Stability domains of actin genes and genomic evolution

In eukaryotic genes the protein coding sequence is split into several fragments, the exons, separated by non-coding DNA stretches, the introns. Prokaryotes do not have introns in their genome. We report the calculations of stability domains of actin genes for various organisms in the animal, plant and fungi kingdoms. Actin genes have been chosen because they have been highly conserved during evolution. In these genes all introns were removed so as to mimic ancient genes at the time of the early eukaryotic development, i.e. before introns insertion. Common stability boundaries are found in evolutionary distant organisms, which implies that these boundaries date from the early origin of eukaryotes. In general boundaries correspond with introns positions of vertebrates and other animals actins, but not much for plants and fungi. The sharpest boundary is found in a locus where fungi, algae and animals have introns in positions separated by one nucleotide only, which identifies a hot-spot for insertion. These results suggest that some introns may have been incorporated into the genomes through a thermodynamic driven mechanism, in agreement with previous observations on human genes. They also suggest a different mechanism for introns insertion in plants and animals.Comment: 9 Pages, 7 figures. Phys. Rev. E in pres

Exons, introns and DNA thermodynamics

The genes of eukaryotes are characterized by protein coding fragments, the exons, interrupted by introns, i.e. stretches of DNA which do not carry any useful information for the protein synthesis. We have analyzed the melting behavior of randomly selected human cDNA sequences obtained from the genomic DNA by removing all introns. A clear correspondence is observed between exons and melting domains. This finding may provide new insights in the physical mechanisms underlying the evolution of genes.Comment: 4 pages, 8 figures - Final version as published. See also Phys. Rev. Focus 15, story 1

Crackling Noise, Power Spectra and Disorder Induced Critical Scaling

Crackling noise is observed in many disordered non-equilibrium systems in response to slowly changing external conditions. Examples range from Barkhausen noise in magnets to acoustic emission in martensites to earthquakes. Using the non-equilibrium random field Ising model, we derive universal scaling predictions for the dependence of the associated power spectra on the disorder and field sweep rate, near an underlying disorder-induced non-equilibrium critical point. Our theory applies to certain systems in which the crackling noise results from avalanche-like response to a (slowly) increasing external driving force, and is characterized by a broad power law scaling regime of the power spectra. We compute the critical exponents and discuss the relevance of the results to experiments.Comment: 27 Latex Pages, 14 eps figure

Dietary omega-3 fatty acids modulate the eicosanoid profile in man primarily via the CYP-epoxygenase pathway

Cytochrome P450 (CYP)-dependent metabolites of arachidonic acid (AA) contribute to the regulation of cardiovascular function. CYP enzymes also accept eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) to yield more potent vasodilatory and potentially anti-arrhythmic metabolites, suggesting that the endogenous CYP-eicosanoid profile can be favorably shifted by dietary omega-3 fatty acids. To test this hypothesis, 20 healthy volunteers were treated with an EPA/DHA-supplement and analyzed for concomitant changes in the circulatory and urinary levels of AA-, EPA-, and DHA-derived metabolites produced by the cyclooxygenase-, lipoxygenase- and CYP-dependent pathways. Raising the Omega-3 Index from about 4 to 8 primarily resulted in a large increase of EPA-derived CYP-dependent epoxy-metabolites followed by increases of EPA- and DHA-derived lipoxygenase-dependent monohydroxy-metabolites including the precursors of resolvin E and D families; resolvins themselves were not detected. The metabolite/precursor fatty acid ratios indicated that CYP epoxygenases metabolized EPA with an 8.6-fold and DHA with a 2.2-fold higher efficiency than AA. Effects on leukotriene, prostaglandin E, prostacyclin, and thromboxane formation remained rather weak. We propose that CYP-dependent epoxy-metabolites of EPA and DHA may function as mediators of the vasodilatory and cardioprotective effects of omega-3 fatty acids and could serve as biomarkers in clinical studies investigating the cardiovascular effects of EPA/DHA-supplementation

Breathing dynamics in heteropolymer DNA

While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule spectroscopy. The dynamical opening of DNA bubbles (DNA breathing) is supposedly crucial for biological functioning during, for instance, transcription initiation and DNA's interaction with selectively single-stranded DNA binding proteins. Motivated by this, we consider the bubble breathing dynamics in a heteropolymer DNA based on a (2+1)-variable master equation and complementary stochastic Gillespie simulations, providing the bubble size and the position of the bubble along the sequence as a function of time. We utilize new experimental data that independently obtain stacking and hydrogen bonding contributions to DNA stability. We calculate the spectrum of relaxation times and the experimentally measurable autocorrelation function of a fluorophore-quencher tagged base-pair, and demonstrate good agreement with fluorescence correlation experiments. A significant dependence of opening probability and waiting time between bubble events on the local DNA sequence is revealed and quantified for a promoter sequence of the T7 phage. The strong dependence on sequence, temperature and salt concentration for the breathing dynamics of DNA found here points at a good potential for nanosensing applications by utilizing short fluorophore-quencher dressed DNA constructs.Comment: 11 pages, 8 figure

First order phase transition in a 1+1-dimensional nonequilibrium wetting process

A model for nonequilibrium wetting in 1+1 dimensions is introduced. It comprises adsorption and desorption processes with a dynamics which generically does not obey detailed balance. Depending on the rates of the dynamical processes the wetting transition is either of first or second order. It is found that the wet (unbound) and the non-wet (pinned) states coexist and are both thermodynamically stable in a domain of the dynamical parameters which define the model. This is in contrast with equilibrium transitions where coexistence of thermodynamically stable states takes place only on the transition line.Comment: 4 pages, RevTeX, including 4 eps figure

