SILAC-Pulse Proteolysis: A Mass Spectrometry-Based Method for Discovery and Cross-Validation in Proteome-Wide Studies of Ligand Binding

Reported here is the use of stable isotope labeling with amino acids in cell culture (SILAC) and pulse proteolysis (PP) for detection and quantitation of protein–ligand binding interactions on the proteomic scale. The incorporation of SILAC into PP enables the PP technique to be used for the unbiased detection and quantitation of protein–ligand binding interactions in complex biological mixtures (e.g., cell lysates) without the need for prefractionation. The SILAC-PP technique is demonstrated in two proof-of-principle experiments using proteins in a yeast cell lysate and two test ligands including a well-characterized drug, cyclosporine A (CsA), and a non-hydrolyzable adenosine triphosphate (ATP) analogue, adenylyl imidodiphosphate (AMP-PNP). The well-known tight-binding interaction between CsA and cyclophilin A was successfully detected and quantified in replicate analyses, and a total of 33 proteins from a yeast cell lysate were found to have AMP-PNP-induced stability changes. In control experiments, the method’s false positive rate of protein target discovery was found to be in the range of 2.1% to 3.6%. SILAC-PP and the previously reported stability of protein from rates of oxidation (SPROX) technique both report on the same thermodynamic properties of proteins and protein–ligand complexes. However, they employ different probes and mass spectrometry-based readouts. This creates the opportunity to cross-validate SPROX results with SILAC-PP results, and vice-versa. As part of this work, the SILAC-PP results obtained here were cross-validated with previously reported SPROX results on the same model systems to help differentiate true positives from false positives in the two experiments. Graphical Abstract

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Thermal,Mechanical and Morphological Behavior of Poly(propylene)/Wood Flour Composites

The comparative studies on the thermal, mechanical and morphological behavior of compression molded poly(propylene) (PP)/wood flour (WF) composites were performed using wood flours (WFs) of different origins. The comparison has been made on the basis of results obtained from thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), scanning electron microscopy (SEM) and tensile testing. It has been demonstrated that an addition of 5 wt.-% of maleic anhydride grafted polypropylene (PP-g-MA) has a significant effect on the morphological and thermomechanical behavior of the composites. Although, microscopic examinations revealed no significant differences in the morphology of the compatibilized composites, a remarkable improvement of thermal degradation behavior was observed. From the view point of mechanical properties, the composites with high amount of filler (60 wt.-%) showed similar behavior irrespective of the origin of wood flour.     

Calix[4]pyrrole‐Based Heteroditopic Ion‐Pair Receptor That Displays Anion‐Modulated,Cation‐Binding Behavior

A new ditopic ion‐pair receptor 1 was designed, synthesized, and characterized. Detailed binding studies served to confirm that this receptor binds fluoride and chloride ions (studied as their tetraalkylammonium salts) and forms stable 1:1 complexes in CDCl₃. Treatment of the halide‐ion complexes of 1 with Group I and II metal ions (Li⁺, Na⁺, K⁺, Cs⁺, Mg²⁺, and Ca²⁺; studied as their perchlorate salts in CD₃CN) revealed unique interactions that were found to depend on both the choice of the added cation and the precomplexed anion. In the case of the fluoride complex [ 1? F]^? (preformed as the tetrabutylammonium (TBA⁺) complex), little evidence of interaction with the K⁺ ion was seen. In contrast, when this same complex (i.e., [ 1? F]^? as the TBA⁺ salt) was treated with the Li⁺ or Na⁺ ions, complete decomplexation of the receptor‐bound fluoride ion was observed. In sharp contrast to what was seen with Li⁺, Na⁺, and K⁺, treating complex [ 1? F]^? with the Cs⁺ ion gave rise to a stable, receptor‐bound ion‐pair complex [Cs ?1? F] that contains the Cs⁺ ion complexed within the cup‐like cavity of the calix[4]pyrrole, which in turn was stabilized in its cone conformation. Different complexation behavior was observed in the case of the chloride complex [ 1? Cl]^?. In this case, no appreciable interaction was observed with Na⁺ or K⁺. In addition, treating [ 1? Cl]^? with Li⁺ produces a tightly hydrated dimeric ion‐pair complex [ 1? LiCl(H₂O)]₂ in which two Li⁺ ions are bound to the crown moiety of the two receptors. In analogy to what was seen in the case of [ 1? F]^?, exposure of [ 1? Cl]^? to the Cs⁺ ion gives rise to an ion‐pair complex [Cs ?1? Cl] in which the cation is bound within the cup of the calix[4]pyrrole. Different complexation modes were also observed when the binding of the fluoride ion was studied by using the tetramethylammonium and tetraethylammonium salts.     

