Using electrostatic potentials to predict DNA-binding sites on DNA-binding proteins

A method to detect DNA-binding sites on the surface of a protein structure is important for functional annotation. This work describes the analysis of residue patches on the surface of DNA-binding proteins and the development of a method of predicting DNA-binding sites using a single feature of these surface patches. Surface patches and the DNA-binding sites were initially analysed for accessibility, electrostatic potential, residue propensity, hydrophobicity and residue conservation. From this, it was observed that the DNA-binding sites were, in general, amongst the top 10% of patches with the largest positive electrostatic scores. This knowledge led to the development of a prediction method in which patches of surface residues were selected such that they excluded residues with negative electrostatic scores. This method was used to make predictions for a data set of 56 non-homologous DNA-binding proteins. Correct predictions made for 68% of the data set

Stress-induced nuclear accumulation is dispensable for Hog1-dependent gene expression and virulence in a fungal pathogen

The authors thank E. Veal for intellectual input. This work was funded by the UK Biotechnology and Biological Research Council [J.Q. BB/K016393/1; A.J.P.B. BB/K017365/1], the National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) [D.M.M. NC/N002482/1] and the Wellcome Trust Strategic Award in Medical Mycology and Fungal Immunology [097377]). D.M.M. and A.J.P.B. are also supported by the MRC Centre for Medical Mycology at the University of Aberdeen (MR/N006364/1).Peer reviewedPublisher PD

Predictors and outcomes of sustained, intermittent or never achieving remission in patients with recent onset inflammatory polyarthritis:Results from the Norfolk Arthritis Register

Objectives: Early remission is the current treatment strategy for patients with inflammatory polyarthritis (IP) and RA. Our objective was to identify baseline factors associated with achieving remission: sustained (SR), intermittent (IR) or never (NR) over a 5-year period in patients with early IP.  Methods: Clinical and demographic data of patients with IP recruited to the Norfolk Arthritis Register (NOAR) were obtained at baseline and years 1, 2, 3 and 5. Remission was defined as no tender or swollen joints (out of 51). Patients were classified as NR or PR, respectively, if they were in remission at: no assessment or ⩾3 consecutive assessments after baseline, and IR otherwise. Ordinal regression and a random effects model, respectively, were used to examine the association between baseline factors, remission group and HAQ scores over time.  Results: A total of 868 patients (66% female) were included. Of these, 54%, 34% and 12% achieved NR, IR and SR, respectively. In multivariate analysis, female sex (odds ratio, OR 0.47, 95% CI: 0.35, 0.63), higher tender joint count (OR = 0.94, 95% CI: 0.93, 0.96), higher HAQ (OR = 0.59, 95% CI: 0.48, 0.74), being obese (OR = 0.70, 95% CI: 0.50, 0.99), hypertensive (OR = 0.67, 95% CI: 0.50, 0.90) or depressed (OR = 0.74, 95% CI: 0.55, 1.00) at baseline were independent predictors of being in a lower remission group. IR and SR were associated with lower HAQ scores over time and lower DAS28 at year 5.  Conclusion: Women with higher tender joint count and disability at baseline, depression, obesity and hypertension were less likely to achieve remission. This information could help when stratifying patients for more aggressive therapy

The Factors of Interest Group Networks and Success: Organization, Issues and Resources

While interest groups use a variety of techniques to exert influence, coalition strategies are the dominant lobbying technique. However, many questions remain about such coalitions. This paper is the second in a series of social network analyses of purposive and coordinated interest group relationships. We utilize a network measure based on cosigner status to United States Supreme Court amicus curiae, or friend of the court briefs. The illuminated structures lend insight into the central players and overall formation of the network over the first several years of the 21st century. The factions are tied together by various central players, who act as hubs, leaving a disparate collection of organizations that work alone. Using an exponential-family random graph model (ERGM), we find that graph-theorectic and organizational characteristics, such as size and budget, as well as policy interests explain interest group network formation

Invaluable Involvement: Purposive Interest Group Networks in the 21st Century

We present the first social network analysis of purposive and coordinated interest group relationships. We utilize a network measure based on cosigner status to United States Supreme Court amicus curiae, or friend of the court briefs. The illuminated structures lend insight into the central players and overall formation of the network over the first seven years of the 21st century. We find that the majority of interest groups primarily partake in coalition strategies with other groups of similar policy interest and ideological character. This is in contrast to previous literature that focused only on one or the other. The factions are tied together by various central players, who act as hubs, leaving a disparate collection of organizations that work alone. Network analysis provides evidence, for example, that the National Wildlife Foundation, the National Association of Criminal Defense Lawyers and the American Civil Liberties Union are all particularly strong groups, but exploit different central roles. Ultimately, our work and data suggest several subsequent questions and opportunities pertaining to the coalition strategies of interest groups

A randomised trial evaluating Bevacizumab as adjuvant therapy following resection of AJCC stage IIB, IIC and III cutaneous melanoma : an update

At present, there are no standard therapies for the adjuvant treatment of malignant melanoma. Patients with primary tumours with a high-Breslow thickness (stages IIB and IIC) or with resected loco-regional nodal disease (stage III) are at high risk of developing metastasis and subsequent disease-related death. Given this, it is important that novel therapies are investigated in the adjuvant melanoma setting. Since angiogenesis is essential for primary tumour growth and the development of metastasis, anti-angiogenic agents are attractive potential therapeutic candidates for clinical trials in the adjuvant setting. Therefore, we initiated a phase II trial in resected high-risk cutaneous melanoma, assessing the efficacy of bevacizumab versus observation. In the interim safety data analysis, we demonstrate that bevacizumab is a safe therapy in the adjuvant melanoma setting with no apparent increase in the surgical complication rate after either primary tumour resection and/or loco-regional lymphadenectomy