Characteristic bimodal profiles of RNA polymerase II at thousands of active mammalian promoters.

BACKGROUND: In mammals, ChIP-seq studies of RNA polymerase II (PolII) occupancy have been performed to reveal how recruitment, initiation and pausing of PolII may control transcription rates, but the focus is rarely on obtaining finely resolved profiles that can portray the progression of PolII through sequential promoter states. RESULTS: Here, we analyze PolII binding profiles from high-coverage ChIP-seq on promoters of actively transcribed genes in mouse and humans. We show that the enrichment of PolII near transcription start sites exhibits a stereotypical bimodal structure, with one peak near active transcription start sites and a second peak 110 base pairs downstream from the first. Using an empirical model that reliably quantifies the spatial PolII signal, gene by gene, we show that the first PolII peak allows for refined positioning of transcription start sites, which is corroborated by mRNA sequencing. This bimodal signature is found both in mouse and humans. Analysis of the pausing-related factors NELF and DSIF suggests that the downstream peak reflects widespread pausing at the +1 nucleosome barrier. Several features of the bimodal pattern are correlated with sequence features such as CpG content and TATA boxes, as well as the histone mark H3K4me3. CONCLUSIONS: We thus show how high coverage DNA sequencing experiments can reveal as-yet unnoticed bimodal spatial features of PolII accumulation that are frequent at individual mammalian genes and reminiscent of transcription initiation and pausing. The initiation-pausing hypothesis is corroborated by evidence from run-on sequencing and immunoprecipitation in other cell types and species.

Diseño de filtros Bulk Acoustic Wave con topología en escalera de altas prestaciones

Degut als avenços als dispositius de telecomunicacions durant l’última dècada, els filtres integrats en aquests dispositius requereixen de millors prestacions, baix cost i, per sobre de tot, requereixen unes dimensions el més reduïdes possibles. Tot i que avui dia encara s’utilitzen el filtres SAW en aquests dispositius, cada cop més s’estan substituint pels filtres amb tecnologia BAW, ja que tenen millors prestacions. En l’actualitat la topologia BAW més extensa i utilitzada és la topologia en escala. En aquest projecte s’ha portat a terme un estudi en profunditat de les limitacions dels filtres en escala. A partir de les limitacions detectades s’ha presentat una nova estructura de disseny per aquest tipus de filtres que redueix les dimensions d’aquests i millora considerablement algunes de les limitacions de l’estructura convencional. Paral·lelament s’ha desenvolupat una metodologia sistemàtica pròpia pel disseny de la nova estructura.

Facing the challenge: The impact of the recession and unemployment on men's health in Ireland

The economic recession with its accompanying rise in unemployment rates is linked to extremely adverse effects for men’s mental health. This research report Facing the Challenge – The Impact of the Recession and Unemployment on Men’s Health in Ireland identifies a strong expectation of increased mental health problems for men given the very strong correlation between unemployment and male mental ill health. The report is the result of a research and consultation process carried out, in Northern Ireland and the Republic of Ireland, by Nexus Research Co-operative on behalf of IPH. 93% of frontline organisations, North and South, in contact with unemployed men linked health challenges to unemployment and recession and all organisations surveyed noted adverse health challenges for men they work with. In addition to health challenges being higher for unemployed men, they were also very high for men who saw themselves as being threatened with unemployment. The organisations surveyed and the men who were interviewed identified the challenges to health as:•    High levels of stress or anxiety•    Dependency on or over-use of alcohol/other drugs•    Deterioration in physical health•    Development of conflict in family or close personal relationships•    Isolation (including sharing or communicating problems)•    A reluctance to approach services or seek help

