Folding and unfolding of a triple-branch DNA molecule with four conformational states

Single-molecule experiments provide new insights into biological processes hitherto not accessible by measurements performed on bulk systems. We report on a study of the kinetics of a triple-branch DNA molecule with four conformational states by pulling experiments with optical tweezers and theoretical modelling. Three distinct force rips associated with different transitions between the conformational states are observed in the folding and unfolding trajectories. By applying transition rate theory to a free energy model of the molecule, probability distributions for the first rupture forces of the different transitions are calculated. Good agreement of the theoretical predictions with the experimental findings is achieved. Furthermore, due to our specific design of the molecule, we found a useful method to identify permanently frayed molecules by estimating the number of opened basepairs from the measured force jump values.Comment: 17 pages, 12 figure

Radiative two-pion decay of the tau lepton

We consider the bremsstrahlung and model-dependent contributions to the radiative decay $\tau^- \to \pi^-\pi^0\nu_{\tau}\gamma$ in the context of a meson dominance model. We focus on several observables related to this decay, including the branching ratio and the photon and di-pion spectra. Particular attention is paid to the sensitivity of different observables upon the effects of model-dependent contributions and of the magnetic dipole moment of the $\rho^-(770)$ vector meson. Important numerical differences are found with respect to results obtained in the framework of chiral perturbation theory.Comment: 14 pages, 8 figures, submitted for publicatio

Inter-Particle Distribution Functions for One-Species Diffusion-Limited Annihilation, A+A->0

Diffusion-limited annihilation, $A+A\to 0$, and coalescence, $A+A\to A$, may both be exactly analyzed in one dimension. While the concentrations of $A$ particles in the two processes bear a simple relation, the inter-particle distribution functions (IPDF) exhibit remarkable differences. However, the IPDF is known exactly only for the coalescence process. We obtain the IPDF for the annihilation process, based on the Glauber spin approach and assuming that the IPDF's of nearest-particle pairs are statistically independent. This assumption is supported by computer simulations. Our analysis sheds further light on the relationship between the annihilation and the coalescence models.Comment: 15 pages, plain TeX, 3 figures - available upon request (snail mail

Reactive dynamics on fractal sets: anomalous fluctuations and memory effects

We study the effect of fractal initial conditions in closed reactive systems in the cases of both mobile and immobile reactants. For the reaction $A+A\to A$, in the absence of diffusion, the mean number of particles $A$ is shown to decay exponentially to a steady state which depends on the details of the initial conditions. The nature of this dependence is demonstrated both analytically and numerically. In contrast, when diffusion is incorporated, it is shown that the mean number of particles $$ decays asymptotically as $t^{-d_f/2}$, the memory of the initial conditions being now carried by the dynamical power law exponent. The latter is fully determined by the fractal dimension $d_f$ of the initial conditions.Comment: 7 pages, 2 figures, uses epl.cl

Fish health challenge after stress : indicators of immunocompetence

Changes in the nervous and endocrine systems of fish after stress episodes have consequences on their immune system and thereby affect the ability to maintain immunocompetence. Fish mainly depend upon innate immune responses, which include a rich and powerful array of mechanisms, that appear to be more potent than in higher vertebrates. Thus, fish provide a unique model to understand the evolution of immune defence system. When the organism is challenged by an antigen or by stressors, a number of responses of reactive nature are engaged in an attempt to counteract the threat and recover homeostasis. However, if the challenge is maintained, changes in the immune system become chronic, and suppression can be observed in several key immune mechanisms, leading to maladaptation. Therefore, the time factor is of key importance in immune assessment. Taking into account this dynamic pattern of infection and stress, specific indicators should be identified in order to detect functional changes in the immune system. Furthermore, there is a need for specific markers that reflect either activation in the initial stages or suppression in response to a chronic challenge.Els canvis en els sistemes nerviós i endocrí després d'episodis d'estrès generen conseqüències en el sistema immunitari que influeixen en la capacitat de mantenir la immunocompetència. Els peixos depenen especialment de la resposta immunitària innata, un ampli conjunt de mecanismes que sembla que actuïn amb més potència que en vertebrats superiors. Així, els peixos es troben en una posició evolutiva única per a comprendre els models de mecanismes de defensa en els vertebrats. Quan l'organisme és afectat per un antigen o per situacions que provoquen estrès, s'inicien una sèrie de respostes de naturalesa reactiva per a contrarestar-ne els efectes i recobrar l'homeòstasi. Altrament, els canvis en el sistema immunitari esdevenen crònics i es pot observar una depressió en alguns mecanismes immunitaris que acaben amb una mala adaptació. Per tant, el factor temps és clau en la determinació de la resposta immunitària. Tenint en compte aquest patró dinàmic en la infecció i l'estrès, és important determinar indicadors específics que detectin canvis funcionals del sistema immunitari dels peixos. Els marcadors més apropiats són els que indiquen tant una activació dels mecanismes immunitaris en els estadis inicials com una depressió en situacions cròniques

