Recognition of DNA Supercoil Geometry by Mycobacterium tuberculosis Gyrase

Mycobacterium tuberculosis encodes only a single type II topoisomerase, gyrase. As a result, this enzyme likely carries out the cellular functions normally performed by canonical gyrase and topoisomerase IV, both in front of and behind the replication fork. In addition, it is the sole target for quinolone antibacterials in this species. Because quinolone-induced DNA strand breaks generated on positively supercoiled DNA ahead of replication forks and transcription complexes are most likely to result in permanent genomic damage, the actions of M. tuberculosis gyrase on positively supercoiled DNA were investigated. Results indicate that the enzyme acts rapidly on overwound DNA and removes positive supercoils much faster than it introduces negative supercoils into relaxed DNA. Canonical gyrase and topoisomerase IV distinguish supercoil handedness differently during the DNA cleavage reaction: while gyrase maintains lower levels of cleavage complexes on overwound DNA, topoisomerase IV maintains similar levels of cleavage complexes on both over- and underwound substrates. M. tuberculosis gyrase maintained lower levels of cleavage complexes on positively supercoiled DNA in the absence and presence of quinolone-based drugs. By retaining this important feature of canonical gyrase, the dual function M. tuberculosis type II enzyme remains a safe enzyme to act in front of replication forks and transcription complexes. Finally, the N-terminal gate region of the enzyme appears to be necessary to distinguish supercoil handedness during DNA cleavage, suggesting that the capture of the transport segment may influence how gyrase maintains cleavage complexes on substrates with different topological states

Association between the oxytocin receptor (OXTR) gene and mesolimbic responses to rewards

10.1186/2040-2392-5-7Molecular Autism51

Action research in physical education: focusing beyond myself through cooperative learning

This paper reports on the pedagogical changes that I experienced as a teacher engaged in an action research project in which I designed and implemented an indirect, developmentally appropriate and child‐centred approach to my teaching. There have been repeated calls to expunge – or at least rationalise – the use of traditional, teacher‐led practice in physical education. Yet despite the advocacy of many leading academics there is little evidence that such a change of approach is occurring. In my role as teacher‐as‐researcher I sought to implement a new pedagogical approach, in the form of cooperative learning, and bring about a positive change in the form of enhanced pupil learning. Data collection included a reflective journal, post‐teaching reflective analysis, pupil questionnaires, student interviews, document analysis, and non‐participant observations. The research team analysed the data using inductive analysis and constant comparison. Six themes emerged from the data: teaching and learning, reflections on cooperation, performance, time, teacher change, and social interaction. The paper argues that cooperative learning allowed me to place social and academic learning goals on an even footing, which in turn placed a focus on pupils’ understanding and improvement of skills in athletics alongside their interpersonal development

Flow Analysis, Linearity, and PTIME

Abstract. Flow analysis is a ubiquitous and much-studied component of compiler technology—and its variations abound. Amongst the most well known is Shivers ’ 0CFA; however, the best known algorithm for 0CFA requires time cubic in the size of the analyzed program and is unlikely to be improved. Consequently, several analyses have been de-signed to approximate 0CFA by trading precision for faster computation. Henglein’s simple closure analysis, for example, forfeits the notion of di-rectionality in flows and enjoys an “almost linear ” time algorithm. But in making trade-offs between precision and complexity, what has been given up and what has been gained? Where do these analyses differ and where do they coincide? We identify a core language—the linear λ-calculus—where 0CFA, simple closure analysis, and many other known approximations or restrictions to 0CFA are rendered identical. Moreover, for this core language, analysis corresponds with (instrumented) evaluation. Because analysis faithfully captures evaluation, and because the linear λ-calculus is complete for ptime, we derive ptime-completeness results for all of these analyses.

Wholesale pricing in a small open economy

This paper addresses the empirical analysis of wholesale profit margins using data of the Dutch wholesale sector, 1986. At the heart of the analysis is the typical nature of wholesale production: wholesalers do not produce a tangible product, but offer a service capacity. This has an immediate impact on the identification, interprelation and measurement of determinants of profit variations. A model is set up to explain variations in wholesale profit margins, which is inspired by two widely applied approaches to industry pricing: the behavioural mark-up model and the marginalist price-cost model

