Location of Novel Benzanthrone Dyes in Model Membranes as Revealed by Resonance Energy Transfer

Förster resonance energy transfer (FRET) between anthrylvinyl-labeled phosphatidylcholine (AV-PC) as a donor and newly synthesized benzanthrones (referred to here as A8, A6, AM12, AM15 and AM18) as acceptors has been examined to gain insight into molecular level details of the interactions between benzanthrone dyes and model lipid membranes composed of zwitterionic lipid phosphatidylcholine and its mixtures with anionic lipids cardiolipin (CL) and phosphatidylglycerol (PG). FRET data were quantitatively analyzed in terms of the model of energy transfer in two-dimensional systems taking into account the distance dependence of orientation factor. Evidence for A8 location in phospholipid headgroup region has been obtained. Inclusion of CL and PG into PC bilayer has been found to induce substantial relocation of A6, AM12, AM15 and AM18 from hydrophobic membrane core to lipid-water interface.     

Medium-high resolution electrochemical genotyping of HLA-DQ2/DQ8 for detection of predisposition to coeliac disease

Coeliac disease is a small intestinal disorder, induced by ingestion of gluten in genetically predisposed individuals. Coeliac disease has been strongly linked to human leukocyte antigens (HLA) located on chromosome 6, with almost 100 % of coeliac disease sufferers carrying either a HLA-DQ2 or HLA-DQ8 heterodimer, with the majority carrying HLA-DQ2 encoded by the DQA1*05:01/05:05, DQB1*02:01/02:02 alleles, whereas the remaining carry the HLA-DQ8 encoded by the DQA1*03:01, DQB1*03:02 alleles. In this work, we present the development of a multiplex electrochemical genosensor array of 36 electrodes, housed within a dedicated microfluidic platform and using a total of 10 sequence-specific probes for rapid medium-high resolution HLA-DQ2/DQ8 genotyping. An evaluation of the selectivity of the designed probes was carried out with the target sequences and 44 potentially interfering alleles, including single base mismatch differentiations; good selectivity was demonstrated. The performance of the electrochemical genosensor array was validated, analyzing real human samples for the presence of HLA-DQ2/DQ8 alleles, and compared with those obtained using laboratory-based HLA typing, and an excellent correlation was obtained.

Context-specific independence in graphical log-linear models

Log-linear models are the popular workhorses of analyzing contingency tables. A log-linear parameterization of an interaction model can be more expressive than a direct parameterization based on probabilities, leading to a powerful way of defining restrictions derived from marginal, conditional and context-specific independence. However, parameter estimation is often simpler under a direct parameterization, provided that the model enjoys certain decomposability properties. Here we introduce a cyclical projection algorithm for obtaining maximum likelihood estimates of log-linear parameters under an arbitrary context-specific graphical log-linear model, which needs not satisfy criteria of decomposability. We illustrate that lifting the restriction of decomposability makes the models more expressive, such that additional context-specific independencies embedded in real data can be identified. It is also shown how a context-specific graphical model can correspond to a non-hierarchical log-linear parameterization with a concise interpretation. This observation can pave way to further development of non-hierarchical log-linear models, which have been largely neglected due to their believed lack of interpretability.     

Self-assembled carbon nanotubes on gold: polarization-modulated infrared reflection-absorption spectroscopy, high-resolution X-ray photoemission spectroscopy, and near-edge X-ray absorption fine structure spectroscopy study

