Translocation of biomolecules through solid‐state nanopores: Theory meets experiments

The interest in polynucleotide translocation through nanopores has moved from purely biological to the need of realizing nanobiotechnological applications related to personalized genome sequencing. Polynucleotide translocation is a process in which biomolecules, like DNA or RNA, are electrophoretically driven through a narrow pore and their passage can be monitored by the change in the ionic current through the pore. Such a translocation process, which will be described here offers a very promising technology aiming at ultra‐fast low‐cost sequencing of DNA, though its realization is still confronted with challenges and drawbacks. In this review, we present the main aspects involved in the polynucleotide translocation through solid‐state nanopores by discussing the most relevant experimental, theoretical, and computational approaches and the way these can supplement each other. The discussion will expose the goals that have been reached so far, the open questions, and contains an outlook to the future of nanopore sequencing. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 985–1011, 2011     

Asymptotics of LRS Bianchi type I cosmological models with elastic matter

In this paper, we report on results in the study of spatially homogeneous cosmological models with elastic matter. We show that the behavior of elastic solutions is fundamentally different from that of perfect fluid solutions already in the case of locally rotationally symmetric Bianchi type I models; this is true even when the elastic material resembles a perfect fluid very closely. In particular, the approach to the initial singularity is characterized by an intricate oscillatory behavior of the scale factors, while the future asymptotic behavior is described by isotropization rates that differ significantly from those of perfect fluids.     

Tetraphenylethylene-BODIPY aggregation-induced emission luminogens for near-infrared polymer light-emitting diodes

The aggregation-induced emission(AIE) phenomenon provides a new direction for the development of organic light-emitting devices. Here, we present a new class of emitters based on 4,4-difluoro-4-bora-3 a,4 a-diaza-s-indacene(BODIPY), functionalized at different positions with tetraphenylethylene(TPE), which is one of the most famous AIE luminogens. Thanks to this modification, we were able to tune the photoluminescence of the BODIPY moiety from the green to the near-infrared(NIR)spectral range and achieve PL efficiencies of ~50% in the solid state. Remarkably, we observed an enhancement of the AIE and up to ~100% photoluminescence efficiencies by blending the TPE-substituted BODIPY fluorophores with a poly[(9,9-di-noctylfluorene-2,7-diyl)-alt-(benzo[2,1,3]thiadiazol-4,7-diyl)](F8 BT) matrix. By incorporating these blends in organic lightemitting diodes(OLEDs), we obtained electroluminescence peaked in the range 650–700 nm with up to 1.8% external quantum efficiency and ~2 m W/cm2 radiance, a remarkable result for red/NIR emitting and solution-processed OLEDs.     

Horizontal comparative fluorescence two‐dimensional gel electrophoresis for improved spot coordinate detection

Vertical comparative 2D fluorescence gel electrophoresis (CoFGE) has recently been shown to increase the reproducibility of coordinate assignment for protein spots, in particular in singular experiments, which cannot be investigated using DIGE. The method applies a standardized marker grid formed by a set of purified proteins to the sample proteome in a conglomerate of 1DE, 2DE, and DIGE. Here, improvements are demonstrated by transferring CoFGE to horizontal 2DE. These include the elimination of the protein modification by residual acrylamide monomer unavoidable in vertical CoFGE, reduced buffer volumes, and highly efficient laboratory procedures. Spot patterns are well defined and can be easily analyzed using commercially available warping algorithms. With horizontal CoFGE also a correction for changes in pI was introduced using a third fluorescent dye. Horizontal CoFGE holds high promises in comparative proteomics.     

Rapid liquid chromatography–tandem mass spectrometry analysis of 4-hydroxynonenal for the assessment of oxidative degradation and safety of vegetable oils

