Improving the Selectivity of the Phosphoric Acid β-Elimination on a Biotinylated Phosphopeptide

This study aims at improving the MALDI-TOF detection of a phosphorylated peptide containing a cysteine residue by ??-elimination of H₃PO₄ hardly enriched by classical methods. The experimental conditions were optimized on this phosphopeptide (biot-pAdd) and its nonphosphorylated counterpart (biot-Add). The major side-reactions were H₂S elimination on the cysteine residues and H₂O elimination on the non phosphorylated serine residue of biot-Add. The former dilutes the MALDI-TOF signal for the desired species. The latter gives a product similar to what is obtained by H₃PO₄ elimination and should prompt to caution when working with a mixture between phosphorylated and non phosphorylated peptides. Modifications on the solvent, the reaction temperature and time, the nature, and concentration of the base were made. Major improvement of the selectivity of the reaction was observed in 30?% ACN, at room temperature for 4?h. However, these optimizations are specific to these sequences and should be performed anew for different peptides. The selectivity of the reaction towards H₃PO₄ elimination is improved, but the persistence of side-reactions renders a previous sample fractionation necessary. In these optimized conditions, the ionization enhancement is 3-fold and the detection limits for biot-pAdd are similar to biot-Add (100?fmol).     

An integrated chemical biology approach provides insight into cdk2 functional redundancy and inhibitor sensitivity

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Highlights? Demonstration that Cdk2 is rate-limiting for DNA replication due to insufficient Cdk1 activity ? A simple bioinformatic approach to design inhibitor resistant mutations in kinases ? Demonstration of distinct binding modes and selectivity of Cdk inhibitors ? Identification of kinetic and structural mechanisms of inhibitor resistance     

Identification and structural characterization of the synthetic cannabinoid 3‐(1‐adamantoyl)‐1‐pentylindole as an additive in ‘herbal incense’

Since the end of 2010, more than 20 synthetic cannabimimetics have been identified in ‘Spice’ products, demonstrating the enormous dynamic in this field. In an effort to cope with the problem, many countries have already undertaken legal measures by putting some of these compounds under control. Nevertheless, once a number of compounds were scheduled, they were soon replaced by other synthetic cannabinoids. In this article, we report the identification of a new – and due to its substitution pattern rather uncommon – cannabimimetic found in several ‘herbal incense’ products. The GC–EI mass spectrum first led to misidentification as the alpha‐methyl‐derivative of JWH‐250. However, since both substances show different retention indices, thin‐layer chromatography was used to isolate the unknown compound. After application of nuclear magnetic resonance spectroscopy, high‐resolution MS and GC–MS/MS techniques, the compound was identified as 3‐(1‐adamantoyl)‐1‐pentylindole, a derivative of JWH‐018 carrying an adamantoyl moiety instead of a naphthoyl group. This finding supports that the listing of synthetic cannabinoids as prohibited substances triggers the appearance of compounds with uncommon substituents. Moreover, it emphasizes the necessity of being aware of the risk of misidentification when using techniques sometimes providing only limited structural information like GC–MS. Copyright © 2012 John Wiley & Sons, Ltd.     

Density functional theory on phase space

Forty‐five years after the point de départ [Hohenberg and Kohn, Phys Rev, 1964, 136, B864] of density functional theory, its applications in chemistry and the study of electronic structures keep steadily growing. However, the precise form of the energy functional in terms of the electron density still eludes us—and possibly will do so forever [Schuch and Verstraete, Nat Phys, 2009, 5, 732]. In what follows we examine a formulation in the same spirit with phase space variables. The validity of Hohenberg–Kohn–Levy‐type theorems on phase space is recalled. We study the representability problem for reduced Wigner functions, and proceed to analyze properties of the new functional. Along the way, new results on states in the phase space formalism of quantum mechanics are established. Natural Wigner orbital theory is developed in depth, with the final aim of constructing accurate correlation‐exchange functionals on phase space. A new proof of the overbinding property of the Müller functional is given. This exact theory supplies its home at long last to that illustrious ancestor, the Thomas–Fermi model. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

A Rigorous Proof of the Landau-Peierls Formula and much more

We present a rigorous mathematical treatment of the zero-field orbital magnetic susceptibility of a non-interacting Bloch electron gas, at fixed temperature and density, for both metals and semiconductors/insulators. In particular, we obtain the Landau-Peierls formula in the low temperature and density limit as conjectured by Kjeldaas and Kohn (Phys Rev 105:806–813, 1957).     

In Defense of Logical Universalism: Taking Issue with Jean van Heijenoort

Van Heijenoort??s main contribution to history and philosophy of modern logic was his distinction between two basic views of logic, first, the absolutist, or universalist, view of the founding fathers, Frege, Peano, and Russell, which dominated the first, classical period of history of modern logic, and, second, the relativist, or model-theoretic, view, inherited from Boole, Schr?der, and L?wenheim, which has dominated the second, contemporary period of that history. In my paper, I present the man Jean van Heijenoort (Sect. 1); then I describe his way of arguing for the second view (Sect. 2); and finally I come down in favor of the first view (Sect. 3). There, I specify the version of universalism for which I am prepared to argue (Sect. 3, introduction). Choosing ZFC to play the part of universal, logical (in a nowadays forgotten sense) system, I show, through an example, how the usual model theory can be naturally given its proper place, from the universalist point of view, in the logical framework of ZFC; I outline another, not rival but complementary, semantics for admissible extensions of ZFC in the very same logical framework; I propose a way to get universalism out of the predicaments in which universalists themselves believed it to be (Sect. 3.1). Thus, if universalists of the classical period did not, in fact, construct these semantics, it was not that their universalism forbade them, in principle, to do so. The historical defeat of universalism was not technical in character. Neither was it philosophical. Indeed, it was hardly more than the victory of technicism over the very possibility of a philosophical dispute (Sect. 3.2).     

Sensitivity kernel for surface scattering in a waveguide

Using the Born approximation, a linearized sensitivity kernel is derived to describe the relationship between a local change at the free surface and its effect on the acoustic propagation in the water column. The structure of the surface scattering kernel is investigated numerically and experimentally for the case of a waveguide at the ultrasonic scale. To better demonstrate the sensitivity of the multipath propagation to the introduction of a localized perturbation at the air-water interface, the kernel is formulated both in terms of point-to-point and beam-to-beam representations. Agreement between theory and experiment suggests applications to sensitivity analysis of the wavefield for sea surface perturbations.     

Enhancing the emergence rate of coherent wavefronts from ocean ambient noise correlations using spatio-temporal filters

Extracting coherent wavefronts between passive receivers using cross-correlations of ambient noise (CAN) provides a means for monitoring the seismoacoustic environment without using active sources. However, using cross-correlations between single receivers can require a long recording time in order to extract stable coherent arrivals from CAN. This becomes an issue if the propagation medium fluctuates significantly during the recording period. To address this issue, this article presents a general spatio-temporal filtering procedure to enhance the emergence rate for coherent wavefronts extracted from time-averaged ambient noise correlations between two spatially separated arrays. The robustness of this array-based CAN technique is investigated using ambient shipping noise recorded over 24?h in the frequency band [250-850 Hz] on two vertical line arrays deployed 143?m apart in shallow water (depth 20?m). Experimental results confirm that the array-based CAN technique can significantly reduce the recording duration (e.g., from 22?h to 30?min) required for extracting coherent wavefronts of sufficient amplitude (e.g., 20?dB over residual temporal fluctations) when compared to conventional CAN implementations between single pairs of hydrophones. These improvements of the CAN technique could benefit the development of noise-based ocean monitoring applications such as passive acoustic tomography.