NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study.

We investigate nuclear magnetic resonance (NMR) parameters of the rhodopsin chromophore in the dark state of the protein and in the early photointermediate bathorhodopsin via first-principles molecular dynamics simulations and NMR chemical shift calculations in a hybrid quantum/classical (QM/MM) framework. NMR parameters are particularly sensitive to structural properties and to the chemical environment, which allows us to address different questions about the retinal chromophore in situ. Our calculations show that both the 13C and the 1H NMR chemical shifts are rather insensitive to the protonation state of Glu181, an ionizable amino acid side chain located in the vicinity of the isomerizing 11-cis bond. Thus, other techniques should be better suited to establish its protonation state. The calculated chemical shifts for bathorhodopsin further support our previously published theoretical structure, which is in very good agreement with more recent X-ray data.

Molecular mechanism of a green-shifted, pH-dependent red fluorescent protein mKate variant.

Fluorescent proteins that can switch between distinct colors have contributed significantly to modern biomedical imaging technologies and molecular cell biology. Here we report the identification and biochemical analysis of a green-shifted red fluorescent protein variant GmKate, produced by the introduction of two mutations into mKate. Although the mutations decrease the overall brightness of the protein, GmKate is subject to pH-dependent, reversible green-to-red color conversion. At physiological pH, GmKate absorbs blue light (445 nm) and emits green fluorescence (525 nm). At pH above 9.0, GmKate absorbs 598 nm light and emits 646 nm, far-red fluorescence, similar to its sequence homolog mNeptune. Based on optical spectra and crystal structures of GmKate in its green and red states, the reversible color transition is attributed to the different protonation states of the cis-chromophore, an interpretation that was confirmed by quantum chemical calculations. Crystal structures reveal potential hydrogen bond networks around the chromophore that may facilitate the protonation switch, and indicate a molecular basis for the unusual bathochromic shift observed at high pH. This study provides mechanistic insights into the color tuning of mKate variants, which may aid the development of green-to-red color-convertible fluorescent sensors, and suggests GmKate as a prototype of genetically encoded pH sensors for biological studies.

Epigenetic regulatory elements: Recent advances in understanding their mode of action and use for recombinant protein production in mammalian cells.

Successful generation of high producing cell lines requires the generation of cell clones expressing the recombinant protein at high levels and the characterization of the clones' ability to maintain stable expression levels. The use of cis-acting epigenetic regulatory elements that improve this otherwise long and uncertain process has revolutionized recombinant protein production. Here we review and discuss new insights into the molecular mode of action of the matrix attachment regions (MARs) and ubiquitously-acting chromatin opening elements (UCOEs), i.e. cis-acting elements, and how these elements are being used to improve recombinant protein production. These elements can help maintain the chromatin environment of the transgene genomic integration locus in a transcriptionally favorable state, which increases the numbers of positive clones and the transgene expression levels. Moreover, the high producing clones tend to be more stable in long-term cultures even in the absence of selection pressure. Therefore, by increasing the probability of isolating a high producing clone, as well as by increasing transcription efficiency and stability, these elements can significantly reduce the time and cost required for producing large quantities of recombinant proteins.