Nanotermoparells: heterounions de nanowires

Projecte de recerca elaborat a partir d’una estada a la University of California a Irvine, EEUU, entre juliol del 2007 i gener del 2008. Els termoparells són actualment els sensors de temperatura més populars i més utilitzats per a un ampli rang d’aplicacions: industrials, domèstiques, etc. Aconseguir miniaturar els dispositius fins a dimensions extremadament petites obra un ampli rang de noves aplicacions per aquests dispositius, per exemple, en el camp de la tecnologia lab-on-a-chip. En aquesta investigació, el concepte de termoparell, és a dir, dos cables de diferent metall connectats per un extrem s’ha extrapolat a l’escala nanomètrica, utilitzant nanowires com a element de construcció. Aquests nanowires s’han sintetitzat a través d’un nou procediment desenvolupat en el grup d’investigació de la Universitat de California, Irvine, que ha permès treballar amb nanowires de diferents dimensions (control independent de l’alçada i amplada) i un major grau d’èxit en la fabricació d’aquests termometres. El mètode també permet dipositar aquestes nanoestructures sobre substractes no conductors de manera controlable, simplificant notablement tot el procés de fabricació. L’obtenció d’aquests dispositius ha permès demostrar que, a part de ser bons sensors de temperatura a nivell macroscòpic (fonts de calor ambientals), també permet la determinació de temperatura a nivell microscòpic (fonts de calor focalitzada, com és el cas de feixos làser). Per a la seva caracterització ha estat necessari l’ús de tecnologia puntera (làsers, amplificadors, microscopis de forces atòmiques) i inclòs el disseny de nous dispositius. Aquests nanotermoparells presenten propietats extraordinàries, com una gran sensitivitat, gran velocitat de resposta a estímuls tèrmics, i un comportament estable vers l’ús i el temps.

Generation of polycyclic aromatic hydrocarbons (PAHs) during woodworking operations.

Occupational exposures to wood dust have been associated with an elevated risk of sinonasal cancer (SNC). Wood dust is recognized as a human carcinogen but the specific cancer causative agent remains unknown. One possible explanation is a co-exposure to; wood dust and polycyclic aromatic hydrocarbons (PAHs). PAHs could be generated during incomplete combustion of wood due to heat created by use of power tools. To determine if PAHs are generated from wood during common wood working operations, PAH concentrations in wood dust samples collected in an experimental chamber operated under controlled conditions were analyzed. In addition, personal air samples from workers exposed to wood dust (n = 30) were collected. Wood dust was generated using three different power tools: vibrating sander, belt sander, and saw; and six wood materials: fir, Medium Density Fiberboard (MDF), beech, mahogany, oak and wood melamine. Monitoring of wood workers was carried out by means of personal sampler device during wood working operations. We measured 21 PAH concentrations in wood dust samples by capillary gas chromatography-ion trap mass spectrometry (GC-MS). Total PAH concentrations in wood dust varied greatly (0.24-7.95 ppm) with the lowest being in MDF dust and the highest in wood melamine dust. Personal PAH exposures were between 37.5-119.8 ng m(-3) during wood working operations. Our results suggest that PAH exposures are present during woodworking operations and hence could play a role in the mechanism of cancer induction related to wood dust exposure.

Report of the Tribunal of Inquiry into the Infection with HIV and Hepatitis C of Persons with Haemophilia and Related Matters

Pursuant to a resolution of Dail Eireann passed on the 2nd day of June 1999 and a resolution of Seanad Eireann on the 2nd day of June 1999, the Minister for Health & Children, Brian Cowen, T.D., on the 8th of September 1999 made an Order appointing a Tribunal to which the Tribunals of Inquiry (Evidence) Act 1921 (as adapted and amended) applied, to inquire urgently into and report and make such findings and recommendations as it saw fit to the Clerk of Dail Eireann on the definite matters of urgent public importance set out in sub-paragraphs 1 to 14 of the resolutions passed by Dail Eireann and Seanad Eireann.   Download document here   • Appendix 1-5 (4.03 MB)• Appendix 6-10 (13.7 MB)• Appendix 11-14 (1.06 MB)• Appendix 15-19 (1.25 MB)• Appendix 20-25 (2.75 MB)• Appendix 26-30 (1.59 MB)• Appendix 31-35 (2.12 MB)• Appendix 36-40 (4.13 MB• Appendix 41-45 (613 KB)• Appendix 46-50 (884 KB)• Appendix 51-54 (6.08 MB)

