The effects of sequence context on DNA curvature.

Recent experiments have exposed significant discrepancies between experimental data and predictive models for DNA structure. These results strongly suggest that DNA structural parameters incorporated in the models are not always sufficient to account for the influence of sequence context and of specific ion effects. In an attempt to evaluate these two effects, we have investigated repetitive DNA sequences with the sequence motif GAGAG.CTCTC located in different helical phasing arrangements with respect to poly(A) tracts and GGGCCC.GGGCCC sequence motifs. Methods used are ligase-mediated cyclization and gel mobility experiments along with DNase I cutting and chemical probe studies. The results provide new evidence for curvature in poly(A) tracts. They also show that the sequence context in which bending and flexible sequence elements are found is an important aspect of sequence-dependent DNA conformation. Although dinucleotide models generally have good predictive power, this work demonstrates that in some instances sequence elements larger than the dinucleotide must be taken into account, and hence it provides a starting point for the appropriate modification and refinement of existing structural models for DNA.

Mutational properties of the primary aflatoxin B1-DNA adduct.

The mutagenic activity of the major DNA adduct formed by the liver carcinogen aflatoxin B1 (AFB1) was investigated in vivo. An oligonucleotide containing a single 8,9-dihydro-8-(N7-guanyl)-9-hydroxyaflatoxin B1 (AFB1-N7-Gua) adduct was inserted into the single-stranded genome of bacteriophage M13. Replication in SOS-induced Escherichia coli yielded a mutation frequency for AFB1-N7-Gua of 4%. The predominant mutation was G --> T, identical to the principal mutation in human liver tumors believed to be induced by aflatoxin. The G --> T mutations of AFB1-N7-Gua, unlike those (if the AFB1-N7-Gua-derived apurinic site, were much more strongly dependent on MucAB than UmuDC, a pattern matching that in intact cells treated with the toxin. It is concluded that the AFB1-N7-Gua adduct, and not the apurinic site, has genetic requirements for mutagenesis that best explain mutations in aflatoxin-treated cells. While most mutations were targeted to the site of the lesion, a significant fraction (13%) occurred at the base 5' to the modified guanine. In contrast, the apurinic site-containing genome gave rise only to targeted mutations. The mutational asymmetry observed for AFB1-N7-Gua is consistent with structural models indicating that the aflatoxin moiety of the aflatoxin guanine adduct is covalently intercalated on the 5' face of the guanine residue. These results suggest a molecular mechanism that could explain an important step in the carcinogenicity of aflatoxin B1.

Structure of the sodium channel pore revealed by serial cysteine mutagenesis.

The pores of voltage-gated cation channels are formed by four intramembrane segments that impart selectivity and conductance. Remarkably little is known about the higher order structure of these critical pore-lining or P segments. Serial cysteine mutagenesis reveals a pattern of side-chain accessibility that contradicts currently favored structural models based on alpha-helices or beta-strands. Like the active sites of many enzymes of known structure, the sodium channel pore consists of irregular loop regions.

Subunit-destabilizing mutations in Drosophila copper/zinc superoxide dismutase: neuropathology and a model of dimer dysequilibrium.

Mutations in Cu/Zn superoxide dismutase (SOD), a hallmark of familial amyotrophic lateral sclerosis (FALS) in humans, are shown here to confer striking neuropathology in Drosophila. Heterozygotes with one wild-type and one deleted SOD allele retain the expected 50% of normal activity for this dimeric enzyme. However, heterozygotes with one wild-type and one missense SOD allele show lesser SOD activities, ranging from 37% for a heterozygote carrying a missense mutation predicted from structural models to destabilize the dimer interface, to an average of 13% for several heterozygotes carrying missense mutations predicted to destabilize the subunit fold. Genetic and biochemical evidence suggests a model of dimer dysequilibrium whereby SOD activity in missense heterozygotes is reduced through entrapment of wild-type subunits into unstable or enzymatically inactive heterodimers. This dramatic impairment of the activity of wild-type subunits in vivo has implications for our understanding of FALS and for possible therapeutic strategies.

