Detecting sequence dependent transcriptional pauses from RNA and protein number time series

Background: Evidence suggests that in prokaryotes sequence-dependent transcriptional pauses a?ect the dynamics of transcription and translation, as well as of small genetic circuits. So far, a few pause-prone sequences have been identi?ed from in vitro measurements of transcription elongation kinetics.

Results: Using a stochastic model of gene expression at the nucleotide and codon levels with realistic parameter values, we investigate three di?erent but related questions and present statistical methods for their analysis. First, we show that information from in vivo RNA and protein temporal numbers is su?cient to discriminate between models with and without a pause site in their coding sequence. Second, we demonstrate that it is possible to separate a large variety of models from each other with pauses of various durations and locations in the template by means of a hierarchical clustering and a random forest classi?er. Third, we introduce an approximate likelihood function that allows to estimate the location of a pause site.

Conclusions: This method can aid in detecting unknown pause-prone sequences from temporal measurements of RNA and protein numbers at a genome-wide scale and thus elucidate possible roles that these sequences play in the dynamics of genetic networks and phenotype.

From Frank Miller to Zack Snyder, and Return: Contemporary Superhero Comics and Post-Classical Hollywood

Film adaptations of superhero comic-books offer a particularly rich case study to analyse narrative strategies of contemporary Hollywood cinema. The serial structures adopted by the comics they are based on, as well as their use of the spectacular potential of the image, provide a successful model for current audiovisual productions. Without completely abandoning classical techniques, these adaptations try to find a new balance between narrative and digital phantasmagoria. This paper discusses some significant examples of this genre, including adaptations of classical DC and Marvel franchises and more recent series, as well as other comic-book influenced films such as The Matrix and Unbreakable.

A Variant in LDLR is Associated with Abdominal Aortic Aneurysm

Background—Abdominal aortic aneurysm (AAA) is a common cardiovascular disease among older people and demonstrates significant heritability. In contrast to similar complex diseases, relatively few genetic associations with AAA have been confirmed. We reanalysed our genome-wide study and carried through to replication suggestive discovery associations at a lower level of significance.

Methods and Results—A genome-wide association study was conducted using 1,830 cases from the UK, New Zealand and Australia with infra-renal aorta diameter =30mm or ruptured AAA and 5,435 unscreened controls from the 1958 Birth Cohort and National Blood Service cohort from the Wellcome Trust Case Control Consortium. Eight suggestive associations with P<1x10-4 were carried through to in silico replication in 1,292 AAA cases and 30,503 controls. One SNP associated with P<0.05 after Bonferroni correction in the in silico study underwent further replication (706 AAA cases and 1,063 controls from the UK, 507 AAA cases and 199 controls from Denmark and 885 AAA cases and 1,000 controls from New Zealand). Low density lipoprotein receptor (LDLR) rs6511720 A, was significantly associated overall and in three of five individual replication studies. The full study showed an association that reached genome-wide significance (odds ratio 0.76; 95% confidence interval 0.70 to 0.83; P=2.08x10-10).

Conclusions—LDLR rs6511720 is associated with abdominal aortic aneurysm. This finding is consistent with established effects of this variant on coronary artery disease. Shared aetiological pathways with other cardiovascular diseases may present novel opportunities for preventative and therapeutic strategies for AAA.

The role of adiposity in cardiometabolic traits:a Mendelian randomization analysis

The association between adiposity and cardiometabolic traits is well known from epidemiological studies. Whilst the causal relationship is clear for some of these traits, for others it is not. We aimed to determine whether adiposity is causally related to various cardiometabolic traits using the Mendelian randomization approach.

'Frank Pig Says Hello' by Pat McCabe

This theatre performance, produced in association with An Grianan Theatre, Letterkenny, contributes to two strands of research: theatre and mental health and Irish Physical Theatre in the 1990s.

Accumulation of the PX domain mutant Frank-ter Haar syndrome protein Tks4 in aggresomes

BACKGROUND: Cells deploy quality control mechanisms to remove damaged or misfolded proteins. Recently, we have reported that a mutation (R43W) in the Frank-ter Haar syndrome protein Tks4 resulted in aberrant intracellular localization.

RESULTS: Here we demonstrate that the accumulation of Tks4(R43W) depends on the intact microtubule network. Detergent-insoluble Tks4 mutant colocalizes with the centrosome and its aggregate is encaged by the intermediate filament protein vimentin. Both the microtubule inhibitor nocodazole and the histone deacetylase inhibitor Trichostatin A inhibit markedly the aggresome formation in cells expressing Tks4(R43W). Finally, pretreatment of cells with the proteasome inhibitor MG132 markedly increases the level of aggresomes formed by Tks4(R43W). Furthermore, two additional mutant Tks4 proteins (Tks4(1-48) or Tks4(1-341)) have been investigated. Whereas the shorter Tks4 mutant, Tks4(1-48), shows no expression at all, the longer Tks4 truncation mutant accumulates in the nuclei of the cells.