Condiciones para una arquitectura radical

La investigación Condiciones para una arquitectura radical se ha desarrollado en el marco de la beca FI 2009-12; y también incluye una beca de movilidad BE-DGR 2009 por un período de seis meses de 2010 en Princeton University School of Architecture. Condiciones para una arquitectura radical tiene un objetivo general: trabajar las relaciones entre límite, experiencia y comunidad a partir de dos pilares: arte y tecnología. Son tres familias de conceptos y sus articulaciones complejas en el espacio común: para definir en última instancia, otros procesos posibles de gestión en la ciudad. La lucha ideológica está en pensar cual debería ser el futuro de las ciudades. El objetivo concreto de la tesis es la búsqueda de herramientas para abrir nuevos espacios en la ciudad donde materializar un cambio social y urbano. Para entender esta aproximación la investigación indaga en los momentos de acercamiento y simbiosis de la arquitectura a las tesis del arte y la tecnología: una mirada atenta a las condiciones de contexto. Se explora el cruce de algunas ideas emancipadoras que se formularon en diferentes momentos de la cultura - desde las vanguardias históricas hasta ahora- en los que se intuyó la importancia del sistema abierto -el paso del objeto al proceso- y su trasposición en arquitectura: una arquitectura y un urbanismo open source; son episodios en los que ha existido un cuestionamiento de las fronteras disciplinares y un interés por la apropiación convivencial de lo público. Algunas de aquellas ideas pueden repetirse en el contexto activo de unas nuevas condiciones.

Messenger RNA expression of transporter and ion channel genes in undifferentiated and differentiated Caco-2 cells compared to human intestines.

PURPOSE: The purpose of this work was to study the influence of cell differentiation on the mRNA expression of transporters and channels in Caco-2 cells and to assess Caco-2 cells as a model for carrier-mediated drug transport in the intestines. METHOD: Gene mRNA expression was measured using a custom-designed microarray chip with 750 deoxyoligonucleotide probes (70mers). Each oligomer was printed four times on poly-lysine-coated glass slides. Expression profiles were expressed as ratio values between fluorescence intensities of Cy3 and Cy5 dye-labeled cDNA derived from poly(A) + RNA samples of Caco-2 cells and total RNA of human intestines. RESULTS: Significant differences in the mRNA expression profile of transporters and channels were observed upon differentiation of Caco-2 cells from 5 days to 2 weeks in culture, including changes for MAT8, S-protein, and Nramp2. Comparing Caco-2 cells of different passage number revealed few changes in mRNAs except for GLUT3, which was down-regulated 2.4-fold within 13 passage numbers. Caco-2 cells had a similar expression profile when either cultured in flasks or on filters but differed more strongly from human small and large intestine, regardless of the differentiation state of Caco-2 cells. Expression of several genes highly transcribed in small or large intestines differed fourfold or more in Caco-2 cells. CONCLUSIONS: Although Caco-2 cells have proven a suitable model for studying carrier-mediated transport in human intestines, the expression of specific transporter and ion channel genes may differ substantially.

Sleep loss reduces the DNA-binding of BMAL1, CLOCK, and NPAS2 to specific clock genes in the mouse cerebral cortex.

We have previously demonstrated that clock genes contribute to the homeostatic aspect of sleep regulation. Indeed, mutations in some clock genes modify the markers of sleep homeostasis and an increase in homeostatic sleep drive alters clock gene expression in the forebrain. Here, we investigate a possible mechanism by which sleep deprivation (SD) could alter clock gene expression by quantifying DNA-binding of the core-clock transcription factors CLOCK, NPAS2, and BMAL1 to the cis-regulatory sequences of target clock genes in mice. Using chromatin immunoprecipitation (ChIP), we first showed that, as reported for the liver, DNA-binding of CLOCK and BMAL1 to target clock genes changes in function of time-of-day in the cerebral cortex. Tissue extracts were collected at ZT0 (light onset), -6, -12, and -18, and DNA enrichment of E-box or E'-box containing sequences was measured by qPCR. CLOCK and BMAL1 binding to Cry1, Dbp, Per1, and Per2 depended on time-of-day, with maximum values reached at around ZT6. We then observed that SD, performed between ZT0 and -6, significantly decreased DNA-binding of CLOCK and BMAL1 to Dbp, consistent with the observed decrease in Dbp mRNA levels after SD. The DNA-binding of NPAS2 and BMAL1 to Per2 was also decreased by SD, although SD is known to increase Per2 expression in the cortex. DNA-binding to Per1 and Cry1 was not affected by SD. Our results show that the sleep-wake history can affect the clock molecular machinery directly at the level of chromatin binding thereby altering the cortical expression of Dbp and Per2 and likely other targets. Although the precise dynamics of the relationship between DNA-binding and mRNA expression, especially for Per2, remains elusive, the results also suggest that part of the reported circadian changes in DNA-binding of core clock components in tissues peripheral to the suprachiasmatic nuclei could, in fact, be sleep-wake driven.

