Statistical Methods for Conservation and Alignment Quality in Proteins

Construction of multiple sequence alignments is a fundamental task in Bioinformatics. Multiple sequence alignments are used as a prerequisite in many Bioinformatics methods, and subsequently the quality of such methods can be critically dependent on the quality of the alignment. However, automatic construction of a multiple sequence alignment for a set of remotely related sequences does not always provide biologically relevant alignments.Therefore, there is a need for an objective approach for evaluating the quality of automatically aligned sequences. The profile hidden Markov model is a powerful approach in comparative genomics. In the profile hidden Markov model, the symbol probabilities are estimated at each conserved alignment position. This can increase the dimension of parameter space and cause an overfitting problem. These two research problems are both related to conservation. We have developed statistical measures for quantifying the conservation of multiple sequence alignments. Two types of methods are considered, those identifying conserved residues in an alignment position, and those calculating positional conservation scores. The positional conservation score was exploited in a statistical prediction model for assessing the quality of multiple sequence alignments. The residue conservation score was used as part of the emission probability estimation method proposed for profile hidden Markov models. The results of the predicted alignment quality score highly correlated with the correct alignment quality scores, indicating that our method is reliable for assessing the quality of any multiple sequence alignment. The comparison of the emission probability estimation method with the maximum likelihood method showed that the number of estimated parameters in the model was dramatically decreased, while the same level of accuracy was maintained. To conclude, we have shown that conservation can be successfully used in the statistical model for alignment quality assessment and in the estimation of emission probabilities in the profile hidden Markov models.

Estudo ab-initio da a-alanina em meio aquoso

Ab initio Hartree-Fock (HF), Density Functional (B3LYP) and electron correlation (MP2) methods have been used to caracterize the aqueous medium intramolecular hydrogen bond in a-alanine. The 6-31G* and 6-31++G** were taken from Gaussian94 library. We were concerned on the structure of three conformers of a-alanine, in their neutral form plus on the structure of the zwitterionic form (Z). The Z structure is a stationary point at the HF/6-31G* level but it is not when diffuse functions and electron correlation are included. This results shows that the Z form does not exist in the gas phase. The inclusion of solvent effects changed significantly the results obtained in gas phase, therefore this inclusion make the Z form a stationary point within all level of theory, and the relative energy depends dramatically on the level of calculation.

Estimativa por DSC das entalpias de sublimação da etilenouréia e da propilenouréia: algumas correlações empíricas envolvendo amidas e tioamidas

By using DSC data, the enthaplies of sublimation for ethyleneurea and propyleneurea, are calculated as 84 and 89 kJ mol-1 respectively. Using the vaporization enthalpy values for dimethylethyleneurea and dimethylprophyleneurea, as obtained from literature, the empirical relation: Dcrg Hmo (1)/ Dcrg Hmo (2) = Dlg Hmo (1)/ Dlg Hmo(2) = constant, that relate sublimation or vaporization enthalpies of two different substances and of its methylated derivatives, is obtained. Correlations like that are found to another ureas and thioureas.

Fotólise no estado estacionário e com pulso de laser de 1-benzociclanonas e de seus derivados a,a -dimetilados

Laser excitation of 0.01 M solutions of 1-indanone (Ia), 1-tetralone (Ib), 1-benzosuberone (Ic), and their a,a -dimethyl derivatives IIa-c, respectively, in benzene, produced transients with maximum absorption at 425 nm, and lifetimes ranging from 62 ns (IIa) to 5.5ms (Ic). Quenching studies using well known triplet quenchers such as 1,3-cyclohexadiene and oxygen demonstrated the triplet nature of these transients. In the presence of hydrogen donors, such as 2-propanol, the triplet state decay of the ketones Ia-c leads to the formation of the corresponding ketyl radicals, i.e. IIIa-c, which show absorption spectra very similar to the parent ketone, with lmax at 430 nm and lifetime in excess of 20 ms. Steady state irradiations show that the a,a -dimethyl ketones IIa and IIc form ortho-alkyl benzaldehydes probably derived from an initial a-cleavage of the corresponding triplet excited states.

