A Rapidly Reversible Chemical Dimerizer System to Study Lipid Signaling in Living Cells

Chemical dimerizers are powerful tools for non‐invasive manipulation of enzyme activities in intact cells. Here we introduce the first rapidly reversible small‐molecule‐based dimerization system and demonstrate a sufficiently fast switch‐off to determine kinetics of lipid metabolizing enzymes in living cells. We applied this new method to induce and stop phosphatidylinositol 3‐kinase (PI3K) activity, allowing us to quantitatively measure the turnover of phosphatidylinositol 3,4,5‐trisphosphate (PIP₃) and its downstream effectors by confocal fluorescence microscopy as well as standard biochemical methods.     

Distributed and multicore QuBiLS-MIDAS software v2.0: Computing chiral,fuzzy, weighted and truncated geometrical molecular descriptors based on tensor algebra

Advances to the distributed, multi-core and fully cross-platform QuBiLS-MIDAS software v2.0 ( http://tomocomd.com/qubils-midas ) are reported in this article since the v1.0 release. The QuBiLS-MIDAS software is the only one that computes atom-pair and alignment-free geometrical MDs (3D-MDs) from several distance metrics other than the Euclidean distance, as well as alignment-free 3D-MDs that codify structural information regarding the relations among three and four atoms of a molecule. The most recent features added to the QuBiLS-MIDAS software v2.0 are related (a) to the calculation of atomic weightings from indices based on the vertex-degree invariant (e.g., Alikhanidi index); (b) to consider central chirality during the molecular encoding; (c) to use measures based on clustering methods and statistical functions to codify structural information among more than two atoms; (d) to the use of a novel method based on fuzzy membership functions to spherically truncate inter-atomic relations; and (e) to the use of weighted and fuzzy aggregation operators to compute global 3D-MDs according to the importance and/or interrelation of the atoms of a molecule during the molecular encoding. Moreover, a novel module to compute QuBiLS-MIDAS 3D-MDs from their headings was also developed. This module can be used either by the graphical user interface or by means of the software library. By using the library, both the predictive models built with the QuBiLS-MIDAS 3D-MDs and the QuBiLS-MIDAS 3D-MDs calculation can be embedded in other tools. A set of predefined QuBiLS-MIDAS 3D-MDs with high information content and low redundancy on a set comprised of 20,469 compounds is also provided to be employed in further cheminformatics tasks. This set of predefined 3D-MDs evidenced better performance than all the universe of Dragon (v5.5) and PaDEL 0D-to-3D MDs in variability studies, whereas a linear independence study proved that these QuBiLS-MIDAS 3D-MDs codify chemical information orthogonal to the Dragon 0D-to-3D MDs. This set of predefined 3D-MDs would be periodically updated as long as new results be achieved. In general, this report highlights our continued efforts to provide a better tool for a most suitable characterization of compounds, and in this way, to contribute to obtaining better outcomes in future applications.     

Continental and Antarctic Lichens: isolation,identification and molecular modeling of the depside tenuiorin from the Antarctic lichen Umbilicaria antarctica as tau protein inhibitor

Abstract

Alzheimer´s disease (AD) is the most common form of dementia involving Aβ and tau protein. So far, AD cure remains elusive, but considering that AD progresses throughout tau pathology, which turns tau protein an appropriate target, besides tau is also included in other neurodegenerative disorders named as tauopathies. Here, we have isolated seventeen compounds belonging to six lichens species. Due to scarce of spectroscopic data of the compound 5,7-dihydroxy-6-methylphthalide, we explained their structural elucidation based on NMR data. In this study, we show that only tenuiorin from Umbilicaria antarctica inhibited 50% of tau 4R at 100?µM. Then, we shown that molecular interactions of tenuiorin with the steric zipper model of the hexapeptide ³⁰⁶VQIVYK³¹¹ were studied by docking calculations and the results suggested that tenuiorin forms both hydrogen bonds with lysine and glutamine side chains and forms several hydrophobic interactions with valine and lysine from ³⁰⁶VQIVYK³¹¹ motif.     

