Conformational transition of DNA bound to Hfq probed by infrared spectroscopy

Hfq is a bacterial protein involved in RNA metabolism. Besides this, Hfq's role in DNA restructuring has also been suggested. Since this mechanism remains unclear, we examined the DNA conformation upon Hfq binding by combining vibrational spectroscopy and neutron scattering. Our analysis reveals that Hfq, which preferentially interacts with deoxyadenosine rich sequences, induces partial opening of dA-dT sequences accompanied by sugar repuckering of the dA strand and hence results in a heteronomous A/B duplex. Sugar repuckering is probably correlated with a global dehydration of the complex. By taking into account Hfq's preferential binding to A-tracts, which are commonly found in promoters, potential biological implications of Hfq binding to DNA are discussed.     

A geometric representation of improper indefinite affine spheres with singularities

Given a pair of planar curves, one can define its generalized area distance, a concept that generalizes the area distance of a single curve. In this paper, we show that the generalized area distance of a pair of planar curves is an improper indefinite affine spheres with singularities, and, reciprocally, every indefinite improper affine sphere in ${\mathbb {R}^3}$ is the generalized distance of a pair of planar curves. Considering this representation, the singularity set of the improper affine sphere corresponds to the area evolute of the pair of curves, and this fact allows us to describe a clear geometric picture of the former. Other symmetry sets of the pair of curves, like the affine area symmetry set and the affine envelope symmetry set can be also used to describe geometric properties of the improper affine sphere.     

The external constraint 4 nonempty part sandwich problem

List partitions generalize list colourings. Sandwich problems generalize recognition problems. The polynomial dichotomy (NP-complete versus polynomial) of list partition problems is solved for 4-dimensional partitions with the exception of one problem (the list stubborn problem) for which the complexity is known to be quasipolynomial. Every partition problem for 4 nonempty parts and only external constraints is known to be polynomial with the exception of one problem (the 2K₂-partition problem) for which the complexity of the corresponding list problem is known to be NP-complete. The present paper considers external constraint 4 nonempty part sandwich problems. We extend the tools developed for polynomial solutions of recognition problems obtaining polynomial solutions for most corresponding sandwich versions. We extend the tools developed for NP-complete reductions of sandwich partition problems obtaining the classification into NP-complete for some external constraint 4 nonempty part sandwich problems. On the other hand and additionally, we propose a general strategy for defining polynomial reductions from the 2K₂-partition problem to several external constraint 4 nonempty part sandwich problems, defining a class of 2K₂-hard problems. Finally, we discuss the complexity of the Skew Partition Sandwich Problem.     

Re-entrant phase behaviour of network fluids: a patchy particle model with temperature-dependent valence

We study a model consisting of particles with dissimilar bonding sites ("patches"), which exhibits self-assembly into chains connected by Y-junctions, and investigate its phase behaviour by both simulations and theory. We show that, as the energy cost ε(j) of forming Y-junctions increases, the extent of the liquid-vapour coexistence region at lower temperatures and densities is reduced. The phase diagram thus acquires a characteristic "pinched" shape in which the liquid branch density decreases as the temperature is lowered. To our knowledge, this is the first model in which the predicted topological phase transition between a fluid composed of short chains and a fluid rich in Y-junctions is actually observed. Above a certain threshold for ε(j), condensation ceases to exist because the entropy gain of forming Y-junctions can no longer offset their energy cost. We also show that the properties of these phase diagrams can be understood in terms of a temperature-dependent effective valence of the patchy particles.     

Optimization of the extraction conditions of the volatile compounds from chili peppers by headspace solid phase micro-extraction

A method involving headspace-solid phase micro-extraction (HS-SPME), gas chromatography with flame ionization detection (GC-FID) and gas chromatography with mass spectrometry (GC-MS) was developed and optimized to investigate the volatile composition of Capsicum chili peppers. Five SPME fibers were tested for extraction: carboxen/polydimethylsiloxane (CAR/PDMS-75μm), polydimethylsiloxane (PDMS-100μm), divinylbenzene/polydimethylsiloxane (DVB/PDMS-65μm), carbowax/divinylbenzene (CW/DVB-70μm), and divinylbenzene/carboxen/polydimethylsiloxane (DVB/CAR/PDMS-50/30μm), the last of which was shown to be the most efficient fiber to trap the volatile compounds. Optimization of the extraction conditions was carried out using multivariate strategies such as factorial design and response surface methodology. Eighty three compounds were identified by GC-MS when using the optimized extraction conditions, the majority of which were esters.     