Functional impact of genetic variation on gene expression

Numerous links between genetic variants and phenotypes are known and genome-wide association studies dramatically increased the number of genetic variants associated with traits during the last decade. However, how changes in the DNA perturb the molecular mechanisms and impact on the phenotype of an organism remains elusive. Studies suggest that many traitassociated variants are in the non-coding region of the genome and probably act through regulation of gene expression. During my thesis I investigated how genetic variants affect gene expression through gene regulatory mechanisms. The first chapter was a collaborative project with a pharmaceutical company, where we investigated genome-wide copy number variation (CNVs) among Cynomolgus monkeys (Macaca fascicularis) used in pharmaceutical studies, and associated them to changes in gene expression. We found substantial copy number variation and identified CNVs linked to tissue-specific expression changes of proximal genes. The second and third chapters focus on genetic variation in humans and its effects on gene regulatory mechanisms and gene expression. The second chapter studies two human trios, where the allelic effects of genetic variation on genome-wide gene expression, protein-DNA binding and chromatin modifications were investigated. We found abundant allele specific activity across all measured molecular phenotypes and show extended coordinated behavior among them. In the third chapter, we investigated the impact of genetic variation on these phenotypes in 47 unrelated individuals. We found that chromatin phenotypes are organized into local variable modules, often linked to genetic variation and gene expression. Our results suggest that chromatin variation emerges as a result of perturbations of cis-regulatory elements by genetic variants, leading to gene expression changes. The work of this thesis provides novel insights into how genetic variation impacts gene expression by perturbing regulatory mechanisms. -- De nombreux liens entre variations génétiques et phénotypes sont connus. Les études d'association pangénomique ont considérablement permis d'augmenter le nombre de variations génétiques associées à des phénotypes au cours de la dernière décennie. Cependant, comprendre comment ces changements perturbent les mécanismes moléculaires et affectent le phénotype d'un organisme nous échappe encore. Des études suggèrent que de nombreuses variations, associées à des phénotypes, sont situées dans les régions non codantes du génome et sont susceptibles d'agir en modifiant la régulation d'expression des gènes. Au cours de ma thèse, j'ai étudié comment les variations génétiques affectent les niveaux d'expression des gènes en perturbant les mécanismes de régulation de leur expression. Le travail présenté dans le premier chapitre est un projet en collaboration avec une société pharmaceutique. Nous avons étudié les variations en nombre de copies (CNV) présentes chez le macaque crabier (Macaca fascicularis) qui est utilisé dans les études pharmaceutiques, et nous les avons associées avec des changements d'expression des gènes. Nous avons découvert qu'il existe une variabilité substantielle du nombre de copies et nous avons identifié des CNVs liées aux changements d'expression des gènes situés dans leur voisinage. Ces associations sont présentes ou absentes de manière spécifique dans certains tissus. Les deuxième et troisième chapitres se concentrent sur les variations génétiques dans les populations humaines et leurs effets sur les mécanismes de régulation des gènes et leur expression. Le premier se penche sur deux trios humains, père, mère, enfant, au sein duquel nous avons étudié les effets alléliques des variations génétiques sur l'expression des gènes, les liaisons protéine-ADN et les modifications de la chromatine. Nous avons découvert que l'activité spécifique des allèles est abondante abonde dans tous ces phénotypes moléculaires et nous avons démontré que ces derniers ont un comportement coordonné entre eux. Dans le second, nous avons examiné l'impact des variations génétiques de ces phénotypes moléculaires chez 47 individus, sans lien de parenté. Nous avons observé que les phénotypes de la chromatine sont organisés en modules locaux, qui sont liés aux variations génétiques et à l'expression des gènes. Nos résultats suggèrent que la variabilité de la chromatine est due à des variations génétiques qui perturbent des éléments cis-régulateurs, et peut conduire à des changements dans l'expression des gènes. Le travail présenté dans cette thèse fournit de nouvelles pistes pour comprendre l'impact des différentes variations génétiques sur l'expression des gènes à travers les mécanismes de régulation.

AltitudeOmics : Resetting of Cerebrovascular CO2 Reactivity Following Acclimatization to High Altitude.

