Positive Selection Results in Frequent Reversible Amino Acid Replacements in the G Protein Gene of Human Respiratory Syncytial Virus

Human respiratory syncytial virus (HRSV) is the major cause of lower respiratory tract infections in children under 5 years of age and the elderly, causing annual disease outbreaks during the fall and winter. Multiple lineages of the HRSVA and HRSVB serotypes co-circulate within a single outbreak and display a strongly temporal pattern of genetic variation, with a replacement of dominant genotypes occurring during consecutive years. In the present study we utilized phylogenetic methods to detect and map sites subject to adaptive evolution in the G protein of HRSVA and HRSVB. A total of 29 and 23 amino acid sites were found to be putatively positively selected in HRSVA and HRSVB, respectively. Several of these sites defined genotypes and lineages within genotypes in both groups, and correlated well with epitopes previously described in group A. Remarkably, 18 of these positively selected tended to revert in time to a previous codon state, producing a ""flipflop'' phylogenetic pattern. Such frequent evolutionary reversals in HRSV are indicative of a combination of frequent positive selection, reflecting the changing immune status of the human population, and a limited repertoire of functionally viable amino acids at specific amino acid sites.

Actions of a Proline Analogue, L-Thiazolidine-4-Carboxylic Acid (T4C), on Trypanosoma cruzi

It is well established that L-proline has several roles in the biology of trypanosomatids. In Trypanosoma cruzi, the etiological agent of Chagas' disease, this amino acid is involved in energy metabolism, differentiation processes and resistance to osmotic stress. In this study, we analyzed the effects of interfering with L-proline metabolism on the viability and on other aspects of the T. cruzi life cycle using the proline analogue L- thiazolidine-4-carboxylic acid (T4C). The growth of epimastigotes was evaluated using different concentrations of T4C in standard culture conditions and at high temperature or acidic pH. We also evaluated possible interactions of this analogue with stress conditions such as those produced by nutrient starvation and oxidative stress. T4C showed a dose-response effect on epimastigote growth (IC(50) = 0.89+/-0.02 mM at 28 degrees C), and the inhibitory effect of this analogue was synergistic (p<0.05) with temperature (0.54+/-0.01 mM at 37 degrees C). T4C significantly diminished parasite survival (p<0.05) in combination with nutrient starvation and oxidative stress conditions. Pre-incubation of the parasites with L-proline resulted in a protective effect against oxidative stress, but this was not seen in the presence of the drug. Finally, the trypomastigote bursting from infected mammalian cells was evaluated and found to be inhibited by up to 56% when cells were treated with non-toxic concentrations of T4C (between 1 and 10 mM). All these data together suggest that T4C could be an interesting therapeutic drug if combined with others that affect, for example, oxidative stress. The data also support the participation of proline metabolism in the resistance to oxidative stress.

Polar organic marker compounds in atmospheric aerosols during the LBA-SMOCC 2002 biomass burning experiment in Rondonia, Brazil: sources and source processes, time series, diel variations and size distributions

