A Clock-independent Model for Real-Time

A new approach for modelling time that does not rely on the concept of a clock is proposed. In order to establish a notion of time, system behaviour is represented as a joint progression of multiple threads of control, which satisfies a certain set of axioms. We show that the clock-independent time model is related to the well-known concept of a global clock and argue that both approaches establish the same notion of time

Molecular perturbations in cholangiocarcinoma: is it time for precision medicine?

The complexity of cholangiocarcinoma (CCA) cellularity and the molecular perturbation mechanisms that underlie the diversity of growth patterns of this malignancy remain a clinical concern. Tumours of the biliary system display significant intrinsic chemoresistance, caused by significant stromal involvement and genome–wide tumour heterogeneity, hampering disease remission and palliation as well as promoting the metastatic behaviour. It is crucial to advance our present understanding of the risk and molecular pathogenesis of CCA. This will facilitate the delineation of patient subsets based on molecular perturbations and adjust for precision therapies

A wildland fire model with data assimilation

A wildfire model is formulated based on balance equations for energy and fuel, where the fuel loss due to combustion corresponds to the fuel reaction rate. The resulting coupled partial differential equations have coefficients that can be approximated from prior measurements of wildfires. An ensemble Kalman filter technique with regularization is then used to assimilate temperatures measured at selected points into running wildfire simulations. The assimilation technique is able to modify the simulations to track the measurements correctly even if the simulations were started with an erroneous ignition location that is quite far away from the correct one.Comment: 35 pages, 12 figures; minor revision January 2008. Original version available from http://www-math.cudenver.edu/ccm/report

Integrated Management of European Cherry Fruit Fly Rhagoletis cerasi (L.): Situation in Switzerland and Europe

Abstract: The European cherry fruit fly, Rhagoletis cerasi (L.) (Diptera: Tephritidae), is a highly destructive pest. The low tolerance for damaged fruit requires preventive insecticide treatments for a marketable crop. The phase-out of old insecticides threatens cherry production throughout the European Union (EU). Consequently, new management techniques and tools are needed. With the increasing number of dwarf tree orchards covered against rain to avoid fruit splitting, crop netting has become a viable, cost-effective method of cherry fruit fly control. Recently, a biocontrol method using the entomopathogenic fungus Beauveria bassiana has been developed for organic agriculture. However, for most situations, there is still a lack of efficient and environmentally sound insecticides to control this pest. This review summarizes the literature from over one hundred years of research on R. cerasi with focus on the biology and history of cherry fruit fly control as well as on antagonists and potential biocontrol organisms. We will present the situation of cherry fruit fly regulation in different European countries, give recommendations for cherry fruit fly control, show gaps in knowledge and identify future research opportunities

How the oxygen tolerance of a [NiFe]-hydrogenase depends on quaternary structure

‘Oxygen-tolerant’ [NiFe]-hydrogenases can catalyze H(2) oxidation under aerobic conditions, avoiding oxygenation and destruction of the active site. In one mechanism accounting for this special property, membrane-bound [NiFe]-hydrogenases accommodate a pool of electrons that allows an O(2) molecule attacking the active site to be converted rapidly to harmless water. An important advantage may stem from having a dimeric or higher-order quaternary structure in which the electron-transfer relay chain of one partner is electronically coupled to that in the other. Hydrogenase-1 from E. coli has a dimeric structure in which the distal [4Fe-4S] clusters in each monomer are located approximately 12 Å apart, a distance conducive to fast electron tunneling. Such an arrangement can ensure that electrons from H(2) oxidation released at the active site of one partner are immediately transferred to its counterpart when an O(2) molecule attacks. This paper addresses the role of long-range, inter-domain electron transfer in the mechanism of O(2)-tolerance by comparing the properties of monomeric and dimeric forms of Hydrogenase-1. The results reveal a further interesting advantage that quaternary structure affords to proteins

The Structure of Hydrogenase-2 from <i>Escherichia coli</i>:Implications for H₂ -Driven Proton Pumping

Under anaerobic conditions Escherichia coli is able to metabolize molecular hydrogen via the action of several [NiFe]-hydrogenase enzymes. Hydrogenase-2, which is typically present in cells at low levels during anaerobic respiration, is a periplasmic-facing membrane-bound complex that functions as a proton pump to convert energy from H2 oxidation into a proton gradient; consequently, its structure is of great interest. Empirically, the complex consists of a tightly-bound core catalytic module, comprising large (HybC) and small (HybO) subunits, which is attached to an Fe-S protein (HybA) and an integral membrane protein, HybB. To date, efforts to gain a more detailed picture have been thwarted by low native expression levels of hydrogenase-2 and the labile interaction between HybOC and HybA/HybB subunits. In this paper we describe a new over-expression system that has facilitated determination of high-resolution crystal structures of HybOC and, hence, a prediction of the quaternary structure of the HybOCAB complex