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)

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

COVID-19, Politics, and Science in Utah: Executive Summary of Research Findings

Daily life in the United States and Utah has changed considerably since the global outbreak of the COVID-19 novel coronavirus. On March 6th, 2020, Gary R. Herbert, Governor of the State of Utah, declared a “State of Emergency” in response to pandemic. On March 27th the Governor then issued the “Stay Safe, Stay Home” Directive, which was much less strict than the shelter in place orders seen in other states as it simply urged residents to leave home infrequently, stay 6 feet away from others outside the home, and banned private gatherings larger than 20. At the end of April, the Utah COVID-19 Public Health Risk Status was moved from Red (High Risk) to Orange (Moderate Risk), meaning the Governor’s recent directive was no longer in place as of May 1st

Utahns’ Generally Agree on Top Environmental Concerns, But Climate Change and Related Issues Reveal Political Polarization

Utah is renowned for its unique landscapes and abundant opportunities to connect with the natural environment. However, the state is currently grappling with serious environmental challenges, including poor air quality, dwindling water supplies, and the alarming desiccation of the Great Salt Lake. These and other issues have major ecological and economic implications, and combating them will likely require large scale efforts. However, rising levels of political polarization are a common problem in the United States that many feel stifles our ability to combat societal problems, including those related to the environment and human health

Word frequency in fast priming: Evidence for immediate cognitive control of eye movements during reading

Numerous studies have demonstrated effects of word frequency on eye movements during reading, but the precise timing of this influence has remained unclear. The fast priming paradigm (Sereno & Rayner, 1992) was previously used to study influences of related versus unrelated primes on the target word. Here, we used this procedure to investigate whether the frequency of the prime word has a direct influence on eye movements during reading when the prime-target relation is not manipulated. We found that with average prime intervals of 32 ms readers made longer single fixation durations on the target word in the low than in the high frequency prime condition. Distributional analyses demonstrated that the effect of prime frequency on single fixation durations occurred very early, supporting theories of immediate cognitive control of eye movements. Finding prime frequency effects only 207 ms after visibility of the prime and for prime durations of 32 ms yields new time constraints for cognitive processes controlling eye movements during reading. Our variant of the fast priming paradigm provides a new approach to test early influences of word processing on eye movement control during reading

impulsivity and the impact of contextual cues on instrumental behavior in alcohol dependence

Alcohol-related cues acquire incentive salience through Pavlovian conditioning and then can markedly affect instrumental behavior of alcohol-dependent patients to promote relapse. However, it is unclear whether similar effects occur with alcohol-unrelated cues. We tested 116 early-abstinent alcohol- dependent patients and 91 healthy controls who completed a delay discounting task to assess choice impulsivity, and a Pavlovian-to-instrumental transfer (PIT) paradigm employing both alcohol-unrelated and alcohol-related stimuli. To modify instrumental choice behavior, we tiled the background of the computer screen either with conditioned stimuli (CS) previously generated by pairing abstract pictures with pictures indicating monetary gains or losses, or with pictures displaying alcohol or water beverages. CS paired to money gains and losses affected instrumental choices differently. This PIT effect was significantly more pronounced in patients compared to controls, and the group difference was mainly driven by highly impulsive patients. The PIT effect was particularly strong in trials in which the instrumental stimulus required inhibition of instrumental response behavior and the background CS was associated to monetary gains. Under that condition, patients performed inappropriate approach behavior, contrary to their previously formed behavioral intention. Surprisingly, the effect of alcohol and water pictures as background stimuli resembled that of aversive and appetitive CS, respectively. These findings suggest that positively valenced background CS can provoke dysfunctional instrumental approach behavior in impulsive alcohol- dependent patients. Consequently, in real life they might be easily seduced by environmental cues to engage in actions thwarting their long-term goals. Such behaviors may include, but are not limited to, approaching alcohol

Recent Developments in Helioseismic Analysis Methods and Solar Data Assimilation

MR and AS have received funding from the European Research Council under the European Union’s Seventh Framework Program (FP/2007-2013)/ERC Grant Agreement no. 307117

Automatisierte Klassifikation nach WRB 2015 mit KA 5-konformen Daten – Qualität der Ableitung bei beschränkten Daten

Zur Verwendung in großen Profildatenbanken wurde eine Datenbankanwendung erstellt, die Bodennamen nach World Reference Base for Soil Resources 2014, update 2015 (WRB) automatisiert aus Profilbeschrieben nach Bodenkundlicher Kartieranleitung und Labordaten ableitet. Mit einem Datensatz von 201 gut beschriebenen Profilen aus Deutschland, Österreich und der Schweiz wurden die Auswirkungen von fehlenden Daten auf die Qualität der Ableitung geprüft. Insbesondere sind Ableitungen allein aus dem Horizontsymbol ebenso wenig erfolgversprechend wie Ableitungen ohne Horizontsymbolinformation. Wir schließen daraus, dass Bodenmerkmale ohne eine grundsätzliche Einordnung in einen genetischen Zusammenhang nicht im Nachhinein genetisch interpretierbar sind. Da die Auswertungen sehr komplex sind, kann dies auch für andere Datenauswertungen als gültig angenommen werden