A técnica da reflectância difusa aplicada ao estudo da fluorescência de 2,3-naftalimidas n-substituídas com grupos alquila incluídas em b-ciclodextrina e adsorvidas em celulose microcristalina

The solution fluorescence of N-alkyl-2,3-naphthalimides (1-4) in polar protic and aprotic solvents was compared to the emission from solid samples resulting from the imide complexation with b-cyclodextrin or adsorption on the surface of microcrystalline cellulose. Solid samples of the inclusion complex 2,3-naphthalimides/b-cyclodextrin show maximum for fluorescence emission significantly different to the observed in methanolic solution. Beside this, a clear effect on the alkyl chain length could be observed for these samples which is probably due to differences in probe location inside the cyclodextrin cavity. The constancy for fluorescence quantum yield and fluorescence lifetime for the imides 1 - 4 adsorbed on microcrystalline cellulose suggests that, independently of the polarity of the solvent used for sample preparation, the probe is preferentially located on the cellulose surface. An increase of fluorescence quantum yield and fluorescence lifetime for solid samples, when compared to the values obtained in solution for the different solvents employed in this study (acetonitrile, methanol and water), is fully in accordance with a decrease of the probe mobility due to inclusion in b-cyclodextrin or to adsorption on cellulose.

Produção de dióxido de manganês eletrolítico para uso em baterias de lítio

The e phase of electrolytic manganese dioxide (EMD) is the structural form most easily converted in the LiMn2O4 spinel used as cathode in lithium batteries. Thus, employing titanium as anode, a study of electrolysis parameters was carried out in order to determine the best conditions to produce an e-EMD suitable for that spinel preparation. The influence of solution temperature (65oC and 90oC) and current density (between 1 mA/cm2 and 17.5 mA/cm2) on the anode potential and the EMD properties was investigated using an aqueous 2.0 mol/L MnSO4 + 0.30 mol/L H2SO4 solution. In any of the electrolysis conditions tested only the e-EMD structure was obtained, but its specific surface area varied with the applied current density and temperature. Drying the e-EMD at temperatures between 60oC and 120oC did not cause any phase changes. To produce a suitable EMD at the highest current density possible without passivation of the titanium anode, the best electrolysis parameters were determined to be 90oC and 15 mA/cm2. The e-EMD thus obtained had a specific surface area (BET) of ca. 65 m2/g.

Elementos da dinâmica química ao nível da teoria variacional do estado de transição com correções interpoladas

In this article are presented some fundamental elements of the conventional and of the variational transition state theories which are needed to carried out calculations of semi-classical chemical dynamics. Some important bottlenecks in building reliable potential energy surfaces using electronic structure calculations are also discussed. It is put emphasis on the methodology of the variational transition state theory with interpolated corrections (VTST-IC), and its application in the calculations of the rate constants and of the kinetic isotope effect (KIE) of CH4 + Cl « CH3 + HCl reaction.

Estado da arte da cromatografia gasosa de alta resolução e alta temperatura

The developments in stationary phase synthesis and capillary column technology, have opened new perspectives in analysis of high molecular mass compounds (³600 daltons) and thermolabile organic compounds by High Temperature High Resolution Gas Chromatography (HT-HRGC). HT-HRGC is a new analytical borderline and its application to the analysis of high molecular mass compounds is still in its infancy. The apolar and medium polar gum phases can now be operated at temperatures up to 400-480ºC, being used for the analysis of n-alcanes up to C-100, lipids, oligosaccharides, industrial resins, polyglycerols, cyclodextrins, porphyrins, etc. This technique should play a leading role as a powerful tool, for many different analysis types, in multidisciplinary fields of Science.

Determinação de carbaril utilizando testes ELISA (Enzyme-linked immunosorbent assay) e CLAE com detecção por arranjo de diodos

ELISAs have been applied to pesticide residue analysis due to their high sensitivity and selectivity. However, some ELISAs performance may be affected by matrix components. In this work, ELISA for carbaryl in water samples was checked for interference by naturally occurring fulvic acids. The results suggested that the high fulvic acid concentration (Symbol>ž³30 mg L-1) and acidic pH conditions (pH 4.0) interfere with the signal detection decreasing the method sensitivity. A dilution of the samples and adjust to pH 8.0 are appropriate to minimize the matrix interferences in the ELISA method. Good correlation between ELISA and HPLC-DAD results was observed.

Caracterização de quitosana por Cromatografia de Permeação em Gel - Influência do método de preparação e do solvente

In this work, samples of chitosan obtained in different conditions were characterized by molecular weight distribution, using Gel Permeation Chromatography (GPC), in two different solvents. It was observed that the increase in the number of deacetylation steps promotes a increase in the degree of deacetylation followed by a decrease in the average of molecular weight and polydispersion. The GPC curves obtained for chitosan samples in the two solvents used (CH3COOH 0.30 mol/dm³ - CH3CONa 0.20 mol/dm³ and CH3COOH 0.10 mol/dm³ - NaCl 0.20 mol/dm³) showed small difference in elution volume, but significant changes in the average molecular weight (Mn and Mw) and polydispersion that, in agree with the values of Huggins constant, present evidences of chitosan aggregates formation in the second solvent.

