Profiling of Complex Microbial Populations by Denaturing Gradient Gel Electrophoresis Analysis of Polymerase Chain Reaction-Amplified Genes Coding for 16S rRNA

We describe a new molecular approach to analyzing the genetic diversity of complex microbial populations. This technique is based on the separation of polymerase chain reaction-amplified fragments of genes coding for 16S rRNA, all the same length, by denaturing gradient gel electrophoresis (DGGE). DGGE analysis of different microbial communities demonstrated the presence of up to 10 distinguishable bands in the separation pattern, which were most likely derived from as many different species constituting these populations, and thereby generated a DGGE profile of the populations. We showed that it is possible to identify constituents which represent only 1% of the total population. With an oligonucleotide probe specific for the V3 region of 16S rRNA of sulfate-reducing bacteria, particular DNA fragments from some of the microbial populations could be identified by hybridization analysis. Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment. The results we obtained demonstrate that this technique will contribute to our understanding of the genetic diversity of uncharacterized microbial populations.

Electrochemical impedance spectroscopy analysis for oxygen reduction reaction in 3.5% NaCl solution

The electrochemical impedance spectroscopy (EIS) at different potentials has been used to study the oxygen reduction reaction (ORR) in 3.5% NaCl solution on glassy carbon (GC) electrode in this work. Results show that ORR consists of three two-electron reaction steps and both superoxide ion (O-2(-)) and hydrogen peroxide (H2O2), which are produced by ORR, obstruct the diffusion of oxygen to the surface of the electrode and make the EIS results change into a transmissive finite diffusion process with the real part contraction and a reflective finite diffusion process from a semi-infinite diffusion process. The values of electron transfer resistance (R-t) and diffusion resistance (R-d) were calculated from EIS. O-2(-) influenced strongly on the Rt values and induced a maximum at -0.45 V.

Descriptive Simulation: Combining Symbolic and Numerical Methods in the Analysis of Chemical Reaction Mechanisms

The Kineticist's Workbench is a computer program currently under development whose purpose is to help chemists understand, analyze, and simplify complex chemical reaction mechanisms. This paper discusses one module of the program that numerically simulates mechanisms and constructs qualitative descriptions of the simulation results. These descriptions are given in terms that are meaningful to the working chemist (e.g., steady states, stable oscillations, and so on); and the descriptions (as well as the data structures used to construct them) are accessible as input to other programs.

Quantitative analysis of the reactivity of formate species seen by DRIFTS over a Au/Ce(La)O2 water–gas shift catalyst: First unambiguous evidence of the minority role of formates as reaction intermediates

The reactivity of the species formed at the surface of a Au/Ce(La)O2 catalyst during the water������¢���¯���¿���½���¯���¿���½gas shift (WGS) reaction were investigated by operando diffuse reflectance Fourier transform spectroscopy (DRIFTS) at the chemical steady state during isotopic transient kinetic analyses (SSITKA). The exchanges of the reaction product CO2 and of formate and carbonate surface species were followed during an isotopic exchange of the reactant CO using a DRIFTS cell as a single reactor. The DRIFTS cell was a modified commercial cell that yielded identical reaction rates to that measured over a quartz plug-flow reactor. The DRIFTS signal was used to quantify the relative oncentrations of the surface species and CO2. The analysis of the formate exchange curves between 428 and 493 K showed that at least two levels of reactivity were present. ������¢���¯���¿���½���¯���¿���½Slow formates������¢���¯���¿���½���¯���¿���½ displayed an exchange rate constant 10- to 20-fold slower than that of the reaction product CO2. ������¢���¯���¿���½���¯���¿���½Fast formates������¢���¯���¿���½���¯���¿���½ were exchanged on a time scale similar to that of CO2. Multiple nonreactive readsorption of CO2 took place, accounting for the kinetics of the exchange of CO2(g) and making it impossible to determine the number of active sites through the SSITKA technique. The concentration (in mol g������¢���¯���¿���½���¯���¿���½1) of formates on the catalyst was determined through a calibration curve and allowed calculation of the specific rate of formate decomposition. The rate of CO2 formation was more than an order of magnitude higher than the rate of decomposition of formates (slow + fast species), indicating that all of the formates detected by DRIFTS could not be the main reaction intermediates in the production of CO2. This work stresses the importance of full quantitative analyses (measuring both rate constants and adsorbate concentrations) when investigating the role of adsorbates as potential reaction intermediates, and illustrates how even reactive species seen by DRIFTS may be unimportant in the overall reaction scheme.