Measurements of polar organic marker compounds were performed on aerosols that were collected at a pasture site in the Amazon basin (Rondonia, Brazil) using a high-volume dichotomous sampler (HVDS) and a Micro-Orifice Uniform Deposit Impactor (MOUDI) within the framework of the 2002 LBA-SMOCC (Large-Scale Biosphere Atmosphere Experiment in Amazonia - Smoke Aerosols, Clouds, Rainfall, and Climate: Aerosols From Biomass Burning Perturb Global and Regional Climate) campaign. The campaign spanned the late dry season (biomass burning), a transition period, and the onset of the wet season (clean conditions). In the present study a more detailed discussion is presented compared to previous reports on the behavior of selected polar marker compounds, including levoglucosan, malic acid, isoprene secondary organic aerosol (SOA) tracers and tracers for fungal spores. The tracer data are discussed taking into account new insights that recently became available into their stability and/or aerosol formation processes. During all three periods, levoglucosan was the most dominant identified organic species in the PM(2.5) size fraction of the HVDS samples. In the dry period levoglucosan reached concentrations of up to 7.5 mu g m(-3) and exhibited diel variations with a nighttime prevalence. It was closely associated with the PM mass in the size-segregated samples and was mainly present in the fine mode, except during the wet period where it peaked in the coarse mode. Isoprene SOA tracers showed an average concentration of 250 ng m(-3) during the dry period versus 157 ng m(-3) during the transition period and 52 ng m(-3) during the wet period. Malic acid and the 2-methyltetrols exhibited a different size distribution pattern, which is consistent with different aerosol formation processes (i.e., gas-to-particle partitioning in the case of malic acid and heterogeneous formation from gas-phase precursors in the case of the 2-methyltetrols). The 2-methyltetrols were mainly associated with the fine mode during all periods, while malic acid was prevalent in the fine mode only during the dry and transition periods, and dominant in the coarse mode during the wet period. The sum of the fungal spore tracers arabitol, mannitol, and erythritol in the PM(2.5) fraction of the HVDS samples during the dry, transition, and wet periods was, on average, 54 ng m(-3), 34 ng m(-3), and 27 ng m(-3), respectively, and revealed minor day/night variation. The mass size distributions of arabitol and mannitol during all periods showed similar patterns and an association with the coarse mode, consistent with their primary origin. The results show that even under the heavy smoke conditions of the dry period a natural background with contributions from bioaerosols and isoprene SOA can be revealed. The enhancement in isoprene SOA in the dry season is mainly attributed to an increased acidity of the aerosols, increased NO(x) concentrations and a decreased wet deposition.

Rapid formation of isoprene photo-oxidation products observed in Amazonia

Isoprene represents the single most important reactive hydrocarbon for atmospheric chemistry in the tropical atmosphere. It plays a central role in global and regional atmospheric chemistry and possible climate feedbacks. Photo-oxidation of primary hydrocarbons (e. g. isoprene) leads to the formation of oxygenated VOCs (OVOCs). The evolution of these intermediates affects the oxidative capacity of the atmosphere (by reacting with OH) and can contribute to secondary aerosol formation, a poorly understood process. An accurate and quantitative understanding of VOC oxidation processes is needed for model simulations of regional air quality and global climate. Based on field measurements conducted during the Amazonian Aerosol Characterization Experiment (AMAZE-08) we show that the production of certain OVOCs (e. g. hydroxyacetone) from isoprene photo-oxidation in the lower atmosphere is significantly underpredicted by standard chemistry schemes. Recently reported fast secondary production could explain 50% of the observed discrepancy with the remaining part possibly produced via a novel primary production channel, which has been proposed theoretically. The observations of OVOCs are also used to test a recently proposed HO(x) recycling mechanism via degradation of isoprene peroxy radicals. If generalized our observations suggest that prompt photochemical formation of OVOCs and other uncertainties in VOC oxidation schemes could result in uncertainties of modelled OH reactivity, potentially explaining a fraction of the missing OH sink over forests which has previously been largely attributed to a missing source of primary biogenic VOCs.

High performance magnetic separation of gold nanoparticles for catalytic oxidation of alcohols

We present the magnetic separation approach to facilitate the recovery of gold nanoparticle (AuNP) catalysts. The use of magnetically recoverable supports for the immobilization of AuNPs instead of traditional oxides, polymers or carbon based solids guarantees facile, clean, fast and efficient separation of the catalyst at the end of the reaction cycle. Magnetic separation can be considered an environmentally benign separation approach, since it minimizes the use of auxiliary substances and energy for achieving catalyst recovery. The catalyst preparation is based on the immobilization of Au(3+) on the surface of core-shell silica-coated magnetite nanoparticles, followed by metal reduction using two different methods. AuNPs were prepared by thermal reduction in air and by hydrogen reduction at mild temperature. Interestingly, the mean particle size of the supported AuNPs was similar (ca. 5.9 nm), but the polydispersity of the samples is quite different. The catalytic activity of both catalysts in the aerobic oxidation of alcohols was investigated and a distinct selectivity for benzyl alcohol oxidation was observed.