Monte Carlo simulation of subsurface ordering kinetics in an fcc-alloy model

Within the atom-vacancy exchange mechanism in a nearest-neighbor interaction model we investigate the kinetics of surface-induced ordering processes close to the (001) surface of an fcc A_3B-alloy. After a sudden quench into the ordered phase with a final temperature above the ordering spinodal, T_f > T_sp, the early time kinetics is dominated by a segregation front which propagates into the bulk with nearly constant velocity. Below the spinodal, T_f < T_sp, motion of the segregation wave reflects a coarsening process which appears to be slower than predicted by the Lifschitz-Allen-Cahn law. In addition, in the front-penetrated region lateral growth differs distinctly from perpendicular growth, as a result of the special structure of antiphase boundaries near the surface. Our results are compared with recent experiments on the subsurface ordering kinetics at Cu_3Au (001).Comment: 10 pages, 9 figures, submitted to Phys. Rev. B, in prin

Virulence of Oomycete Pathogens from \u3cem\u3ePhragmites australis\u3c/em\u3e-Invaded and Noninvaded Soils to Seedlings of Wetland Plant Species

Soil pathogens affect plant community structure and function through negative plant-soil feedbacks that may contribute to the invasiveness of non-native plant species. Our understanding of these pathogen-induced soil feedbacks has relied largely on observations of the collective impact of the soil biota on plant populations, with few observations of accompanying changes in populations of specific soil pathogens and their impacts on invasive and noninvasive species. As a result, the roles of specific soil pathogens in plant invasions remain unknown. In this study, we examine the diversity and virulence of soil oomycete pathogens in freshwater wetland soils invaded by non-native Phragmites australis (European common reed) to better understand the potential for soil pathogen communities to impact a range of native and non-native species and influence invasiveness. We isolated oomycetes from four sites over a 2-year period, collecting nearly 500 isolates belonging to 36 different species. These sites were dominated by species of Pythium, many of which decreased seedling survival of a range of native and invasive plants. Despite any clear host specialization, many of the Pythium species were differentially virulent to the native and non-native plant species tested. Isolates from invaded and noninvaded soils were equally virulent to given individual plant species, and no apparent differences in susceptibility were observed between the collective groups of native and non-native plant species

Susceptibility and Percolation in 2D Random Field Ising Magnets

The ground state structure of the two-dimensional random field Ising magnet is studied using exact numerical calculations. First we show that the ferromagnetism, which exists for small system sizes, vanishes with a large excitation at a random field strength dependent length scale. This {\it break-up length scale} $L_b$ scales exponentially with the squared random field, $\exp(A/\Delta^2)$. By adding an external field $H$ we then study the susceptibility in the ground state. If $L>L_b$, domains melt continuously and the magnetization has a smooth behavior, independent of system size, and the susceptibility decays as $L^{-2}$. We define a random field strength dependent critical external field value $\pm H_c(\Delta)$, for the up and down spins to form a percolation type of spanning cluster. The percolation transition is in the standard short-range correlated percolation universality class. The mass of the spanning cluster increases with decreasing $\Delta$ and the critical external field approaches zero for vanishing random field strength, implying the critical field scaling (for Gaussian disorder) $H_c \sim (\Delta -\Delta_c)^\delta$, where $\Delta_c = 1.65 \pm 0.05$ and $\delta=2.05\pm 0.10$. Below $\Delta_c$ the systems should percolate even when H=0. This implies that even for H=0 above $L_b$ the domains can be fractal at low random fields, such that the largest domain spans the system at low random field strength values and its mass has the fractal dimension of standard percolation $D_f = 91/48$. The structure of the spanning clusters is studied by defining {\it red clusters}, in analogy to the ``red sites'' of ordinary site-percolation. The size of red clusters defines an extra length scale, independent of $L$.Comment: 17 pages, 28 figures, accepted for publication in Phys. Rev.

CGILS: Results From The First Phase of An International Project to Understand The Physical Mechanisms of Low Cloud Feedbacks in Single Column Models

CGILS—the CFMIP-GASS Intercomparison of Large Eddy Models (LESs) and single column models (SCMs)—investigates the mechanisms of cloud feedback in SCMs and LESs under idealized climate change perturbation. This paper describes the CGILS results from 15 SCMs and 8 LES models. Three cloud regimes over the subtropical oceans are studied: shallow cumulus, cumulus under stratocumulus, and well-mixed coastal stratus/stratocumulus. In the stratocumulus and coastal stratus regimes, SCMs without activated shallow convection generally simulated negative cloud feedbacks, while models with active shallow convection generally simulated positive cloud feedbacks. In the shallow cumulus alone regime, this relationship is less clear, likely due to the changes in cloud depth, lateral mixing, and precipitation or a combination of them. The majority of LES models simulated negative cloud feedback in the well-mixed coastal stratus/stratocumulus regime, and positive feedback in the shallow cumulus and stratocumulus regime. A general framework is provided to interpret SCM results: in a warmer climate, the moistening rate of the cloudy layer associated with the surface-based turbulence parameterization is enhanced; together with weaker large-scale subsidence, it causes negative cloud feedback. In contrast, in the warmer climate, the drying rate associated with the shallow convection scheme is enhanced. This causes positive cloud feedback. These mechanisms are summarized as the “NESTS” negative cloud feedback and the “SCOPE” positive cloud feedback (Negative feedback from Surface Turbulence under weaker Subsidence—Shallow Convection PositivE feedback) with the net cloud feedback depending on how the two opposing effects counteract each other. The LES results are consistent with these interpretations