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

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

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

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

Utahns are Becoming More Likely to Say Human-Caused Climate Change is Happening

Scientists who study the earth’s climate overwhelmingly agree that human activities are causing rapid change1 . Most Americans also agree that global warming is happening (74%) and caused by humans (61%)2 . However, the same research finds that about one in eight (12%) of Americans do not think global warming is happening. This indicates that despite scientific consensus, some Americans remain skeptical about whether climate change is real and if humans are the cause

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)

Utahns\u27 Perceptions of Climate Change and Disaster Vulnerabilities

Climate change increases the frequency and severity of extreme weather events, making people more vulnerable in a variety of ways1-2. It is essential to determine if individuals believe they are susceptible to the effects of climate change in order to develop effective adaptation strategies. Climate change has contributed to extreme weather occurrences in Utah in recent years. For instance, in the summer of 2022, there was a severe or extreme drought in all of Utah\u27s counties3. Health effects of drought vary with intensity4 and can cause climate related deaths directly and indirectly, such as by worsening air quality which can increase cardiovascular and pulmonary disease5-8. According to most climate models, such events are likely to continue as temperature is expected to increase and snowpack to decrease in the western U.S. and Utah9. A recent statewide survey found that Utahns are concerned about various environmental and climatic issues including increased temperature, poor air quality, drought/lack of water etc10. Moreover, since 2020, more Utahns agree with the scientific consensus that human activities are causing climate change11. This research brief uses representative statewide survey data from the 2023 Utah People and Environment Poll (UPEP) to understand how Utah residents consider themselves vulnerable to climate change, how prepared they think they are for climate change, and if they believe they need to plan or prepare for climate change

The cellular heat shock response monitored by chemical exchange saturation transfer MRI

CEST-MRI of the rNOE signal has been demonstrated in vitro to be closely linked to the protein conformational state. As the detectability of denaturation and aggregation processes on a physiologically relevant scale in living organisms has yet to be verified, the aim of this study was to perform heat-shock experiments with living cells to monitor the cellular heat-shock response of the rNOE CEST signal. Cancer cells (HepG2) were dynamically investigated after a mild, non-lethal heat-shock of 42 °C for 20 min using an MR-compatible bioreactor system at 9.4 T. Reliable and fast high-resolution CEST imaging was realized by a relaxation-compensated 2-point contrast metric. After the heat-shock, a substantial decrease of the rNOE CEST signal by 8.0 ± 0.4% followed by a steady signal recovery within a time of 99.1 ± 1.3 min was observed in two independent trials. This continuous signal recovery is in coherence with chaperone-induced refolding of heat-shock induced protein aggregates. We demonstrated that protein denaturation processes influence the CEST-MRI signal on a physiologically relevant scale. Thus, the protein folding state is, along with concentration changes, a relevant physiological parameter for the interpretation of CEST signal changes in diseases that are associated with pathological changes in protein expression, like cancer and neurodegenerative diseases