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.     

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.     

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.     

Paramagnetic Particles and PNA Probe for Automated Separation and Electrochemical Detection of Influenza

Considerable efforts have been devoted to the development of rapid and sensitive methods allowing the detection of viral nucleic acid. We herein describe an assay for identification of a specific influenza sequence. The suggested method was based on isolation using paramagnetic particles coupled with electrochemical detection of isolated product. Peptide nucleic acid (PNA) was used as a probe for hybridization and identification of the influenza-derived specific sequence. The use of PNA can show numerous benefits: PNA probe is not degradable by enzymes and the duplex of PNA with RNA/DNA is more thermostable and more resistant to pH changes than DNA/DNA or RNA/RNA duplexes. This PNA probe assay can be applied as a magnetically guidable tool for detection of DNA/RNA samples under different conditions.

     

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.     

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.     

Polyacetylene‐Type Networks Prepared by Coordination Polymerization of Diethynylarenes: New Type of Microporous Organic Polymers

Microporous organic polymers (MOP) of a new type have been synthesised in high yields by a simple coordination polymerization of 1,3‐diethynylbenzene, 1,4‐diethynylbenzene and 4,4′‐diethynylbiphenyl catalysed by [Rh(cod)acac] and [Rh(nbd)acac] complexes. The new MOPs are non‐swellable polyacetylene‐type conjugated networks consisting of ethynylaryl‐substituted polyene main chains that are crosslinked by arylene linkers. Prepared MOP samples have a mole fraction of branching units (by ¹³C CP/MAS NMR) from 0.30 to 0.47 and exhibit the BET (Brunaer‐Emmett‐Teller) surface up to 809 m² g⁻¹ and hydrogen uptake up to 0.69 wt% (77 K, H₂ pressure 750 torr).     

Mesoporous Molecular Sieves as Advanced Supports for Olefin Metathesis Catalysts

Summary: Siliceous mesoporous molecular sieves MCM-41, MCM-48 and SBA-15 and organised mesoporous alumina represent progressive supports for new heterogeneous catalysts for olefin metathesis and metathesis polymerization. In combination with Mo and Re oxides they provide catalysts of considerably higher activity in comparison with those based on conventional silica and alumina. Immobilization of Mo and Ru alkylidenes on these materials led to the highly active and selective catalysts with negligible leaching of transition metal.     

Chemical analysis of Gothic mortar from a bridge pier in Roudnice nad Labem (Czech Republic)

In this paper, a Gothic mortar originating from the remains of a bridge pier in Roudnice nad Labem (Czech Republic) was analyzed. The inorganic composition of the mortar showing special mechanical properties was studied using polarizing light microscopy, scanning electron microscopy coupled with energy dispersive X-ray spectrometry, and X-ray diffraction, while the protein content was analyzed by peptide mass mapping using matrix-assisted laser desorption/ionization—time of flight mass spectrometry and nanoliquid chromatography coupled to tandem mass spectrometry. Two types of inorganic binders having a composition similar to mineral wollastonite and hydraulic lime and milk protein additive were detected. We believe that organic and inorganic binders added together to the mortar increase its hardness and firmness in the aquatic environment.