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

Ivermectin and Novel Coronavirus Disease (COVID-19): Keeping Rigor in Times of Urgency.

Ivermectin is a widely used drug for the treatment and control of several neglected tropical diseases.The drug has an excellent safety profile, with more than 2.5 billion doses distributed in the last 30 years, and its potential to reduce malaria transmission by killing mosquitoes is under evaluation in several trials around the world. Ivermectin inhibits the in vitro replication of some positive, single-stranded RNA viruses, namely, dengue virus (DNV), Zika virus, yellow fever virus, and others

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.

Biomolecular characterization of 3500-year-old ancient Egyptian mummification balms from the Valley of the Kings

Ancient Egyptian mummification was practiced for nearly 4000 years as a key feature of some of the most complex mortuary practices documented in the archaeological record. Embalming, the preservation of the body and organs of the deceased for the afterlife, was a central component of the Egyptian mummification process. Here, we combine GC-MS, HT-GC-MS, and LC-MS/MS analyses to examine mummification balms excavated more than a century ago by Howard Carter from Tomb KV42 in the Valley of the Kings. Balm residues were scraped from now empty canopic jars that once contained the mummified organs of the noble lady Senetnay, dating to the 18th dynasty, ca. 1450 BCE. Our analysis revealed balms consisting of beeswax, plant oil, fats, bitumen, Pinaceae resins, a balsamic substance, and dammar or Pistacia tree resin. These are the richest, most complex balms yet identified for this early time period and they shed light on balm ingredients for which there is limited information in Egyptian textual sources. They highlight both the exceptional status of Senetnay and the myriad trade connections of the Egyptians in the 2nd millennium BCE. They further illustrate the excellent preservation possible even for organic remains long removed from their original archaeological context

Effective action for Superconductors and BCS-Bose crossover

A standard perturbative expansion around the mean-field solution is used to derive the low-energy effective action for superconductors at T=0. Taking into account the density fluctuations at the outset we get the effective action where the density $\rho$ is the conjugated momentum to the phase $\theta$ of the order parameter. In the hydrodynamic regime, the dynamics of the superconductor is described by a time dependent non-linear Schr\"odinger equation (TDNLS) for the field $\Psi(x)=\sqrt{\rho/2} e^{i\theta}$. The evolution of the density fluctuations in the crossover from weak-coupling (BCS) to strong-coupling (Bose condensation of localized pairs) superconductivity is discussed for the attractive Hubbard model. In the bosonic limit, the TDNLS equation reduces to the the Gross-Pitaevskii equation for the order parameter, as in the standard description of superfluidity. The conditions under which a phase-only action can be derived in the presence of a long-range interaction to describe the physics of the superconductivity of ``bad metals'' are discussed.Comment: 13 pages, accepted for publication on Phys. Rev.

Real spin glasses relax slowly in the shade of hierarchical trees

The Parisi solution of the mean-field spin glass has been widely accepted and celebrated. Its marginal stability in 3d and its complexity however raised the question of its relevance to real spin glasses. This paper gives a short overview of the important experimental results which could be understood within the mean-field solution. The existence of a true phase transition and the particular behaviour of the susceptibility below the freezing temperature, predicted by the theory, are clearly confirmed by the experimental results. The behaviour of the complex order parameter and of the Fluctuation Dissipation ratio are in good agreement with results of spontaneous noise measurements. The very particular ultrametric symmetry, the key feature of the theory, provided us with a simple description of the rejuvenation and memory effects observed in experiment. Finally, going a step beyond mean-field, the paper shortly discusses new analyses in terms of correlated domains characterized by their length scales, as well as new experiments on superspin glasses which compare well with recent theoretical simulations.Comment: To appear in the proceedings of "Wandering with Curiosity in Complex Landscapes", a scientific conference in honour of Giorgio Parisi for his 60th birthday, Roma, September 8-10 2008 (submitted for the special issue of the Journal of Statistical Physics, 2009

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

On the scaling and ageing behaviour of the alternating susceptibility in spin glasses and local scale-invariance

The frequency-dependent scaling of the dispersive and dissipative parts of the alternating susceptibility is studied for spin glasses at criticality. An extension of the usual $\omega t$-scaling is proposed. Simulational data from the three-dimensional Ising spin glass agree with this new scaling form and moreover reproduce well the scaling functions explicitly calculated for systems satisfying local scale-invariance. There is also a qualitative agreement with existing experimental data.Comment: 19 pages, 2 figures, to appear in special issue of J. Phys. Cond. Matt. dedicated to Lothar Schaefer on the occasion of his 60th birthday, final form with IOP macro

E2F6 initiates stable epigenetic silencing of germline genes during embryonic development.

In mouse development, long-term silencing by CpG island DNA methylation is specifically targeted to germline genes; however, the molecular mechanisms of this specificity remain unclear. Here, we demonstrate that the transcription factor E2F6, a member of the polycomb repressive complex 1.6 (PRC1.6), is critical to target and initiate epigenetic silencing at germline genes in early embryogenesis. Genome-wide, E2F6 binds preferentially to CpG islands in embryonic cells. E2F6 cooperates with MGA to silence a subgroup of germline genes in mouse embryonic stem cells and in embryos, a function that critically depends on the E2F6 marked box domain. Inactivation of E2f6 leads to a failure to deposit CpG island DNA methylation at these genes during implantation. Furthermore, E2F6 is required to initiate epigenetic silencing in early embryonic cells but becomes dispensable for the maintenance in differentiated cells. Our findings elucidate the mechanisms of epigenetic targeting of germline genes and provide a paradigm for how transient repression signals by DNA-binding factors in early embryonic cells are translated into long-term epigenetic silencing during mouse development

The {\eta}'-carbon potential at low meson momenta

The production of $\eta^\prime$ mesons in coincidence with forward-going protons has been studied in photon-induced reactions on $^{12}$C and on a liquid hydrogen (LH$_2$) target for incoming photon energies of 1.3-2.6 GeV at the electron accelerator ELSA. The $\eta^\prime$ mesons have been identified via the $\eta^\prime\rightarrow \pi^0 \pi^0\eta \rightarrow 6 \gamma$ decay registered with the CBELSA/TAPS detector system. Coincident protons have been identified in the MiniTAPS BaF$_2$ array at polar angles of $2^{\circ} \le \theta _{p} \le 11^{\circ}$. Under these kinematic constraints the $\eta^\prime$ mesons are produced with relatively low kinetic energy ($\approx$ 150 MeV) since the coincident protons take over most of the momentum of the incident-photon beam. For the C-target this allows the determination of the real part of the $\eta^\prime$-carbon potential at low meson momenta by comparing with collision model calculations of the $\eta^\prime$ kinetic energy distribution and excitation function. Fitting the latter data for $\eta^\prime$ mesons going backwards in the center-of-mass system yields a potential depth of V = $-$(44 $\pm$ 16(stat)$\pm$15(syst)) MeV, consistent with earlier determinations of the potential depth in inclusive measurements for average $\eta^\prime$ momenta of $\approx$ 1.1 GeV/$c$. Within the experimental uncertainties, there is no indication of a momentum dependence of the $\eta^\prime$-carbon potential. The LH$_2$ data, taken as a reference to check the data analysis and the model calculations, provide differential and integral cross sections in good agreement with previous results for $\eta^\prime$ photoproduction off the free proton.Comment: 9 pages, 13 figures. arXiv admin note: text overlap with arXiv:1608.0607