Genome dynamics explain the evolution of flowering time CCT domain gene families in the Poaceae

Numerous CCT domain genes are known to control flowering in plants. They belong to the CONSTANS-like (COL) and PREUDORESPONSE REGULATOR (PRR) gene families, which in addition to a CCT domain possess B-box or response-regulator domains, respectively. Ghd7 is the most recently identified COL gene to have a proven role in the control of flowering time in the Poaceae. However, as it lacks B-box domains, its inclusion within the COL gene family, technically, is incorrect. Here, we show Ghd7 belongs to a larger family of previously uncharacterized Poaceae genes which possess just a single CCT domain, termed here CCT MOTIF FAMILY (CMF) genes. We molecularly describe the CMF (and related COL and PRR) gene families in four sequenced Poaceae species, as well as in the draft genome assembly of barley (Hordeum vulgare). Genetic mapping of the ten barley CMF genes identified, as well as twelve previously unmapped HvCOL and HvPRR genes, finds the majority map to colinear positions relative to their Poaceae orthologues. Combined inter-/intra-species comparative and phylogenetic analysis of CMF, COL and PRR gene families indicates they evolved prior to the monocot/dicot divergence ~200 mya, with Poaceae CMF evolution described as the interplay between whole genome duplication in the ancestral cereal, and subsequent clade-specific mutation, deletion and duplication events. Given the proven role of CMF genes in the modulation of cereals flowering, the molecular, phylogenetic and comparative analysis of the Poaceae CMF, COL and PRR gene families presented here provides the foundation from which functional investigation can be undertaken.

The population dynamics of disease on short and long time-scales

Observational evidence is scarce concerning the distribution of plant pathogen population sizes or densities as a function of time-scale or spatial scale. For wild pathosystems we can only get indirect evidence from evolutionary patterns and the consequences of biological invasions.We have little or no evidence bearing on extermination of hosts by pathogens, or successful escape of a host from a pathogen. Evidence over the last couple of centuries from crops suggest that the abundance of particular pathogens in the spectrum affecting a given host can vary hugely on decadal timescales. However, this may be an artefact of domestication and intensive cultivation. Host-pathogen dynamics can be formulated mathematically fairly easily–for example as SIR-type differential equation or difference equation models, and this has been the (successful) focus of recent work in crops. “Long-term” is then discussed in terms of the time taken to relax from a perturbation to the asymptotic state. However, both host and pathogen dynamics are driven by environmental factors as well as their mutual interactions, and both host and pathogen co-evolve, and evolve in response to external factors. We have virtually no information about the importance and natural role of higher trophic levels (hyperpathogens) and competitors, but they could also induce long-scale fluctuations in the abundance of pathogens on particular hosts. In wild pathosystems the host distribution cannot be modelled as either a uniform density or even a uniform distribution of fields (which could then be treated as individuals). Patterns of short term density-dependence and the detail of host distribution are therefore critical to long-term dynamics. Host density distributions are not usually scale-free, but are rarely uniform or clearly structured on a single scale. In a (multiply structured) metapopulation with coevolution and external disturbances it could well be the case that the time required to attain equilibrium (if it exists) based on conditions stable over a specified time-scale is longer than that time-scale. Alternatively, local equilibria may be reached fairly rapidly following perturbations but the meta-population equilibrium be attained very slowly. In either case, meta-stability on various time-scales is a more relevant than equilibrium concepts in explaining observed patterns.

Long-lived excited-state dynamics of i-motif structures probed by time-resolved infrared spectroscopy

UV-generated excited states of cytosine (C) nucleobases are precursors to mutagenic photoproduct formation. The i-motif formed from C-rich sequences is known to exhibit high yields of long-lived excited states following UV absorption. Here the excited states of several i-motif structures have been characterized following 267 nm laser excitation using time-resolved infrared spectroscopy (TRIR). All structures possess a long-lived excited state of ~300 ps and notably in some cases decays greater than 1 ns are observed. These unusually long-lived lifetimes are attributed to the interdigitated DNA structure which prevents direct base stacking overlap.

