Hydration and mobility of HO-(aq)

The hydroxide anion plays an essential role in many chemical and biochemical reactions. But a molecular-scale description of its hydration state, and hence also its transport, in water is currently controversial. The statistical mechanical quasi-chemical theory of solutions suggests that HO[H2O]3- is the predominant species in the aqueous phase under standard conditions. This result is in close agreement with recent spectroscopic studies on hydroxide water clusters, and with the available thermodynamic hydration free energies. In contrast, a recent ab initio molecular dynamics simulation has suggested that HO[H_2O]4- is the only dominant aqueous solution species. We apply adiabatic ab initio molecular dynamics simulations, and find good agreement with both the quasi-chemical theoretical predictions and experimental results. The present results suggest a picture that is simpler, more traditional, but with additional subtlety. These coordination structures are labile but the tri-coordinate species is the prominent case. This conclusion is unaltered with changes in the electronic density functional. No evidence is found for rate-determining activated inter-conversion of a HO[H2O]4- trap structure to HO[H2O]3-, mediating hydroxide transport. The view of HO- diffusion as the hopping of a proton hole has substantial validity, the rate depending largely on the dynamic disorder of the water hydrogen-bond network.Comment: 7 pages, 5 figures, additional results include

Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response

Background Sensing and responding to ambient temperature is important for controlling growth and development of many organisms, in part by regulating mRNA levels. mRNA abundance can change with temperature, but it is unclear whether this results from changes in transcription or decay rates, and whether passive or active temperature regulation is involved. Results Using a base analog labelling method, we directly measured the temperature coefficient, Q10, of mRNA synthesis and degradation rates of the Arabidopsis transcriptome. We show that for most genes, transcript levels are buffered against passive increases in transcription rates by balancing passive increases in the rate of decay. Strikingly, for temperature-responsive transcripts, increasing temperature raises transcript abundance primarily by promoting faster transcription relative to decay and not vice versa, suggesting a global transcriptional process exists that controls mRNA abundance by temperature. This is partly accounted for by gene body H2A.Z which is associated with low transcription rate Q10, but is also influenced by other marks and transcription factor activities. Conclusions Our data show that less frequent chromatin states can produce temperature responses simply by virtue of their rarity and the difference between their thermal properties and those of the most common states, and underline the advantages of directly measuring transcription rate changes in dynamic systems, rather than inferring rates from changes in mRNA abundance. Background The mechanism for ambient temperature sensing in plants is unclear. Control of transcript levels is believed to be important in responses to temperature [1-4] but affects of ambient temperature on transcription and mRNA decay rates have not been measured. According to the work of Arrhenius [5] the temperature coefficient (Q10) of biochemical reactions is expected to be 2 to 3 at biological temperatures: yet less than 2% of Arabidopsis thaliana genes have a two-fold or greater difference in expression level between 17°C and 27°C [6]. The remaining genes either have rates buffered against changing temperatures, or passive increases in transcription rate must be offset by a balanced increase in decay rate, leading to higher turnover but static steady state levels. Despite this fundamental uncertainty, steady state transcriptomic responses to ambient temperature have been used to infer a role for chromatin modifications in temperature signaling [2,7]. 4-Thiouracil (4SU) is a non-toxic base analogue that has been shown to be incorporated into mammalian and yeast mRNA during transcription [8-12]. Biotinylation and column separation allow 4SU-labeled RNA to be separated from unlabeled RNA, and transcriptomic analysis using the separated samples can be used to simultaneously calculate mRNA synthesis and decay rates [8]. Here we use 4SU labeling to measure transcription rates and determine the Q10 genome-wide of mRNA synthesis and decay rates in Arabidopsis thaliana. We show that ambient temperature has large passive effects on both mRNA synthesis and decay rates, and that where temperature controls transcript abundance it does so by regulating transcription relative to decay and not vice versa. Our analysis suggests that transcription factor binding sites and epigenetic state combine to create a complex network of temperature responses in plants. Results Cells incorporate 4SU into RNA and this has been exploited in mammalian cells [8,11,12] and in yeast [13] to measure mRNA synthesis and decay rates. In order to determine whether plants can take up 4SU we floated intact seedlings in MS medium and monitored 4SU incorporation into RNA by biotinylation and dot blot (Figure S1a in Additional file 1). This clearly showed that plants incorporate 4SU from the environment into RNA and that concentrations as low as 1 mM lead to a signal detectable above background within 1 hour (Figure 1B). The resulting RNA could be separated from unlabeled RNA by biotinylation and passage through a streptavidin column as described previously. At 1.5 mM the flow-through can be depleted of detectable 4SU-labeled RNA, whilst labeled plant RNA is highly concentrated in the fraction recovered from the column [8,13] (Figure S1c in Additional file 1). To maximize recovery we chose a low concentration of 4SU at 1.5 mM [8] as high labeling frequencies are known to lead to binding of fewer more frequently labeled transcripts to the columns and reduce recovery. At this concentration Arabidopsis plants treated with 4SU showed the same growth and survival as control plants (Figure S2a in Additional file 1), suggesting 4SU has low toxicity in plants, as in other organisms. Therefore, 4SU dynamics in Arabidopsis seedlings resemble those described for other experimental systems. Preliminary experiments showed that RNA turnover was faster at 27°C compared to 12°C (Figure S2b in Additional file 1), suggesting that temperature generally affected transcription rates

