Base sequence dependent sliding of proteins on DNA

The possibility that the sliding motion of proteins on DNA is influenced by the base sequence through a base pair reading interaction, is considered. Referring to the case of the T7 RNA-polymerase, we show that the protein should follow a noise-influenced sequence-dependent motion which deviate from the standard random walk usually assumed. The general validity and the implications of the results are discussed.Comment: 12 pages, 3 figure

Violator Spaces: Structure and Algorithms

Sharir and Welzl introduced an abstract framework for optimization problems, called LP-type problems or also generalized linear programming problems, which proved useful in algorithm design. We define a new, and as we believe, simpler and more natural framework: violator spaces, which constitute a proper generalization of LP-type problems. We show that Clarkson's randomized algorithms for low-dimensional linear programming work in the context of violator spaces. For example, in this way we obtain the fastest known algorithm for the P-matrix generalized linear complementarity problem with a constant number of blocks. We also give two new characterizations of LP-type problems: they are equivalent to acyclic violator spaces, as well as to concrete LP-type problems (informally, the constraints in a concrete LP-type problem are subsets of a linearly ordered ground set, and the value of a set of constraints is the minimum of its intersection).Comment: 28 pages, 5 figures, extended abstract was presented at ESA 2006; author spelling fixe

Compendium for precise ac measurements of the quantum Hall resistance

In view of the progress achieved in the field of the ac quantum Hall effect, the Working Group of the Comite Consultatif d'Electricite et Magnetisme (CCEM) on the AC Quantum Hall Effect asked the authors of this paper to write a compendium which integrates their experiences with ac measurements of the quantum Hall resistance. In addition to the important early work performed at the Bureau International des Poids et Mesures and the National Physical Laboratory, UK, further experience has been gained during a collaboration of the authors' institutes NRC, METAS, and PTB, and excellent agreement between the results of different national metrology institutes has been achieved. This compendium summarizes the present state of the authors' knowledge and reviews the experiences, tests and precautions that the authors have employed to achieve accurate measurements of the ac quantum Hall effect. This work shows how the ac quantum Hall effect can be reliably used as a quantum standard of ac resistance having a relative uncertainty of a few parts in 10^8.Comment: 26 pages, 8 figure

Forming a Mogi Doughnut in the Years Prior to and Immediately Before the 2014 M8.1 Iquique, Northern Chile, Earthquake

Asperities are patches where the fault surfaces stick until they break in earthquakes. Locating asperities and understanding their causes in subduction zones is challenging because they are generally located offshore. We use seismicity, interseismic and coseismic slip, and the residual gravity field to map the asperity responsible for the 2014M8.1 Iquique, Chile, earthquake. For several years prior to the mainshock, seismicity occurred exclusively downdip of the asperity. Two weeks before the mainshock, a series of foreshocks first broke the upper plate then the updip rim of the asperity. This seismicity formed a ring around the slip patch (asperity) that later ruptured in the mainshock. The asperity correlated both with high interseismic locking and a circular gravity low, suggesting that it is controlled by geologic structure. Most features of the spatiotemporal seismicity pattern can be explained by a mechanical model in which a single asperity is stressed by relative plate motion

Root-root interactions: extending our perspective to be more inclusive of the range of theories in ecology and agriculture using in-vivo analyses

Background There is a large body of literature on competitive interactions among plants, but many studies have only focused on above-ground interactions and little is known about root-root dynamics between interacting plants. The perspective on possible mechanisms that explain the outcome of root-root interactions has recently been extended to include non-resource-driven mechanisms (as well as resource-driven mechanisms) of root competition and positive interactions such as facilitation. These approaches have often suffered from being static, partly due to the lack of appropriate methodologies for in-situ non-destructive root characterization. Scope Recent studies show that interactive effects of plant neighbourhood interactions follow non-linear and non-additive paths that are hard to explain. Common outcomes such as accumulation of roots mainly in the topsoil cannot be explained solely by competition theory but require a more inclusive theoretical, as well as an improved methodological framework. This will include the question of whether we can apply the same conceptual framework to crop versus natural species. Conclusions The development of non-invasive methods to dynamically study root-root interactions in vivo will provide the necessary tools to study a more inclusive conceptual framework for root-root interactions. By following the dynamics of root-root interactions through time in a whole range of scenarios and systems, using a wide variety of non-invasive methods, (such as fluorescent protein which now allows us to separately identify the roots of several individuals within soil), we will be much better equipped to answer some of the key questions in root physiology, ecology and agronom

Expression of adhesion molecules and cytokines after coronary artery bypass grafting during normothermic and hypothermic cardiac arrest