Comparative study of the adsorption and dissociation of vinylacetic acid and acrylic acid on silicon (001)

In this work, we employ the state of the art pseudopotential method, within a generalized gradient approximation to the density functional theory, to investigate the adsorption process of acrylic acid (AAc) and vinylacetic acid (VAA) on the silicon surface. Our total energy calculations support the proposed experimental process, as it indicates that the chemisorption of the molecule is as follows: The gas phase VAA (AAc) adsorbs molecularly to the electrophilic surface Si atom and then dissociates into H(2)C = CH - COO and H, bonded to the electrophilic and nucleophilic surface silicon dimer atoms, respectively. The activation energy for both processes correspond to thermal activations that are smaller than the usual growth temperature. In addition, the electronic structure, calculated vibrational modes, and theoretical scanning tunneling microscopy images are discussed, with a view to contribute to further experimental investigations.

4-(2,5-Dioxo-2,5-dihydro-1H-pyrrol-1-yl)benzoic acid: X-ray and DFT-calculated structure

In the title compound, C(11)H(7)NO(4), there is a dihedral angle of 45.80 (7)degrees between the planes of the benzene and maleimide rings. The presence of O-H...O hydrogen bonding and weak C-H...O interactions allows the formation of R (3) 3(19) edge-connected rings parallel to the (010) plane. Structural, spectroscopic and theoretical studies were carried out. Density functional theory (DFT) optimized structures at the B3LYP/6-311 G(d,p) and 6-31++G(d,p) levels are compared with the experimentally determined molecular structure in the solid state. Additional IR and UV theoretical studies allowed the presence of functional groups and the transition bands of the system to be identified.

Development and validation of a fast RP-HPLC method to determine the analogue of the thyroid hormone, 3,5,3 '-triiodothyroacetic acid (TRIAC), in polymeric nanoparticles

The objective of this work was to develop and validate a rapid Reversed-Phase High-Performance Liquid Chromatography method for the quantification of 3,5,3 '-triiodothyroacetic acid (TRIAC) in nanoparticles delivery system prepared in different polymeric matrices. Special attention was given to developing a reliable reproductive technique for the pretreatment of the samples. Chromatographic runs were performed on an Agilent 1200 Series HPLC with a RP Phenomenex (R) Gemini C18 (150 x 4, 6 mm i.d., 5 mu m) column using acetonitrile and triethylamine buffer 0.1% (TEA) (40 : 60 v/v) as a mobile phase in an isocratic elution, pH 5.6 at a flow rate of 1 ml min(-1). TRIAC was detected at a wavelength of 220 nm. The injection volume was 20 mu l and the column temperature was maintained at 35 degrees C. The validation characteristics included accuracy, precision, specificity, linearity, recovery, and robustness. The standard curve was found to have a linear relationship (r(2) - 0.9996) over the analytical range of 5-100 mu g ml(-1) . The detection and quantitation limits were 1.3 and 3.8 mu g ml(-1), respectively. The recovery and loaded TRIAC in colloidal system delivery was nearly 100% and 98%, respectively. The method was successfully applied in polycaprolactone, polyhydroxybutyrate, and polymethylmethacrylate nanoparticles.

2-(Phenylcarbonothioylsulfanyl)acetic acid

The title compound, C(9)H(8)O(2)S(2), can be used as a chain transfer agent and may be used to control the behavior of polymerization reactions. O-H center dot center dot center dot O hydrogen bonds of moderate character link the molecules into dimers. In the crystal, the dimers are linked into sheets by C-H center dot center dot center dot O interactions, forming R(4)(2)(12) and R(2)(2)(8) edge-fused rings running parallel to [101]. There are no intermolecular interactions involving the S atoms.