HSE Crisis Pregnancy Programme annual report 2010.

January 2010 saw the former Crisis Pregnancy Agencyâ?Ts integration into the Health Service Executive to become the HSE Crisis Pregnancy Programme. For most of 2010, the Programme was located in Children and Family Social Services Care Group in the Integrated Services Directorate and reported to Assistant National Director for Children and Family Social Services. The Programme commenced the process of forging links and relationships within the wider HSE and with services which support and add value to the work of the Programme. The Programme also made efforts to identify areas where it could share its expertise in the areas of crisis pregnancy and sexual health. In the latter part of 2010, the Programme was moved to Public Health with the aim of improving the alignment of the Programme to achieve better integration and create more opportunity to synchronise approaches with other related parts of the health service and to work more effectively at long term integration and planning 2012 - 2016.This resource was contributed by The National Documentation Centre on Drug Use.

Soilse annual review 2010.

Soilse, the HSE addiction rehabilitation programme in Dublin North Central, experienced another challenging year in 2010. However, despite budget constraints and logistical and building difficulties, we prioritised the needs of recovering drug abusers with considerable success. Throughout the year, we had enquiries, referrals, programme uptake and successful outcomes. In terms of addiction, the problems are as enduring as ever with complex needs and limited progression opportunities. The rehabilitation strategy published in 2007 has had no practical effect. Yet Soilse saw a clear and positive impact from our work in terms of: stabilising service users; achieving detox; encouraging participants to move from our prescribed medication to our drugfree service; and consolidating these outcomes. Our evidence base continually validates our approach with people who want to become independent of services being facilitated to do so. Soilse did well in 2010 in terms of educational and vocational outcomes, particularly through FETAC but also through comprehensive care planning. We faced protracted difficulties as a result of the staff moratorium and budget cuts, but continued to deliver a professional service, keeping morale and performance high. Our service is based on the following practice standards: holistic assessment care planning care management interagency work quality assurance, and customer service involvementThis resource was contributed by The National Documentation Centre on Drug Use.