Novel approaches to the analysis of the Maillard reaction of proteins

The Maillard reaction comprises a complex network of reactions which has proven to be of great importance in both food science and medicine. The majority of methods developed for studying the Maillard reaction in food have focused on model systems containing amino acids and monosaccharides. In this study, a number of electrophoretic techniques, including two-dimensional gel electrophoresis and capillary electrophoresis, are presented. These have been developed specifically for the analysis of the Maillard reaction of food proteins, and are giving important insights into this complex process.

Kinetic analysis of the reaction between electrogenerated superoxide and carbon dioxide in the room temperature ionic liquids 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide and hexyltriethylammonium bis(trifluoromethylsulfonyl)imide

The reduction of oxygen in the presence of carbon dioxide has been investigated by cyclic voltammetry at a gold microdisk electrode in the two room-temperature ionic liquids 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)imide ([EMIM][N(Tf)(2)]) and hexyltriethylammonium bis(trifluoromethylsulfonyl)imide ([N-6222] [N(Tf)(2)]). With increasing levels of CO2, cyclic voltammetry shows an increase in the reductive wave and diminishing of the oxidative wave, indicating that the generated superoxide readily reacts with carbon dioxide. The kinetics of this reaction are investigated in both ionic liquids. The reaction was found to proceed via a DISP1 type mechanism in [EMIM][N(Tf)(2)] with an overall second-order rate constant of 1.4 +/- 0.4 x 10(3) M-1 s(-1). An ECE or DISP1 mechanism was determined to be the most likely pathway for the reaction in [N-6222][N(Tf)(2)], with an overall second-order rate constant of 1.72 +/- 0.45 x 10(3) m(-1) s(-1).

Determination of polyphenols in wines by reaction with 4-aminoantipyrine and photometric flow-injection analysis

A new flow-injection analytical procedure is proposed for the determination of the total amount of polyphenols in wines; the method is based on the formation of a colored complex between 4-aminoantipyrine and phenols, in the presence of an oxidizing reagent. The oxidizing agents hexacyanoferrate(III), peroxodisulfate, and tetroxoiodate(VII) were tested. Batch trials were first performed to select appropriate oxidizing agents, pH, and concentration ratios of reagents, on the basis of their effect on the stability of the colored complex. Conditions selected as a result of these trials were implemented in a flow-injection analytical system in which the influence of injection volume, flow rate, and reaction- coil length, was evaluated. Under the optimum conditions the total amount of polyphenols, expressed as gallic acid, could be determined within a concentration range of 36 to 544 mg L–1, and with a sensitivity of 344 L mol–1 cm–1 and an RSD <1.1%. The reproducibility of analytical readings was indicative of standard deviations <2%. Interference from sugars, tartaric acid, ascorbic acid, methanol, ammonium sulfate, and potassium chloride was negligible. The proposed system was applied to the determination of total polyphenols in red wines, and enabled analysis of approximately 55 samples h–1. Results were usually precise and accurate; the RSD was <3.9% and relative errors, by the Folin–Ciocalteu method, <5.1%.

Evaluation of multiple reaction monitoring cubed for the analysis of tachykinin related peptides in rat spinal cord using a hybrid triple quadrupole–linear ion trap mass spectrometer

Targeted peptide methods generally use HPLC-MS/MRM approaches. Although dependent on the instrumental resolution, interferences may occur while performing analysis of complex biological matrices. HPLC-MS/MRM3 is a technique, which provides a significantly better selectivity, compared with HPLC-MS/MRM assay. HPLC-MS/MRM3 allows the detection and quantitation by enriching standard MRM with secondary product ions that are generated within the linear ion trap. Substance P (SP) and neurokinin A (NKA) are tachykinin peptides playing a central role in pain transmission. The objective of this study was to verify whether HPLC-HPLCMS/ MRM3 could provide significant advantages over a more traditional HPLC-MS/MRM assay for the quantification of SP and NKA in rat spinal cord. The results suggest that reconstructed MRM3 chromatograms display significant improvements with the nearly complete elimination of interfering peaks but the sensitivity (i.e. signal-to-noise ratio) was severely reduced. The precision (%CV) observed was between 3.5% - 24.1% using HPLC-MS/MRM and in the range of 4.3% - 13.1% with HPLC-MS/MRM3, for SP and NKA. The observed accuracy was within 10% of the theoretical concentrations tested. HPLC-MS/MRM3 may improve the assay sensitivity to detect difference between samples by reducing significantly the potential of interferences and therefore reduce instrumental errors.