Global dynamics of Chua Corsage Memristor circuit family: fixed-point loci,Hopf bifurcation,and coexisting dynamic attractors

Nonlinear Dynamics - This paper presents an in-depth and rigorous mathematical analysis of a family of nonlinear dynamical circuits whose only nonlinear component is a Chua Corsage Memristor (CCM)...     

Generalized Rabi oscillations in a three-level metastable system under periodic and quasiperiodic perturbations

The quantum dynamics of prototypical three-level metastable system under external perturbations, both time-independent and time-dependent, are studied numerically as well as analytically. The regular Rabi oscillations generated in the system under a monochromatic perturbation are shown to develop additional features when the system has a metastable state. The autocorrelation function of ψ(t) reveals nondecaying, almost quasiperiodic, behavior in such systems. The Rabi oscillations turn more complex when a bichromatic perturbation with two incommensurate frequencies is allowed to interact with the three-level system, irrespective of the presence or absence of a metastable state. A rapid decay in the autocorrelation function of the wavefunction [ψ(t)] is observed in such cases. © 1996 Wiley & Sons, Inc.     

Elastic instability of bilayer graphene using atomistic finite element

In-plane elastic instability of bilayer graphene sheets is investigated using atomistic finite element approaches. The equivalent homogenised properties of graphene sheet are expressed in terms of the thickness, equilibrium lengths and force-field models used to represent the C–C bonds of the graphene lattice. The covalent bonds are represented as structural beams with stretching, bending, torsional and shear deformation, and the strain energies associated to affine deformation mechanisms. The overall mechanical properties and geometric configurations of the nano-structures represented as truss assemblies are then calculated minimising the total potential energy associated to the loading, thickness and average equilibrium lengths of the bonds. Different boundary conditions and aspect ratios are considered for both bilayer and single-layer graphene sheets. The bilayer graphene sheets are found to be offering remarkably higher buckling strengths as compared to single-layer sheets.     

Studies on third-order nonlinear optical properties and reverse saturable absorption in polythiophene/poly (methylmethacrylate) composites

We report here the studies on third-order nonlinear optical properties of two novel polythiophene composite films investigated using the Z-scan technique. The measurements were carried out using a Q-switched, frequency doubled Nd:YAG laser producing 7 nanosecond laser pulses at 532 nm. Z-scan results reveal that the composite films exhibit self-defocusing nonlinearity. The real and imaginary parts of the third-order nonlinear optical susceptibility were of the order 10⁻¹² esu. The effective excited-state absorption cross section was found to be larger than the ground state absorption cross section, indicating that the operating nonlinear mechanism is reverse saturable absorption (RSA). The polythiophene composite films also exhibit good optical power limiting of the nanosecond laser pulses. The nonlinear optical parameters are found to increase on increasing the strength of the electron-donor group, indicating the dependence of χ ⁽³⁾ on the electron-donor/acceptor units of polythiophenes.     

Remarks on some zero-sum problems

Let Z denote the ring of integers and for a prime p and positive integers r and d, let f_r(P, d) denote the smallest positive integer such that given any sequence of f_r(p, d) elements in (Z/pZ(^d, there exists a subsequence of (rp) elements whose sum is zero in (Z/pZ(^d. That f₁(p, 1) = 2p − 1, is a classical result due to Erdős, Ginzburg and Ziv. Whereas the determination of the exact value of f₁(p, 2) has resisted the attacks of many well known mathematicians, we shall see that exact values of f_r(p, 1) for r ≥ 1 can be easily obtained from the above mentioned theorem of Erdős, Ginzburg and Ziv and those of f_r(p, 2) for r ≥ 2 can be established by the existing techniques developed by Alon, Dubiner and Rónyai in connection with obtaining good upper bounds for f₁(p, 2). We shall also take this opportunity to describe some of the early results in the introduction.     

Remarks on some zero-sum theorems

In the present paper, we give a new proof of a weighted generalization of a result of Gao in a particular case. We also give new methods for determining the weighted Davenport constant and another similar constant for some particular weights.     

Uncertainty modeling of carbon nanotube terahertz oscillators

Significant uncertainties have been reported in the material properties of carbon nanotubes. In this paper, a probabilistic approach to take account of these uncertainties is proposed. The probability density function of the natural frequencies is derived in closed-form. The new results are compared with high-fidelity stochastic finite element simulations.