Electrochemical genosensors for the detection of Bonamia parasite. Selection of single strand-DNA (ssDNA) probes by simulation of the secondary structure folding

A post-PCR nucleic acid work by comparing experimental data, from electrochemical genosensors, and bioinformatics data, derived from the simulation of the secondary structure folding and prediction of hybridisation reaction, was carried out in order to rationalize the selection of ssDNA probes for the detection of two Bonamia species, B. exitiosa and B. ostreae, parasites of Ostrea edulis.Six ssDNA probes (from 11 to 25 bases in length, 2 thiolated and 4 biotinylated) were selected within different regions of B. ostreae and B. exitiosa PCR amplicons (300 and 304 bases, respectively) with the aim to discriminate between these parasite species. ssDNA amplicons and probes were analyzed separately using the “Mfold Web Server” simulating the secondary structure folding behaviour. The hybridisation of amplicon-probe was predicted by means of “Dinamelt Web Server”. The results were evaluated considering the number of hydrogen bonds broken and formed in the simulated folding and hybridisation process, variance in gaps for each sequence and number of available bases. In the experimental part, thermally denatured PCR products were captured at the sensor interface via sandwich hybridisation with surface-tethered probes (thiolated probes) and biotinylated signalling probes. A convergence between analytical signals and simulated results was observed, indicating the possibility to use bioinformatic data for ssDNA probes selection to be incorporated in genosensors.     

Gas phase charged aggregates of bis(2-ethylhexyl)sulfosuccinate (AOT) and divalent metal ions: first evidence of AOT solvated aggregates

Assembling and chelating properties of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) towards divalent metal ions have been investigated in the gas phase by electrospray ionization mass spectrometry. A variety of positively charged monometallated and mixed metal aggregates are formed. Interestingly, several ions contain solvent (MeOH, H(2)O) molecules and constitute the most abundant AOT cationic aggregates not containing sodium. These species are the first example of solvated AOT-metal ion aggregates in the gas phase. By increasing the surfactant aggregation number, the abundance of solvated species becomes lower than that of unsolvated ones. Decompositions of ionic species have been studied by tandem mass spectrometry, and their stability has been determined through energy resolved mass spectrometry. In contrast with positively charged AOT-alkaline metal ion aggregates, whose decompositions are dominated by the loss of individual surfactant molecules, AOTNa-divalent ion aggregates mainly dissociate through the cleavage of the AOT H(2)C-O bond followed by further intramolecular fragmentations. This finding, that is consistent with an enhanced chelation of divalent ions with AOT(-) head groups, has been taken as an indication that such aggregates are characterized by a reverse micelle-like organization with a ionic core formed by the metal cations interacting with the negatively charged surfactant polar heads, whereas the surfactant alkyl chains point outside.     

Effects of the net charge on abundance and stability of supramolecular surfactant aggregates in gas phase

Self-assembling of amphiphilic molecules under electrospray ionization (ESI) conditions is characterized by quite unexpected phenomenology. The noticeable differences with respect to the condensed phase are attributable to the absence of the surfactant-solvent interactions, the presence of net charge in the aggregates, and the strong deviation from equilibrium conditions. Aiming to investigate the effects of the net charge on abundance and stability of supramolecular surfactant aggregates, positively and negatively charged aggregates of sodium bis(2-ethylhexyl)sulfosuccinate (AOT) and sodium methane sulfonate (MetS), butane sulfonate (ButS) and octane sulfonate (OctS) have been studied by ESI mass spectrometry, energy resolved mass spectrometry and density functional theory calculations. The negatively charged aggregates are found to be less stable than their positive counterparts. The results are consistent with a self-assembling pattern dominated by electrostatic interactions involving the counterions and head groups of the investigated amphiphilic compounds while the alkyl chains point outwards, protecting the aggregates from unlimited growth processes.     

Chemical fingerprinting of Equisetum arvense L. using HPTLC densitometry and HPLC

Equisetum arvense L. is a herbaceous medicinal plant, commonly known as horsetail, whose extracts have been reported to possess diuretic and haemostatic properties. The aim of this study was to evaluate the use of fingerprint chromatographic methods on commercially available raw materials or preparations of E. arvense L. in order to ascertain their quality and identify possible adulterants using HPLC and HPTLC densitometry. Two chromatographic methods were used to determine the chemical fingerprints of E. arvense and other allied species. The first was based on HPTLC identification followed by densitometric measurement at 350?nm. The second was based on HPLC separation. The ease of sample preparation and the possibility of simultaneous analysis of several samples in a short time make HPTLC a method of choice for the comprehensive quality evaluation of herbal products.     

The derivation of EOQ/EPQ inventory models with two backorders costs using analytic geometry and algebra

The EOQ model will have a century of its discovery in two years, and recently still, many researchers have been using alternative approaches to model and solve inventory systems. The EOQ/EPQ models have been developed using different optimization methods. However, in many of the works that deal with the EOQ/EPQ with backorders only linear backorders cost is considered. This paper proposes another easy method which uses basic concepts of analytic geometric and algebra. The proposed method finds the optimal lot size and backorders level considering both linear and fixed backorders costs. Additionally, this paper presents a review of the different optimization methods utilized in inventory theory.     