Origin of the asymmetric magnetization reversal behavior in exchange-biased systems: competing anisotropies

The magnetization reversal in exchange-biased ferromagnetic-antiferromagnetic (FM-AFM) bilayers is investigated. Different reversal pathways on each branch of the hysteresis loop, i.e., asymmetry, are obtained both experimentally and theoretically when the magnetic field is applied at certain angles from the anisotropy direction. The range of angles and the magnitude of this asymmetry are determined by the ratio between the FM anisotropy and the interfacial FM-AFM exchange anisotropy. The occurrence of asymmetry is linked with the appearance of irreversibility, i.e., finite coercivity, as well as with the maximum of exchange bias, increasing for larger anisotropy ratios. Our results indicate that asymmetric hysteresis loops are intrinsic to exchange-biased systems and the competition between anisotropies determines the asymmetric behavior of the magnetization reversal.     

Measurement of geometric phase for mixed states using single photon interferometry

Geometric phase may enable inherently fault-tolerant quantum computation. However, due to potential decoherence effects, it is important to understand how such phases arise for mixed input states. We report the first experiment to measure mixed-state geometric phases in optics, using a Mach-Zehnder interferometer, and polarization mixed states that are produced in two different ways: decohering pure states with birefringent elements; and producing a nonmaximally entangled state of two photons and tracing over one of them, a form of remote state preparation.     

The hydrogen atom as a projection of an homogeneous space

The Kustaanheimo-Stiefel transformation as applied to the nonrelativistic hydrogen atom provides one of the rare examples of a free particle moving on a four-dimensional homogeneous space.     

Diffusion in a one-dimensional gas of hard point particles

We simulate the classical diffusion of a particle of massM in an infinite one-dimensional system of hard point particles of massm in equilibrium. Each computer run corresponds to about 10⁸ collisions of the diffusive particle. We find that (t) 1/t fort large enough, and a crossover from an M m regime where=2 to=3 forM=m. The diffusion constant has a sharp maximum atM=m. We study moments x(t)² and x(t)⁴, and examine the behavior ofq ² (t)=x(t)⁴/3x(t)²². We find thatq(t)1 (consistent with a normal distribution) in theM limit (for all timest) and in the t limit for allM. On sabbatical leave from IVIC-Instituto Venezolano de Investigaciones Cientificas.     

Thermodynamics based on the principle of least abbreviated action: Entropy production in a network of coupled oscillators

We present some novel thermodynamic ideas based on the Maupertuis principle. By considering Hamiltonians written in terms of appropriate action-angle variables we show that thermal states can be characterized by the action variables and by their evolution in time when the system is nonintegrable. We propose dynamical definitions for the equilibrium temperature and entropy as well as an expression for the nonequilibrium entropy valid for isolated systems with many degrees of freedom. This entropy is shown to increase in the relaxation to equilibrium of macroscopic systems with short-range interactions, which constitutes a dynamical justification of the Second Law of Thermodynamics. Several examples are worked out to show that this formalism yields the right microcanonical (equilibrium) quantities. The relevance of this approach to nonequilibrium situations is illustrated with an application to a network of coupled oscillators (Kuramoto model). We provide an expression for the entropy production in this system finding that its positive value is directly related to dissipation at the steady state in attaining order through synchronization.     

Unexpected reactivity of pyridinium salts toward alkynyl Fischer complexes to produce oxo‐heterocycles

The unprecedented reaction of ketone‐containing aromatic pyridinium salts 3a ‐ e and alkynyl Fischer complexes 1a ‐ f proceeds via a mild domino process to provide 4,6‐disubstituted pyran‐2‐ones 5a ‐ k and 2,3,5‐trisubstituted furans 6a ‐ h (45‐97%). According of the results of isotopic labeling experiments, a mechanism involving an initial Michael addition appears to be the key step, obtaining a mesomeric structure responsible for the formation of both products.