Volunteer Engagement: Does Engagement Predict the Degree of Satisfaction among New Volunteers and the Commitment of Those who have been Active Longer?

This study examines the concept of engagement in samples of volunteers from different non-profit organisations. Study 1 analyzes the psychometric properties of the abbreviated version of the Utrecht Work Engagement Scale (UWES) (Schaufeli, Bakker, & Salanova, 2006a). Two factorial structures are examined: one-dimensional and three-dimensional structures. Based on the Three-Stage Model of Volunteers’ Duration of Service (Chacón, Vecina, & Dávila, 2007), Study 2 investigates the relationship between engagement, volunteer satisfaction, and intention to remain in a sample of new volunteers and the relationship between engagement, organisational commitment, and intention to remain in a sample of veteran volunteers. Moderated mediation analysis is provided using duration of service as a moderator in order to set a splitting point between new and veteran volunteers. The results of the confirmatory factor analysis suggest that the three-factor model fits better to the data. Regarding the structural models, the first one shows that engagement is crucial to volunteer satisfaction during the first stage, while volunteer satisfaction is the key variable in explaining intention to continue. The second structural model shows that engagement reinforces the participant’s commitment to the organisation, while organizational commitment predicts intention to continue. Both models demonstrate a notable decline when samples are changed.

Adoção de práticas de gestão ambiental e seus efeitos nos desempenhos ambiental e financeiro de acordo com a percepção dos gestores: uma survey

Alterações nos regulamentos, mudanças no comportamento do consumidor e potenciais ganhos de competitividade são alguns dos motivos citados por gestores como motivadores para a adoção de várias práticas de gestão ambiental. Estas práticas afetam, de acordo com outros estudos, os desempenhos ambiental e financeiro das empresas. No entanto, práticas diferentes afetam de forma diferente os desempenhos mencionados, ou ainda algumas práticas podem ser usadas de forma propagandísticas, podendo afetar o desempenho financeiro, mas não necessariamente o desempenho ambiental.. Assim, este trabalho tem como objetivo verificar se há relação entre as práticas de gestão ambiental (aqui divididas em \'práticas de planejamento e organização\', \'práticas operacionais\' e \'práticas comunicacionais\') utilizadas pelas empresas e os desempenhos ambiental e financeiro destas por meio da análise de empresas do setor químico brasileiro, utilizando modelagem de equações estruturais (Structural Equation Modeling - SEM) e uma survey para coleta dos dados subjetivoprimários (percepção dos gestores). Para tanto, foi desenvolvido um modelo teórico e construído um diagrama de caminhos de relações causais que foi convertido em um conjunto de modelos estruturais e de mensuração. Para testar o modelo proposto, um teste empírico foi aplicado em empresas do setor químico brasileiro. Os resultados deste teste foram os seguintes: (a) PGAs de planejamento e organização possuem uma relação positiva com o desempenho ambiental e o com desempenho financeiro; (b) PGAs operacionais possuem uma relação negativa com o desempenho financeiro; (c) PGAs comunicacionais possuem uma relação positiva com o desempenho financeiro; (d) Não há relação estatisticamente significativa entre as PGAs operacionais e o desempenho ambiental; (e) Não há relação estatisticamente significativa entre as PGAs comunicacionais e o desempenho ambiental; (f) Não há relação estatisticamente significativa entre o desempenho ambiental e o desempenho financeiro. Neste estudo, as práticas de gestão ambiental se relacionam mais significativamente com o desempenho financeiro, podendo indicar, na amostra estudada, um perfil menos proativo de gestão ambiental, com foco na adequação legar para a continuar com um bom desempenho financeiro.

An explanatory model of academic achievement based on aptitudes, goal orientations, self-concept and learning strategies

As a result of studies examining factors involved in the learning process, various structural models have been developed to explain the direct and indirect effects that occur between the variables in these models. The objective was to evaluate a structural model of cognitive and motivational variables predicting academic achievement, including general intelligence, academic self-concept, goal orientations, effort and learning strategies. The sample comprised of 341 Spanish students in the first year of compulsory secondary education. Different tests and questionnaires were used to evaluate each variable, and Structural Equation Modelling (SEM) was applied to contrast the relationships of the initial model. The model proposed had a satisfactory fit, and all the hypothesised relationships were significant. General intelligence was the variable most able to explain academic achievement. Also important was the direct influence of academic self-concept on achievement, goal orientations and effort, as well as the mediating ability of effort and learning strategies between academic goals and final achievement.

