Sequence Dependence of Transcription Factor-Mediated DNA Looping

DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA looping in transcriptional regulation in both prokaryotes and eukaryotes. These kinds of regulatory problems are now becoming amenable to systematic quantitative dissection with a powerful dialogue between theory and experiment. Here we use a single-molecule experiment in conjunction with a statistical mechanical model to test quantitative predictions for the behavior of DNA looping at short length scales, and to determine how DNA sequence affects looping at these lengths. We calculate and measure how such looping depends upon four key biological parameters: the strength of the transcription factor binding sites, the concentration of the transcription factor, and the length and sequence of the DNA loop. Our studies lead to the surprising insight that sequences that are thought to be especially favorable for nucleosome formation because of high flexibility lead to no systematically detectable effect of sequence on looping, and begin to provide a picture of the distinctions between the short length scale mechanics of nucleosome formation and looping.Comment: Nucleic Acids Research (2012); Published version available at http://nar.oxfordjournals.org/cgi/content/abstract/gks473? ijkey=6m5pPVJgsmNmbof&keytype=re

Reclaiming heritage: colourization, culture wars and the politics of nostalgia

This article considers the discursive continuities between a specifically liberal defence of cultural patrimony, evident in the debate over film colourization, and the culture war critique associated with neo-conservatism. It examines how a rhetoric of nostalgia, linked to particular ideas of authenticity,canonicity and tradition,has been mobilized by the right and the left in attempts to stabilize the confguration and perceived transmission of American cultural identity. While different in scale, colourization and multiculturalism were seen to create respective (postmodern) barbarisms against which defenders of culture, heritage and good taste could unite. I argue that in its defence of the ‘classic’ work of art, together with principles of aesthetic distinction and the value of cultural inheritance,the anti-colourization lobby helped enrich and legitimize a discourse of tradition that, at the end of the 1980s, was beginning to reverberate powerfully in the conservative challenge to a ‘crisis’ within higher education and the humanities. This article attempts to complicate the contemporary politics of nostalgia, showing how a defence of cultural patrimony has distinguished major and minor culture wars, engaging left and right quite differently but with similar presuppositions

On ecological conceptualizations of perceptual systems and action systems

This article examines Gibson's concept of perceptual system and Reed's concept of action system. After discussing several assumptions underlying these concepts, the ontological status of these systems is considered. It is argued that perceptual systems and action systems should be conceptualized neither as parts of an animal's body nor as softly (temporarily) assembled devices; rather, they are best understood as animals' abilities to achieve functional relationships, that is, as dispositional properties. This conceptualization entails that these systems are relatively permanent properties of the animal that are causally supported by, though not identical to, anatomical substrates. Further, it entails that it is the animal that perceives and acts, not its perceptual and action systems

Peri-operative red blood cell transfusion in neonates and infants: NEonate and Children audiT of Anaesthesia pRactice IN Europe: A prospective European multicentre observational study

BACKGROUND: Little is known about current clinical practice concerning peri-operative red blood cell transfusion in neonates and small infants. Guidelines suggest transfusions based on haemoglobin thresholds ranging from 8.5 to 12 g dl-1, distinguishing between children from birth to day 7 (week 1), from day 8 to day 14 (week 2) or from day 15 (≥week 3) onwards. OBJECTIVE: To observe peri-operative red blood cell transfusion practice according to guidelines in relation to patient outcome. DESIGN: A multicentre observational study. SETTING: The NEonate-Children sTudy of Anaesthesia pRactice IN Europe (NECTARINE) trial recruited patients up to 60 weeks' postmenstrual age undergoing anaesthesia for surgical or diagnostic procedures from 165 centres in 31 European countries between March 2016 and January 2017. PATIENTS: The data included 5609 patients undergoing 6542 procedures. Inclusion criteria was a peri-operative red blood cell transfusion. MAIN OUTCOME MEASURES: The primary endpoint was the haemoglobin level triggering a transfusion for neonates in week 1, week 2 and week 3. Secondary endpoints were transfusion volumes, 'delta haemoglobin' (preprocedure - transfusion-triggering) and 30-day and 90-day morbidity and mortality. RESULTS: Peri-operative red blood cell transfusions were recorded during 447 procedures (6.9%). The median haemoglobin levels triggering a transfusion were 9.6 [IQR 8.7 to 10.9] g dl-1 for neonates in week 1, 9.6 [7.7 to 10.4] g dl-1 in week 2 and 8.0 [7.3 to 9.0] g dl-1 in week 3. The median transfusion volume was 17.1 [11.1 to 26.4] ml kg-1 with a median delta haemoglobin of 1.8 [0.0 to 3.6] g dl-1. Thirty-day morbidity was 47.8% with an overall mortality of 11.3%. CONCLUSIONS: Results indicate lower transfusion-triggering haemoglobin thresholds in clinical practice than suggested by current guidelines. The high morbidity and mortality of this NECTARINE sub-cohort calls for investigative action and evidence-based guidelines addressing peri-operative red blood cell transfusions strategies. TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT02350348

Political travel across the ‘Iron Curtain’ and Communist youth identities in West Germany and Greece in the 1970s and 1980s

This article explores tours through the Iron Curtain arranged by West German and Greek pro-Soviet Communist youth groups, in an attempt to shed light on the transformation of European youth cultures beyond the ‘Americanisation’ story. It argues that the concept of the ‘black box’, employed by Rob Kroes to describe the influence of American cultural patterns on Western European youth, also applies to the reception of Eastern Bloc policies and norms by the Communists under study. Such selective reception was part of these groups’ efforts to devise a modernity alternative to the ‘capitalist’ one, an alternative modernity which tours across the Iron Curtain would help establish. Nevertheless, the organisers did not wish such travel to help eliminate American/Western influences on youth lifestyles entirely: the article analyses the excursions’ aims with regard to two core components of youth lifestyles in Western Europe since the 1960s, which have been affected by intra-Western flows, the spirit of ‘doing one’s own thing’ and transformations of sexual practices. The article also addresses the experience of the travellers in question, showing that they felt an unresolved tension: the tours neither served as a means of Sovietisation nor as an impulse to develop an openly anti-Soviet stance.PostprintPeer reviewe

Expert recommendations on the assessment of wall shear stress in human coronary arteries : existing methodologies, technical considerations, and clinical applications

The aim of this manuscript is to provide guidelines for appropriate use of CFD to obtain reproducible and reliable wall shear stress maps in native and instrumented human coronary arteries. The outcome of CFD heavily depends on the quality of the input data, which include vessel geometrical data, proper boundary conditions, and material models. Available methodologies to reconstruct coronary artery anatomy are discussed in ‘Imaging coronary arteries: a brief review’ section. Computational procedures implemented to simulate blood flow in native coronary arteries are presented in ‘Wall shear stress in native arteries’ section. The effect of including different geometrical scales due to the presence of stent struts in instrumented arteries is highlighted in ‘Wall shear stress in stents’ section. The clinical implications are discussed in ‘Clinical applications’ section, and concluding remarks are presented in ‘Concluding remarks’ section