Divergent RNA transcription:A role in promoter unwinding?

New approaches using biotinylated-psoralen as a probe for investigating DNA structure have revealed new insights into the relationship between DNA supercoiling, transcription and chromatin compaction. We explore a hypothesis that divergent RNA transcription generates negative supercoiling at promoters facilitating initiation complex formation and subsequent promoter clearance

An aesthetics of touch: investigating the language of design relating to form

How well can designers communicate qualities of touch? This paper presents evidence that they have some capability to do so, much of which appears to have been learned, but at present make limited use of such language. Interviews with graduate designer-makers suggest that they are aware of and value the importance of touch and materiality in their work, but lack a vocabulary to fully relate to their detailed explanations of other aspects such as their intent or selection of materials. We believe that more attention should be paid to the verbal dialogue that happens in the design process, particularly as other researchers show that even making-based learning also has a strong verbal element to it. However, verbal language alone does not appear to be adequate for a comprehensive language of touch. Graduate designers-makers’ descriptive practices combined non-verbal manipulation within verbal accounts. We thus argue that haptic vocabularies do not simply describe material qualities, but rather are situated competences that physically demonstrate the presence of haptic qualities. Such competencies are more important than groups of verbal vocabularies in isolation. Design support for developing and extending haptic competences must take this wide range of considerations into account to comprehensively improve designers’ capabilities

Public Interest Litigation and Social Change in South Africa: Strategies, Tactics and Lessons

In 2007, The Atlantic Philanthropies approached two legal practitioners, Gilbert Marcus SC and Steven Budlender, to conduct an evaluation of public interest litigation in South Africa, following The Atlantic Philanthropies' substantial investment in the field. The resulting report -- A strategic evaluation of public interest litigation in South Africa -- was published in 2008. This 2008 report has now evolved into a book entitled Public interest litigation and social change in South Africa: Strategies, tactics and lessons, with a further co-author, Nick Ferreira. The book is a revised and substantially expanded version of the initial study, providing new insights and covering post-2008 developments in the field of public interest litigation in South Africa. The book will be relevant to anyone interested in how to best use rights, law and litigation to advance social change

Star Formation History of a Young Super-Star Cluster in NGC 4038/39: Direct Detection of Low Mass Pre-Main Sequence Stars

We present an analysis of the near-infrared spectrum of a young massive star cluster in the overlap region of the interacting galaxies NGC 4038/39 using population synthesis models. Our goal is to model the cluster population as well as provide rough constraints on its initial mass function (IMF). The cluster shows signs of youth such as thermal radio emission and strong hydrogen emission lines in the near-infrared. Late-type absorption lines are also present which are indicative of late-type stars in the cluster. The strength and ratio of these absorption lines cannot be reproduced through either late-type pre-main sequence (PMS) stars or red supergiants alone. Thus we interpret the spectrum as a superposition of two star clusters of different ages, which is feasible since the 1" spectrum encompasses a physical region of ~90 pc and radii of super-star clusters are generally measured to be a few parsecs. One cluster is young (<= 3 Myr) and is responsible for part of the late-type absorption features, which are due to PMS stars in the cluster, and the hydrogen emission lines. The second cluster is older (6 Myr - 18 Myr) and is needed to reproduce the overall depth of the late-type absorption features in the spectrum. Both are required to accurately reproduce the near-infrared spectrum of the object. Thus we have directly detected PMS objects in an unresolved super-star cluster for the first time using a combination of population synthesis models and pre-main sequence tracks. This analysis serves as a testbed of our technique to constrain the low-mass IMF in young super-star clusters as well as an exploration of the star formation history of young UC HII regions.Comment: 26 pages, 5 figures, accepted for publication in the Astrophysical Journa

Our Space: Being a Responsible Citizen of the Digital World

Our Space is a set of curricular materials designed to encourage high school students to reflect on the ethical dimensions of their participation in new media environments. Through role-playing activities and reflective exercises, students are asked to consider the ethical responsibilities of other people, and whether and how they behave ethically themselves online. These issues are raised in relation to five core themes that are highly relevant online: identity, privacy, authorship and ownership, credibility, and participation.Our Space was co-developed by The Good Play Project and Project New Media Literacies (established at MIT and now housed at University of Southern California's Annenberg School for Communications and Journalism). The Our Space collaboration grew out of a shared interest in fostering ethical thinking and conduct among young people when exercising new media skills

