High‐throughput workflow for identification of phosphorylated peptides by LC‐MALDI‐TOF/TOF‐MS coupled to in situ enrichment on MALDI plates functionalized by ion landing

We report an MS‐based workflow for identification of phosphorylated peptides from trypsinized protein mixtures and cell lysates that is suitable for high‐throughput sample analysis. The workflow is based on an in situ enrichment on matrix‐assisted laser desorption/ionization (MALDI) plates that were functionalized by TiO₂ using automated ion landing apparatus that can operate unsupervised. The MALDI plate can be functionalized by TiO₂ into any array of predefined geometry (here, 96 positions for samples and 24 for mass calibration standards) made compatible with a standard MALDI spotter and coupled with high‐performance liquid chromatography. The in situ MALDI plate enrichment was compared with a standard precolumn‐based separation and achieved comparable or better results than the standard method. The performance of this new workflow was demonstrated on a model mixture of proteins as well as on Jurkat cells lysates. The method showed improved signal‐to‐noise ratio in a single MS spectrum, which resulted in better identification by MS/MS and a subsequent database search. Using the workflow, we also found specific phosphorylations in Jurkat cells that were nonspecifically activated by phorbol 12‐myristate 13‐acetate. These phosphorylations concerned the mitogen‐activated protein kinase/extracellular signal‐regulated kinase signaling pathway and its targets and were in agreement with the current knowledge of this signaling cascade. Control sample of non‐activated cells was devoid of these phosphorylations. Overall, the presented analytical workflow is able to detect dynamic phosphorylation events in minimally processed mammalian cells while using only a short high‐performance liquid chromatography gradient. Copyright © 2015 John Wiley & Sons, Ltd.     

Comparison of Transcriptomic Profiles of MiaPaCa-2 Pancreatic Cancer Cells Treated with Different Statins

Statins have been widely used for the treatment of hypercholesterolemia due to their ability to inhibit HMG-CoA reductase, the rate-limiting enzyme of de novo cholesterol synthesis, via the so-called mevalonate pathway. However, their inhibitory action also causes depletion of downstream intermediates of the pathway, resulting in the pleiotropic effects of statins, including the beneficial impact in the treatment of cancer. In our study, we compared the effect of all eight existing statins on the expression of genes, the products of which are implicated in cancer inhibition and suggested the molecular mechanisms of their action in epigenetic and posttranslational regulation, and in cell-cycle arrest, death, migration, or invasion of the cancer cells.     

In-bone protein digestion followed by LC-MS/MS peptide analysis as a new way towards the routine proteomic characterization of human maxillary and mandibular bone tissue in oral surgery

Proteomic characterization of alveolar bones in oral surgery represents an analytical challenge due to their insoluble character. The implementation of a straightforward technique could lead to the routine use of proteomics in this field. This work thus developed a simple technique for the characterization of bone tissue for human maxillary and mandibular bones. It is based on the direct in-bone tryptic digestion of proteins in both healthy and pathological human maxillary and mandibular bone samples. The released peptides were then identified by the LC-MS/MS. Using this approach, a total of 1120 proteins were identified in the maxillary bone and 1151 proteins in the mandibular bone. The subsequent partial least squares–discrimination analysis (PLS-DA) of protein data made it possible to reach 100% discrimination between the samples of healthy alveolar bones and those of the bone tissue surrounding the inflammatory focus. These results indicate that the in-bone protein digestion followed by the LC-MS/MS and subsequent statistical analysis can provide a deeper insight into the field of oral surgery at the molecular level. Furthermore, it could also have a diagnostic potential in the differentiation between the proteomic patterns of healthy and pathological alveolar bone tissue. Data are available via ProteomeXchange with the identifier PXD026775.     

Pd-catalysed conjugate addition of arylboronic acids to <Emphasis Type="Italic">α,β</Emphasis>-unsaturated ketones under microwave irradiation

The Pd-catalysed conjugate addition of arylboronic acids to α,β-unsaturated cyclic ketones was studied under controlled microwave irradiation conditions. A variety of catalysts, bases and solvents was explored in order to achieve optimum yields in the shortest possible reaction time. Under optimised conditions (Pd(OAc)₂/2,2′-bipyridine and KF in a mixture of toluene, water, and acetic acid and 10 min microwave irradiation), a range of arylboronic acids was successfully added to several cyclic enones. With chiral phosphane ligands, a promising enantioselectivity was obtained (85 % ee).     

Relativistic four-component calculations of Buckingham birefringence using London atomic orbitals

We present the first relativistic study of the electric-field-gradient induced birefringence (Buckingham birefringence), with application to the series of molecules CX₂ (X?=?O, S, Se, Te). A recently developed atomic-orbital-driven scheme for the calculation of time-dependent molecular properties using one-, two- and four-component relativistic wave functions (Bast et?al. in Chem Phys 356:177, 2009) is extended to first-order frequency-dependent magnetic-field perturbations, using London atomic orbitals to ensure gauge-origin independent results and to improve basis-set convergence. Calculations are presented at the Hartree?CFock and Kohn?CSham levels of theory and results for CO₂ and CS₂ are compared with previous high-level coupled-cluster calculations. Except for the heaviest member of the series, relativistic effects are small??in particular for the temperature-independent contribution to the birefringence. By contrast, the effects of electron correlation are significant. However, the reliability of standard exchange-correlation functionals in describing Buckingham birefringence remains unclear based on the comparison with high-level coupled-cluster singles-and-doubles calculations.     

Blended silicone-ionic liquid membranes: Transport properties of butan-1-ol vapor

This paper is focused on modeling of sorption and desorption kinetics as well as on equilibrium butan-1-ol vapor sorption in blended poly(dimethylsiloxane)-benzyl-3-butylimidazolium tetrafluoroborate membranes. Based on the generalized Fick’s second law, on time-dependent boundary conditions and on two models of equilibrium sorption, the diffusion coefficients of butan-1-ol were calculated from the experimental data using the finite difference modeling. Although anomalous sorption occurred at higher concentrations of butan-1-ol, the diffusion coefficients calculated from the data on sorption and desorption kinetics were in a good agreement. The increase of the ionic liquid content in poly(dimethylsiloxane) elevated the butan-1-ol equilibrium concentration in the membrane, and, at the same time, decreased the values of butan-1-ol diffusion coefficient.     

Eigenvalue estimates for Schrödinger operators on metric trees

We consider Schrödinger operators on radial metric trees and prove Lieb–Thirring and Cwikel–Lieb–Rozenblum inequalities for their negative eigenvalues. The validity of these inequalities depends on the volume growth of the tree. We show that the bounds are valid in the endpoint case and reflect the correct order in the weak or strong coupling limit.     

On the semiclassical analysis of the ground state energy of the Dirichlet Pauli operator III: magnetic fields that change sign

We consider the semiclassical Dirichlet Pauli operator in bounded connected domains in the plane. Rather optimal results have been obtained in previous papers by Ekholm–Kova?ík–Portmann and Helffer–Sundqvist for the asymptotics of the ground state energy in the semiclassical limit when the magnetic field has constant sign. In this paper, we focus on the case when the magnetic field changes sign. We show, in particular, that the ground state energy of this Pauli operator will be exponentially small as the semiclassical parameter tends to zero and give lower bounds and upper bounds for this decay rate. Concrete examples of magnetic fields changing sign on the unit disk are discussed. Various natural conjectures are disproved, and this leaves the research of an optimal result in the general case still open.