Previous studies reported enhanced cerebrovascular CO2 reactivity upon ascent to high altitude using linear models. However, there is evidence that this response may be sigmoidal in nature. Moreover, it was speculated that these changes at high altitude are mediated by alterations in acid-base buffering. Accordingly, we reanalyzed previously published data to assess middle cerebral blood flow velocity (MCAv) responses to modified rebreathing at sea level (SL), upon ascent (ALT1) and following 16 days of acclimatization (ALT16) to 5260 m in 21 lowlanders. Using sigmoid curve fitting of the MCAv responses to CO2, we found the amplitude (95 vs. 129%, SL vs. ALT1, 95% confidence intervals (CI) [77, 112], [111, 145], respectively, P = 0.024) and the slope of the sigmoid response (4.5 vs. 7.5%/mmHg, SL vs. ALT1, 95% CIs [3.1, 5.9], [6.0, 9.0], respectively, P = 0.026) to be enhanced at ALT1, which persisted with acclimatization at ALT16 (amplitude: 177, 95% CI [139, 215], P < 0.001; slope: 10.3%/mmHg, 95% CI [8.2, 12.5], P = 0.003) compared to SL. Meanwhile, the sigmoidal response midpoint was unchanged at ALT1 (SL: 36.5 mmHg; ALT1: 35.4 mmHg, 95% CIs [34.0, 39.0], [33.1, 37.7], respectively, P = 0.982), while it was reduced by ~7 mmHg at ALT16 (28.6 mmHg, 95% CI [26.4, 30.8], P = 0.001 vs. SL), indicating leftward shift of the cerebrovascular CO2 response to a lower arterial partial pressure of CO2 (PaCO2) following acclimatization to altitude. Sigmoid fitting revealed a leftward shift in the midpoint of the cerebrovascular response curve which could not be observed with linear fitting. These findings demonstrate that there is resetting of the cerebrovascular CO2 reactivity operating point to a lower PaCO2 following acclimatization to high altitude. This cerebrovascular resetting is likely the result of an altered acid-base buffer status resulting from prolonged exposure to the severe hypocapnia associated with ventilatory acclimatization to high altitude.

"La influencia de Internet en la participación: ¿menor relevancia de la motivación política?"

In this paper we aim to investigate the relationship between Internet use, motivation and political participation. In particular, we aim to find out if, by reducing participation costs, use of the Internet changes the importance of motivation in the classic explanations of participation. In order to explore this question, we have used data from survey 2736 by the Centro de Investigaciones Sociológicas (CIS), which addresses the issue of political participation andInternet use. The analysis shows that Internet use has a direct impact on participation, regardless of motivation, and that skilled Internet users do not need to be motivated or interested in politics in order to participate in at least one online political activity.

Síntese e caracterização estrutural de complexos mono e bimetálicos de paládio e platina com ligantes contendo nitrogênio e enxofre

The synthesis of several mono- and bimetallic platinum and palladium complexes are reported. The monometallic complexes are of the type MCl2(PEt3)2L (L=2-aminothiazol; benzothiazol; 2-imidazolidithione; M=Pt; Pd), and the bimetallic complexes (M2Cl4(PEt3) 2L) are derived from them. Infrared spectroscopic characterization of the monometallic complexes shows that the metal centre are coordinated through the N-endocyclic (L=2-aminothiazol; benzothiazol) and through the sulphur when L=2-imidazolidithione. Coordination of a second metal fragment occurs via the sulphur atom (L=2-aminothiazol; benzothiazol) according to infrared studies. 31P{¹H} NMR spectroscopy suggest that the complexes have a cis- configuration since the ¹J Pt-P are around the value found for this type of compound.

Termodinâmica estatística de líquidos com o método de Monte Carlo. II. O líquido clorofórmio

Thermodynamic properties and radial distribution functions for liquid chloroform were calculated using the Monte Carlo method implemented with Metropolis algorithm in the NpT ensemble at 298 K and 1 atm. A five site model was developed to represent the chloroform molecules. A force field composed by Lennard-Jones and Coulomb potential functions was used to calculate the intermolecular energy. The partial charges needed to represent the Coulombic interactions were obtained from quantum chemical ab initio calculations. The Lennard-Jones parameters were adjusted to reproduce experimental values for density and enthalpy of vaporization for pure liquid. All thermodynamic results are in excelent agreement with experimental data. The correlation functions calculated are in good accordance with theoretical results avaliable in the literature. The free energy for solvating one chloroform molecule into its own liquid at 298 K and 1 atm was computed as an additional test of the potential model. The result obtained compares well with the experimental value. The medium effects on cis/trans convertion of a hypotetical solute in water TIP4P and chloroform solvents were also accomplished. The results obtained from this investigation are in agreement with estimates of the continuous theory of solvation.

