Evolution of transcriptional networks in yeast: Alternative teams of transcriptional factors for different species

Background: The diversity in eukaryotic life reflects a diversity in regulatory pathways. Nocedal and Johnson argue that the rewiring of gene regulatory networks is a major force for the diversity of life, that changes in regulation can create new species. Results: We have created a method (based on our new "ping-pong algorithm) for detecting more complicated rewirings, where several transcription factors can substitute for one or more transcription factors in the regulation of a family of co-regulated genes. An example is illustrative. A rewiring has been reported by Hogues et al. that RAP1 in Saccharomyces cerevisiae substitutes for TBF1/CBF1 in Candida albicans for ribosomal RP genes. There one transcription factor substitutes for another on some collection of genes. Such a substitution is referred to as a "rewiring". We agree with this finding of rewiring as far as it goes but the situation is more complicated. Many transcription factors can regulate a gene and our algorithm finds that in this example a "team" (or collection) of three transcription factors including RAP1 substitutes for TBF1 for 19 genes. The switch occurs for a branch of the phylogenetic tree containing 10 species (including Saccharomyces cerevisiae), while the remaining 13 species (Candida albicans) are regulated by TBF1. Conclusions: To gain insight into more general evolutionary mechanisms, we have created a mathematical algorithm that finds such general switching events and we prove that it converges. Of course any such computational discovery should be validated in the biological tests. For each branch of the phylogenetic tree and each gene module, our algorithm finds a sub-group of co-regulated genes and a team of transcription factors that substitutes for another team of transcription factors. In most cases the signal will be small but in some cases we find a strong signal of switching. We report our findings for 23 Ascomycota fungi species. © 2016 The Author(s)

Critical wetting of a class of nonequilibrium interfaces: A mean-field picture

A self-consistent mean-field method is used to study critical wetting transitions under nonequilibrium conditions by analyzing Kardar-Parisi-Zhang (KPZ) interfaces in the presence of a bounding substrate. In the case of positive KPZ nonlinearity a single (Gaussian) regime is found. On the contrary, interfaces corresponding to negative nonlinearities lead to three different regimes of critical behavior for the surface order-parameter: (i) a trivial Gaussian regime, (ii) a weak-fluctuation regime with a trivially located critical point and nontrivial exponents, and (iii) a highly non-trivial strong-fluctuation regime, for which we provide a full solution by finding the zeros of parabolic-cylinder functions. These analytical results are also verified by solving numerically the self-consistent equation in each case. Analogies with and differences from equilibrium critical wetting as well as nonequilibrium complete wetting are also discussed.Comment: 11 pages, 2 figure

Tissue distribution of mercury and its relationship with selenium in atlantic bluefin tuna (Thunnus thynnus l.)

Mercury (Hg) is an important heavy metal to consider in marine predators, while selenium (Se) has a natural antagonistic effect on this metal in fish. The Atlantic bluefin tuna (ABFT, Thunnus thynnus) is a pelagic top-level predator of the trophic web and their Hg muscular content is an object of concern in food safety. Nevertheless, little is known about levels of this metal in remaining tissues, which may be important as by-product source, and its relationship with Se. Thus, concentration of both elements in liver, kidney, brain, gill and bone, in addition to muscle, of ABFT were determined. The kidney was the tissue with the highest concentration of Hg (Total-Hg, THg) and Se, and the Se/THg concentration ratio was similar in all tissues, except bone and muscle. The Selenium Health Benefit Value (HBVSe ) was positive in each specimen and tissue, indicating that the Se plays an important role against Hg not only in the muscle. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.Preprin

Finite size effects in nonequilibrium wetting

Models with a nonequilibrium wetting transition display a transition also in finite systems. This is different from nonequilibrium phase transitions into an absorbing state, where the stationary state is the absorbing one for any value of the control parameter in a finite system. In this paper, we study what kind of transition takes place in finite systems of nonequilibrium wetting models. By solving exactly a microscopic model with three and four sites and performing numerical simulations we show that the phase transition taking place in a finite system is characterized by the average interface height performing a random walk at criticality and does not discriminate between the bounded-KPZ classes and the bounded-EW class. We also study the finite size scaling of the bKPZ universality classes, showing that it presents peculiar features in comparison with other universality classes of nonequilibrium phase transitions.Comment: 14 pages, 6figures, major change

Diagnosis and numerical simulations of a heavy rain event in the Western Mediterranean Basin

