Dynamic disorder in simple enzymatic reactions induces stochastic amplification of substrate

A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon, termed dynamic disorder, has become possible due to advances in single-molecule enzymology measurement techniques, through which the catalytic activity of individual enzyme molecules can be tracked in time. The biological role and importance of these fluctuations in a system with a small number of enzymes such as a living cell have only recently started being explored. In this work, we examine a simple stochastic reaction system consisting of an inflowing substrate and an enzyme with a randomly fluctuating catalytic reaction rate that converts the substrate into an outflowing product. To describe analytically the effect of rate fluctuations on the average substrate abundance at steady-state, we derive an explicit formula that connects the relative speed of enzymatic fluctuations with the mean substrate level. We demonstrate that the relative speed of rate fluctuations can have a dramatic effect on the mean substrate, and lead to large positive deviations from predictions based on the assumption of deterministic enzyme activity. Our results also establish an interesting connection between the amplification effect and the mixing properties of the Markov process describing the enzymatic activity fluctuations, which can be used to easily predict the fluctuation speed above which such deviations become negligible. As the techniques of single-molecule enzymology continuously evolve, it may soon be possible to study the stochastic phenomena due to enzymatic activity fluctuations within living cells. Our work can be used to formulate experimentally testable hypotheses regarding the magnitude of these fluctuations, as well as their phenotypic consequences.Comment: 7 Figure

Relation between TMAOase activity and content of formaldehyde in fillet minces and bellyflap minces from gadoid fishes

Minced fish is a significant component of a number of frozen fishery products like fish fingers, cakes and patties. Predominately minced fish is produced from gadoid species (Alaska pollack, cod, saithe, hake and others) possessing the enzyme trimethylamine oxide demethylase (TMAOase, E.C. 4.1.2.32) (Rehbein and Schreiber 1984). TMAOase catalyses the degradation of trimethylamine oxide (TMAO) to formaldehyde (FA) and dimethylamine (DMA), preferentially during frozen storage of products (Hultin 1992). In most gadoid species light muscle contains only low activity of TMAOase, the activity of red muscle and bellyflaps being somewhat higher. In contrast, the TMAOase activity in blood, kidney and other tissues, residues of which may contaminate minced fish flesh, may be higher for several orders of magnitude (Rehbein and Schreiber 1984)

Local environment of Nitrogen in GaN{y}As{1-y} epilayers on GaAs (001) studied using X-ray absorption near edge spectroscopy

X-ray absorption near-edge spectroscopy (XANES) is used to study the N environment in bulk GaN and in GaN{y}As{1-y} epilayers on GaAs (001), for y \~5%. Density-functional optimized structures were used to predict XANES via multiple-scattering theory. We obtain striking agreement for pure GaN. An alloy model with nitrogen pairs on Ga accurately predicts the threshold energy, the width of the XANES ``white line'', and features above threshold, for the given X-ray polarization. The presence of N-pairs may point to a role for molecular N_2 in epitaxial growth kinetics.Comment: Four pages (PRL style) with two figure

Fish Habitat Utilization Patterns and Evaluation of the Efficacy of Marine Protected Areas in Hawaii: Integration of NOAA Digital Benthic Habitat Mapping and Coral Reef Ecological Studies

Over the past four decades, the state of Hawaii has developed a system of eleven Marine Life Conservation Districts (MLCDs) to conserve and replenish marine resources around the state. Initially established to provide opportunities for public interaction with the marine environment, these MLCDs vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning marine protected area (MPA) design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Team developed digital benthic habitat maps for all MLCD and adjacent habitats. These maps were used to evaluate the efficacy of existing MLCDs for biodiversity conservation and fisheries replenishment, using a spatially explicit stratified random sampling design. Coupling the distribution of habitats and species habitat affinities using GIS technology elucidates species habitat utilization patterns at scales that are commensurate with ecosystem processes and is useful in defining essential fish habitat and biologically relevant boundaries for MPAs. Analysis of benthic cover validated the a priori classification of habitat types and provided justification for using these habitat strata to conduct stratified random sampling and analyses of fish habitat utilization patterns. Results showed that the abundance and distribution of species and assemblages exhibited strong correlations with habitat types. Fish assemblages in the colonized and uncolonized hardbottom habitats were found to be most similar among all of the habitat types. Much of the macroalgae habitat sampled was macroalgae growing on hard substrate, and as a result showed similarities with the other hardbottom assemblages. The fish assemblages in the sand habitats were highly variable but distinct from the other habitat types. Management regime also played an important role in the abundance and distribution of fish assemblages. MLCDs had higher values for most fish assemblage characteristics (e.g. biomass, size, diversity) compared with adjacent fished areas and Fisheries Management Areas (FMAs) across all habitat types. In addition, apex predators and other targeted resources species were more abundant and larger in the MLCDs, illustrating the effectiveness of these closures in conserving fish populations. Habitat complexity, quality, size and level of protection from fishing were important determinates of MLCD effectiveness with respect to their associated fish assemblages. (PDF contains 217 pages

