Twist/Writhe Partitioning in a Coarse-Grained DNA Minicircle Model

Here we present a systematic study of supercoil formation in DNA minicircles under varying linking number by using molecular dynamics simulations of a two-bead coarse-grained model. Our model is designed with the purpose of simulating long chains without sacrificing the characteristic structural properties of the DNA molecule, such as its helicity, backbone directionality and the presence of major and minor grooves. The model parameters are extracted directly from full-atomistic simulations of DNA oligomers via Boltzmann inversion, therefore our results can be interpreted as an extrapolation of those simulations to presently inaccessible chain lengths and simulation times. Using this model, we measure the twist/writhe partitioning in DNA minicircles, in particular its dependence on the chain length and excess linking number. We observe an asymmetric supercoiling transition consistent with experiments. Our results suggest that the fraction of the linking number absorbed as twist and writhe is nontrivially dependent on chain length and excess linking number. Beyond the supercoiling transition, chains of the order of one persistence length carry equal amounts of twist and writhe. For longer chains, an increasing fraction of the linking number is absorbed by the writhe.Comment: 21 pages, 7 figures, 1 tabl

Environmental challenges to operationalisation of South African rainfall enhancement

Most of the atmospheric moisture in systems moving across South Africa leaves the sub-continent as the weather systems move out over the ocean, only a tenth of it falls on the landmass as rain. An increase in the efficiency of the atmospheric moisture delivery system by means of rainfall enhancement is therefore an attractive concept. Rainfall enhancement functions by either providing additional Cloud Condensation Nuclei or Ice forming Nuclei that will beneficially influence the precipitation formation process, improving the efficiency of moisture to rainfall conversion. Systematic South African research into rainfall enhancement started in the 1970s. The South African Rainfall Enhancement Programme (SAREP), initiated in the late 1990\'s, is the most recent in a series of studies and was the first semi-operational rainfall enhancement project to occur in South Africa as a response to drought conditions. In a recent study (DWAF, 2004 in prep) to finalise SAREP and provide guidance on operationalising rainfall enhancement, it was recommended that environmental impact assessment must be undertaken before this technology is implemented further. Rainfall enhancement falls specifically within the jurisdiction of the National Water Act (NWA) and the National Environmental Management Act (NEMA). A licence to undertake rainfall enhancement activities is required from the Minister of Water Affairs and Forestry after an appropriate environmental impact assessment has been undertaken to inform his decision. This paper proposes an approach to fulfil the legal requirements for operationalising future rainfall enhancement. The interaction between the science of rainfall enhancement and the ability of scientific disciplines to determine relevant environmental impacts, to appropriately inform the decision-making process, is specifically highlighted. The data requirements identified by scientists during the study varies in duration and resource needs and does not differentiate between ongoing scientific research and the requisite information required for informed decision making. This paper contemplates an approach which provides for holistic and co-ordinated investigation of South African rainfall enhancement into the future. Water SA Vol. 30 (5) 2005: pp.88-9

Polymer reptation and nucleosome repositioning

We consider how beads can diffuse along a chain that wraps them, without becoming displaced from the chain; our proposed mechanism is analogous to the reptation of "stored length" in more familiar situations of polymer dynamics. The problem arises in the case of globular aggregates of proteins (histones) that are wound by DNA in the chromosomes of plants and animals; these beads (nucleosomes) are multiply wrapped and yet are able to reposition themselves over long distances, while remaining bound by the DNA chain.Comment: 9 pages, including 2 figures, to be published in Phys. Rev. Let

The occurrence of dental caries is associated with atherosclerosis

OBJECTIVE: Previous studies have suggested that marginal periodontitis is a risk factor for developing atherosclerosis. The objective of this study was to determine whether caries may also be associated with atherosclerosis. METHODS: The computed tomography data sets of 292 consecutive patients, 137 women and 155 men with a mean age of 54.1±17.3 years, were analyzed. Caries were quantified based on the number of decayed surfaces of all the teeth, and periodontitis was quantified on the basis of the horizontal bone loss in the jaw. The presence of chronic apical periodontitis (CAP) was assessed, and the aortic atherosclerotic burden was quantified using a calcium scoring method. RESULTS: The patients wit

Constraints, Histones, and the 30 Nanometer Spiral

We investigate the mechanical stability of a segment of DNA wrapped around a histone in the nucleosome configuration. The assumption underlying this investigation is that the proper model for this packaging arrangement is that of an elastic rod that is free to twist and that writhes subject to mechanical constraints. We find that the number of constraints required to stabilize the nuclesome configuration is determined by the length of the segment, the number of times the DNA wraps around the histone spool, and the specific constraints utilized. While it can be shown that four constraints suffice, in principle, to insure stability of the nucleosome, a proper choice must be made to guarantee the effectiveness of this minimal number. The optimal choice of constraints appears to bear a relation to the existence of a spiral ridge on the surface of the histone octamer. The particular configuration that we investigate is related to the 30 nanometer spiral, a higher-order organization of DNA in chromatin.Comment: ReVTeX, 15 pages, 18 figure

Older Veteran Digital Disparities: Examining the Potential for Solutions Within Social Networks