Molecular dynamics simulation of organic-inorganic nanocomposites: Layering behavior and interlayer structure of organoclays

Isothermal-isobaric (NPT) molecular dynamics simulation has been performed to investigate the layering behavior and structure of nanoconfined quaternary alkylammoniums in organoclays. This work is focused on systems consisting of two clay layers and a number of alkylammoniums, and involves the use of modified Dreiding force field. The simulated basal spacings of organoclays agree satisfactorily with the experimental results in the literature. The atomic density profiles in the direction normal to the clay surface indicate that the alkyl chains within the interlayer space of montmorillonite exhibit an obvious layering behavior. The headgroups of long alkyl chains are distributed within two layers close to the clay surface, whereas the distributions of methyl and methylene groups are strongly dependent on the alkyl chain length and clay layer charge. Monolayer, bilayer, and pseudo-trilayer structures are found in organoclays modified with single long alkyl chains, which are identical to the structural models based on the measured basal spacings. A pseudo-quadrilayer structure, for the first time to our knowledge, is also identified in organoclays with double long alkyl chains. In the mixture structure of paraffin-type and multilayer, alkyl chains do not lie flat within a single layer but interlace, and also jump to the next layer in pseudo-trilayer as well as next nearest layer in pseudo-quadrilayer.

Optimal design for model discrimination and parameter estimation for itraconazole population pharmacokinetics in cystic fibrosis patients

Optimal sampling times are found for a study in which one of the primary purposes is to develop a model of the pharmacokinetics of itraconazole in patients with cystic fibrosis for both capsule and solution doses. The optimal design is expected to produce reliable estimates of population parameters for two different structural PK models. Data collected at these sampling times are also expected to provide the researchers with sufficient information to reasonably discriminate between the two competing structural models.

Analysis of population pharmacokinetic data using NONMEM and WinBUGS

The aim of this report is to describe the use of WinBUGS for two datasets that arise from typical population pharmacokinetic studies. The first dataset relates to gentamicin concentration-time data that arose as part of routine clinical care of 55 neonates. The second dataset incorporated data from 96 patients receiving enoxaparin. Both datasets were originally analyzed by using NONMEM. In the first instance, although NONMEM provided reasonable estimates of the fixed effects parameters it was unable to provide satisfactory estimates of the between-subject variance. In the second instance, the use of NONMEM resulted in the development of a successful model, albeit with limited available information on the between-subject variability of the pharmacokinetic parameters. WinBUGS was used to develop a model for both of these datasets. Model comparison for the enoxaparin dataset was performed by using the posterior distribution of the log-likelihood and a posterior predictive check. The use of WinBUGS supported the same structural models tried in NONMEM. For the gentamicin dataset a one-compartment model with intravenous infusion was developed, and the population parameters including the full between-subject variance-covariance matrix were available. Analysis of the enoxaparin dataset supported a two compartment model as superior to the one-compartment model, based on the posterior predictive check. Again, the full between-subject variance-covariance matrix parameters were available. Fully Bayesian approaches using MCMC methods, via WinBUGS, can offer added value for analysis of population pharmacokinetic data.

A quantum yield map for synthetic eumelanin

The quantum yield of synthetic eumelanin is known to be extremely low and it has recently been reported to be dependent on excitation wavelength. In this paper, we present quantum yield as a function of excitation wavelength between 250 and 500 nm, showing it to be a factor of 4 higher at 250 nm than at 500 nm. In addition, we present a definitive map of the steady-state fluorescence as a function of excitation and emission wavelengths, and significantly, a three-dimensional map of the specific quantum yield: the fraction of photons absorbed at each wavelength that are subsequently radiated at each emission wavelength. This map contains clear features, which we attribute to certain structural models, and shows that radiative emission and specific quantum yield are negligible at emission wavelengths outside the range of 585 and 385 nm (2.2 and 3.2 eV), regardless of excitation wavelength. This information is important in the context of understanding melanin biofunctionality, and the quantum molecular biophysics therein. (c) 2005 American Institute of Physics.