Enlightening the influence of mordant, dyeing technique and photodegradation on the colour hue of textiles dyed with madder - A chromatographic and spectrometric approach

Wool samples were dyed with madder and alum, copper, and iron salts at different concentration by pre-mordanting (MD) and simultaneous mordanting (M + D) procedures. Samples were artificially aged to identify the influence of the mordant on the madder chromophores photodegradation. A set of analytical techniques was used for complete characterisation of the dyed fibres before and after light exposure, which included colour and chromophore analysis (colourimetry and LC-ESI-MS/MS analysis), determination of mordant ions amounts in the fibres (FAAS and ICP-OES analysis), morphological characterisation of the fibres and punctual chemical analysis (SEM-EDS studies).Fibre colour hue was found to be dependent on the mordant ion nature, mordant bath concentration and dyeing procedure. Mordant ion quantification showed that the uptake of metal ion by the fibres is relatively small, with the Cu ion presenting the highest affinity for the fibre. MD method yields fibres with higher amounts of metal ions and larger chromophore chromatographic peak areas corresponding, in general, to stronger colour hues. Photodegradation was more severe in alum mordant samples and in the first 480 h of light exposure. Chromophore degradation rates are unequal and dependent on the mordant nature, contributing for colour changes observed after light exposure.     

Infrared (810 nm) low-level laser therapy in rat achilles tendinitis: a consistent alternative to drugs

Nonsteroidal anti-inflammatory drugs (NSAIDs) are widely used and can reduce musculoskeletal pain in spite of the cost of adverse reactions like gastrointestinal ulcers or cardiovascular events. The current study investigates if a safer treatment such as low-level laser therapy (LLLT) could reduce tendinitis inflammation, and whether a possible pathway could be through inhibition of either of the two-cyclooxygenase (COX) isoforms in inflammation. Wistar rats (six animals per group) were injected with saline (control) or collagenase in their Achilles tendons. Then, we treated them with three different doses of IR LLLT (810 nm; 100 mW; 10 s, 30 s and 60 s; 3.57 W cm(-2); 1 J, 3 J, 6 J) at the sites of the injections, or intramuscular diclofenac, a nonselective COX inhibitor/NSAID. We found that LLLT dose of 3 J significantly reduced inflammation through less COX-2-derived gene expression and PGE(2) production, and less edema formation compared to nonirradiated controls. Diclofenac controls exhibited significantly lower PGE(2) cytokine levels at 6 h than collagenase control, but COX isoform 1-derived gene expression and cytokine PGE(2) levels were not affected by treatments. As LLLT seems to act on inflammation through a selective inhibition of the COX-2 isoform in collagenase-induced tendinitis, LLLT may have potential to become a new and safer nondrug alternative to coxibs.     

Determination of triamcinolone in human plasma by a sensitive HPLC-ESI-MS/MS method: application for a pharmacokinetic study using nasal spray formulation

A liquid chromatography-electrospray ionization tandem mass spectrometry (HPLC-ESI-MS/MS) method for the quantitation of triamcinolone in human plasma after nasal spray application was developed and validated. Betamethasone was used as internal standard (IS). The analytes were extracted by a liquid-liquid procedure and separated on a Zorbax Eclipse XDB C(18) column with a mobile phase composed of 2 mM aqueous ammonium acetate pH 3.2 and acetonitrile (55:45). Selected reaction monitoring was performed using the transitions m/z 435 → 415 and m/z 393 → 373 to quantify triamcinolone acetonide and betamethasone, respectively. Calibration curve was constructed over the range of 20-2000 pg/ml for triamcinolone acetonide. The lower limit of quantitation was 20 pg/ml. The mean RSD values were 4.6% and 5.7% for the intra-run and inter-run precision, respectively. The mean accuracy value was 98.5% and a recovery rate corresponding to 97.5% was achieved. No matrix effect was detected in the samples. The validated method was successfully applied to determine the plasma concentrations of triamcinolone acetonide in healthy volunteers, in a pharmacokinetic study with nasal spray formulation.     

