Nucleosomal arrangement affects single-molecule transcription dynamics.

In eukaryotes, gene expression depends on chromatin organization. However, how chromatin affects the transcription dynamics of individual RNA polymerases has remained elusive. Here, we use dual trap optical tweezers to study single yeast RNA polymerase II (Pol II) molecules transcribing along a DNA template with two nucleosomes. The slowdown and the changes in pausing behavior within the nucleosomal region allow us to determine a drift coefficient, χ, which characterizes the ability of the enzyme to recover from a nucleosomal backtrack. Notably, χ can be used to predict the probability to pass the first nucleosome. Importantly, the presence of a second nucleosome changes χ in a manner that depends on the spacing between the two nucleosomes, as well as on their rotational arrangement on the helical DNA molecule. Our results indicate that the ability of Pol II to pass the first nucleosome is increased when the next nucleosome is turned away from the first one to face the opposite side of the DNA template. These findings help to rationalize how chromatin arrangement affects Pol II transcription dynamics

Institutional settings and urban sprawl: evidence from Europe

This article explores the role of institutional settings in determining spatial variation in urban sprawl across Europe. We first synthesize the emerging literature that links land use policies and local fiscal incentives to urban sprawl. Next, we compile a panel dataset on various measures of urban sprawl for European countries using high-resolution satellite images. We document substantial variation in urban sprawl across countries. This variation remains roughly stable over the period of our analysis (1990-2012). Urban sprawl is particularly pronounced in emerging Central and Eastern Europe but is comparatively low in Northern European countries. Urban sprawl – especially outside functional urban areas – is strongly negatively associated with real house price growth, suggesting a trade-off between urban containment and housing affordability. Our main novel empirical findings are that decentralization and local political fragmentation are significantly positively associated with urban sprawl. Decentralized countries have a 25 to 30 percent higher sprawl index than centralized ones. This finding is consistent with the proposition that in decentralized countries fiscal incentives at local level may provide strong incentives to permit residential development at the outskirts of existing development

Random Walks for Spike-Timing Dependent Plasticity

Random walk methods are used to calculate the moments of negative image equilibrium distributions in synaptic weight dynamics governed by spike-timing dependent plasticity (STDP). The neural architecture of the model is based on the electrosensory lateral line lobe (ELL) of mormyrid electric fish, which forms a negative image of the reafferent signal from the fish's own electric discharge to optimize detection of sensory electric fields. Of particular behavioral importance to the fish is the variance of the equilibrium postsynaptic potential in the presence of noise, which is determined by the variance of the equilibrium weight distribution. Recurrence relations are derived for the moments of the equilibrium weight distribution, for arbitrary postsynaptic potential functions and arbitrary learning rules. For the case of homogeneous network parameters, explicit closed form solutions are developed for the covariances of the synaptic weight and postsynaptic potential distributions.Comment: 18 pages, 8 figures, 15 subfigures; uses revtex4, subfigure, amsmat

Mounding Instability and Incoherent Surface Kinetics

Mounding instability in a conserved growth from vapor is analysed within the framework of adatom kinetics on the growing surface. The analysis shows that depending on the local structure on the surface, kinetics of adatoms may vary, leading to disjoint regions in the sense of a continuum description. This is manifested particularly under the conditions of instability. Mounds grow on these disjoint regions and their lateral growth is governed by the flux of adatoms hopping across the steps in the downward direction. Asymptotically ln(t) dependence is expected in 1+1- dimensions. Simulation results confirm the prediction. Growth in 2+1- dimensions is also discussed.Comment: 4 pages, 4 figure

Insight into Bio-metal Interface Formation in vacuo: Interplay of S-layer Protein with Copper and Iron