Efeito da substituição por átomos de flúor no equilíbrio conformacional de chalcona

Chalcone (1) and its fluorinated derivatives 2-4, as well as their cyclic analogues 5-10, were synthesized through an aldol condensation reaction between the corresponding ketone and aldehyde. These compounds were characterized by IR, EIMS and ¹H and 13C NMR spectral data. Modern NMR techniques allowed us to conclude that the compounds obtained show E configuration. These techniques were also employed to investigate the equilibrium involving the s-cis and s-trans conformations of 1-4, with this equilibrium being dependent on the fluorine substitution on both aromatic rings, A or B. IR studies indicated that the yield of the s-cis conformation in the fluorinated derivatives is 57.4±1.4; 88.1±0.4 and 66.4±0.7%, for 2, 3 and 4, respectively, based on previous ¹H NMR calculations for chalcone. Theoretical calculations, using the MMX method, were employed to justify the variation of chemical shifts for the fluorinated derivatives and cyclic analogues. These chemical shifts are consequence of the anisotropic effect showed by the carbonyl group on these compounds.

Borohidreto complexos de cobre (I) contendo difosfinas: caracterização espectroscópica e comportamento térmico

Tetrahydroborate complexes of copper (I) with bidentate phosphines, [Cu(eta²-BH4)(dppm)] (1), [Cu(eta²-BH4)(dppe)] (2), [Cu(eta²-BH4)(cis-dppet)] (3) and [Cu(eta²-BH4)(dppb)] (4) (dppm = bis(diphenylphosphino)methane; dppe = 1,2-bis(diphenylphosphino) ethane; cis-dppet = 1,2-cis(diphenylphosphino)ethene; dppb = 1,4-bis(diphenylphosphino)butane) were prepared and characterized by elemental analysis, infrared spectroscopy, NMR and thermogravimetric analysis. The IR data for 1-4 showed bands typical of a bidentate coordination of BH4 group to the copper atom and the 31P{¹H} NMR spectra indicated that the phosphorous atoms are chelating the metal centre. The thermal behavior of the compounds was investigated and suggested that their thermal stability is influenced by the phosphines. Their thermal stability decreased as follows: [Cu(eta²-BH4)(dppe)] (2) > [Cu(eta²-BH4)(dppm)] (1) > [Cu(eta²-BH4)(dppb)] (4) > [Cu(eta²-BH4)(cis-dppet)] (3). According to thermal analysis and X-ray diffraction patterns all compounds decomposed giving Cu(BO2)2, CuO, CuO2 and Cu as final products.

Aplicação de lipases microbianas na obtenção de concentrados de ácidos graxos poliinsaturados

Several polyunsaturated fatty acids (PUFA) belonging to the ômega 6 series, such as cis-6,9,12 gamma-linolenic acid, as well as those of the ômega 3 series, such as cis-5,8,11,14,17-eicosapentaenoic acid and cis-4,7,10,13,16,19-docosahexaenoic acid are of considerable interest due to their nutritional and therapeutic properties. Methods used for the concentration of PUFA from natural sources include urea adduct formation, solvent winterization, supercritical fluid extraction and lipase-catalyzed reaction. Lipases are known to have little reactivity on PUFA and these acids can be enriched by selective hydrolysis, direct esterification of glycerol with PUFA and interesterification. Since lipase reactions are advantageous with respect to fatty acid, positional specificities and mild incubation condition, these enzymes are considered to be suitable for the production of PUFA concentrates for medical purposes.

Compostos voláteis em méis florais

A review about origin, composition and importance of volatile compounds in floral honeys is presented. Hydrocarbons, aromatic components, acids, diacids, terpenoids, ketones, aldehydes, esters and alcohols have been found in honey aroma of different botanical origin. Cis-rose oxide has been proposed as an indicator for Tilia cordata honey. Citrus honeys are known to contain methyl anthranilate, a compound which other honeys virtually lack. Linalool, phenylethylalcohol, phenylacetaldehyde, p-anisaldehyde and benzaldehyde are important contributors for the aroma of different unifloral honeys. Both isovaleric acid, gama-decalactone and benzoic acid appears to be important odourants for Anarcadium occidentale and Croton sp. honeys from Brazil. The furfurylmercaptan, benzyl alcohol, delta-octalactone, eugenol, phenylethylalcohol and guaiacol appear to be only relevant compounds for Anarcadium occidentale. The vanillin was considered an important odourant only for Croton sp..

