Propidium monoazide (PMA) and ethidium bromide monoazide(EMA) improve DNA array and high-throughput sequencing ofporcine reproductive and respiratory syndrome virus identification

Pan-viral DNA array (PVDA) and high-throughput sequencing (HTS) are useful tools to identify novel viruses of emerging diseases. However, both techniques have difficulties to identify viruses in clinical samples because of the host genomic nucleic acid content (hg/cont). Both propidium monoazide (PMA) and ethidium bromide monoazide (EMA) have the capacity to bind free DNA/RNA, but are cell membrane-impermeable. Thus, both are unable to bind protected nucleic acid such as viral genomes within intact virions. However, EMA/PMA modified genetic material cannot be amplified by enzymes. In order to assess the potential of EMA/PMA to lower the presence of amplifiable hg/cont in samples and improve virus detection, serum and lung tissue homogenates were spiked with porcine reproductive and respiratory virus (PRRSV) and were processed with EMA/PMA. In addition, PRRSV RT-qPCR positive clinical samples were also tested. EMA/PMA treatments significantly decreased amplifiable hg/cont and significantly increased the number of PVDA positive probes and their signal intensity compared to untreated spiked lung samples. EMA/PMA treatments also increased the sensitivity of HTS by increasing the number of specific PRRSV reads and the PRRSV percentage of coverage. Interestingly, EMA/PMA treatments significantly increased the sensitivity of PVDA and HTS in two out of three clinical tissue samples. Thus, EMA/PMA treatments offer a new approach to lower the amplifiable hg/cont in clinical samples and increase the success of PVDA and HTS to identify viruses.

Vibrational intensities VIII: CH3- and CD3- chloride, bromide and iodide

Absolute intensity measurements have been made on the fundamental vibrations of methyl chloride, bromide, and iodide, and their fully deuterated derivatives, by integrating the optical density over the absorption bands. The bands were fully pressure broadened by using up to 80 atmos of foreign gas. Band separations were made graphically. The results are analyzed in terms of the dipole moment derivatives with respect to symmetry coordinates in the molecule, (∂p/∂Si). The data on the different isotopic species are shown to yield consistent results, and this requirement of consistency has also been used as an aid in the analysis. In the E‐class vibrations the signs of the dipole moment derivatives have been determined unambiguously by assuming the permanent dipole to be directed CH3+☒X—.

Coordination behavior of pyridylmethylthioether system with cupric chloride and cupric bromide: CS bond cleavage and crystal structures

The coordination behavior of pyridylmethylthioether type of organic moieties having N2S2 donor set [L-1=1,2-bis(2-pyridylmethylthio)ethane, L-2 = 1,3-bis(2-pyridylmethyl-thio)propane and L-3 = 1,4-bis(2-pyridylmethylthio)butane] with copper(II) chloride and copper(II) bromide have been studied in different chemical environments. Copper(II) chloride assisted C-S bond cleavage of the organic moieties leading to the formation of copper(II) picolinate derivatives, whereas, under similar experimental conditions, no C-S bond cleavage was observed in the reaction with copper(II) bromide. The resulted copper(II) complexes isolated from the different mediums have been characterized by spectroscopic and X-ray crystallographic tools.

Lysozyme binding to poly(4-vinyl-N-alkylpyridinium bromide)