CONCLUSIONS: Our results suggest that misfolded Frank-ter Haar syndrome protein Tks4(R43W) is transported via the microtubule system to the aggresomes. Lack of expression of Tks4(1-48) or aberrant intracellular expressions of Tks4(R43W) and Tks4(1-341) strongly suggest that these mutations result in dysfunctional proteins which are not capable of operating properly, leading to the development of FTHS.

‘Twenty-six things at once’: Pragmatic perspectives on Frank O’Hara and Norman Bluhm’s Poem-Paintings

Created over a couple of Sunday mornings in the Fall of 1960, the twenty-six collaborative Poem-Paintings of the artist Norman Bluhm and the poet Frank O'Hara represent what Bluhm later called a spontaneous 'conversation' between the painter and the poet. In this essay, Catherine Gander adopts a number of pragmatist positions to reconsider these overlooked works as essential examples of verbal-visual interaction that extend their 'conversation' to greet and involve us in a relationship that is at once interpersonal, integrated, and embodied. The works, Gander argues, constitute what John Dewey terms 'art as experience'; in their back and forth exchange of verbal and visual gesture, abstraction and denotation, the Poem-Paintings are the 'cumulative continuity' of 'the process of living', dramatising the shifting, spontaneous and multiple dimensions of interpersonal conversation, and in so doing, indicating a new path toward interconnective and equal exchange between word and image.

Adiposity as a cause of cardiovascular disease: a Mendelian randomization study

Background: Adiposity, as indicated by body mass index (BMI), has been associated with risk of cardiovascular diseases in epidemiological studies. We aimed to investigate if these associations are causal, using Mendelian randomization (MR) methods.

Methods: The associations of BMI with cardiovascular outcomes [coronary heart disease (CHD), heart failure and ischaemic stroke], and associations of a genetic score (32 BMI single nucleotide polymorphisms) with BMI and cardiovascular outcomes were examined in up to 22 193 individuals with 3062 incident cardiovascular events from nine prospective follow-up studies within the ENGAGE consortium. We used random-effects meta-analysis in an MR framework to provide causal estimates of the effect of adiposity on cardiovascular outcomes.

Results: There was a strong association between BMI and incident CHD (HR = 1.20 per SD-increase of BMI, 95% CI, 1.12–1.28, P = 1.9·10−7), heart failure (HR = 1.47, 95% CI, 1.35–1.60, P = 9·10−19) and ischaemic stroke (HR = 1.15, 95% CI, 1.06–1.24, P = 0.0008) in observational analyses. The genetic score was robustly associated with BMI (β = 0.030 SD-increase of BMI per additional allele, 95% CI, 0.028–0.033, P = 3·10−107). Analyses indicated a causal effect of adiposity on development of heart failure (HR = 1.93 per SD-increase of BMI, 95% CI, 1.12–3.30, P = 0.017) and ischaemic stroke (HR = 1.83, 95% CI, 1.05–3.20, P = 0.034). Additional cross-sectional analyses using both ENGAGE and CARDIoGRAMplusC4D data showed a causal effect of adiposity on CHD.

Conclusions: Using MR methods, we provide support for the hypothesis that adiposity causes CHD, heart failure and, previously not demonstrated, ischaemic stroke.

Truth at 24 frames a second? A working dialogue between a film-maker and a historical consultant about the making of The Enigma of Frank Ryan

We employ a practice-based methodology based on a ‘live’ film project to explore the different ways that film-makers and historians narrate the past. Through a case-study of the production and exhibition of a drama-documentary feature-film, The Enigma of Frank Ryan, on which both authors (film-maker Bell and historian McGarry) worked respectively as director and historical consultant, we explore a range of critical issues arising from our collaboration. Through a dialogue between a director and a historian, a model of good practice between historians and film-makers emerges.

Dos décadas de una atormentada relación: Martin Heidegger y Edmund Husserl 1909-1929

La publicación reciente de documentos y la consulta directa en archivos posibilita un acercamiento renovado a la conflictiva relación entre Edmund Husserl y Martin Heidegger. El artículo lleva a cabo esto mediante una revisión del camino académico de Heidegger a la sombra de su protector Husserl. De ese modo se dejan ver las escisiones anímicas del joven Heidegger, su apropiación de la fenomenología husserliana y a la vez su distanciamiento del maestro. Con ello también se muestra que el rompimiento entre ambos pensadores no tiene su origen en los compromisos políticos de Heidegger en 1933, sino que era algo que latía desde el inicio de la relación.

Dr. Rómulo Guillermo Jordan Sotelo 1929- 2007: biólogo marino cultor de principios ecológico-pesquero

Biografía y relación de artículos científicos.

M. Frank Polk [sous-secrétaire d'Etat aux Affaires étrangères des États-Unis] (Central News, New York) : [photographie de presse] / [Agence Rol]

Référence bibliographique : Rol, 58548