Recently we reported noncovalent functionalization of nanotubes in an aqueous medium with ionic liquid-based surfactants, 1-dodecyl-3-methylimidazolium bromide (1) and 1-(12-mercaptododecyl)-3-methylimidazolium bromide (2), resulting in positively charged single-wall carbon nanotube (SWNT)-1,2 composites. Thiolation of SWNTs with 2 provides their self-assembly on gold as well as templating gold nanoparticles on SWNT sidewalls via a covalent -S-Au bond. In this investigation, we studied the electronic structure, intermolecular interactions, and packing within noncovalently thiolated SWNTs and also nanotube alignment in the bulk of SWNT-2 dried droplets and self-assembled submonolayers (SAMs) on gold by high-resolution X-ray photoemission spectroscopy (HRXPS), C K-edge X-ray absorption fine structure (NEXAFS) spectroscopy, and polarization-modulated infrared reflection-absorption spectroscopy (PM-IRRAS). HRXPS data confirmed the noncovalent nature of interactions within the nanocomposite of thiolated nanotubes. In PM-IRRAS spectra of SWNT SAMs on gold, the IR-active vibrational SWNT modes have been observed and identified. According to PM-IRRAS data, the hydrocarbon chains of 2 are oriented with less tilt angle to the bare gold normal in a SAM deposited from an SWNT-2 dispersion than those of 1 deposited from an SWNT-1 dispersion on the mercaptoethanesulfonic acid-primed gold. For both the dried SWNT-2 bulk and the SWNT-2 SAM on gold, the C K-edge NEXAFS spectra revealed the presence of CH-pi interactions between hydrocarbon chains of 2 and the pi electronic nanotube structure due to the highly resolved vibronic fine structure of carbon 1s --> R*/sigma*C-H series of states in the alkyl chain of 2. For the SWNT-2 bulk, the observed splitting and upshift of the SWNT pi* orbitals in the NEXAFS spectrum indicated the presence of pi-pi interactions. In the NEXAFS spectrum of the SWNT-2 SAM on gold, the upshifted values of the photon energy for R*/sigma*C-H transitions indicated close contact of 2 with nanotubes and with a gold surface. The angle-dependent NEXAFS for the SWNT-2 bulk showed that most of the molecules of 2 are aligned along the nanotubes, which are self-organized with orientation parallel to the substrate plane, whereas the NEXAFS for the SWNT-2 SAM revealed a more normal orientation of functionality 2 on gold compared with that in the SWNT-2 bulk.     

Structural Characteristics of Hydrogenated Carbon and Boron Nitride Nanotubes: Impact of H?H Interactions

The structural characteristics of perhydrogenated carbon and boron nitride nanotubes are determined by means of quantum chemical calculations. Two families of nanotubes are systematically studied for both carbon and boron nitride, the nanotubes being derived from the perhydrogenated (110) and (111) sheets of diamond and cubic boron nitride. Single‐walled perhydrogenated carbon nanotubes prefer structures analogous to the (111) sheet. In clear contrast, the single‐walled perhydrogenated boron nitride nanotubes prefer structures analogous to the (110) sheet. The significantly different structural characteristics are due to the polarization of hydrogen atoms in the perhydrogenated boron nitride nanotubes. The presence of attractive electrostatic H? H interactions leads to a strong preference for multilayering of the boron nitride sheets and nanotubes. The results are expected to provide new insights into the structural characteristics of main‐group binary hydrides.     

Proteomic analysis of cartilage- and bone-associated samples

The skeleton of the human body is built of cartilage and bone, which are tissues that contain extensive amounts of extracellular matrix (ECM). In bone, inorganic mineral hydroxyapatite forms 50-70% of the whole weight of the tissue. Although the organic matrix of bone consists of numerous proteins, 90% of it is composed of type I collagen. In cartilage, ECM forms a major fraction of the tissue, type II collagen and aggrecans being the most abundant macromolecules. It is obvious that the high content of ECM components causes analytical problems in the proteomic analysis of cartilage and bone, analogous to those in the analysis of low-abundance proteins present in serum. The massive contents of carbohydrates present in cartilage proteoglycans, and hydroxyapatite in bone, further complicate the situation. However, the development of proteomic tools makes them more and more tempting also for research of musculoskeletal tissues. Application of proteomic techniques to the research of chondrocytes, osteoblasts, osteocytes, and osteoclasts in cell cultures can immediately benefit from the present knowledge. Here we make an overview to previous proteomic research of cartilage- and bone-associated samples and evaluate the future prospects of applying proteomic techniques to investigate key events, such as cellular signal transduction, in cartilage- and bone-derived cells.     