A novel method for the UHPLC–MS/MS analysis of (E)-4-hydroxynonenal (4-HNE) is described. The method is based on derivatization of 4-HNE with pentafluorophenylhydrazine (1) or 4-trifluoromethylphenylhydrazine (2) in acetonitrile in the presence of trifluoroacetic acid as catalyst at room temperature and allows complete analysis of one sample of vegetable oil in only 21 min, including sample preparation and chromatography. The method involving hydrazine 1, implemented in an ion trap instrument with analysis of the transition m/z 337 → 154 showed LOD = 10.9 nM, average accuracy of 101% and precision ranging 2.5–4.0% RSD intra-day (2.7–4.1% RSD inter-day), with 4-HNE standard solutions. Average recovery from lipid matrices was 96.3% from vaseline oil, 91.3% from sweet almond oil and 105.3% from olive oil. The method was tested on the assessment of safety and oxidative degradation of seven samples of dietary oil (soybean, mixed seeds, corn, peanut, sunflower, olive) and six cosmetic-grade oils (avocado, blackcurrant, apricot kernel, echium, sesame, wheat germ) and effectively detected increased 4-HNE levels in response to chemical (Fenton reaction), photochemical, or thermal stress and aging, aimed at mimicking typical oxidation associated with storage or industrial processing. The method is a convenient, cost-effective and reliable tool to assess quality and safety of vegetable oils.     

Selective Coordination of Gallium(III), Zinc(II), and Copper(II) by an Asymmetric Dinucleating Ligand: A Model for Metallophosphatases

Complexation studies of the dinucleating ligand H₃L (H₃L=2‐{[bis(pyridin‐2‐ylmethyl)amino]methyl}‐6‐{[bis(6‐pivaloylamidopyridin‐2‐ylmethyl)amino]methyl}‐4‐methylphenol), with metal‐binding sites A and B, which both provide four donors to a metal ion; a tertiary amine; two pyridines (substituted with amide hydrogen‐bond donors in site B), and a bridging phenolate, with Zn^II, Cu^II, and Ga^III are reported. The titration of H₃L with the three metal ions in solution was monitored by NMR spectroscopy or EPR and UV/Vis/near‐IR spectroscopy, as well as by ESI‐MS to analyze the selectivity of the two metal‐ion sites A and B of this model ligand for metallophosphatases; the spectroscopic assignments are supported by X‐ray crystallography results. The first Zn^II ion coordinates to site A with unsubstituted pyridine donors and, upon addition of a second equivalent of Zn^II, this coordinates to the sterically less accessible site B. From a similar titration with Ga^III, it emerges that only a mononuclear complex is obtained, with the Ga^III center coordinated to site A. When one equivalent of Ga^III is reacted with the mononuclear Zn^II complex, Zn^II is forced by Ga^III to exchange the site; this results in a dinuclear complex with Ga^III in site A and Zn^II in site B. With Cu^II, two isomers are observed: one with and the other without a bridging phenolate; these differ significantly in their spectroscopic and magnetic properties.     

Multitarget quantitative metabolic profiling of hydrophilic metabolites in fermentation broths of β-lactam antibiotics production by HILIC–ESI–MS/MS

The presented work deals with the development and comprehensive validation of a quantitative LC–electrospray ionization (ESI)–tandem mass spectrometry (MS/MS) method using a triple quadrupole instrument in the MRM mode for the metabolic profiling of amino acids, organic acids, vitamins, some biogenic amines, secondary metabolites of β-lactam antibiotics biosynthesis as well as their intermediates, and degradation products in fermentation broths of β-lactam antibiotics production (in total 57 hydrophilic compounds). A great number of chromatographic systems (22 different stationary phase/mobile phase conditions) were screened for their adequate chromatographic selectivity to cope with isobaric compounds and other critical analyte pairs. Finally, a hydrophilic interaction liquid chromatography (HILIC) method employing a zwitterionic ZIC-HILIC column was selected as best compromise. Particular focus was given on the elucidation of absolute and relative matrix effects via comparison of slopes of calibration functions of spiked matrix and standard solutions. These data as well as precision and accuracy data confirm suitability of the HILIC–ESI–MS/MS assay for metabolic profiling studies in fermentation samples. Detailed comprehensive data sets are presented which should illustrate critical issues, problems, and challenges of multitarget quantitative metabolic profiling and should outline possible strategies to circumvent pitfalls and overcome common problems.     

