A model for melting of confined DNA

When DNA molecules are heated they denature. This occurs locally so that loops of molten single DNA strands form, connected by intact double-stranded DNA pieces. The properties of this "melting" transition have been intensively investigated. Recently there has been a surge of interest in this question, caused by experiments determining the properties of partially bound DNA confined to nanochannels. But how does such confinement affect the melting transition? To answer this question we introduce, and solve a model predicting how confinement affects the melting transition for a simple model system by first disregarding the effect of self-avoidance. We find that the transition is smoother for narrower channels. By means of Monte-Carlo simulations we then show that a model incorporating self-avoidance shows qualitatively the same behaviour and that the effect of confinement is stronger than in the ideal case.Comment: 5 pages, 4 figures, supplementary materia

Intrinsic protein disorder in histone lysine methylation

Histone lysine methyltransferases (HKMTs), catalyze mono-, di- and trimethylation of lysine residues, resulting in a regulatory pattern that controls gene expression. Their involvement in many different cellular processes and diseases makes HKMTs an intensively studied protein group, but scientific interest so far has been concentrated mostly on their catalytic domains. In this work we set out to analyze the structural heterogeneity of human HKMTs and found that many contain long intrinsically disordered regions (IDRs) that are conserved through vertebrate species. Our predictions show that these IDRs contain several linear motifs and conserved putative binding sites that harbor cancer-related SNPs. Although there are only limited data available in the literature, some of the predicted binding regions overlap with interacting segments identified experimentally. The importance of a disordered binding site is illustrated through the example of the ternary complex between MLL1, menin and LEDGF/p75. Our suggestion is that intrinsic protein disorder plays an as yet unrecognized role in epigenetic regulation, which needs to be further elucidated through structural and functional studies aimed specifically at the disordered regions of HKMTs. Reviewers: This article was reviewed by Arne Elofsson and Piotr Zielenkiewicz. © 2016 The Author(s)

Validation of the self regulation questionnaire as a measure of health in quality of life research

<p>Abstract</p> <p>Objectives</p> <p>Several epidemiological studies address psychosomatic 'self regulation' as a measure of quality of life aspects. However, although widely used in studies with a focus on complementary cancer treatment, and recognized to be associated with better survival of cancer patients, it is unclear what the 'self regulation' questionnaire exactly measures.</p> <p>Design and setting</p> <p>In a sample of 444 individuals (27% healthy, 33% cancer, 40% other internal diseases), we performed reliability and exploratory factor analyses, and correlated the 16-item instrument with external measures such as the Hospital Anxiety and Depression Scale, the Herdecke Quality of Life questionnaire, and autonomic regulation questionnaire.</p> <p>Results</p> <p>The 16-item pool had a very good internal consistency (Cronbach's alpha = 0.948) and satisfying/good (r_rt= 0.796) test-retest reliability after 3 months. Exploratory factor analysis indicated 2 sub-constructs: (1) Ability to change behaviour in order to reach goals, and (2) Achieve satisfaction and well-being. Both sub-scales correlated well with quality of life aspects, particularly with Initiative Power/Interest, Social Interactions, Mental Balance, and negatively with anxiety and depression.</p> <p>Conclusions</p> <p>The Self Regulation Questionnaire (SRQ) was found to be a valid and reliable tool which measures unique psychosomatic abilities. Self regulation deals with competence and autonomy and can be regarded as a problem solving capacity in terms of an active adaptation to stressful situations to restore wellbeing. The tool is an interesting option to be used particularly in complementary medicine research with a focus on behavioural modification.</p

Probing the Solar Atmosphere Using Oscillations of Infrared CO Spectral Lines

Oscillations were observed across the whole solar disk using the Doppler shift and line depth of spectral lines from the CO molecule near 4666~nm with the National Solar Observatory's McMath/Pierce solar telescope. Power, coherence, and phase spectra were examined, and diagnostic diagrams reveal power ridges at the solar global mode frequencies to show that these oscillations are solar p-modes. The phase was used to determine the height of formation of the CO lines by comparison with the IR continuum intensity phase shifts as measured in Kopp et al., 1992; we find the CO line formation height varies from 425 < z < 560 km as we move from disk center towards the solar limb 1.0 > mu > 0.5. The velocity power spectra show that while the sum of the background and p-mode power increases with height in the solar atmosphere as seen in previous work, the power in the p-modes only (background subtracted) decreases with height, consistent with evanescent waves. The CO line depth weakens in regions of stronger magnetic fields, as does the p-mode oscillation power. Across most of the solar surface the phase shift is larger than the expected value of 90 degrees for an adiabatic atmosphere. We fit the phase spectra at different disk positions with a simple atmospheric model to determine that the acoustic cutoff frequency is about 4.5 mHz with only small variations, but that the thermal relaxation frequency drops significantly from 2.7 to 0 mHz at these heights in the solar atmosphere

Removal of Spectro-Polarimetric Fringes by 2D Pattern Recognition

We present a pattern-recognition based approach to the problem of removal of polarized fringes from spectro-polarimetric data. We demonstrate that 2D Principal Component Analysis can be trained on a given spectro-polarimetric map in order to identify and isolate fringe structures from the spectra. This allows us in principle to reconstruct the data without the fringe component, providing an effective and clean solution to the problem. The results presented in this paper point in the direction of revising the way that science and calibration data should be planned for a typical spectro-polarimetric observing run.Comment: ApJ, in pres