PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins

Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination of individual PTM states is a key to modulate cellular functions as became evident in a few well-studied proteins. This combinatorial setting, dubbed the PTM code, has been proposed to be extended to whole proteomes in eukaryotes. Although we are still far from deciphering such a complex language, thousands of protein PTM sites are being mapped by high-throughput technologies, thus providing sufficient data for comparative analysis. PTMcode (http://ptmcode.embl.de) aims to compile known and predicted PTM associations to provide a framework that would enable hypothesis-driven experimental or computational analysis of various scales. In its first release, PTMcode provides PTM functional associations of 13 different PTM types within proteins in 8 eukaryotes. They are based on five evidence channels: a literature survey, residue co-evolution, structural proximity, PTMs at the same residue and location within PTM highly enriched protein regions (hotspots). PTMcode is presented as a protein-based searchable database with an interactive web interface providing the context of the co-regulation of nearly 75 000 residues in >10 000 proteins

Switching of Magnetic Moments of Nanoparticles by Surface Acoustic Waves

We report evidence of the magnetization reversal in nanoparticles by surface acoustic waves (SAWs). The experimental system consists of isolated magnetite nanoparticles dispersed on a piezoelectric substrate. Magnetic relaxation from a saturated state becomes significantly enhanced in the presence of the SAW at a constant temperature of the substrate. The dependence of the relaxation on SAW power and frequency has been investigated. The effect is explained by the effective ac magnetic field generated by the SAW in the nanoparticles.Comment: Accepted in Europhysics Letter

Tuning Magnetic Avalanches in Mn12-ac

Using micron-sized Hall sensor arrays to obtain time-resolved measurements of the local magnetization, we report a systematic study in the molecular magnet Mn$_{12}$-acetate of magnetic avalanches controllably triggered in different fixed external magnetic fields and for different values of the initial magnetization. The speeds of propagation of the spin-reversal fronts are in good overall agreement with the theory of magnetic deflagration of Garanin and Chudnovsky \cite{Garanin}.Comment: 8 pages, 7 figures; discussion expanded and revise

PTMcode v2: a resource for functional associations of post-translational modifications within and between proteins

The post-translational regulation of proteins is mainly driven by two molecular events, their modification by several types of moieties and their interaction with other proteins. These two processes are interdependent and together are responsible for the function of the protein in a particular cell state. Several databases focus on the prediction and compilation of protein-protein interactions (PPIs) and no less on the collection and analysis of protein post-translational modifications (PTMs), however, there are no resources that concentrate on describing the regulatory role of PTMs in PPIs. We developed several methods based on residue co-evolution and proximity to predict the functional associations of pairs of PTMs that we apply to modifications in the same protein and between two interacting proteins. In order to make data available for understudied organisms, PTMcode v2 (http://ptmcode.embl.de) includes a new strategy to propagate PTMs from validated modified sites through orthologous proteins. The second release of PTMcode covers 19 eukaryotic species from which we collected more than 300 000 experimentally verified PTMs (>1 300 000 propagated) of 69 types extracting the post-translational regulation of >100 000 proteins and >100 000 interactions. In total, we report 8 million associations of PTMs regulating single proteins and over 9.4 million interplays tuning PPIs

Field induced magnetic transition and metastability in Co substituted Mn2SbMn_{2}Sb

A detailed investigation of first order ferrimagnetic (FRI) to antiferromagnetic (AFM) transition in Co (15%) doped $Mn_2Sb$ is carried out. These measurements demonstrate anomalous thermomagnetic irreversibility and glass-like frozen FRI phase at low temperatures. The irreversibility arising between the supercooling and superheating spinodals is distinguised in an ingenious way from the irreversibility arising due to kinetic arrest. Field annealing measurements shows reentrant FRI-AFM-FRI transition with increasing temperature. These measurements also show that kinetic arrest band and supercooling band are anitcorrelated i.e regions which are kinetically arrested at higher temperature have lower supercooling temperature and vice versa.Comment: 10 pages, 8 figure

Coherent radiation by molecular magnets

The possibility of coherent radiation by molecular magnets is investigated. It is shown that to realize the coherent radiation, it is necessary to couple the considered sample to a resonant electric circuit. A theory for describing this phenomenon is developed, based on a realistic microscopic Hamiltonian, including the Zeeman terms, single-site anisotropy, and dipole interactions. The role of hyperfine interactions between molecular and nuclear spins is studied. Numerical solutions of the spin evolution equations are presented.Comment: Latex file, 11 pages, 3 figure

Augmented Reality for Real-time Navigation Assistance to Wheelchair Users with Obstacles' Management

International audienceDespite a rapid technological evolution in the field of technical assistance for people with motor disabilities, their ability to move independently in a wheelchair is still limited. New information and communication technologies (NICT) such as augmented reality (AR) are a real opportunity to integrate people with disabilities into their everyday life and work. AR can afford real-time information about buildings and locations' accessibility through mobile applications that allow the user to have a clear view of the building details. By interacting with augmented environments that appear in the real world using a smart device, users with disabilities have more control of their environment. In this paper, we propose a decision support system using AR for motor disabled people navigation assistance. We describe a real-time wheelchair navigation system equipped with geological mapping that indicates access path to a desired location, the shortest route towards it and identifies obstacles to avoid. The prototyped wheelchair navigation system was developed for use within the University of Lille campus