Dendritic chelating agents. 1. Cu(II) binding to ethylene diamine core poly(amidoamine) dendrimers in aqueous solutions

This paper describes an investigation of the uptake of Cu(II) by poly(amidoamine) (PAMAM) dendrimers with an ethylenediamine (EDA) core in aqueous solutions. We use bench scale measurements of proton and metal ion binding to assess the effects of (i) metal ion-dendrimer loading, (ii) dendrimer generation/terminal group chemistry, and (iii) solution pH on the extent of binding of Cu(II) in aqueous solutions of EDA core PAMAM dendrimers with primary amine, succinamic acid, glycidol, and acetamide terminal groups. We employ extended X-ray absorption fine structure (EXAFS) spectroscopy to probe the structures of Cu(II) complexes with Gx-NH2 EDA core PAMAM dendrimers in aqueous solutions at pH 7.0. The overall results of the proton and metal ion binding measurements suggest that the uptake of Cu(II) by EDA core PAMAM dendrimers involves both the dendrimer tertiary amine and terminal groups. However, the extents of protonation of these groups control the ability of the dendrimers to bind Cu(II). Analysis of the EXAFS spectra suggests that Cu(II) forms octahedral complexes involving the tertiary amine groups of Gx-NH2 EDA core PAMAM dendrimers at pH 7.0. The central Cu(II) metal ion of each of these complexes appears to be coordinated to 2-4 dendrimer tertiary amine groups located in the equatorial plane and 2 axial water molecules. Finally, we combine the results of our experiments with literature data to formulate and evaluate a phenomenological model of Cu(II) uptake by Gx-NH2 PAMAM dendrimers in aqueous solutions. At low metal ion-dendrimer loadings, the model provides a good fit of the measured extent of binding of Cu(II) in aqueous solutions of G4-NH2 and G5-NH2 PAMAM dendrimers at pH 7.0.     

X-ray absorption fine structure spectroscopic studies of Octakis(DMSO)lanthanoid(III) complexes in solution and in the solid iodides

Octakis(DMSO)lanthanoid(III) iodides (DMSO = dimethylsulfoxide), [Ln(OS(CH3)2)8]I3, of most lanthanoid(III) ions in the series from La to Lu have been studied in the solid state and in DMSO solution by extended X-ray absorption fine structure (EXAFS) spectroscopy. L3-edge and also some K-edge spectra were recorded, which provided mean Ln-O bond distances for the octakis(DMSO)lanthanoid(III) complexes. The agreement with the average of the Ln-O bond distances obtained in a separate study by X-ray crystallography was quite satisfactory. The crystalline octakis(DMSO)lanthanoid(III) iodide salts have a fairly broad distribution of Ln-O bond distances, ca. 0.1 A, with a few disordered DMSO ligands. Their EXAFS spectra are in excellent agreement with those obtained for the solvated lanthanoid(III) ions in DMSO solution, both of which show slightly asymmetric distributions of the Ln-O bond distances. Hence, all lanthanoid(III) ions are present as octakis(DMSO)lanthanoid(III) complexes in DMSO solution, with the mean Ln-O distances centered at 2.50 (La), 2.45 (Pr), 2.43 (Nd), 2.41 (Sm), 2.40 (Eu), 2.39 (Gd), 2.37 (Tb), 2.36 (Dy), 2.34 (Ho), 2.33 (Er), 2.31 (Tm), and 2.29 A (Lu). This decrease in the Ln-O bond distances is larger than expected from the previously established ionic radii for octa-coordination. This indicates increasing polarization of the LnIII-O(DMSO) bonds with increasing atomic number. However, the S(1s) electron transition energies in the sulfur K-edge X-ray absorption near-edge structure (XANES) spectra, probing the unoccupied molecular orbitals of lowest energy of the DMSO ligands for the [Ln(OS(CH3)2)8](3+) complexes, change only insignificantly from Ln = La to Lu. This indicates that there is no appreciable change in the sigma-contribution to the S-O bond, probably due to a corresponding increase in the contribution from the sulfur lone pair to the bonding.     

Critical Quantum Metrology in the Non-Linear Quantum Rabi Model

The quantum Rabi model (QRM) with linear coupling between light mode and qubit exhibits the analog of a second-order phase transition for vanishing mode frequency which allows for criticality-enhanced quantum metrology in a few-body system. We show that the QRM including a nonlinear coupling term exhibits much higher measurement precisions due to its first-order-like phase transition at finite frequency, avoiding the detrimental slowing-down effect close to the critical point of the linear QRM. When a bias term is added to the Hamiltonian, the system can be used as a fluxmeter or magnetometer if implemented in circuit QED platforms.