Nature and modulation of the higher order chromatin fibre

The bulk of eukaryotic cellular DNA is compacted into chromatin, a nucleoprotein complex that is responsible for packaging DNA into the nucleus and regulating gene transcription. The chromatin fibre is a dynamic structure which is able to accommodate the many complex processes which occur simultaneously in a living cell. The fundamental building blocks of the lower order chromatin fibre have been studied extensively, providing us with a detailed understanding of the structures present; much is known about how these structures are modulated to allow processes like gene transcription and replication to occur in an organised fashion. In contrast to our detailed knowledge of the fundamental building blocks of chromatin, little is known about the conformation of the higher order chromatin fibre. This lack of understanding is due, predominantly, to the inaccessibility of the higher order fibre for study, and that much of the research to date has considered the conformation of the higher order fibre to be uniform. In this project I have analysed and modulated the higher order chromatin fibre to assess the role this fibre plays in the regulation of cellular processes.The conformation of the higher order chromatin fibre is often thought to change during the differentiation of cells. To study this alteration in conformation I have undertaken a detailed analysis of the higher order chromatin fibre from cells with different differentiation potentials and during their differentiation process. Using a hydrodynamic sedimentation approach to assess the conformation of the chromatin fibre I was unable to find any differences in its conformation. However, I have found that these chromatin fibres do have inherent differences in their nuclease sensitivities, suggesting that although the overall conformation of the fibres are similar, there are chromatin- related differences between cells with various differentiation potentials.To study the uniformity of the higher order chromatin fibre at different chromosomal locations I have analysed the chromatin structure found at centromeres to determine whether there is an alteration in the conformation of the chromatin fibre, which might affect the function of centromeres. My results clearly show that in mouse and human cells the chromatin fibre found at inner centromeric regions is more compact than the chromatin fibre present at outer centromeric regions, and in turn this is more compact than the bulk chromatin fibre. To determine the molecular basis for this, I have analysed acetylated centromeric heterochromatin from embryonic stem (ES) cells and heterochromatin associated with undermethylated centromeric DNA from F9 cells. My results demonstrate that this special chromatin architecture found at centromeres appears to be independent of histone acetylation and DNA methylation.To establish whether an alteration in the chromatin conformation will alter a cell's differentiation potential I have expressed histone H5, a replacement linker histone normally found in nucleated erythrocytes, in pluripotential ES cells. My results show that the constitutive expression of H5 in ES cells causes substantial cell death. I have therefore constructed a regulated, tetracycline based, histone H5 expression system in ES cells, but I was unable to express H5 in a controlled manner to investigate the underlying chromatin structure of these cells. In addition, I expressed histone H5 DNA -binding mutants in ES cells which also caused substantial cell death. I was therefore unable to determine whether the cellular phenotype obtained from expressing H5 in ES cells was due to an alteration in chromatin structure or a non- specific effect from expressing a positively charged molecule. As a first step towards studying the expression of linker histones in living cells and during development, I constructed and analysed a green fluorescent protein (GFP)- histone H5 fusion. As for histone H5, the GFP -H5 fusion protein is correctly expressed in a variety of cell types, but is lethal to cells when expressed at high levels for longer periods of time

Characterisation of osteoprotegerin autoantibodies in coeliac disease

Objectives: Autoantibodies neutralising the effect of the bone regulatory cytokine osteoprotegerin (OPG) have been described in a patient with severe osteoporosis and coeliac disease. This study aimed to determine the prevalence and epitope specificity of autoantibodies to OPG in patients with coeliac disease, and correlate their presence with bone mineral density.   Methods: A direct enzyme linked immunosorbent assay was developed and used to screen patients with coeliac disease for autoantibodies to OPG. Recombinant fragments of OPG were made to evaluate the epitope specificity and affinity of these antibodies. Phenotype information of the patients was obtained by case note review.   Results: Raised titres of antibodies to OPG were found in 7/71 (9.8%) patients with coeliac disease, compared with 1/72 (1.4%) non-coeliac osteoporosis clinic control patients (p<0.05). Our results suggest a polyclonal antibody response to OPG is raised in these patients capable of recognising different epitopes of OPG with varying affinity. The titre of OPG antibodies was associated with lower bone mineral density Z score of the hip in coeliac patients on univariate (p<0.05) and multivariate analysis including age, sex height and weight as covariates (p<0.01).   Conclusion: Polyclonal antibodies to OPG are more common in patients with coeliac disease and are independently associated with lower bone mineral density Z scores of the hip. Further work is required to establish the clinical utility of testing for OPG antibodies

Building solidarity without Big Tech? Moving beyond the problems of today’s digital platforms

Today we spend much of our lives on digital platforms. But what has been the impact for political exchange and mobilisation? Algorithms that seek to polarise by amplifying inflammatory rhetoric and extreme views are undermining public debate and consensus-building. In advance of an LSE public event tomorrow (28 March) on “Digital Platforms and the Future of Political Solidarity,” Nick Couldry and Jeremy Gilbert ask: Can we imagine a different model, where digital spaces and media enhance solidarity rather than eroding it

Lactate, a product of glycolytic metabolism, inhibits histone deacetylase activity and promotes changes in gene expression

Chemical inhibitors of histone deacetylase (HDAC) activity are used as experimental tools to induce histone hyperacetylation and deregulate gene transcription, but it is not known whether the inhibition of HDACs plays any part in the normal physiological regulation of transcription. Using both in vitro and in vivo assays, we show that lactate, which accumulates when glycolysis exceeds the cell’s aerobic metabolic capacity, is an endogenous HDAC inhibitor, deregulating transcription in an HDAC-dependent manner. Lactate is a relatively weak inhibitor (IC(50) 40 mM) compared to the established inhibitors trichostatin A and butyrate, but the genes deregulated overlap significantly with those affected by low concentrations of the more potent inhibitors. HDAC inhibition causes significant up and downregulation of genes, but genes that are associated with HDAC proteins are more likely to be upregulated and less likely to be downregulated than would be expected. Our results suggest that the primary effect of HDAC inhibition by endogenous short-chain fatty acids like lactate is to promote gene expression at genes associated with HDAC proteins. Therefore, we propose that lactate may be an important transcriptional regulator, linking the metabolic state of the cell to gene transcription