Thermalization after holographic bilocal quench

We study thermalization in the holographic (1+1)-dimensional CFT after simultaneous generation of two high-energy excitations in the antipodal points on the circle. The holographic picture of such quantum quench is the creation of BTZ black hole from a collision of two massless particles. We perform holographic computation of entanglement entropy and mutual information in the boundary theory and analyze their evolution with time. We show that equilibration of the entanglement in the regions which contained one of the initial excitations is generally similar to that in other holographic quench models, but with some important distinctions. We observe that entanglement propagates along a sharp effective light cone from the points of initial excitations on the boundary. The characteristics of entanglement propagation in the global quench models such as entanglement velocity and the light cone velocity also have a meaning in the bilocal quench scenario. We also observe the loss of memory about the initial state during the equilibration process. We find that the memory loss reflects on the time behavior of the entanglement similarly to the global quench case, and it is related to the universal linear growth of entanglement, which comes from the interior of the forming black hole. We also analyze general two-point correlation functions in the framework of the geodesic approximation, focusing on the study of the late time behavior.Comment: 75 pages, 41 figure, v2: typos corrected, references and minor comments added, v3: published versio

BPS Solutions in D=5 Dilaton-Axion Gravity

We show that the D=5 dilaton-axion gravity compactified on a 2-torus possesses the SL(4,R)/SO(4) matrix formulation. It is used for construction of the SO(2,2)-invariant BPS solution depended on the one harmonic function.Comment: presented at GR1

Distributed PC Based Routers: Bottleneck Analysis and Architecture Proposal

Recent research in the different functional areas of modern routers have made proposals that can greatly increase the efficiency of these machines. Most of these proposals can be implemented quickly and often efficiently in software. We wish to use personal computers as forwarders in a network to utilize the advances made by researchers. We therefore examine the ability of a personal computer to act as a router. We analyze the performance of a single general purpose computer and show that I/O is the primary bottleneck. We then study the performance of distributed router composed of multiple general purpose computers. We study the performance of a star topology and through experimental results we show that although its performance is good, it lacks flexibility in its design. We compare it with a multistage architecture. We conclude with a proposal for an architecture that provides us with a forwarder that is both flexible and scalable.© IEE

Efficacy of first-line sodium thiosulphate administration in a case of potassium cyanide poisoning

Cyanide poisoning may occur following accidental fire-smoke inhalation or deliberate ingestion of salts. Hydroxocobalamin represents a first-line life-saving antidote. Although hydroxocobalamin represents a first-line lifesaving antidote, it is still not promptly available in the emergency department. Sodium thiosulfate can be administered in association with hydroxocobalamin whereas the delayed onset of clinical response makes sodium thiosulfate less suitable for emergency use. We describe a case of cyanide intoxication of a 43-year-old man who ingested an unknown amount of potassium cyanide, purchased via the Internet, in an attempted suicide. At admission to the emergency department, the patient presented GCS 3 with severe lactic acidosis. Orotracheal intubation, gastric lavage and oral activated charcoal were applied. Sodium thiosulfate was available in the emergency department and 10 grams were infused over a 30 minute period. Hydroxocobalamin was prescribed by the poison control centre and 5 grams were infused 2 hours after admission. Following sodium thiosulfate administration the patient was arousable and lactate concentration improved. No adverse effects were noted. Metabolic acidosis completely resolved 12 hours later. Cyanide concentration performed on blood samples collected at admission confirmed high cyanide blood levels (15 mg/L). This report highlights as the first-line administration of sodium thiosulfate, in rapid infusion, resulted effective and safe for cyanide poisoning. Our report suggests that sodium thiosulfate should be considered when hydroxocobalamin is not promptly available in an emergency settin

WHAT IS THE LENGTH OF A SNAKE?

The way that herpetologists have traditionally measuredlive snakes is by stretching them on a ruler andrecording the total length (TL). However, due to the thinconstitution of the snake, the large number of intervertebraljoints, and slim muscular mass of most snakes,it is easier to stretch a snake than it is to stretch anyother vertebrate. The result of this is that the length ofa snake recorded is infl uenced by how much the animalis stretched. Stretching it as much as possible is perhapsa precise way to measure the length of the specimenbut it might not correspond to the actual length ofa live animal. Furthermore, it may seriously injure a livesnake. Another method involves placing the snake in aclear plexiglass box and pressing it with a soft materialsuch as rubber foam against a clear surface. Measuringthe length of the snake may be done by outlining itsbody with a string (Fitch 1987; Frye 1991). However, thismethod is restricted to small animals that can be placedin a box, and in addition, no indications of accuracy of thetechnique are given. Measuring the snakes with a fl exibletape has also been reported (Blouin-Demers 2003)but when dealing with a large animals the way the tapeis positioned can produce great variance on the fi nal outcome.In this contribution we revise alternative ways tomeasuring a snake and propose a method that offers repeatableresults. We further analyze the precision of thismethod by using a sample of measurements taken fromwild populations of green anacondas (Eunectes murinus)with a large range of sizes