The mechanisms of interaction between inorganic matter and biomolecules, as well as properties of resulting hybrids, are receiving growing interest due to the rapidly developing field of bionanotechnology. The majority of potential applications for metal-biohybrid structures require stability of these systems under vacuum conditions, where their chemistry is elusive, and may differ dramatically from the interaction between biomolecules and metal ions in vivo. Here we report for the first time a photoemission and X-ray absorption study of the formation of a hybrid metal-protein system, tracing step-by-step the chemical interactions between the protein and metals (Cu and Fe) in vacuo. Our experiments reveal stabilization of the enol form of peptide bonds as the result of protein-metal interactions for both metals. The resulting complex with copper appears to be rather stable. In contrast, the system with iron decomposes to form inorganic species like oxide, carbide, nitride, and cyanide

Current-Induced Step Bending Instability on Vicinal Surfaces

We model an apparent instability seen in recent experiments on current induced step bunching on Si(111) surfaces using a generalized 2D BCF model, where adatoms have a diffusion bias parallel to the step edges and there is an attachment barrier at the step edge. We find a new linear instability with novel step patterns. Monte Carlo simulations on a solid-on-solid model are used to study the instability beyond the linear regime.Comment: 4 pages, 4 figure

Vacuum oscillation solution to the solar neutrino problem in standard and non-standard pictures

The neutrino long wavelength (just-so) oscillation is revisited as a solution to the solar neutrino problem. We consider just-so scenario in various cases: in the framework of the solar models with relaxed prediction of the boron neutrino flux, as well as in the presence of the non-standard weak range interactions between neutrino and matter constituents. We show that the fit of the experimental data in the just-so scenario is not very good for any reasonable value of the $^8B$ neutrino flux, but it substantially improves if the non-standard $\tau$-neutrino--electron interaction is included. These new interactions could also remove the conflict of the just-so picture with the shape of the SN 1987A neutrino spectrum. Special attention is devoted to the potential of the future real-time solar neutrino detectors as are Super-Kamiokande, SNO and BOREXINO, which could provide the model independent tests for the just-so scenario. In particular, these imply specific deformation of the original solar neutrino energy spectra, and time variation of the intermediate energy monochromatic neutrino ($^7Be$ and $pep$) signals.Comment: Latex, 14 pages, 9 figures (avalilable by fax or postscript files requested to [email protected]) -- some textual and Latex errors are corrected and few references adde

Measurements and modeling of optical-equivalent snow grain sizes under arctic low-sun conditions

The size and shape of snow grains directly impacts the reflection by a snowpack. In this article, different approaches to retrieve the optical-equivalent snow grain size (r$_{opt}$) or, alternatively, the specific surface area (SSA) using satellite, airborne, and ground-based observations are compared and used to evaluate ICON-ART (ICOsahedral Nonhydrostatic—Aerosols and Reactive Trace gases) simulations. The retrieval methods are based on optical measurements and rely on the r$_{opt}$-dependent absorption of solar radiation in snow. The measurement data were taken during a three-week campaign that was conducted in the North of Greenland in March/April 2018, such that the retrieval methods and radiation measurements are affected by enhanced uncertainties under these low-Sun conditions. An adjusted airborne retrieval method is applied which uses the albedo at 1700 nm wavelength and combines an atmospheric and snow radiative transfer model to account for the direct-to-global fraction of the solar radiation incident on the snow. From this approach, we achieved a significantly improved uncertainty (<25%) and a reduced effect of atmospheric masking compared to the previous method. Ground-based in situ measurements indicated an increase of r$_{opt}$ of 15 µm within a five-day period after a snowfall event which is small compared to previous observations under similar temperature regimes. ICON-ART captured the observed change of r$_{opt}$ during snowfall events, but systematically overestimated the subsequent snow grain growth by about 100%. Adjusting the growth rate factor to 0.012 µm$^{2}$ s$^{-1}$ minimized the difference between model and observations. Satellite-based and airborne retrieval methods showed higher r$_{opt}$ over sea ice (<300 µm) than over land surfaces (<100 µm) which was reduced by data filtering of surface roughness features. Moderate-Resolution Imaging Spectroradiometer (MODIS) retrievals revealed a large spread within a series of subsequent individual overpasses, indicating their limitations in observing the snow grain size evolution in early spring conditions with low Sun