3-Nitrobenzoic acid-3-methyl-4-nitropyridine 1-oxide (1/1)

The title adduct, C(7)H(5)NO(4)center dot C(6)H(6)N(2)O(3), forms part of an ongoing study of the design of non-centrosymmetric systems based on 3-methy-4-nitropyridine 1-oxide. The components of the adduct are linked by intermolecular O-H center dot center dot center dot O hydrogen bonds. The rings of the two components are nearly planar, with a dihedral angle of 11.9 (2)degrees between the planes. The supramolecular structure shows that molecules of the title complex are linked into sheets by a combination of strong O-H center dot center dot center dot O and weak C-H center dot center dot center dot O hydrogen bonds.

Screening of Microorganisms Producing Cold-Active Oxidoreductases to Be Applied in Enantioselective Alcohol Oxidation. An Antarctic Survey

Several microorganisms were isolated from soil/sediment samples of Antarctic Peninsula. The enrichment technique using (RS)-.1-(phenyl) ethanol as a carbon source allowed us to isolate 232 psychrophile/psychrotroph microorganisms. We also evaluated the enzyme activity (oxidoreductases) for enantioselective oxidation reactions, by using derivatives of (RS)-.1-(phenyl) ethanol as substrates. Among the studied microorganisms, 15 psychrophile/psychrotroph strains contain oxidoreductases that catalyze the (S)-.enantiomer oxidation from racemic alcohols to their corresponding ketones. Among the identified microorganisms, Flavobacterium sp. and Arthrobacter sp. showed excellent enzymatic activity. These new bacteria strains were selected for optimization study, in which the (RS)-.1-(4-.methyl-.phenyl) ethanol oxidation was evaluated in several reaction conditions. From these studies, it was observed that Flavobacterium sp. has an excellent enzymatic activity at 10 degrees C and Arthrobacter sp. at 15 and 25 degrees C. We have also determined the growth curves of these bacteria, and both strains showed optimum growth at 25 degrees C, indicating that these bacteria are psychrotroph.

DNA oxidation, strand-breaks and etheno-adducts formation promoted by Cu, Zn-superoxide dismutase-H(2)O(2) in the presence and absence of bicarbonate

Biomolecule oxidation promoted by Cu, Zn-superoxide dismutase (SOD1) has been studied because of its potential role in neurodegenerative diseases. We studied the mechanism of DNA damage promoted by the SOD1-H(2)O(2) system. The system promoted the formation of strand breaks in plasmid DNA and the formation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodGuo) in calf thymus DNA. We were also able to detect, for the. first time, 1,N(2)-etheno-2'-deoxyguanosine (1,N(2)-epsilon dGuo) in calf thymus DNA exposed to SOD1-H(2)O(2). The addition of a copper chelator caused a decrease in the frequency of 8-oxodGuo and 1,N(2)-epsilon dGuo, indicating the participation of copper ions lost from SOD1 active sites. The addition of bicarbonate increased the levels of both DNA lesions. We conclude that copper liberated from SOD1 active sites has a central role in the mechanism of DNA damage promoted by SOD1 in the presence of H(2)O(2), and that bicarbonate can modulate the reactivity of released copper.

DNA damage by sulfite autoxidation catalyzed by cobalt complexes

DNA damage was investigated in the presence of sulfite, dissolved oxygen and cobalt(II) complexes with glycylglycylhistidine, glycylhistidyllysine, glycylglycyltyrosylarginine and tetraglycine. These studies indicated that only Co(II) complexed with glycylglycylhistidine (GGH) induced DNA strand breaks at low sulfite concentrations (1-80 mu M) via strong oxidants formed in the reaction. In the presence of the other complexes, some damage occurred only in the presence of high sulfite concentrations (0.1-2.0 mM) after incubation for 4 h. In the presence of GGH, Co(II) and dissolved O(2), DNA damage must involve a reactive high-valent cobalt complex. The damaging effect was increased by adding S(IV), due to the oxysulfur radicals formed as intermediates in S(IV) autoxidation catalyzed by the complex. SO(3)(center dot)-S-, HO(center dot) and H(center dot) radicals were detected by EPR-spin trapping experiments with DMPO (5,5-dimethyl-1-pyrroline N-oxide). The results indicate that Co(II) binds O2 in the presence of GGH, and leads to the formation of a DMPO-HO(center dot) adduct without first forming free superoxide or hydroxyl radical, supporting the participation of a reactive high-valent cobalt complex.