The role of CTCFL/BORIS in Meiosis

The complexity of mammalian genome organization demands a complex interplay of DNA and proteins to orchestrate proper gene regulation. CTCF, a highly conserved, ubiquitously expressed protein has been postulated as a primary organizer of genome architecture because of its roles in transcriptional activation/repression, insulation and imprinting. Diverse regulatory functions are exerted through genome wide binding via a central eleven zinc finger DNA binding domain and an array of diverse protein-protein interactions through N- and C- terminal domains. CTCFL has been identified as a paralog of CTCF expressed only in spermatogenic cells of the testis. CTCF and CTCFL have a highly homologous DNA-binding domain, while the flanking amino acid sequences exhibit no significant similarity. Genome- wide mapping of CTCF binding sites has been carried out in many cell types, but no data exist for CTCFL apart from a few identified loci. The lack of high quality antibodies prompted us to generate an endogenously flag-tagged CTCFL mouse model using BAC recombination. IHC staining using anti-flag antibodies confirmed CTCFL localization to type Β spermatogonia and preleptotene spermatocytes and a mutually exclusive pattern of expression with CTCF. ChIP followed by high-throughput sequencing identified 10,382 binding sites showing 70% overlap but representing only 20% of CTCF sites. Consensus sequence analysis identified a significantly longer binding motif with prominently less ambiguity of base calling at every position. The significant difference between CTCF and CTCFL genomic binding patterns proposes that their binding to DNA is differentially regulated. Analysis of CTCFL binding to methylated regions on a genome wide scale identified approximately 1,000 loci. Methylation-independent binding of CTCFL might be at least one of the mechanisms that ensures distinct binding patterns of CTCF and CTCFL since CTCF binding is methylation- sensitive. Co-localization of CTCF with cohesin has been well established and analysis of CTCFL and SMC3 overlap identified around 3,300 binding sites from which two related but distinct consensus sequence motifs were derived. Because virtually all data for cohesin binding originate from mitotically proliferating cells, the anticipated overlap is expected to be considerably higher in meiotic cells. Meiosis-specific cohesin subunit Rec8 is specific for spermatocytes and 6 out of the 12 identified binding sites are also bound by CTCFL. In conclusion, this was the first genome-wide mapping of CTCFL binding sites in spermatocytes, the only cell type where CTCF is not expressed. CTCFL has a unique binding site repertoire distinct from CTCF, binds to methylated sequences and shows a significant overlap with cohesin binding sites. Future efforts will be oriented towards deciphering the role CTCFL plays in conversion of chromatin structure and function from mitotic to meiotic chromosomes. - La complexité de l'organisation du génome des mammifères exige une interaction particulière entre ADN et protéines pour orchestrer une régulation appropriée de l'expression des gènes. CTCFL, une protéine ubiquitaire très conservée, serait le principal organisateur de l'architecture du génome de par son rôle dans l'activation / la répression de la transcription, la protection et la localisation des gènes. Diverses régulations sont opérées, d'une part au travers d'interactions à différents endroits du génome par le biais d'un domaine protéique central de liaison à l'ADN à onze doigts de zinc, et d'autre part par des interactions protéine-protéine variées au niveau de leur domaine N- et C-terminal. CTCFL a été identifié comme un paralogue de CTCF exprimé uniquement dans les cellules spermatiques du testicule. CTCFL et CTCF ont un domaine de liaison à l'ADN très homologue, tandis que les séquences d'acides aminés situées de part et d'autre de ce domaine ne présentent aucune similitude. Une cartographie générale des sites de liaison au CTCF a été réalisée pour de nombreux types cellulaires, mais il n'existe aucune donnée pour CTCFL à l'exception de l'identification de quelques loci. L'absence d'anticorps de bonne qualité nous a conduit à générer un modèle murin portant un CTCFL endogène taggué grâce à un procédé de recombinaison BAC. Une coloration IHC à l'aide d'anticorps anti-FLAG a confirmé la présence de CTCFL au niveau des spermatogonies de type Β et des spermatocytes au stade préleptotène, et une distribution mutuellement exclusive avec CTCF. Une méthode de Chromatine Immunoprecipitation (ChIP) suivie d'un séquençage à haut débit a permis d'identifier 10.382 sites de liaison montrant 70% d'homologie mais ne représentant que 20% des sites CTCF. L'analyse de la séquence consensus révèle un motif de fixation à l'ADN nettement plus long et qui comporte bien moins de bases aléatoires à chaque position nucléotidique. La différence significative entre les séquences génomiques des sites de liaison au CTCF et CTCFL suggère que leur fixation à l'ADN est régulée différemment. Appliquée à l'échelle du génome, l'étude de l'interaction de CTCFL avec des régions méthylées de l'ADN a permis d'identifier environ 1.000 loci. Contrairement à CTCFL, la liaison de CTCF dépend de l'état de méthylation de l'ADN ; cette modification épigénétique constitue donc au moins un des mécanismes de régulation expliquant une localisation de CTCF et CTCFL à des sites distincts du génome. La co- localisation de CTCF avec la cohésine étant établie, l'analyse de la superposition des séquences de CTCFL avec la sous-unité SMC3 identifie environ 3.300 sites de liaison parmi lesquels deux mêmes motifs consensus distincts par leur séquence sont mis en évidence. La presque quasi-totalité des données sur la cohésine ayant été établie à partir de cellules en prolifération mitotique, il est probable que la similitude au sein des séquences consensus soit encore plus grande dans le cas des cellules en méiose. La sous-unité Rec8 de la cohésine propre à l'état de méiose est spécifiquement exprimée dans les spermatocytes. Or 6 des 12 sites de liaison identifiés sont également utilisés par CTCFL. Pour conclure, ce travail constitue la première cartographie à l'échelle du génome des sites de liaison de CTCFL dans les spermatocytes, seul type cellulaire où CTCFL n'est pas exprimé. CTCFL possède un répertoire unique de sites de fixation à l'ADN distinct de CTCF, se lie à des séquences méthylées et présente un nombre important de sites de liaison communs avec la cohésine. Les perspectives futures sont d'élucider le rôle de CTCFL dans le remodelage de la structure de la chromatine et de définir sa fonction dans le processus de méiose.