Development and validation of a high-performance liquid chromatography-electrospray ionization-MS/MS method for the simultaneous quantitation of levodopa and carbidopa in human plasma

A sensitive and fast high‐performance liquid chromatography–electrospray ionization–MS/MS method for the simultaneous quantitation of levodopa and carbidopa in human plasma was developed and validated. A simple protein precipitation step with perchloric acid was used for the cleanup of plasma, and methyldopa was added as an internal standard. The analyses were carried out using an ACE C₁₈ column (50 × 4.6 mm i.d.; 5 µm particle size) and a mobile phase consisting of 0.2% formic acid and acetonitrile (90:10). The triple‐quadrupole mass spectrometer equipped with an electrospray source in positive mode was set up in the selective reaction monitoring mode to detect the ion transitions m/z 198.1 → m/z 107.0, m/z 227.2 → m/z 181.0, and m/z 212.1 → m/z 139.2 for levodopa, carbidopa, and methyldopa, respectively. The method was validated and proved to be linear, accurate, and precise over the range 50–5000 ng/mL for levodopa and 3–600 ng/mL for carbidopa. The proposed method was successfully applied in a pharmacokinetic study with a levodopa/carbidopa tablet formulation in healthy volunteers. Copyright © 2011 John Wiley & Sons, Ltd.     

Synthesis and application of imprinted polyvinylimidazole-silica hybrid copolymer for Pb2+ determination by flow-injection thermospray flame furnace atomic absorption spectrometry

A novel ion imprinted polyvinylimidazole-silica hybrid copolymer (IIHC) was synthesized and used as a selective solid sorbent for Pb(2+) ions preconcentration using an on-line solid phase extraction (SPE) system coupled to TS-FF-AAS. The ionic hybrid sorbent was prepared using 1-vinylimidazole and 3-(trimethoxysilyl)propylmethacrylate as monomers, Pb(2+) ions as template, tetraethoxysilane as reticulating agent and 2,2'-azobis-isobutyronitrile as initiator. The best on-line SPE conditions concerning sorption behavior, including sample pH (6.46), buffer concentration (9.0 mmol L(-1)), eluent (HNO(3)) concentration (0.5 mol L(-1)) and preconcentration flow rate (4.0 mL min(-1)), were optimized by means of full factorial design and Doehlert matrix. The analytical curve ranged from 2.5 to 65.0 μg L(-1) (r=0.999) with limit of detection of 0.75 μg L(-1); the precision (repeatability) calculated as relative standard deviation (n=10) was 5.0 and 3.6% for Pb(2+) concentration of 10.0 and 60.0 μg L(-1), respectively. From on-line breakthrough curve, column capacity was 3.5 mg g(-1). Preconcentration factor (PF), consumptive index (CI) and concentration efficiency (CE) were 128.0, 0.16 mL and 25.6 min(-1), respectively. The selective performance of the sorbent, based on relative selectivity coefficient, was compared to NIC (non imprinted copolymer) for the binary mixture Pb(2+)/Cd(2+), Pb(2+)/Cu(2+) and Pb(2+)/Zn(2+). The results showed that ion imprinted polyvinylimidazole-silica hybrid polymer had higher selectivity for Pb(2+) than NIC at 64.9, 16.0 and 8.8 folds. The developed method was successfully applied for highly sensitive and selective Pb(2+) determination in different kinds of water samples, parenteral solutions and urine. Accuracy was also assessed by analyzing certified reference fish protein (DORM-3) and marine sediment (MESS-3 and PACS-2) with satisfactory results.