Spectral characterisation of eight glycerolipids and their detection in natural samples using time‐of‐flight secondary ion mass spectrometry

In recent years, time‐of‐flight secondary ion mass spectrometry (ToF‐SIMS) with cluster ion sources has opened new perspectives for the analysis of lipid biomarkers in geobiology and organic geochemistry. However, published ToF‐SIMS reference spectra of relevant compounds are still sparse, and the influence of the chemical environment (matrix) on the ionisation of molecules and their fragmentation is still not well explored. This study presents ToF‐SIMS spectra of eight glycerolipids as common target compounds in biomarker studies, namely ester‐ and ether‐bound phosphatidylethanolamine, ester‐ and ether‐bound phosphatidylcholine, ester‐bound phosphatidylglycerol, ester‐ and ether‐bound diglycerides and archaeol, obtained with a Bi cluster ion source. For all of these compounds, the spectra obtained in positive and negative analytical modes showed characteristic fragments that could clearly be assigned to e.g. molecular ions, functional groups and alkyl chains. By comparison with the reference spectra, it was possible to track some of these lipids in a pre‐characterised organic extract and in cryosections of microbial mats. The results highlight the potential of ToF‐SIMS for the laterally resolved analysis of organic biomarkers in environmental materials. The identification of the target compounds, however, may be hampered by matrix effects (e.g. adduct formation) and often require careful consideration of all spectral features and taking advantage of the molecular imaging capability of ToF‐SIMS. Copyright © 2009 John Wiley & Sons, Ltd.     

Asymmetric Markovian analysis of the polymerization mechanism of propene by ziegler-natta catalysis and external alkoxysilane donors

The formulae for conditional probabilities are derived with the term of NMR triad tacticities for the polymers whose polymerization process is described by an asymmetric Markovian process. The formulae obtained are applied to the polypropylene polymerized by Ziegler-Natta catalysis with external alkoxysilane donors. For both, unfractionated samples and heptane-insoluble fractions, four evidences are clarified as follows: Don the transformation from symmetric to (fluctuating) asymmetric sites the transformation of one (hereafter, L) site is much more enhanced than that of the other (D) site, 2) monotonous increase of isotacticity with an increase of the concentration of the donor is due to the increase of p_LL, 3) aromatic donors are more effective than aliphatic ones for the improvement of isotacticity, and 4) the improvement of isotacticity after an addition of alkoxysilane is not due to the contribution from both of L and D sites, but the competition between the larger positive contribution from the former and the smaller negative one from the latter.     

Investigation of the microstructure of metallocene-catalyzed norbornene–ethylene copolymers using NMR spectroscopy

Norbornene–ethylene copolymers were prepared using the metallocene catalyst ethylene bis (indenyl) zirconium dichloride with MAO, and their microstructure was characterized with ¹H-NMR and ¹³C-NMR methods. From a Cosy ¹H-NMR spectrum it was found that all norbornene units are enchained in the exo-configuration. The sequence distribution of norbornene units was investigated using ¹³C-¹H correlations, hmqc for one-bond correlations, and hmbc for two- or three-bond correlations. It was shown that norbornene diads were formed at a high norbornene content (45 mol %). When further increasing the norbornene incorporation (66 mol %) a number of new signals were obtained. A Cosy ¹H-NMR spectrum revealed a new crosspeak which, according to the corresponding ¹³C-NMR shifts (hmqc), correlated well with a terminal unit of a trimer of norbornene. This means that at very high norbornene contents, norbornene triads can be formed. Because the formation of isotactic norbornene triads is very difficult to understand from a sterical point of view, an epimerization process causing stereoirregularities in the norbornene triad is proposed. © 1998 John Wiley & Sons, Inc. J Polym Sci A: Polym Chem 36: 1633–1638, 1998     

Solubilization of polyaniline in water by interpolymer complexation

Water solubility of electro-active polymers in their doped state may provide a possibility for environmentally feasible manufacturing processes. Because previous results in this direction require expensive modifications or impractical template polymerization methods, we created a simple method of mixing components with a large molecular weight difference. The polymer which acts as an acidic dopant and provides water solubility, has to have the higher molecular weight. The formed complex resembles a block copolymer but in this case the polyaniline block is attached to the sulfonated polystyrene chain by strong physical interactions instead of chemical end-to-end linkage.