1,268 research outputs found
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
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