CHARGED PARTICLE DYNAMICS IN TIME DEPENDENT MAGNETIC FIELDS

In this work we study the behavior of charged particles immersed in a peculiar configuration of magnetic fields, which has a main constant field B(0) and a superimposed, transversal perturbation field B(1) sin(omega(p)t), with B(1) << B(0). By taking Cartesian coordinates and placing B(0) along the z axis and B(1) sin (omega(p)t) on the x axis, an analytical solution for y(t) may be obtained by solving an integrodifferential equation. Besides, the solution z(t) also exhibits a very interesting dynamics, and the entire system is conditioned by resonances between the particle orbit frequencies and the frequency of the magnetic transversal perturbation, omega(p). In this work we also discuss numerical simulations for the related particle trajectories, as well as potential applications in the context of separation phenomena.

Coordinate and time-dependent diffusion dynamics in protein folding

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Noncommutative fluid dynamics in the Snyder space-time

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Scaling dynamics for a particle in a time-dependent potential well

Some dynamical properties for a classical particle confined in an infinitely deep box of potential containing a periodically oscillating square well are studied. The dynamics of the system is described by using a two-dimensional non-linear area-preserving map for the variables energy and time. The phase space is mixed and the chaotic sea is described using scaling arguments. Scaling exponents are obtained as a function of all the control parameters, extending the previous results obtained in the literature. (c) 2012 Elsevier B.V. All rights reserved.

CRITICAL EXPONENTS and SCALING PROPERTIES FOR THE CHAOTIC DYNAMICS of A PARTICLE IN A TIME-DEPENDENT POTENTIAL BARRIER

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Dynamics in discrete phase spaces and time interval operators

The von Neumann-Liouville time evolution equation is represented in a discrete quantum phase space. The mapped Liouville operator and the corresponding Wigner function are explicitly written for the problem of a magnetic moment interacting with a magnetic field and the precessing solution is found. The propagator is also discussed and a time interval operator, associated to a unitary operator which shifts the energy levels in the Zeeman spectrum, is introduced. This operator is associated to the particular dynamical process and is not the continuous parameter describing the time evolution. The pair of unitary operators which shifts the time and energy is shown to obey the Weyl-Schwinger algebra. (C) 1999 Elsevier B.V. B.V. All rights reserved.

Electromagnetic form factor of the pion in the space- and time-like regions within the front-form dynamics

The pion electromagnetic form factor is calculated in the space- and time-like regions from -10 (GeV/c)2 up to 10 (GeV/c)2, within a front-form model. The dressed photon vertex where a photon decays in a quark-antiquark pair is depicted generalizing the vector meson dominance ansatz, by means of the vector meson vertex functions. An important feature of our model is the description of the on-mass-shell vertex functions in the valence sector, for the pion and the vector mesons, through the front-form wave functions obtained within a realistic quark model. The theoretical results show an excellent agreement with the data in the space-like region, while in the time-like region the description is quite encouraging. © 2003 Elsevier B.V. All rights reserved.

Dynamics of handling time and functional response by larvae of Chrysomya albiceps (Dipt., Calliphoridae) on different prey species

One way to understand the behavioural patterns exhibited by a predator in response to prey density is to evaluate its functional response. Such evaluation yields information about basic mechanisms of prey-predator dynamics, and is an essential component of prey-predator models. In this paper we analysed experimentally the functional response and the handling time spent by Chrysomya albiceps on different prey species and larval instars of blowflies. The type II functional response was observed when second instar larvae of Chrysomya megacephala and Chrysomya macellaria were consumed. The handling time spent by the predator was significantly different between instars and species. The implications of the functional response and handling time for the interaction dynamics of Brazilian Chrysomyinae species are discussed.

Time-like and space-like pion form factors within front-form dynamics

An approach for a unified description of the pion electromagnetic form factor in the space- and time-like regions, within a constituent quark model on the light front is briefly illustrated. Three main ingredients enter our approach: i) the on-shell quark-hadron vertex functions in the valence sector, ii) the dressed photon vertex where a photon decays in a quark-antiquark pair, and iii) the emission and absorption amplitudes of a pion by a quark. © 2005 American Institute of Physics.

