Modulation of plant growth in vivo and identification of kinase substrates using an analog-sensitive variant of CYCLIN-DEPENDENT KINASE A;1

BACKGROUND: Modulation of protein activity by phosphorylation through kinases and subsequent de-phosphorylation by phosphatases is one of the most prominent cellular control mechanisms. Thus, identification of kinase substrates is pivotal for the understanding of many – if not all – molecular biological processes. Equally, the possibility to deliberately tune kinase activity is of great value to analyze the biological process controlled by a particular kinase. RESULTS: Here we have applied a chemical genetic approach and generated an analog-sensitive version of CDKA;1, the central cell-cycle regulator in Arabidopsis and homolog of the yeast Cdc2/CDC28 kinases. This variant could largely rescue a cdka;1 mutant and is biochemically active, albeit less than the wild type. Applying bulky kinase inhibitors allowed the reduction of kinase activity in an organismic context in vivo and the modulation of plant growth. To isolate CDK substrates, we have adopted a two-dimensional differential gel electrophoresis strategy, and searched for proteins that showed mobility changes in fluorescently labeled extracts from plants expressing the analog-sensitive version of CDKA;1 with and without adding a bulky ATP variant. A pilot set of five proteins involved in a range of different processes could be confirmed in independent kinase assays to be phosphorylated by CDKA;1 approving the applicability of the here-developed method to identify substrates. CONCLUSION: The here presented generation of an analog-sensitive CDKA;1 version is functional and represent a novel tool to modulate kinase activity in vivo and identify kinase substrates. Our here performed pilot screen led to the identification of CDK targets that link cell proliferation control to sugar metabolism, proline proteolysis, and glucosinolate production providing a hint how cell proliferation and growth are integrated with plant development and physiology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0900-7) contains supplementary material, which is available to authorized users

Aging in the Relaxor Ferroelectric PMN/PT

The relaxor ferroelectric (PbMn$_{1/3}$Nb$_{2/3}$O$_3$)$_{1-x}$(PbTiO$_3$)$_{x}$, $x=0.1$, (PMN/PT(90/10)) is found to exhibit several regimes of complicated aging behavior. Just below the susceptibility peak there is a regime exhibiting rejuvenation but little memory. At lower temperature, there is a regime with mainly cumulative aging, expected for simple domain-growth. At still lower temperature, there is a regime with both rejuvenation and memory, reminiscent of spin glasses. PMN/PT (88/12) is also found to exhibit some of these aging regimes. This qualitative aging behavior is reminiscent of that seen in reentrant ferromagnets, which exhibit a crossover from a domain-growth ferromagnetic regime into a reentrant spin glass regime at lower temperatures. These striking parallels suggest a picture of competition in PMN/PT (90/10) between ferroelectric correlations formed in the domain-growth regime with glassy correlations formed in the spin glass regime. PMN/PT (90/10) is also found to exhibit frequency-aging time scaling of the time-dependent part of the out-of-phase susceptibility for temperatures 260 K and below. The stability of aging effects to thermal cycles and field perturbations is also reported.Comment: 8 pages RevTeX4, 11 figures; submitted to Phys. Rev.

The relative influences of disorder and of frustration on the glassy dynamics in magnetic systems

The magnetisation relaxations of three different types of geometrically frustrated magnetic systems have been studied with the same experimental procedures as previously used in spin glasses. The materials investigated are Y$_2$Mo$_2$O$_7$ (pyrochlore system), SrCr$_{8.6}$Ga$_{3.4}$O$_{19}$ (piled pairs of Kagom\'e layers) and (H$_3$O)Fe$_3$(SO$_4$)$_2$(OH)$_6$ (jarosite compound). Despite a very small amount of disorder, all the samples exhibit many characteristic features of spin glass dynamics below a freezing temperature $T_g$, much smaller than their Curie-Weiss temperature $\theta$. The ageing properties of their thermoremanent magnetization can be well accounted for by the same scaling law as in spin glasses, and the values of the scaling exponents are very close. The effects of temperature variations during ageing have been specifically investigated. In the pyrochlore and the bi-Kagom\'e compounds, a decrease of temperature after some waiting period at a certain temperature $T_p$ re-initializes ageing and the evolution at the new temperature is the same as if the system were just quenched from above $T_g$. However, as the temperature is raised back to $T_p$, the sample recovers the state it had previously reached at that temperature. These features are known in spin glasses as rejuvenation and memory effects. They are clear signatures of the spin glass dynamics. In the Kagom\'e compound, there is also some rejuvenation and memory, but much larger temperature changes are needed to observe the effects. In that sense, the behaviour of this compound is quantitatively different from that of spin glasses.Comment: latex VersionCorrigee4.tex, 4 files, 3 figures, 5 pages (Proceedings of the International Conference on Highly Frustrated Magnetism (HFM2003), August 26-30, 2003, Institut Laue Langevin (ILL), Grenoble, France

Aging, rejuvenation and memory effects in Ising and Heisenberg spin glasses

We have compared aging phenomena in the Fe_{0.5}Mn_{0.5}TiO_3 Ising spin glass and in the CdCr_{1.7}In_{0.3}S_4 Heisenberg-like spin glass by means of low-frequency ac susceptibility measurements. At constant temperature, aging obeys the same `$\omega t$ scaling' in both samples as in other systems. Investigating the effect of temperature variations, we find that the Ising sample exhibits rejuvenation and memory effects which are qualitatively similar to those found in other spin glasses, indicating that the existence of these phenomena does not depend on the dimensionality of the spins. However, systematic temperature cycling experiments on both samples show important quantitative differences. In the Ising sample, the contribution of aging at low temperature to aging at a slightly higher temperature is much larger than expected from thermal slowing down. This is at variance with the behaviour observed until now in other spin glasses, which show the opposite trend of a free-energy barrier growth as the temperature is decreased. We discuss these results in terms of a strongly renormalized microscopic attempt time for thermal activation, and estimate the corresponding values of the barrier exponent $\psi$ introduced in the scaling theories.Comment: 8 pages, including 6 figure