Investigation on different composition of powder metallurgy electrode (Cu-W) in high performance edm (HPEDM) on AISI D2 hardened steel

The ideal selection of manufacturing conditions is one of the most important aspects to take into consideration in the majority of manufacturing processes and particularly in processes related to Electrical Discharge Machining (EDM). EDM die sinking machines are used to machine conductive metals of any hardness or difficult to machine with traditional methods. The problem in the capabilities of tool electrodes which are not utilized at the optimum levels of the operating parameters has attracted the attention of researchers and practicing engineers to manufacture tool electrodes with highly great performance. In this work, an experimental design was conducted to characterize the machining performances and surface integrity of three different composition of copper tungsten (CuW) tool electrode in EDM of D2 hardened steel (58-62 HRC). Machining performances i.e. material removal rate (MRR), tool wear rate (TWR), workpiece surface roughness (Ra) and micro-hardness (MH) were studied for the three different composition of CuW tool electrode made through powder metallurgy (PM) method. Machining variables were peak current and pulse duration, meanwhile machining voltage, depth of cut and duty factor were kept constant. The 65%W electrode is the best choice of CuW electrode on machining D2 hardened steel due to the highest machining rate, reasonable tool wear rate and acceptable surface characteristics. The improvement of MRR is obviously affected by the increment of current intensity. MRR increased as the value of peak current increased. The increment of pulse duration is not essentially improving MRR. There is no clear relation between the alteration of pulse duration and MRR. However, the MRR becomes the optimum at an optimal set of variables which is set at 40A and 400µs. The results of the machining performance can extent the availability of database on EDM machinability and surface characteristics of D2 hardened steel for machinist practices in industrial application of roughing operation

Droplet actuation induced by coalescence: experimental evidences and phenomenological modeling

This paper considers the interaction between two droplets placed on a substrate in immediate vicinity. We show here that when the two droplets are of different fluids and especially when one of the droplet is highly volatile, a wealth of fascinating phenomena can be observed. In particular, the interaction may result in the actuation of the droplet system, i.e. its displacement over a finite length. In order to control this displacement, we consider droplets confined on a hydrophilic stripe created by plasma-treating a PDMS substrate. This controlled actuation opens up unexplored opportunities in the field of microfluidics. In order to explain the observed actuation phenomenon, we propose a simple phenomenological model based on Newton's second law and a simple balance between the driving force arising from surface energy gradients and the viscous resistive force. This simple model is able to reproduce qualitatively and quantitatively the observed droplet dynamics

High performance mixed bisimide resins and composites based thereon

Mixtures of bismaleimide/biscitraconirnide resins produces materials which have better handling, processing or mechanical and thermal properties, particularly in graphite composites, than materials made with the individual resins. The mechanical strength of cured graphite composites prepared from a 1:1 copolymer of such bisimide resins is excellent at both ambient and elevated temperatures. The copolymer mixture provides improved composites which are lighter than metals and replace metals in many aerospace applications

Modeled channel distributions explain extracellular recordings from cultured neurons sealed to microelectrodes

Amplitudes and shapes of extracellular recordings from single neurons cultured on a substrate embedded microelectrode depend not only on the volume conducting properties of the neuron-electrode interface, but might also depend on the distribution of voltage-sensitive channels over the neuronal membrane. In this paper, finite-element modeling is used to quantify the effect of these channel distributions on the neuron-electrode contact. Slight accumulation or depletion of voltage-sensitive channels in the sealing membrane of the neuron results in various shapes and amplitudes of simulated extracellular recordings. However, estimation of channel-specific accumulation factors from extracellular recordings can be obstructed by co-occuring ion currents and defect sealing. Experimental data from cultured neuron-electrode interfaces suggest depletion of sodium channels and accumulation of potassium channels