Objective: Cardiac surgery with cardiopulmonary bypass (CPB) results in vascular injury and tissue damage which involves leukocyte-endothelial interactions mediated by cytokines and adhesion molecules. This study was designed to demonstrate the effect of normothermic and hypothermic CPB to cytokine and soluble adhesion molecule levels in adults and to determine whether these levels correlate to the patients postoperative course. Design and patients: In 25 patients after normothermic and in 25 patients after hypothermic coronary artery bypass grafting with cardiopulmonary bypass (CPB), blood samples for cytokine and soluble adhesion molecule analysis were taken preoperatively, 24, 36, 48 h, and 6 days postoperatively. Soluble adhesion molecules (sE-selectin, sICAM-1) were measured by ELISA and cytokines (TNF-α, IL-6, IL-8) by chemilumenscent-immunoassay. Clinical data were collected prospectively. Results: Postoperatively, adhesion molecule and cytokine levels were significantly elevated after CPB. Mean plasma levels of sICAM-1 was 2.4-fold higher after 6 days. Mean plasma concentration of sE-selectin peaked after 48 h with a 2-fold increase compared to normothermic conditions. In the hypothermia group sICAM-1, sE-selectin, IL-6, and IL-8 showed significantly higher levels (P≪0.0057, P≪0.0012, P≪0.0419, P≪0.0145) after 24 h compared to the normothermia group. No clinical differences were seen. Conclusion: Adhesion molecules and cytokines are elevated after CPB. Patients after hypothermic CPB show significant higher sICAM-1, sE-selectin, IL-6, and IL-8 levels after 24 h compared to normothermic conditions. These results are mainly due to longer CPB and crossclamp times but do not alter the patient's postoperative cours

Pseudomonas fluorescens CHA0 maintains carbon delivery to Fusarium graminearum-infected roots and prevents reduction in biomass of barley shoots through systemic interactions

Soil bacteria such as pseudomonads may reduce pathogen pressure for plants, both by activating plant defence mechanisms and by inhibiting pathogens directly due to the production of antibiotics. These effects are hard to distinguish under field conditions, impairing estimations of their relative contributions to plant health. A split-root system was set up with barley to quantify systemic and local effects of pre-inoculation with Pseudomonas fluorescens on the subsequent infection process by the fungal pathogen Fusarium graminearum. One root half was inoculated with F. graminearum in combination with P. fluorescens strain CHA0 or its isogenic antibiotic-deficient mutant CHA19. Bacteria were inoculated either together with the fungal pathogen or in separate halves of the root system to separate local and systemic effects. The short-term plant response to fungal infection was followed by using the short-lived isotopic tracer 11CO2 to track the delivery of recent photoassimilates to each root half. In the absence of bacteria, fungal infection diverted carbon from the shoot to healthy roots, rather than to infected roots, although the overall partitioning from the shoot to the entire root system was not modified. Both local and systemic pre-inoculation with P. fluorescens CHA0 prevented the diversion of carbon as well as preventing a reduction in plant biomass in response to F. graminearum infection, whereas the non-antibiotic-producing mutant CHA19 lacked this ability. The results suggest that the activation of plant defences is a central feature of biocontrol bacteria which may even surpass the effects of direct pathogen inhibition

Twist and writhe dynamics of stiff filaments

This letter considers the dynamics of a stiff filament, in particular the coupling of twist and bend via writhe. The time dependence of the writhe of a filament is $W_r^2\sim L t^{1/4}$ for a linear filament and $W_r^2\sim t^{1/2} / L$ for a curved filament. Simulations are used to study the relative importance of crankshaft motion and tube like motion in twist dynamics. Fuller's theorem, and its relation with the Berry phase, is reconsidered for open filamentsComment: 7 Pages with 2 figure

The crust in the pamir: Insights from receiver functions

The Cenozoic convergence between India and Asia has created Earth's thickest crust in the Pamir‐Tibet Plateau by extreme crustal shortening. Here we study the crustal structure of the Pamir and western Tian Shan, the adjacent margins of the Tajik, Tarim, and Ferghana Basins, and the Hindu Kush, using data collected by temporary seismic experiments. We derive, compare, and combine independent observations from P and S receiver functions. The obtained Moho depth varies from ~40 km below the basins to a double‐normal thickness of 65–75 km underneath the Pamir and Hindu Kush. A Moho doublet—with the deeper interface down to a depth of ~90 km—coincides with the arc of intermediate‐depth seismicity underneath the Pamir, where Asian continental lower crust delaminates and rolls back. The crust beneath most of the Central and South Pamir has a low Vp/Vs ratio (<1.70), suggesting a dominantly felsic composition, probably a result of delamination/foundering of the mafic rocks of the lower crust. Beneath the Cenozoic gneiss domes of the Central and South Pamir, which represent extensional core complexes, the Vp/Vs ratios are moderate to high (~1.75), consistent with the previously observed, midcrustal low‐velocity zones, implying the presence of crustal partial melts. Even higher crustal average Vp/Vs ratios up to 1.90 are found in the sedimentary basins and along the Main Pamir Thrust. The ratios along the latter—the active thrust front of the Pamir—may reflect fluid accumulations within a strongly fractured fault system