Generalized Metropolis dynamics with a generalized master equation: An approach for time-independent and time-dependent Monte Carlo simulations of generalized spin systems

The extension of Boltzmann-Gibbs thermostatistics, proposed by Tsallis, introduces an additional parameter q to the inverse temperature beta. Here, we show that a previously introduced generalized Metropolis dynamics to evolve spin models is not local and does not obey the detailed energy balance. In this dynamics, locality is only retrieved for q = 1, which corresponds to the standard Metropolis algorithm. Nonlocality implies very time-consuming computer calculations, since the energy of the whole system must be reevaluated when a single spin is flipped. To circumvent this costly calculation, we propose a generalized master equation, which gives rise to a local generalized Metropolis dynamics that obeys the detailed energy balance. To compare the different critical values obtained with other generalized dynamics, we perform Monte Carlo simulations in equilibrium for the Ising model. By using short-time nonequilibrium numerical simulations, we also calculate for this model the critical temperature and the static and dynamical critical exponents as functions of q. Even for q not equal 1, we show that suitable time-evolving power laws can be found for each initial condition. Our numerical experiments corroborate the literature results when we use nonlocal dynamics, showing that short-time parameter determination works also in this case. However, the dynamics governed by the new master equation leads to different results for critical temperatures and also the critical exponents affecting universality classes. We further propose a simple algorithm to optimize modeling the time evolution with a power law, considering in a log-log plot two successive refinements.

Dynamics of Shifting Cultivation Landscapes in Northern Lao PDR Between 2000 and 2009 Based on an Analysis of MODIS Time Series and Landsat Images

The rotational nature of shifting cultivation poses several challenges to its detection by remote sensing. Consequently, there is a lack of spatial data on the dynamics of shifting cultivation landscapes on a regional, i.e. sub-national, or national level. We present an approach based on a time series of Landsat and MODIS data and landscape metrics to delineate the dynamics of shifting cultivation landscapes. Our results reveal that shifting cultivation is a land use system still widely and dynamically utilized in northern Laos. While there is an overall reduction in the areas dominated by shifting cultivation, some regions also show an expansion. A review of relevant reports and articles indicates that policies tend to lead to a reduction while market forces can result in both expansion and reduction. For a better understanding of the different factors affecting shifting cultivation landscapes in Laos, further research should focus on spatially explicit analyses.

Effects of forest management and time on herbaceous species dynamics in the western Upper Peninsula of Michigan

The herbaceous layer is a dynamic layer in a forest ecosystem which often contains the highest species richness in northern temperate forests. Few long-term studies exist in northern hardwood forests with consistent management practices to observe herbaceous species dynamics. The Ford Forest (Michigan Technological University) reached its 50th year of management during the winter of 2008-2009. Herbaceous species were sampled during the summers pre- and post-harvest. Distinct herbaceous communities developed in the 13-cm diameter-limit treatment and the uncut control. After the harvest, the diameter-limit treatments had herbaceous communities more similar to the 13-cm diameter-limit treatment than the uncut control; the herbaceous layer contained more exotic and early successional species. Fifty years of continuous management changed the herbaceous community especially in the diameter-limit treatments. Sites used in the development of habitat classification systems based on the presence and absence of certain herbaceous species can also be used to monitor vegetation change over time. The Guide to Forest Communities and Habitat Types of Michigan was developed to aid forest managers in understanding the potential productivity of a stand, and often aid in the development of ecologically-based forest management practices. Subsets of plots used to create the Western Upper Peninsula Guide were resampled after 10 years. During the resampling, both spring and summer vegetation were sampled and earthworm populations were estimated through liquid extraction. Spring sampling observed important spring ephemerals missed during summer sampling. More exotic species were present during the summer 2010 sampling than the summer 2000 sampling. Invasive European earthworms were also observed at all sample locations in all habitat types; earthworm densities increased with increasing habitat richness. To ensure the accuracy of the guide book, plots should be monitored to see how herbaceous communities are changing. These plots also offer unique opportunities to monitor for invasive species and the effects of a changing climate.