Estabilidade relativa de alcenos: análise dos critérios encontrados nos livros textos de graduação e uma proposta de explicação operacional para alcenos dissubstituídos

Despite of being used as thermodynamic criterion to rank alkene stability in a number of undergraduate textbooks, the heat of hydrogenation does not describe adequately the relative stability of disubstituted alkenes. In this work, both the heat of formation and the heat of combustion were used as thermodynamic criteria to rank correctly the stability of alkenes according to the degree of alkyl substitution and also in the disubstituted series (geminal > trans > cis). An operational model based on molecular orbital and valence bond representations of hyperconjugation is proposed to show how this effect can explain the order of stability of this class of compounds.

A carboxylesterase, Esterase-6, modulates sensory physiological and behavioural response dynamics to pheromone in Drosophila

Background: Insects respond to the spatial and temporal dynamics of a pheromone plume, which implies not only a strong response to"odor on", but also to"odor off". This requires mechanisms geared toward a fast signal termination. Several mechanisms may contribute to signal termination, among which odorant-degrading enzymes. These enzymes putatively play a role in signal dynamics by a rapid inactivation of odorants in the vicinity of the sensory receptors, although direct in vivo experimental evidences are lacking. Here we verified the role of an extracellular carboxylesterase, esterase-6 (Est-6), in the sensory physiological and behavioral dynamics of Drosophila melanogaster response to its pheromone, cis-vaccenyl acetate (cVA). Est-6 was previously linked to post-mating effects in the reproductive system of females. As Est-6 is also known to hydrolyze cVA in vitro and is expressed in the main olfactory organ, the antenna, we tested here its role in olfaction as a putative odorant-degrading enzyme. Results: We first confirm that Est-6 is highly expressed in olfactory sensilla, including cVA-sensitive sensilla, and we show that expression is likely associated with non-neuronal cells. Our electrophysiological approaches show that the dynamics of olfactory receptor neuron (ORN) responses is strongly influenced by Est-6, as in Est-6° null mutants (lacking the Est-6 gene) cVA-sensitive ORN showed increased firing rate and prolonged activity in response to cVA. Est-6° mutant males had a lower threshold of behavioral response to cVA, as revealed by the analysis of two cVAinduced behaviors. In particular, mutant males exhibited a strong decrease of male-male courtship, in association with a delay in courtship initiation. Conclusions: Our study presents evidence that Est-6 plays a role in the physiological and behavioral dynamics of sex pheromone response in Drosophila males and supports a role of Est-6 as an odorant-degrading enzyme (ODE) in male antennae. Our results also expand the role of Est-6 in Drosophila biology, from reproduction to olfaction, and highlight the role of ODEs in insect olfaction. Keywords: carboxylesterase, esterase 6, olfaction, pheromone, signal termination

Aplicação da técnica de dispersão da matriz em fase sólida (DMFS) na análise de pesticidas em quiabo por CG-EM

A matrix solid phase dispersion and gas chromatography-mass selective detection method for the simultaneous determination of monocrotophos, methyl parathion, cypermethrin and deltamethrin in okra is described. Analyses of 2 g of fortified okra (0.05-0.75 mg kg-1) showed an average recovery of 96.2% (71.4-128.4%) and average relative standard deviation of 11.7% (1.4-37.1%). The cypermethrin recovery at the lower level was above 130%. The limit of detection ranged from 0.02 to 0.15 mg kg-1. The procedure was applied to the okra samples and has found 0.56 mg kg-1 of cypermethrin-cis, 0.75 mg kg-1 of cypermethrin-trans and 2.71 mg kg-1 of deltamethrin.