Isolation of chromosome clusters from metaphase-arrested HeLa cells

We have developed a simplified approach for the isolation of metaphase chromosomes from HeLa cells. In this method, all the chromosomes from a cell remain together in a bundle which we call a “metaphase chromosome cluster”. Cells are arrested to 90–95% in metaphase, collected by centrifugation, extracted with non-ionic detergent in a low ionic strength buffer at neutral pH, and homogenised to strip away the cytoskeleton. The chromosome clusters which are released can then be isolated in a crude state by pelleting or they can be purified away from nearly all the interphase nuclei and cytoplasmic debris by banding in a Percoll TM density gradient. — This procedure has the advantages that it is quick and easy, metaphase chromatin is recovered in high yield, and Ca ++ is not needed to stabilise the chromosomes. Although the method does not yield individual chromosomes, it is nevertheless very useful for both structural and biochemical studies of mitotic chromatin. The chromosome clusters also make possible biochemical and structural studies of what holds the different chromosomes together. Such information could be useful in improving chromosome isolation procedures and for understanding suprachromosomal organisation of the nucleus.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47359/1/412_2004_Article_BF00327351.pd

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

Background Previous studies using candidate gene and genome-wide approaches have identified epigenetic changes in DNA methylation (DNAm) associated with posttraumatic stress disorder (PTSD). Methods In this study, we performed an EWAS of PTSD in a cohort of Veterans (n = 378 lifetime PTSD cases and 135 controls) from the Translational Research Center for TBI and Stress Disorders (TRACTS) cohort assessed using the Illumina EPIC Methylation BeadChip which assesses DNAm at more than 850,000 sites throughout the genome. Our model included covariates for ancestry, cell heterogeneity, sex, age, and a smoking score based on DNAm at 39 smoking-associated CpGs. We also examined in EPIC-based DNAm data generated from pre-frontal cortex (PFC) tissue from the National PTSD Brain Bank (n = 72). Results The analysis of blood samples yielded one genome-wide significant association with PTSD at cg19534438 in the gene G0S2 (p = 1.19 x 10(-7), p(adj) = 0.048). This association was replicated in an independent PGC-PTSD-EWAS consortium meta-analysis of military cohorts (p = 0.0024). We also observed association with the smoking-related locus cg05575921 in AHRR despite inclusion of a methylation-based smoking score covariate (p = 9.16 x 10(-6)), which replicates a previously observed PGC-PTSD-EWAS association (Smith et al. 2019), and yields evidence consistent with a smoking-independent effect. The top 100 EWAS loci were then examined in the PFC data. One of the blood-based PTSD loci, cg04130728 in CHST11, which was in the top 10 loci in blood, but which was not genome-wide significant, was significantly associated with PTSD in brain tissue (in blood p = 1.19 x 10(-5), p(adj) = 0.60, in brain, p = 0.00032 with the same direction of effect). Gene set enrichment analysis of the top 500 EWAS loci yielded several significant overlapping GO terms involved in pathogen response, including "Response to lipopolysaccharide" (p = 6.97 x 10(-6), p(adj) = 0.042). Conclusions The cross replication observed in independent cohorts is evidence that DNA methylation in peripheral tissue can yield consistent and replicable PTSD associations, and our results also suggest that that some PTSD associations observed in peripheral tissue may mirror associations in the brain.Stress-related psychiatric disorders across the life spa

Factors Associated with Revision Surgery after Internal Fixation of Hip Fractures

Background: Femoral neck fractures are associated with high rates of revision surgery after management with internal fixation. Using data from the Fixation using Alternative Implants for the Treatment of Hip fractures (FAITH) trial evaluating methods of internal fixation in patients with femoral neck fractures, we investigated associations between baseline and surgical factors and the need for revision surgery to promote healing, relieve pain, treat infection or improve function over 24 months postsurgery. Additionally, we investigated factors associated with (1) hardware removal and (2) implant exchange from cancellous screws (CS) or sliding hip screw (SHS) to total hip arthroplasty, hemiarthroplasty, or another internal fixation device. Methods: We identified 15 potential factors a priori that may be associated with revision surgery, 7 with hardware removal, and 14 with implant exchange. We used multivariable Cox proportional hazards analyses in our investigation. Results: Factors associated with increased risk of revision surgery included: female sex, [hazard ratio (HR) 1.79, 95% confidence interval (CI) 1.25-2.50; P = 0.001], higher body mass index (fo

Seasonal yield and fuel consumed for domestic, organic waste collections in currently operational door-to-door and bring-type collection systems

The European Commission is tightening waste laws, and many local authorities, particularly in countries with low recycling rates, face the question of what system to introduce for the source-separate collection of food waste from householders. This study provides empirical data in form of fuel consumed and waste yield from four councils that already have source separate organic waste collections in operation. Two systems were compared: (i) door-to-door collection and (ii) bring systems where the householder walks to the bin in her/his street to drop off organic waste. Fuel consumption for the collection operation with the bring system was dramatically lower compared to the door-to-door system. Organic waste yield was constant over the observation year in the door-to-door system employing small 20- to 30-litre bins, but increased notably in the summer with the bring system that used 240-litre bins. The metric used to quantify seasonality was the summer/winter yield ratio. As commercial waste companies do not normally allow the making of data public, this is a rare opportunity to learn from collection systems currently in operation