Spin Glasses: Model systems for non-equilibrium dynamics

Spin glasses are frustrated magnetic systems due to a random distribution of ferro- and antiferromagnetic interactions. An experimental three dimensional (3d) spin glass exhibits a second order phase transition to a low temperature spin glass phase regardless of the spin dimensionality. In addition, the low temperature phase of Ising and Heisenberg spin glasses exhibits similar non-equilibrium dynamics and an infinitely slow approach towards a thermodynamic equilibrium state. There are however significant differences in the detailed character of the dynamics as to memory and rejuvenation phenomena and the influence of critical dynamics on the behaviour. In this article, some aspects of the non-equilibrium dynamics of an Ising and a Heisenberg spin glass are briefly reviewed and some comparisons are made to other glassy systems that exhibit magnetic non-equilibrium dynamics.Comment: To appear in J. Phys.: Condens. Matter, Proceedings from HFM2003, Grenobl

Aging and memory properties of topologically frustrated magnets

The model 2d kagome system (H3O)Fe3(SO4)2(OH)6 and the 3d pyrochlore Y2Mo2O7 are two well characterized examples of low-disordered frustrated antiferromagnets which rather then condensing into spin liquid have been found to undergo a freezing transition with spin glass-like properties. We explore more deeply the comparison of their properties with those of spin glasses, by the study of characteristic rejuvenation and memory effects in the non-stationary susceptibility. While the pyrochlore shows clear evidence for these non-trivial effects, implying temperature selective aging, that is characteristic of a wide hierarchical distribution of equilibration processes, the kagome system does n not show clearly these effects. Rather, it seems to evolve towards the same final state independently of temperature.Comment: submitted for the proceedings of the 46th MMM conference (Seattle, 2001

Numerical Study on Aging Dynamics in the 3D Ising Spin-Glass Model. II. Quasi-Equilibrium Regime of Spin Auto-Correlation Function

Using Monte Carlo simulations, we have studied isothermal aging of three-dimensional Ising spin-glass model focusing on quasi-equilibrium behavior of the spin auto-correlation function. Weak violation of the time translational invariance in the quasi-equilibrium regime is analyzed in terms of {\it effective stiffness} for droplet excitations in the presence of domain walls. Within the range of computational time window, we have confirmed that the effective stiffness follows the expected scaling behavior with respect to the characteristic length scales associated with droplet excitations and domain walls, whose growth law has been extracted from our simulated data. Implication of the results are discussed in relation to experimental works on ac susceptibilities.Comment: 18 pages, 6 figure

Domain growth by isothermal aging in 3d Ising and Heisenberg spin glasses

Non-equilibrium dynamics of three dimensional model spin glasses - the Ising system Fe$_{0.50}$Mn$_{0.50}$TiO$_3$ and the Heisenberg like system Ag(11 at% Mn) - has been investigated by measurements of the isothermal time decay of the low frequency ac-susceptibility after a quench from the paramagnetic to the spin glass phase. It is found that the relaxation data measured at different temperatures can be scaled according to predictions from the droplet scaling model, provided that critical fluctuations are accounted for in the analyzes.Comment: 5 pages, 3 figure

Photoproduction of eta mesons from the neutron: cross sections and double polarization observable E

Photoproduction of $\eta$ mesons from neutrons} \abstract{Results from measurements of the photoproduction of $\eta$ mesons from quasifree protons and neutrons are summarized. The experiments were performed with the CBELSA/TAPS detector at the electron accelerator ELSA in Bonn using the $\eta\to3\pi^{0}\to6\gamma$ decay. A liquid deuterium target was used for the measurement of total cross sections and angular distributions. The results confirm earlier measurements from Bonn and the MAMI facility in Mainz about the existence of a narrow structure in the excitation function of $\gamma n\rightarrow n\eta$. The current angular distributions show a forward-backward asymmetry, which was previously not seen, but was predicted by model calculations including an additional narrow $P_{11}$ state. Furthermore, data obtained with a longitudinally polarized, deuterated butanol target and a circularly polarized photon beam were analyzed to determine the double polarization observable $E$. Both data sets together were also used to extract the helicity dependent cross sections $\sigma_{1/2}$ and $\sigma_{3/2}$. The narrow structure in the excitation function of $\gamma n\rightarrow n\eta$ appears associated with the helicity-1/2 component of the reaction

Aging in an infinite-range Hamiltonian system of coupled rotators

We analyze numerically the out-of-equilibrium relaxation dynamics of a long-range Hamiltonian system of $N$ fully coupled rotators. For a particular family of initial conditions, this system is known to enter a particular regime in which the dynamic behavior does not agree with thermodynamic predictions. Moreover, there is evidence that in the thermodynamic limit, when $N\to \infty$ is taken prior to $t\to \infty$, the system will never attain true equilibrium. By analyzing the scaling properties of the two-time autocorrelation function we find that, in that regime, a very complex dynamics unfolds in which {\em aging} phenomena appear. The scaling law strongly suggests that the system behaves in a complex way, relaxing towards equilibrium through intricate trajectories. The present results are obtained for conservative dynamics, where there is no thermal bath in contact with the system. This is the first time that aging is observed in such Hamiltonian systems.Comment: Figs. 2-4 modified, minor changes in text. To appear in Phys. Rev.