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

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 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.

Atmospheric drivers of Greenland surface melt revealed by self-organizing maps

Recent acceleration in surface melt on the Greenland ice sheet (GrIS) has occurred concurrently with a rapidly warming Arctic and has been connected to persistent, anomalous atmospheric circulation patterns over Greenland. To identify synoptic setups favoring enhanced GrIS surface melt and their decadal changes, we develop a summer Arctic synoptic climatology by employing self-organizing maps. These are applied to daily 500 hPa geopotential height fields obtained from the Modern Era Retrospective Analysis for Research and Applications reanalysis, 1979–2014. Particular circulation regimes are related to meteorological conditions and GrIS surface melt estimated with outputs from the Modèle Atmosphérique Régional. Our results demonstrate that the largest positive melt anomalies occur in concert with positive height anomalies near Greenland associated with wind, temperature, and humidity patterns indicative of strong meridional transport of heat and moisture. We find an increased frequency in a 500 hPa ridge over Greenland coinciding with a 63% increase in GrIS melt between the 1979–1988 and 2005–2014 periods, with 75.0% of surface melt changes attributed to thermodynamics, 17% to dynamics, and 8.0% to a combination. We also confirm that the 2007–2012 time period has the largest dynamic forcing relative of any period but also demonstrate that increased surface energy fluxes, temperature, and moisture separate from dynamic changes contributed more to melt even during this period. This implies that GrIS surface melt is likely to continue to increase in response to an ever warmer future Arctic, regardless of future atmospheric circulation patterns

Quasi-stationary trajectories of the HMF model: a topological perspective

We employ a topological approach to investigate the nature of quasi-stationary states of the Mean Field XY Hamiltonian model that arise when the system is initially prepared in a fully magnetized configuration. By means of numerical simulations and analytical considerations, we show that, along the quasi-stationary trajectories, the system evolves in a manifold of critical points of the potential energy function. Although these critical points are maxima, the large number of directions with marginal stability may be responsible for the slow relaxation dynamics and the trapping of the system in such trajectories.Comment: 5 pages, 4 figure

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.

Oxidant-controlled regioselectivity in the oxidative arylation of N-acetylindoles

N-Acetylindoles can be oxidatively coupled with arenes such as benzene or pentafluorobenzene in dioxane. The use of Cu(OAc)2 as the stoichiometric oxidant produces selective arylation at the 3-position of indole while AgOAc produces selective arylation at indole’s 2-position. [Refer to PDF for graphical abstract

Stratigraphic analysis of firn cores from an antarctic ice shelf firn aquifer

Indexación ScopusIn recent decades, several large ice shelves in the Antarctic Peninsula region have experienced significant ice loss, likely driven by a combination of oceanic, atmospheric and hydrological processes. All three areas need further research, however, in the case of the role of liquid water the first concern is to address the paucity of field measurements. Despite this shortage of field observations, several authors have proposed the existence of firn aquifers on Antarctic ice shelves, however little is known about their distribution, formation, extension and role in ice shelf mechanics. In this study we present the discovery of saturated firn at three drill sites on the Müller Ice Shelf (67°14' S; 66°52' W), which leads us to conclude that either a large contiguous or several disconnected smaller firn aquifers exist on this ice shelf. From the stratigraphic analysis of three short firn cores extracted during February 2019 we describe a new classification system to identify the structures and morphological signatures of refrozen meltwater, identify evidence of superficial meltwater percolation, and use this information to propose a conceptual model of firn aquifer development on the Müller Ice Shelf. The detailed stratigraphic analysis of the sampled cores will provide an invaluable baseline for modelling studies. © 2021 by the authors. Licensee MDPI, Basel, Switzerland.https://www.mdpi.com/2073-4441/13/5/73

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

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