The adsorption behavior of polycations at ionic strengths (1) ranging from 0.001 to 0.1 onto silicon wafers was studied by means of ellipsometry, contact angle measurements and atomic force microscopy (AFM). Polycations chosen were bromide salts of poly(4-vinylpyridine) N-alkyl quaternized with linear aliphatic chains of 2 and 5 carbon atoms, QPVP-C2 and QPVP-C5, respectively. Under 1 0.001 the reduction of screening effects led to low adsorbed amounts of QPVP-C2 or QPVP-C5 (1.0 +/- 0.1 mg/m(2)), arising from the adsorption of extended chains. Upon increasing l to 0.1, screening effects led to conformational changes of polyelectrolyte chains ill Solution and to higher adsorbed amount values (1.9 +/- 0.2 mg/m(2)). Advancing contact angle theta(a) measurements performed with water drops onto QPVP-C2 and QPVP-C5 adsorbed layers varied from (45 +/- 2)degrees to (50 +/- 5)degrees, evidencing the exposure of both hydrophobic alkyl groups and charged moieties. The adsorption of lysozyme (LYZ) molecules to QPVP-C5 layers was more pronounced than to QPVP-C2 films. Antimicrobial effect of LYZ bound to QPVP-C2 or QPVP-C5 layers or to Si wafers was evaluated with enzymatic assays using Micrococcus luteus as Substrates. The adsorption behavior of QPVP-C2 and QPVP-C5 at the water-air interface was studied by means Of surface tension measurements. Only QPVP-C5 was able to reduce water Surface tension. Mixtures of LYZ and QPVP-C5 were more efficient in reducing Surface tension than pure LYZ solution, evidencing co-adsorption at liquid-air interface. Moreover, antimicrobial action observed for mixtures of LYZ and QPVP-C5 was more pronounced than that measured for pure LYZ. Hydrophobic interaction between LYZ and QPVP-C5 ill Solution seems to drive the binding and to preserve LYZ secondary structure. (c) 2008 Elsevier Inc. All rights reserved.

Thiothionyl bromide (S=SBr2): The elusive isomer of dibromodisulfane (BrSSBr)

CCSD(T) with a series of correlation consistent basis up to quadruple-zeta is used to investigate the structures, vibrational spectra, relative stability, heats of formation, and barrier to isomerization of S=SBr2 and BrSSBr. It represents the most accurate and detailed characterization of these molecules to date. We show that the frequency mode at 302 cm(-1), detected in various studies and assigned to impurities by some authors, and to the anti-symmetric SBr stretch in BrSSBr by others, thus in fact corresponds to the anti-symmetric SBr stretch in the elusive S=SBr2 species; it thus corroborates and complements an earlier partial IR spectra study attributable to S=SBr2. Including corrections for relativistic and core-valence correlation effects, we also predict 26.33 (12.74) kcal/mol for Delta H-f (298.15 K) of S=SBr2 (BrSSBr). For the S=SBr2 -> BrSSBr reaction, our best estimates for the Gibbs free energy and the enthalpy of the reaction at 298.15 K are -13.71 and -13.44 kcal/mol, respectively. For a value of Delta G(#) equal to 23.52 kcal/mol, we estimate a TST rate constant, at 298.15 K, of 3.57 x 10(-5) s(-1). (c) 2007 Elsevier B.V. All rights reserved.

Ooplast-mediated developmental rescue of bovine oocytes exposed to ethidium bromide

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

The vinyl bromide optically pumped far infrared laser: New large offset emissions

We present the results of a study on vinyl bromide for the search for new far infrared (FIR) laser lines. As the pump source, we use a CW waveguide CO2 laser with a tunability of 290 MHz around each line in order to pump large offset vibrational transitions. As a consequence, we obtained 28 new FIR laser emissions; 24 of them have wavelengths greater than 500 mum and are, therefore, suitable to be used in high-field EPR spectroscopy, For each of the new lines, we give the wavelength, the offset of the pumping transition with respect to the center Frequency of the CO2 emission, the polarization relative to that of the pumping laser line, the operating pressure, and the relative intensity. We also present a catalog including data of all of the FIR laser lines observed from this molecule up to now.