Retinoic Acid-Treated Pluripotent Stem Cells Undergoing Neurogenesis Present Increased Aneuploidy and Micronuclei Formation

The existence of loss and gain of chromosomes, known as aneuploidy, has been previously described within the central nervous system. During development, at least one-third of neural progenitor cells (NPCs) are aneuploid. Notably, aneuploid NPCs may survive and functionally integrate into the mature neural circuitry. Given the unanswered significance of this phenomenon, we tested the hypothesis that neural differentiation induced by all-trans retinoic acid (RA) in pluripotent stem cells is accompanied by increased levels of aneuploidy, as previously described for cortical NPCs in vivo. In this work we used embryonal carcinoma (EC) cells, embryonic stem (ES) cells and induced pluripotent stem (iPS) cells undergoing differentiation into NPCs. Ploidy analysis revealed a 2-fold increase in the rate of aneuploidy, with the prevalence of chromosome loss in RA primed stem cells when compared to naive cells. In an attempt to understand the basis of neurogenic aneuploidy, micronuclei formation and survivin expression was assessed in pluripotent stem cells exposed to RA. RA increased micronuclei occurrence by almost 2-fold while decreased survivin expression by 50%, indicating possible mechanisms by which stem cells lose their chromosomes during neural differentiation. DNA fragmentation analysis demonstrated no increase in apoptosis on embryoid bodies treated with RA, indicating that cell death is not the mandatory fate of aneuploid NPCs derived from pluripotent cells. In order to exclude that the increase in aneuploidy was a spurious consequence of RA treatment, not related to neurogenesis, mouse embryonic fibroblasts were treated with RA under the same conditions and no alterations in chromosome gain or loss were observed. These findings indicate a correlation amongst neural differentiation, aneuploidy, micronuclei formation and survivin downregulation in pluripotent stem cells exposed to RA, providing evidence that somatically generated chromosomal variation accompanies neurogenesis in vitro.

Ionic mobility of the solvated proton and acid-base titration in a four-compartment capillary electrophoresis system

Although H(+) and OH(-) are the most common ions in aqueous media, they are not usually observable in capillary electrophoresis (CE) experiments, because of the extensive use of buffer solutions as the background electrolyte. In the present work, we introduce CE equipment designed to allow the determination of such ions in a similar fashion as any other ion. Basically, it consists of a four-compartment piece of equipment for electrolysis-separated experiments (D. P. de Jesus et at, Anal. Chem., 2005, 77, 607). In such a system, the ends of the capillary are placed in two reservoirs, which are connected to two other reservoirs through electrolyte-filled tubes. The electrodes of the high-voltage power source are positioned in these reservoirs. Thus, the electrolysis products are kept away from the inputs of the capillary. The detection was provided by two capacitively coupled contactless conductivity detectors (CD), each one positioned about 11 cm from the end of the capillary. Two applications were demonstrated: titration-like procedures for nanolitre samples and mobility measurements. Strong and weak acids (pK(a) < 5), pure or mixtures, could be titrated. The analytical curve is linear from 50 mu M up to 10 mM of total dissociable hydrogen (r = 0.99899 for n =10) in 10-nL samples. By including D(2)O in the running electrolyte, we could demonstrate how to measure the mixed proton/deuteron mobility. When H(2)O/D(2)O (9 : 1 v/v) was used as the solvent, the mobility was 289.6 +/- 0.5 x 10(-5) cm(2) V(-1) s(-1). Due to the fast conversion of the species, this value is related to the overall behaviour of all isotopologues and isotopomers of the Zundel and Eigen structures, as well as the Stokesian mobility of proton and deuteron. The effect of neutral (o-phenanthroline) and negatively charged (chloroacetate) bases and aprotic solvent (DMSO) over the H(+) mobility was also demonstrated.