On slowdown and speedup of transient random walks in random environment

We consider one-dimensional random walks in random environment which are transient to the right. Our main interest is in the study of the sub-ballistic regime, where at time $n$ the particle is typically at a distance of order $O(n^\kappa)$ from the origin, $\kappa\in(0,1)$. We investigate the probabilities of moderate deviations from this behaviour. Specifically, we are interested in quenched and annealed probabilities of slowdown (at time $n$, the particle is at a distance of order $O(n^{\nu_0})$ from the origin, $\nu_0\in (0,\kappa)$), and speedup (at time $n$, the particle is at a distance of order $n^{\nu_1}$ from the origin, $\nu_1\in (\kappa,1)$), for the current location of the particle and for the hitting times. Also, we study probabilities of backtracking: at time $n$, the particle is located around $(-n^\nu)$, thus making an unusual excursion to the left. For the slowdown, our results are valid in the ballistic case as well.Comment: 43 pages, 4 figures; to appear in Probability Theory and Related Field

ChromID identifies the protein interactome at chromatin marks

ISSN:1546-1696ISSN:1087-015

P53 expression is significantly correlated with high risk of malignancy and epithelioid differentiation in GISTs. An immunohistochemical study of 104 cases

<p>Abstract</p> <p>Background</p> <p>Molecular analyses of the <it>c-kit </it>and <it>PDGFRα </it>genes have contributed greatly to our understanding of the development of gastrointestinal stromal tumors (GISTs), but little is known about their malignant potential. The aim of our study was to evaluate cell cycle regulators as potential prognostic markers in GISTs.</p> <p>Methods</p> <p>We investigated 104 KIT positive GISTs from various tumor sites in immunoassays on CD34, Ki67 and particularly on P53, BCL-2 and Cyclin D1. The results were compared with tumor size, mitotic rate, proliferative activity, histological subtype, nuclear atypia and risk assessment according to Fletcher and Miettinen. Occurrence of metastases and survival were also taken into account.</p> <p>Results</p> <p>The expression of P53 was significantly correlated with high risk criteria towards malignancy and epithelioid differentiation in GISTs. Likewise P53 label correlated significantly with the established prognostic indicators: tumor size, mitotic rate, nuclear atypia and proliferative activity. Regarding the site of tumor presentation, P53 was not a decisive factor. BCL-2 and Cyclin D1 expression was not related to any of the prognostic indicators.</p> <p>Conclusion</p> <p>The present data identified P53 being a recommendable marker for predicting the risk of malignancy in GISTs. In addition, we found P53 significantly correlated with epithelioid tumor differentiation, independent of tumor site. BCL-2 and Cyclin D1, however, did not prove to be deciding markers for diagnosis and prognosis.</p

Competitive advantage of Rumex obtusifolius L. might increase in intensively managed temperate grasslands under drier climate

Climate models predict decreasing amounts of precipitation for future summers in Switzerland. Since grasslands cover about one quarter of the area, severe consequences might be expected for Swiss agriculture, ranging from loss of grassland productivity to changes in vegetation composition. Since stressed ecosystems are also more susceptible to invasion, future drier conditions might favour the emergence of weeds. However, the response of temperate grasslands to drought has not been investigated in great detail so far. Using transparent rain shelters, we simulated extreme summer drought conditions in intensively managed temperate grassland in the Swiss lowlands at 400 m (Chamau, located near the city of Lucerne) and studied the drought response of Rumex obtusifolius, one of the most troublesome weeds for forage production. We quantified above-ground biomass and assessed the resource use in terms of carbon, nitrogen and water. R. obtusifolius increased its above-ground biomass production in response to drought, comprising up to 80% of the total community biomass in 2006. Within the drought plots, highest pre-dawn leaf water potentials, high values for midday leaf water potentials, stomatal conductance and assimilation clearly indicated that R. obtusifolius was much less affected by drought than other plant species. In general, no significant differences were found for these variables between drought and control R. obtusifolius plants, in contrast to the other plant species. Higher water use efficiency together with a change in N acquisition patterns resulted in a competitive advantage of R. obtusifolius over other species, favouring the spread of this weed. Thus, our results suggest a potential increase of weed pressure by R. obtusifolius under future climatic conditions, demanding additional management measures to limit its success. © 2009 Elsevier B.V. All rights reserved

Dynamics of the Internal Water Molecules in Squid Rhodopsin

Understanding the mechanism of G-protein coupled receptors action is of major interest for drug design. The visual rhodopsin is the prototype structure for the family A of G-protein coupled receptors. Upon photoisomerization of the covalently bound retinal chromophore, visual rhodopsins undergo a large-scale conformational change that prepares the receptor for a productive interaction with the G-protein. The mechanism by which the local perturbation of the retinal cis-trans isomerization is transmitted throughout the protein is not well understood. The crystal structure of the visual rhodopsin from squid solved recently suggests that a chain of water molecules extending from the retinal toward the cytoplasmic side of the protein may play a role in the signal transduction from the all-trans retinal geometry to the activated receptor. As a first step toward understanding the role of water in rhodopsin function, we performed a molecular dynamics simulation of squid rhodopsin embedded in a hydrated bilayer of polyunsaturated lipid molecules. The simulation indicates that the water molecules present in the crystal structure participate in favorable interactions with side chains in the interhelical region and form a persistent hydrogen-bond network in connecting Y315 to W274 via D80

Publisher Correction: ChromID identifies the protein interactome at chromatin marks

An amendment to this paper has been published and can be accessed via a link at the top of the paper