Crystallization and preliminary X-ray diffraction analysis of an acidic phospholipase A(2) complexed with p-bromophenacyl bromide and alpha-tocopherol inhibitors at 1.9-and 1.45-A resolution

An acidic phospholipase A(2) (PLA(2)) isolated from Bothrops jararacussu snake venom was crystallized with two inhibitors: alpha-tocopherol (vitamin E) and p-bromophenacyl bromide (BPB). The crystals diffracted at 1.45- and 1.85-Angstrom resolution, respectively, for the complexes with alpha-tocopherol and p-bromophenacyl bromide. The crystals are not isomorphous with those of the native protein, suggesting the inhibitors binding was successful and changes in the quaternary structure may have occurred. (C) 2004 Elsevier B.V. All rights reserved.

Structure of BthA-I complexed with p-bromophenacyl bromide: possible correlations with lack of pharmacological activity

The crystal structure of an acidic phospholipase A(2) isolated from Bothrops jararacussu venom (BthA-I) chemically modified with p-bromophenacyl bromide (BPB) has been determined at 1.85 angstrom resolution. The catalytic, platelet-aggregation inhibition, anticoagulant and hypotensive activities of BthA-I are abolished by ligand binding. Electron-density maps permitted unambiguous identification of inhibitor covalently bound to His48 in the substrate-binding cleft. The BthA-I-BPB complex contains three structural regions that are modified after inhibitor binding: the Ca2+-binding loop, ss-wing and C-terminal regions. Comparison of BthA-I-BPB with two other BPB-inhibited PLA(2) structures suggests that in the absence of Na+ ions at the Ca2+- binding loop, this loop and other regions of the PLA(2)s undergo structural changes. The BthA-I-BPB structure reveals a novel oligomeric conformation. This conformation is more energetically and conformationally stable than the native structure and the abolition of pharmacological activities by the ligand may be related to the oligomeric structural changes. A residue of the `pancreatic' loop (Lys69), which is usually attributed as providing the anticoagulant effect, is in the dimeric interface of BthA-I-BPB, leading to a new hypothesis regarding the abolition of this activity by BPB.

Crystallization and preliminary X-ray diffraction analysis of a myotoxic Lys49-PLA(2) from Bothrops jararacussu venom complexed with p-bromophenacyl bromide

For the first time, a non-catalytic and myotoxic Lys49-PLA(2) (BthTX-I from Bothrops jararacussu venom) has been crystallized with BPB inhibitor. X-ray diffraction data were collected and electron-density calculations showed that the ligand is bound to the His48 residue. BthTX-I with His48 chemically modified by BPB shows strongly reduced myotoxic and cytotoxic activities. This suggests a biological correlation between the modification of His48, which is associated with catalytic activity of PLA(2)s, and other toxicological activities of Lys49-PLA(2)s.

Crystal structure of a phospholipase A(2) homolog complexed with p-bromophenacyl bromide reveals important structural changes associated with the inhibition of myotoxic activity

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Vesicle-micelle transition in aqueous mixtures of the cationic dioctadecyldimethylammonium and octadecyltrimethylammonium bromide surfactants

The vesicle-micelle transition in aqueous mixtures of dioctadecyidimethylammonium and octadecyltrimethylammonium bromide (DODAB and C(18)TAB) cationic surfactants, having respectively double and single chain, was investigated by differential scanning calorimetry (DSQ, steady-state fluorescence, dynamic light scattering (DLS) and surface tension. The experiments performed at constant total surfactant concentration, up to 1.0 mM, reveal that these homologous surfactants mix together to form mixed vesicles and/or micelles, depending on the relative amount of the surfactants. The melting temperature T-m of the mixed DODAB-C(18)TAB vesicles is larger than that for the neat DODAB in water owing to the incorporation of C(18)TAB in the vesicle bilayer. The surface tension decreases sigmoidally with C(18)TAB concentration and the inflection point lies around (XDODAB) approximate to 0.4, indicating the onset of micelle formation owing to saturation of DODAB vesicles by C(18)TAB molecules. When XDODAB > 0.5 C(18)TAB molecules are mainly solubilised by the vesicles, but when XDODAB < 0.25 micelles are dominant. Fluorescence data of the Nile Red probe incorporated in the system at different surfactant molar fractions indicate the formation of micelle and vesicle structures. These structures have apparent hydrodynamic radius RH of about 180 and 500-800 nm, respectively, as obtained by DLS measurements. (C) 2007 Elsevier B.V. All rights reserved.