Kinetic Regimes and Cross-Over Times in Many-Particle Reacting Systems

We study kinetics of single species reactions ("A+A -> 0") for general local reactivity Q and dynamical exponent z (rms displacement x_t ~ t^{1/z}.) For small molecules z=2, whilst z=4,8 for certain polymer systems. For dimensions d above the critical value d_c=z, kinetics are always mean field (MF). Below d_c, the density n_t initially follows MF decay, n_0 - n_t ~ n_0^2 Q t. A 2-body diffusion-controlled regime follows for strongly reactive systems (Q>Qstar ~ n_0^{(z-d)/d}) with n_0 - n_t ~ n_0^2 x_t^d. For Q<Qstar, MF kinetics persist, with n_t ~ 1/Qt. In all cases n_t ~ 1/x_t^d at the longest times. Our analysis avoids decoupling approximations by instead postulating weak physically motivated bounds on correlation functions.Comment: 10 pages, 1 figure, uses bulk2.sty, minor changes, submitted to Europhysics Letter

Quantal distribution functions in non-extensive statistics and an early universe test revisited

Within the context of non-extensive thermostatistics, we use the factorization approximation to study a recently proposed early universe test. A very restrictive bound upon the non-extensive parameter is presented: $|q-1| < 4.01 \times 10^{-3}$.Comment: 4 pages, prl revtex style, no figures. To appear in Physica A, 199

Sub-toxic Ethanol Exposure Modulates Gene Expression and Enzyme Activity of Antioxidant Systems to Provide Neuroprotection in Hippocampal HT22 Cells

Ethanol is known to cause severe systemic damage often explained as secondary to oxidative stress. Brain is particularly vulnerable to ethanol-induced reactive oxygen species (ROS) because the high amounts of lipids, and because nerve cell membranes contain high amounts of peroxidable fatty acids. Usually these effects of ethanol are associated to high and/or chronic exposure to ethanol. However, as we show in this manuscript, a low and acute dose of ethanol trigger a completely different response in hippocampal cells. Thus, we have observed that 0.1% ethanol exposure to HT22 cells, a murine hippocampal-derived cell line, increases the transcriptional expression of different genes belonging to the classical, glutathione/glutaredoxin and thioredoxin/peroxiredoxin antioxidant systems, these including Sod1, Sod2, Gpx1, Gclc, and Txnrd1. Paralleling these changes, enzyme activities of total superoxide dismutase (tSOD), catalase, total glutathione peroxidase (tGPx), glutathione-S-reductase (GSR), and total thioredoxin reductase (tTXNRD), were all increased, while the generation of thiobarbituric acid reactive substances (TBARS), as indicators of lipid peroxidation, and glutathione levels remained unaltered. Ethanol exposure did not affect cell viability or cell growing as assessed by real-time cell culture monitoring, indicating that low ethanol doses are not deleterious for hippocampal cells, but rather prevented glutamate-induced excitotoxicity. In summary, we conclude that sub-toxic exposure to ethanol may well be neuroprotective against oxidative insults in hippocampal cells.Supported by grants SAF2010-22114-C02-01 and SAF2014-52582-R from Ministerio de Economía y Competitividad (Spain). VC and DQ held fellowships from Gobierno de Canarias and Fundación Cajacanarias, respectively.Peer reviewedPeer Reviewe

Criticality of natural absorbing states

We study a recently introduced ladder model which undergoes a transition between an active and an infinitely degenerate absorbing phase. In some cases the critical behaviour of the model is the same as that of the branching annihilating random walk with $N\geq 2$ species both with and without hard-core interaction. We show that certain static characteristics of the so-called natural absorbing states develop power law singularities which signal the approach of the critical point. These results are also explained using random walk arguments. In addition to that we show that when dynamics of our model is considered as a minimum finding procedure, it has the best efficiency very close to the critical point.Comment: 6 page