa in the late 18th century. During the 19th and 20th centuries, their economic success in an institutionally underdeveloped region coupled with a strong religious impetus allowed them to build communal municipal institutions throughout the region that both mimicked and replaced the absent state. The insecurity of postcolonial East Africa, such as the 1964 revolution in Zanzibar and the 1972 Ugandan Asian exodus, forced the Khōjā to further expand their bureaucratic apparatus towards foreign policy- migration to Western Europe and North America and requisite institutionalization. In the 21st century, the Khōjā coordinate these communal networks from North America and Western Europe to Asia and Africa towards a religious based economic development in emerging economies. Their primary identity is religious, defined from within and outwith, using the mechanisms of globalization to further communal aims internationally within a framework of religious nationalism insensible to state nationalism.Key Words: The Khōjā, Religious citizenship, Islam, Madagascar, Diaspora, Identity, Imagined CommunityRésuméLe Khoja africaine sont une caste musulmane Indic, qui a commencé la migration de Sindh et du Gujarat Afrique de l’Est à la fin du 18ème siècle. Au cours des 19e et 20e siècles, leur succès économique dans une région sous-développée sur le plan institutionnel couplé avec une forte impulsion religieuse leur a permis de construire des institutions municipales communales toute la région imité C’est Bothan et substitué à l’Etat absent. L’insécurité de l’Afrique postcoloniale de l’Est, tels que la révolution de 1964 à Zanzibar et 1972 ougandais asiatique exode, a forcé le Khoja à élargir leur appareil bureaucratique de la politique de la migration étrangère à l’Europe occidentale et l’Amérique du Nord et l’institutionnalisation nécessaire. Au 21e siècle, la Khoja coordonner Ces réseaux communautaires d’Amérique du Nord et en Europe occidentale à l’Asie et de l’Afrique vers un développement économique basé sur la religion dans les économies émergentes. Leur identité première est religieuse, définie à partir de l’intérieur et sont sortis, en utilisant les mécanismes de la mondialisation à d’autres objectifs communautaires l’échelle internationale dans le cadre de nationalisme religieux Insensible aux nationalisme d’Etat.Mots clés: Le Khoja, citoyenneté Religieuse, l’islam, Madagascar, la diaspora, identité, communauté Imagin

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background: The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings: As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. © 2011 Dao et al

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