International audienceThe heavy rain event of November 2001 in the western Mediterranean area was synoptically characterized by the presence of a long-lived Omega blocking geopotential pattern. A set of mesoscale numerical simulations using MM5 is performed to investigate the mechanisms responsible for the convection development through several output diagnosis. A potential vorticity evolution showed how dry air masses were extruded from the stratospheric levels promoting strong cyclonic circulation at all levels. Moreover, a deep vertical column of high relative humidity over the Algerian coastline maintained the few and geographically confined convective cells responsible for the heavy precipitation. Mesoscale environment parameters indicated enhanced conditional instability through a deep troposphere layer. Also, strong vertical wind shear values, higher than 50 ms?1 over the troposphere, were derived, indicating enough strength to promote necessary conditions to organize and keep mesoscale convective structures

Stochastic theory of non-equilibrium wetting

We study a Langevin equation describing non-equilibrium depinning and wetting transitions. Attention is focused on short-ranged attractive substrate-interface potentials. We confirm the existence of first order depinning transitions, in the temperature-chemical potential diagram, and a tricritical point beyond which the transition becomes a non-equilibrium complete wetting transition. The coexistence of pinned and depinned interfaces occurs over a finite area, in line with other non-equilibrium systems that exhibit first order transitions. In addition, we find two types of phase coexistence, one of which is characterized by spatio-temporal intermittency (STI). A finite size analysis of the depinning time is used to characterize the different coexisting regimes. Finally, a stationary distribution of characteristic triangles or facets was shown to be responsible for the structure of the STI phase.Comment: To appear in Europhys. Lett. // 3 figure

A Novel Root-Knot Nematode Resistance QTL on Chromosome Vu01 in Cowpea.

The root-knot nematode (RKN) species Meloidogyne incognita and M. javanica cause substantial root system damage and suppress yield of susceptible cowpea cultivars. The narrow-based genetic resistance conferred by the Rk gene, present in some commercial cultivars, is not effective against Rk-virulent populations found in several cowpea production areas. The dynamics of virulence within RKN populations require a broadening of the genetic base of resistance in elite cowpea cultivars. As part of this goal, F1 and F2 populations from the cross CB46-Null (susceptible) x FN-2-9-04 (resistant) were phenotyped for M. javanica induced root-galling (RG) and egg-mass production (EM) in controlled growth chamber and greenhouse infection assays. In addition, F[Formula: see text] families of the same cross were phenotyped for RG on field sites infested with Rk-avirulent M. incognita and M. javanica The response of F1 to RG and EM indicated that resistance to RKN in FN-2-9-04 is partially dominant, as supported by the degree of dominance in the F2 and F[Formula: see text] populations. Two QTL associated with both RG and EM resistance were detected on chromosomes Vu01 and Vu04. The QTL on Vu01 was most effective against aggressive M. javanica, whereas both QTL were effective against avirulent M. incognita Allelism tests with CB46 x FN-2-9-04 progeny indicated that these parents share the same RKN resistance locus on Vu04, but the strong, broad-based resistance in FN-2-9-04 is conferred by the additive effect of the novel resistance QTL on Vu01. This novel resistance in FN-2-9-04 is an important resource for broadening RKN resistance in elite cowpea cultivars

Langevin theory of absorbing phase transitions with a conserved magnitude

The recently proposed Langevin equation, aimed to capture the relevant critical features of stochastic sandpiles, and other self-organizing systems is studied numerically. This equation is similar to the Reggeon field theory, describing generic systems with absorbing states, but it is coupled linearly to a second conserved and static (non-diffusive) field. It has been claimed to represent a new universality class, including different discrete models: the Manna as well as other sandpiles, reaction-diffusion systems, etc. In order to integrate the equation, and surpass the difficulties associated with its singular noise, we follow a numerical technique introduced by Dickman. Our results coincide remarkably well with those of discrete models claimed to belong to this universality class, in one, two, and three dimensions. This provides a strong backing for the Langevin theory of stochastic sandpiles, and to the very existence of this new, yet meagerly understood, universality class.Comment: 4 pages, 3 eps figs, submitted to PR

Springtime coupled modes of regional wind in the Iberian Peninsula and large-scale variability patterns

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Critical wetting of a class of nonequilibrium interfaces: A computer simulation study

Critical wetting transitions under nonequilibrium conditions are studied numerically and analytically by means of an interface-displacement model defined by a Kardar-Parisi-Zhang equation, plus some extra terms representing a limiting, short-ranged attractive wall. Its critical behavior is characterized in detail by providing a set of exponents for both the average height and the surface order-parameter in one dimension. The emerging picture is qualitatively and quantitatively different from recently reported mean-field predictions for the same problem. Evidence is shown that the presence of the attractive wall induces an anomalous scaling of the interface local slopes.Comment: 7 pages, 8 figure