Semi-algebraic methods for symbolic analysis of complex reaction networks

The identification of chemical mechanism that can exhibit oscillatory phenomena in reaction networks are currently of intense interest. In particular, the parametric question of the existence of Hopf bifurcations has gained increasing popularity due to its relation to the oscillatory behavior around the fixed points. However, the detection of oscillations in high-dimensional systems and systems with constraints by the available symbolic methods has proven to be difficult. The development of new efficient methods are therefore required to tackle the complexity caused by the high-dimensionality and non-linearity of these systems. In this thesis, we mainly present efficient algorithmic methods to detect Hopf bifurcation fixed points in (bio)-chemical reaction networks with symbolic rate constants, thereby yielding information about their oscillatory behavior of the networks. The methods use the representations of the systems on convex coordinates that arise from stoichiometric network analysis. One of the methods called HoCoQ reduces the problem of determining the existence of Hopf bifurcation fixed points to a first-order formula over the ordered field of the reals that can then be solved using computational-logic packages. The second method called HoCaT uses ideas from tropical geometry to formulate a more efficient method that is incomplete in theory but worked very well for the attempted high-dimensional models involving more than 20 chemical species. The instability of reaction networks may lead to the oscillatory behaviour. Therefore, we investigate some criterions for their stability using convex coordinates and quantifier elimination techniques. We also study Muldowney's extension of the classical Bendixson-Dulac criterion for excluding periodic orbits to higher dimensions for polynomial vector fields and we discuss the use of simple conservation constraints and the use of parametric constraints for describing simple convex polytopes on which periodic orbits can be excluded by Muldowney's criteria. All developed algorithms have been integrated into a common software framework called PoCaB (platform to explore bio- chemical reaction networks by algebraic methods) allowing for automated computation workflows from the problem descriptions. PoCaB also contains a database for the algebraic entities computed from the models of chemical reaction networks.

An analysis of Samoan reaction to The Orator (O Le Tulafale)’s Fāgogo defining Samoan identity

The Orator (O Le Tulafale) was promoted as the first Samoan language film shot in Samoa with a Samoan cast and crew. Written and directed by Samoan filmmaker Tusi Tamasese, the film succeeded at several of the movie industry’s prestigious festivals. The Orator (O Le Tulafale) is about an outcast family of a dwarf (Saili), his wife and her teenage daughter. As the main protagonist, Saili battles to overcome his fears to become a chief to save his family and land. The film’s themes are courage, love, honour , as well as hypocrisy, violence, and discrimination. A backlash by Samoans was predicted ; however, the opposite occurred. This raised the following questions: first, what is it about the film causing this reaction? It is a 106 -minute film shot in Samoa about Samoans and the Samoan culture . D espite promotional claims about the film , there have been Samoan -produced films in Samoa . Secondly, to what are Samoans really responding? Is it 1) just to the film because it is about Samoa, or 2) are they responding to themselves , and how they reacted during the act of watching the film? This implies levels of reactions in the act of watching, and examining the dominant level of response is important. To explore this, t he Samoan story telling technique of Fāgogo was used to analyse the film’s narration and narrative techniques. R. Allen’s (1993, 1997) concept of projected illusion was employed to discuss the relationship between Samoans and the film developed during the act of watching. An examination of the term Samoan and a description of the framework of Fa’a Samoa (Samoan culture) were provided. Also included were discussions of memory and its impact on Samoan cultural identity. The analysis indicated that The Orator (O Le Tulafale) acted as a memory prompt through which Samoans recalled memories confirming and defining cultural bonds. These memories constituted the essence of being Samoan. These memories were awakened, and shared as oral histories as fāgogo. The receivers appeared to interpret the shared memories to create their own memories and stories to suit their contexts, according to Facebook postings. An interpretation is that the organic sharing of memories as fā gogo created a global definition of Samoan that Samoans internationally claimed.

Suitability of DNA extracted from archival specimens of fruit-eating bats of the genus Artibeus (Chiroptera, Phyllostomidae) for polymerase chain reaction and sequencing analysis

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Symmetry analysis of an integrable reaction-diffusion equation

In this paper, we investigate the invariance and integrability properties of an integrable two-component reaction-diffusion equation. We perform Painleve analysis for both the reaction-diffusion equation modelled by a coupled nonlinear partial differential equations and its general similarity reduced ordinary differential equation and confirm its integrability. Further, we perform Lie symmetry analysis for this model. Interestingly our investigations reveals a rich variety of particular solutions, which have not been reported in the literature, for this model. (C) 2000 Elsevier B.V. Ltd. All rights reserved.