Determinação de baixas concentrações de cobre em águas naturais por espectrofotometria de absorção atômica em chama usando um sistema SIA com uma coluna de poli(etilenimina)

This paper describes a sequential injection analysis (SIA) set-up coupled to a flame atomic absorption spectrometer (FAAS) to accomplish the determination of low concentrations of copper in drinking waters. Copper is first retained under neutral media in an on-line 29x1.6 mm column filled with poly(ethylenimine) immobilised on silica gel. The retained analyte is then eluted by flowing through the column 250 Symbol>mL of a nitric acid solution. The selection of 3.85 ml of sample enabled to obtain a detection limit of 0.27 mug/L and a sampling rate of about 24 samples/h. There was a good agrement between the results of 12 samples furnished by the proposed procedure and by electrothermal atomic absorption spectrometry. Repeatability assessment gave a relative standard deviation of 1.3 % after ten replicate analysis of a sample containing about 70 mug/L in copper..

Preparação e caracterização de pós cerâmicos de aluminatos de lítio

The preparation of gamma-LiAlO2 by coprecipitation and sol-gel synthesis was investigated. Ceramic powders obtained by coprecipitation synthesis were prepared from aqueous solutions of aluminum and lithium nitrates using sodium hydroxide as precipitant agent. By sol-gel synthesis, the ceramic powders were prepared from hydrolysis of aluminum isopropoxide. The materials obtained by two routes of synthesis were dried at 80ºC and calcined at 550, 750, 950 and 1150ºC. The characterization was done by X-ray diffraction, infrared spectroscopy, emission and absorption atomic spectrometry, helium picnometry, specific surface area (BET method) and scanning electronic microscopy. Mixtures of crystalline phases were obtained by coprecipitation synthesis: 80ºC- LiAl2(OH)7.2H2O + Al(OH)3; 550 and 750ºC- alpha-LiAlO2 + eta-Al2O3; 950 and 1150ºC- gamma-LiAlO2 + LiAl5O8. Chemical analysis showed molar ration Al/Li Symbol>@ 3. Crystalline single-phases were obtained by sol-gel synthesis above 550ºC: 550ºC-alpha-LiAlO2; 750, 950 and 1150ºC-gamma-LiAlO2. These powders presented molar ration Al/Li Symbol>@ 1. Thus, gamma-LiAlO2 crystalline phase was obtained at 750ºC by sol-gel synthesis while by coprecipitation synthesis, a mixture of crystalline phases was obtained. These results showed the superiority of the sol-gel synthesis for the preparation of pure gamma-LiAlO2.

Prelude and Fugue in F Major

Fugue in F Major : Recorded in Danish State Radio, Copenhagen, Denmark.

Indicadores naturais de pH: usar papel ou solução?

In this work, the fruit extracts of Morus nigra - mulberry, Syzygium cuminii - jambolão, Vitis vinifera Symbol>¾ grape, Myrciaria cauliflora - jabuticaba are suggested as pH indicators in the form of either solutions or paper. The pH indicator solutions were prepared by soaking the fruits or their peels in ethanol 1:3 (m/V) for 24 h, followed by simple filtration. The pH indicator papers were prepared by imersion of the qualitative filter paper strips in the pH indicator solutions. The different pH leads to color changes in the indicator solutions or papers and it can be used for teaching elementary chemistry concepts.

Terapia fotodinâmica: aspectos farmacológicos, aplicações e avanços recentes no desenvolvimento de medicamentos

Photodynamic Therapy (PDT) is a clinical procedure, which utilize a photosensitive compound and light. This is a new modality of treatment for cancer, aged related macular degenerescence (AMD), psoriasis, arthritis, arterial restenosis, etc which exhibits efficiency, less traumatic effects, low recovery time and few co-lateral effects. The first officially approved drug for PDT by the Food and Drug Administration (EUA) is PhotofrinSymbol>â, which is applied for cancer. A new generation drug for PDT, VisudyneSymbol>â was recently approved to treat AMD; its photoactive compound is BPDMA, a benzoporphyrin mono-acid derivative (chlorin-type molecule). A concise history, technical information and some drugs for PDT are reported.