Solving the vendor–buyer integrated inventory system with arithmetic–geometric inequality

In the past, economic order quantity (EOQ) and economic production quantity (EPQ) were treated independently from the viewpoints of the buyer or the vendor. In most cases, the optimal solution for one player was non-optimal to the other player. In today’s competitive markets, close cooperation between the vendor and the buyer is necessary to reduce the joint inventory cost and the response time of the vendor–buyer system. The successful experiences of National Semiconductor, Wal-Mart, and Procter and Gamble have demonstrated that integrating the supply chain has significantly influenced the company’s performance and market share (Simchi-Levi et al. (2000) [1]). Recently, Yang et al. (2007) [2] presented an inventory model to determine the economic lot size for both the vendor and buyer, and the number of deliveries in an integrated two stage supply chain. In this paper, we present an alternative approach to determine the global optimal inventory policy for the vendor–buyer integrated system using arithmetic–geometric inequality.     

Influence of mixed thiolate/thioether versus dithiolate coordination on the accessibility of the uncommon +I and +III oxidation states for the nickel ion: an experimental and computational study

Sulfur-rich nickel metalloenzymes are capable of stabilizing Ni(I) and Ni(III) oxidation states in catalytically relevant species. In an effort to better understand the structural and electronic features that allow the stabilization of such species, we have investigated the electrochemical properties of two mononuclear N(2)S(2) Ni(II) complexes that differ in their sulfur environment. Complex 1 features aliphatic dithiolate coordination ([NiL], 1), and complex 2I is characterized by mixed thiolate/thioether coordination ([NiL(Me)]I, 2I). The latter results from the methylation of a single sulfur of 1. The X-ray structure of 2I reveals a distorted square planar geometry around the Ni(II) ion, similar to what was previously reported by us for 1. The electrochemical investigation of 1 and 2(+) shows that the addition of a methyl group shifts the potentials of both redox Ni(II)/Ni(I) and Ni(III)/Ni(II) redox couples by about 0.7 and 0.6 V to more positive values. Through bulk electrolyses, only the mononuclear dithiolate [Ni(I)L](-) (1(-)) and the mixed thiolate/thioether [Ni(III)L(Me)](2+) (2(2+)) complexes were generated, and their electronic properties were investigated by UV-vis and EPR spectroscopy. For 1(-) (Ni(I), d(9) configuration) the EPR data are consistent with a d(x(2))(-)(y(2)) based singly occupied molecular orbitals (SOMOs). However, DFT calculations suggest that there is also pronounced radical character. This is consistent with the small g-anisotropy observed in the EPR experiments. The spin population (Mulliken analysis) analysis of 1(-) reveals that the main contribution to the SOMO (64%) is due to the bipyridine unit. Time dependent density functional theory (TD-DFT) calculations attribute the most prominent features observed in the electronic absorption spectrum of 1(-) to metal to ligand charge transfer (MLCT) transitions. Concerning 2(2+), the EPR spectrum displays a rhombic signal with g(x) = 2.236, g(y) = 2.180, and g(z) = 2.039 in CH(3)CN. The g(iso) value is larger than 2.0, which is consistent with metal based oxidation. The unpaired electron (Ni(III), d(7) configuration) occupies a Ni-d(z(2)) based molecular orbital, consistent with DFT calculations. Nitrogen hyperfine structure is observed as a triplet in the g(z) component of the EPR spectrum with A(N) = 51 MHz. This result indicates the coordination of a CH(3)CN molecule in the axial position. DFT calculations confirm that the presence of a fifth ligand in the coordination sphere of the Ni ion is required for the metal-based oxidation process. Finally, we have shown that 1 exhibits catalytic reductive dehalogenation activity below potentials of -2.00 V versus Fc/Fc(+) in CH(2)Cl(2).     

A molecular dynamics study of structure, stability and fragmentation patterns of sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates in vacuo

Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and n(c) additional sodium ions, i.e. [AOT(n)Na(n+n(c))](n(c)), have been investigated by molecular dynamics (MD) simulations for n = 1-20 and n(c) = 0-5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for n(c) = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alkyl chains. Moreover, the aggregate shapes may be approximated by rather flat and elongated ellipsoids whose longer axis increases with n and n(c). The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. In one particular case, for which experimental findings are available in the literature, a good agreement is found with the present fragmentation data.     

Anthraquinone profile, antioxidant and antimicrobial properties of bark extracts of Rhamnus catharticus and R. orbiculatus

The anthraquinone profile, antioxidant and antimicrobial activities as well as the total phenol and total flavonoid contents were determined in methanol extracts of the barks of Rhamnus catharticus L. and R. orbiculatus Bornm. The most abundant anthraquinone derivatives in R. catharticus were physcion (67.8%) and emodin (26.2%), while R. orbiculatus contained mostly physcion (81.3%) and chrysophanol (14.6%). R. catharticus displayed better activity in the beta-carotene-linoleic acid assay, as well as chelating activity, whereas its activity in the reducing power assay was significantly lower than that of R. orbiculatus. Both methanol extracts showed antimicrobial activity against all microbial species tested (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Candida albicans, Aspergillus niger, Microsporum gypseum) with MIC values either equal to or lower than 2.50 mg/mL. R. catharticus and R. orbiculatus contained several anthranoid aglycones and their bark extracts demonstrated notable antioxidant and antimicrobial properties. The results obtained indicate the medicinal potential of these two species.