Interaction of octaethylene glycol n-dodecyl monoether with dioctadecyldimethylammonium bromide and chloride vesicles

Several different methods were used to investigate the vesicle-to-micelle transition induced by the addition of the nonionic surfactant octaethylene glycol n-dodecyl monoether (C12E8) to spontaneously formed vesicle dispersions of dioctadecyldimethylammonium bromide and chloride (DODAX, X = Cl- and Br-). Dynamic light scattering reveals that fast mode micelles are formed upon addition of C12E6. The micellar mode becomes progressively dominant as the C12E8/DODAX molar ratio (R) is increased until the vesicle-to-micelle transition is complete. Turbidity, calorimetry, fluorescence quantum yield, and anisotropy measurements indicate two critical compositions: the first, R-sat, when the vesicle bilayer is saturated with C12E8 and the second, R-sol, which corresponds to the complete vesicle-to-micelle transition. Below R-sat the vesicles swell due to incorporation of the surfactant into the vesicle bilayer, and above R-sat mixed micelles and bilayer structures coexist, the determined R-sat and R-sol range from 0 to 1 and 4 to 6, respectively, depending on the surfactant counterion and the experimental method used. Cryo-transmission electron microscopy micrographs show that when R approximate to 4, micelles coexist with extended bilayer fragments. In pure DODAX (1.0 mM) dispersions, unilamellar vesicles are observed. According to the DSC results, C12E8 lowers the gel-to-liquid crystalline transition temperature, T-m, of DODAX and broadens the main transition peak which disappears around R approximate to 5 and 6 for DODAC and DODAB, respectively.

Vesicle-micelle transition in mixtures of dioctadecyldimethylammonium chloride and bromide with nonionic and zwitterionic surfactants

We have investigated the effect of mixing spontaneously formed dispersions of the cationic vesicle-forming dioctadecyldimethylammonium chloride and bromide (DODAX, with X being anions Cl- (C) or Br- (B)) with solutions of the micelle-forming nonionic ethylene oxide surfactants penta-, hepta-, and octaethyleneglycol mono-n-dodecyl ether, C12En (n = 5, 7, and 8), and the zwitterionic 3-(N-hexadecyl-N,N-dimethylammonio)propane sulfonate (HPS). We used for this purpose differential scanning calorimetry (DSC), turbidity, and steady-state fluorescence spectroscopy to investigate the vesicle-micelle (V-M) transition yielded by adding C12En and HPS to 1.0 mM vesicle dispersions of DODAC and DODAB. The addition of these surfactants lowers the gel-to-liquid crystalline phase transition temperature (T-m) of DODAC and DODAB, and the transition becomes less cooperative, that is, the thermogram transition peak shifts to lower temperature and broadens to disappear when the V-M transition is complete, the vesicle bilayer becomes less organized, and the T., decreases, in agreement with measurements of the fluorescence quantum yield of trans-diphenylpolyene (t-DPO) fluorescence molecules incorporated in the vesicle bilayer. Turbidity data indicate that the V-M transition comes about in three stages: first surfactants are solubilized into the vesicle bilayer; after saturation, the vesicles are ruptured, and, finally, the vesicles are completely solubilized and only mixed micelles are formed. The critical points of bilayer saturation and vesicle solubilization were obtained from the turbidity and fluorescence curves, and are reported in this communication. The solubility of DODAX is stronger for C12En than it is for HPS, meaning that C12En solubilizes DODAX more efficiently than does HPS. The surfactant solubilization depends slightly on the counterion, and varies according to the sequence C12E5 > C12E7 > C12E8 > HPS.