The Marmot Review: Updated data and information 2 years on

To mark the two year anniversary since The Marmot Review ('Fair Society, Healthy Lives') was published, on the 15th of February the UCL Institute of Health Equity published new data on key health inequalities indicators at local authority level in England.Main Findings:Life Expectancy – this has historically been one of the main indicators of health inequalities.The Marmot Indicators from this year’s charts show the average life expectancy for eachlocal authority and the level of inequality within each authority area (7):-While overall life expectancy at birth in England increased by 0.3 years for both menand women between 2007-9 and 2008-10, inequalities in life expectancy betweenneighbourhoods increased by 0.1 years for men and showed no change for women-Among the 150 upper tier local authorities in England, life expectancy improved inthe majority of cases (133 areas saw improvements for men and 125 sawimprovements for women). However inequalities also increased in the majority ofareas (104 for men and 92 for women).-The largest increase in inequality in life expectancy was in West Berkshire for men(2.0 years) and inMiddlesbrough for women (2 years). The largest decreases ininequality were in Kensington and Chelsea for both men and women (1.9 and 1.1years respectively. To find out more, please read: - The press release, including key figures and main findings. - A blog by Michael Marmot about the data and it's implications. - Press coverage of the data in national and local newspapers and websites. - A powerpoint presentation on the key findings.

Comparative transcriptomics of rice reveals an ancient pattern of response to microbial colonization.

Glomalean fungi induce and colonize symbiotic tissue called arbuscular mycorrhiza on the roots of most land plants. Other fungi also colonize plants but cause disease not symbiosis. Whole-transcriptome analysis using a custom-designed Affymetrix Gene-Chip and confirmation with real-time RT-PCR revealed 224 genes affected during arbuscular mycorrhizal symbiosis. We compared these transcription profiles with those from rice roots that were colonized by pathogens (Magnaporthe grisea and Fusarium moniliforme). Over 40% of genes showed differential regulation caused by both the symbiotic and at least one of the pathogenic interactions. A set of genes was similarly expressed in all three associations, revealing a conserved response to fungal colonization. The responses that were shared between pathogen and symbiont infection may play a role in compatibility. Likewise, the responses that are different may cause disease. Some of the genes that respond to mycorrhizal colonization may be involved in the uptake of phosphate. Indeed, phosphate addition mimicked the effect of mycorrhiza on 8% of the tested genes. We found that 34% of the mycorrhiza-associated rice genes were also associated with mycorrhiza in dicots, revealing a conserved pattern of response between the two angiosperm classes.

STAT3 links IL-22 signaling in intestinal epithelial cells to mucosal wound healing.

Signal transducer and activator of transcription (STAT) 3 is a pleiotropic transcription factor with important functions in cytokine signaling in a variety of tissues. However, the role of STAT3 in the intestinal epithelium is not well understood. We demonstrate that development of colonic inflammation is associated with the induction of STAT3 activity in intestinal epithelial cells (IECs). Studies in genetically engineered mice showed that epithelial STAT3 activation in dextran sodium sulfate colitis is dependent on interleukin (IL)-22 rather than IL-6. IL-22 was secreted by colonic CD11c(+) cells in response to Toll-like receptor stimulation. Conditional knockout mice with an IEC-specific deletion of STAT3 activity were highly susceptible to experimental colitis, indicating that epithelial STAT3 regulates gut homeostasis. STAT3(IEC-KO) mice, upon induction of colitis, showed a striking defect of epithelial restitution. Gene chip analysis indicated that STAT3 regulates the cellular stress response, apoptosis, and pathways associated with wound healing in IECs. Consistently, both IL-22 and epithelial STAT3 were found to be important in wound-healing experiments in vivo. In summary, our data suggest that intestinal epithelial STAT3 activation regulates immune homeostasis in the gut by promoting IL-22-dependent mucosal wound healing.