Multilevel Deconstruction of the In Vivo Behavior of Looped DNA-Protein Complexes

Protein-DNA complexes with loops play a fundamental role in a wide variety of cellular processes, ranging from the regulation of DNA transcription to telomere maintenance. As ubiquitous as they are, their precise in vivo properties and their integration into the cellular function still remain largely unexplored. Here, we present a multilevel approach that efficiently connects in both directions molecular properties with cell physiology and use it to characterize the molecular properties of the looped DNA-lac repressor complex while functioning in vivo. The properties we uncover include the presence of two representative conformations of the complex, the stabilization of one conformation by DNA architectural proteins, and precise values of the underlying twisting elastic constants and bending free energies. Incorporation of all this molecular information into gene-regulation models reveals an unprecedented versatility of looped DNA-protein complexes at shaping the properties of gene expression.Comment: Open Access article available at http://www.plosone.org/article/fetchArticle.action?articleURI=info%3Adoi%2F10.1371%2Fjournal.pone.000035

Modeling Slope Instability as Shear Rupture Propagation in a Saturated Porous Medium

When a region of intense shear in a slope is much thinner than other relevant geometric lengths, this shear failure may be approximated as localized slip, as in faulting, with strength determined by frictional properties of the sediment and effective stress normal to the failure surface. Peak and residual frictional strengths of submarine sediments indicate critical slope angles well above those of most submarine slopes—in contradiction to abundant failures. Because deformation of sediments is governed by effective stress, processes affecting pore pressures are a means of strength reduction. However, common methods of exami ning slope stability neglect dynamically variable pore pressure during failure. We examine elastic-plastic models of the capped Drucker-Prager type and derive approximate equations governing pore pressure about a slip surface when the adjacent material may deform plastically. In the process we identify an elastic-plastic hydraulic diffusivity with an evolving permeability and plastic storage term analogous to the elastic term of traditional poroelasticity. We also examine their application to a dynamically propagating subsurface rupture and find indications of downslope directivity.Earth and Planetary SciencesEngineering and Applied Science

Insegurança alimentar em domicílios brasileiros com crianças menores de cinco anos

This article analyzes food insecurity and hunger in Brazilian families with children under five years of age. This was a nationally representative cross-sectional study using data from the National Demographic and Health Survey on Women and Children (PNDS-2006), in which the outcome variable was moderate to severe food insecurity, measured by the Brazilian Food Insecurity Scale (EBIA). Prevalence estimates and prevalence ratios were generated with 95% confidence intervals. The results showed a high prevalence of moderate to severe food insecurity, concentrated in the North and Northeast regions (30.7%), in economic classes D and E (34%), and in beneficiaries of conditional cash transfer programs (36.5%). Multivariate analysis showed that the socioeconomic relative risks (beneficiaries of conditional cash transfers), regional relative risks (North and Northeast regions), and economic relative risks (classes D and E) were 1.8, 2.0 and 2.4, respectively. Aggregation of the three risks showed 48% of families with moderate to severe food insecurity, meaning that adults and children were going hungry during the three months preceding the survey.Se plantea estudiar el proceso de inseguridad alimentaria y el hambre en los hogares brasileños con niños menores de cinco años. Se trata de un estudio transversal a nivel nacional, realizado con datos de la Encuesta Nacional de Demografía y Salud de la Mujer y la Infancia (PNDS 2006), siendo la variable dependiente la inseguridad alimentaria moderada y grave (IAM+G), medidas mediante la Escala Brasileña de Inseguridad Alimentaria (EBIA). Se generaron estimaciones de prevalencia y razón de prevalencia con intervalos de 95% de confianza. Los resultados muestran una alta prevalencia de IAM+G en el Norte y Nordeste (30,7%), en las clases económicas D y E (34%), y entre los beneficiarios de los programas de transferencias de renta (36,5%). El modelo de análisis multivariado descubrió que los riesgos sociales (beneficiario de programas de transferencias de renta), regionales (Norte y Nordeste) y económicos (clases D y E) fueron de 1,8, 2,0 y 2,4, respectivamente. Mediante la agregación de los tres riesgos se encontró el 48% de los hogares en IAM+G, o sea, adultos y niños tuvieron hambre durante los tres meses anteriores a la encuesta.Este artigo se propõe a estudar o processo de insegurança alimentar e fome em domicílios brasileiros com crianças menores de cinco anos. É um estudo transversal com representatividade nacional executado com dados da Pesquisa Nacional de Demografia e Saúde da Criança e da Mulher (PNDS-2006) tendo como variável dependente a insegurança alimentar moderada e grave (IAM+G), medida através da Escala Brasileira de Insegurança Alimentar (EBIA). Foram geradas estimativas de prevalência e razão de prevalência com intervalos de 95% de confiança. Os resultados apontam para alta prevalência de IAM+G concentrada nas regiões Norte e Nordeste (30,7%), nas classes econômicas D e E (34%) e em beneficiários de Programas de Transferência de Renda (PTR; 36,5%). O modelo de análise multivariada constatou que os riscos sociais (beneficiário de PTR), regionais (Norte e Nordeste) e econômicos (classes D e E) eram de 1,8, 2,0 e 2,4, respectivamente. Agregando-se os três riscos observou-se que 48% dos domicílios encontravam-se em IAM+G, ou seja, crianças e adultos passaram fome nos três meses anteriores ao inquérito.Universidade Federal de São Paulo (UNIFESP)Universidade Estadual de Campinas Faculdade de Ciências MédicasUNIFESPSciEL