Quantitative fluorescence excitation spectra of synthetic eumelanin

Previously reported excitation spectra for eumelanin are sparse and inconsistent. Moreover, these studies have failed to account for probe beam attenuation and emission reabsorption within the samples, making them qualitative at best. We report for the first time quantitative excitation spectra for synthetic eumelanin, acquired for a range of solution concentrations and emission wavelengths. Our data indicate that probe beam attenuation and emission reabsorption significantly affect the spectra even in low-concentration eumelanin solutions and that previously published data do not reflect the true excitation profile. We apply a correction procedure (previously applied to emission spectra) to account for these effects. Application of this procedure reconstructs the expected relationship of signal intensity with concentration, and the normalized spectra show a similarity in form to the absorption profiles. These spectra reveal valuable information regarding the photophysics and photochemistry of eumelanin. Most notably, an excitation peak at 365 urn (3.40 eV), whose position is independent of emission wavelength, is possibly attributable to a 5,6-dihydroxyindole-2-carboxylic acid (DHICA) component singly linked to a polymeric structure.

Mimicking the action of GroEL in molecular dynamics simulations: Application to the refinement of protein structures

Bacterial chaperonin, GroEL, together with its co-chaperonin, GroES, facilitates the folding of a variety of polypeptides. Experiments suggest that GroEL stimulates protein folding by multiple cycles of binding and release. Misfolded proteins first bind to an exposed hydrophobic surface on GroEL. GroES then encapsulates the substrate and triggers its release into the central cavity of the GroEL/ES complex for folding. In this work, we investigate the possibility to facilitate protein folding in molecular dynamics simulations by mimicking the effects of GroEL/ES namely, repeated binding and release, together with spatial confinement. During the binding stage, the (metastable) partially folded proteins are allowed to attach spontaneously to a hydrophobic surface within the simulation box. This destabilizes the structures, which are then transferred into a spatially confined cavity for folding. The approach has been tested by attempting to refine protein structural models generated using the ROSETTA procedure for ab initio structure prediction. Dramatic improvements in regard to the deviation of protein models from the corresponding experimental structures were observed. The results suggest that the primary effects of the GroEL/ES system can be mimicked in a simple coarse-grained manner and be used to facilitate protein folding in molecular dynamics simulations. Furthermore, the results Sur port the assumption that the spatial confinement in GroEL/ES assists the folding of encapsulated proteins.

The physical and chemical properties of eumelanin

In this article, we review the current state of knowledge concerning the physical and chemical properties of the eumelanin pigment. We examine properties related to its photoprotective functionality, and draw the crucial link between fundamental molecular structure and observable macroscopic behaviour. Where necessary, we also briefly review certain aspects of the pheomelanin literature to draw relevant comparison. A full understanding of melanin function, and indeed its role in retarding or promoting the disease state, can only be obtained through a full mapping of key structure-property relationships in the main pigment types. We are engaged in such an endeavor for the case of eumelanin.

Radiative relaxation in synthetic pheomelanin

We report a detailed photoluminescence study of cysteinyldopa-melanin ( CDM), the synthetic analogue of pheomelanin. Emission spectra are shown to be a far more sensitive probe of CDM's spectroscopic behavior than are absorption spectra. Although CDM and dopa-melanin ( DM, the synthetic analogue of eumelanin) have very similar absorption spectra, we find that they have very different excitation and emission characteristics; CDM has two distinct photoluminescence peaks that do not shift with excitation wavelength. Additionally, our data suggest that the radiative quantum yield of CDM is excitation energy dependent, an unusual property among biomolecules that is indicative of a chemically disordered system. Finally, we find that the radiative quantum yield for CDM is similar to 0.2%, twice that of DM, although still extremely low. This means that 99.8% of the energy absorbed by CDM is dissipated via nonradiative pathways, consistent with its role as a pigmentary photoprotectant.