BACKGROUND: Older adults typically have less access to the Internet than other age groups, and older Veterans may use the Internet even less due to economic and geographic reasons. OBJECTIVE: To explore solutions to this problem, our study examined older Veterans\u27 reported ability to access technology through their close social ties. METHODS: Data were collected via mail survey from a sample of Veterans aged 65 years and older (N=266). RESULTS: Nearly half (44.0%, 117/266) of the sample reported having no Internet access. Yet, among those without current access, older Veterans reported having a median of 5 (IQR 7) close social ties with home Internet access. These older Veterans also reported that they would feel comfortable asking a median of 2 (IQR 4) social ties for help to access the Internet, and that a median of 2 (IQR 4) social ties would directly access the Internet for the older Veteran to help with health management. CONCLUSIONS: Findings suggest that even older Veterans without current Internet access have at least two social ties with home Internet who could be called upon for technology support. Thus, older Veterans may be willing to call upon these surrogate seekers for technology assistance and support in health management. This has implications for the digital divide, technology design, and health care policy

Sequence Effects on DNA Entropic Elasticity

DNA stretching experiments are usually interpreted using the worm-like chain model; the persistence length A appearing in the model is then interpreted as the elastic stiffness of the double helix. In fact the persistence length obtained by this method is a combination of bend stiffness and intrinsic bend effects reflecting sequence information, just as at zero stretching force. This observation resolves the discrepancy between the value of A measured in these experiments and the larger ``dynamic persistence length'' measured by other means. On the other hand, the twist persistence length deduced from torsionally-constrained stretching experiments suffers no such correction. Our calculation is very simple and analytic; it applies to DNA and other polymers with weak intrinsic disorder.Comment: LaTeX; postscript available at http://dept.physics.upenn.edu/~nelson/index.shtm

Developments and challenges in dermatology: an update from the Interactive Derma Academy (IDeA) 2019

The 2019 Interactive Derma Academy (IDeA) meeting was held in Lisbon, Portugal, 10–12 May, bringing together leading dermatology experts from across Europe, the Middle East and Asia. Over three days, the latest developments and challenges in relation to the pathophysiology, diagnosis, evaluation and management of dermatological conditions were presented, with a particular focus on acne, atopic dermatitis (AD) and actinic keratosis (AK). Interesting clinical case studies relating to these key topics were discussed with attendees to establish current evidence-based best practices. Presentations reviewed current treatments, potential therapeutic approaches and key considerations in the management of acne, AK and AD, and discussed the importance of the microbiome in these conditions, as well as the provision of patient education/support. It was highlighted that active treatment is not always required for AK, depending on patient preferences and clinical circumstances. In addition to presentations, two interactive workshops on the diagnosis and treatment of sexually transmitted infections/diseases (STIs/STDs) presenting to the dermatology clinic, and current and future dermocosmetics were conducted. The potential for misdiagnosis of STIs/STDs was discussed, with dermoscopy and/or reflectance confocal microscopy suggested as useful diagnostic techniques. In addition, botulinum toxin was introduced as a potential dermocosmetic, and the possibility of microbiome alteration in the treatment of dermatological conditions emphasized. Furthermore, several challenges in dermatology, including the use of lasers, the complexity of atopic dermatitis, wound care, use of biosimilars and application of non-invasive techniques in skin cancer diagnosis were reviewed. In this supplement, we provide an overview of the presentations and discussions from the fourth successful IDeA meeting, summarizing the key insights shared by dermatologists from across the globe

DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers

Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric complexes that bind to arrays of PRH binding sites with high affinity and specificity. We have also shown that many PRH target genes contain suitably spaced arrays of PRH sites that allow this protein to bind and regulate transcription. Here, we use analytical ultracentrifugation and electron microscopy to further characterize PRH oligomers. We use the same techniques to show that PRH oligomers bound to long DNA fragments self-associate to form highly ordered assemblies. Electron microscopy and linear dichroism reveal that PRH oligomers can form protein–DNA fibres and that PRH is able to compact DNA in the absence of other proteins. Finally, we show that DNA compaction is not sufficient for the repression of PRH target genes in cells. We conclude that DNA compaction is a consequence of the binding of large PRH oligomers to arrays of binding sites and that PRH is functionally and structurally related to the Lrp/AsnC family of proteins from bacteria and archaea, a group of proteins formerly thought to be without eukaryotic equivalents

DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers

Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric complexes that bind to arrays of PRH binding sites with high affinity and specificity. We have also shown that many PRH target genes contain suitably spaced arrays of PRH sites that allow this protein to bind and regulate transcription. Here, we use analytical ultracentrifugation and electron microscopy to further characterize PRH oligomers. We use the same techniques to show that PRH oligomers bound to long DNA fragments self-associate to form highly ordered assemblies. Electron microscopy and linear dichroism reveal that PRH oligomers can form protein–DNA fibres and that PRH is able to compact DNA in the absence of other proteins. Finally, we show that DNA compaction is not sufficient for the repression of PRH target genes in cells. We conclude that DNA compaction is a consequence of the binding of large PRH oligomers to arrays of binding sites and that PRH is functionally and structurally related to the Lrp/AsnC family of proteins from bacteria and archaea, a group of proteins formerly thought to be without eukaryotic equivalents