The 3D Genome as Moderator of Chromosomal Communication

Proper expression of genes requires communication with their regulatory elements that can be located elsewhere along the chromosome. The physics of chromatin fibers imposes a range of constraints on such communication. The molecular and biophysical mechanisms by which chromosomal communication is established, or prevented, have become a topic of intense study, and important roles for the spatial organization of chromosomes are being discovered. Here we present a view of the interphase 3D genome characterized by extensive physical compartmentalization and insulation on the one hand and facilitated long-range interactions on the other. We propose the existence of topological machines dedicated to set up and to exploit a 3D genome organization to both promote and censor communication along and between chromosomes.National Human Genome Research Institute (U.S.) (Grant R01 HG003143)National Human Genome Research Institute (U.S.) (Grant U54 HG007010)National Human Genome Research Institute (U.S.) (Grant U01 HG007910)National Cancer Institute (U.S.) (Grant U54 CA193419)National Institutes of Health (U.S.) (Grant U54 DK107980)National Institutes of Health (U.S.) (Grant U01 DA 040588)National Institute of General Medical Sciences (U.S.) (Grant R01 GM 112720)National Institute of Allergy and Infectious Diseases (U.S.) (Grant U01 R01 AI 117839

Discrete Breathers in One-Dimensional Diatomic Granular Crystals

We report the experimental observation of discrete breathers in a one-dimensional diatomic granular crystal composed of compressed elastic beads that interact via Hertzian contact. We first characterize their effective linear spectrum both theoretically and experimentally. We then illustrate theoretically and numerically the modulational instability of the lower edge of the optical band. This leads to the dynamical formation of long-lived breather structures, whose families of solutions we compute throughout the linear spectral gap. Finally, we observe experimentally such localized breathing modes with quantitative characteristics that agree with our numerical results.Comment: 5 pages, 4 figure

Welfarism vs. extra-welfarism

'Extra-welfarism' has received some attention in health economics, yet there is little consensus on what distinguishes it from more conventional 'welfarist economics'. In this paper, we seek to identify the characteristics of each in order to make a systematic comparison of the ways in which they evaluate alternative social states. The focus, though this is not intended to be exclusive, is on health. Specifically, we highlight four areas in which the two schools differ: (i) the outcomes considered relevant in an evaluation; (ii) the sources of valuation of the relevant outcomes; (iii) the basis of weighting of relevant outcomes and (iv) interpersonal comparisons. We conclude that these differences are substantive. (C) 2007 Elsevier B.V. All rights reserved

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

How DNA is organized in three dimensions inside the cell nucleus and how this affects the ways in which cells access, read and interpret genetic information are among the longest standing questions in cell biology. Using newly developed molecular, genomic and computational approaches based on the chromosome conformation capture technology (such as 3C, 4C, 5C and Hi-C), the spatial organization of genomes is being explored at unprecedented resolution. Interpreting the increasingly large chromatin interaction data sets is now posing novel challenges. Here we describe several types of statistical and computational approaches that have recently been developed to analyse chromatin interaction data.National Institutes of Health (U.S.)National Human Genome Research Institute (U.S.) (HG003143)National Human Genome Research Institute (U.S.) (HG003143-06S1)W. M. Keck FoundationSpain. Ministerio de Ciencia e Innovación (BFU2010-19310/BMC)Human Frontier Science Program (Strasbourg, France) (RGP0044/2011)European Union (BLUEPRINT project (EU FP7 grant agreement 282510))National Cancer Institute (U.S.) (Physical Sciences Oncology Center at MIT, U54CA143874

Etanol, meio ambiente e tecnologia: reflexões sobre a experiência brasileira.

O trabalho apresenta uma breve reflexão sobre os principais aspectos ambientais e tecnológicos da experiência brasileira voltada à produção e ao uso de etanol a partir da cana-de-açúcar. Ao se analisar toda a cadeia produtiva do etanol, observa-se que o aproveitamento estratégico de todos os subprodutos da cana-de-açúcar é condição essencial para a sustentabilidade do processo produtivo. Por sua vez, a queima da cana-de-açúcar para colheita e a expansão da monocultura canavieira são fatores que requerem maior atenção. O trabalho demonstra que a produção de etanol de cana-deaçúcar contribui para a sustentabilidade ambiental e que seu uso como combustível renovável é favorável em relação aos combustíveis fósseis

Who gets to see themselves as talented? Biased self-concepts contribute to first-generation students' disadvantage in talent-focused environments

Intellectual talent is commonly regarded as an important factor for success – i.e., “what it takes to succeed” in Western educational contexts. Yet, the differential experiences individuals have may not allow everyone to think of themselves as talented - i.e., as having “what it takes to succeed” - to the same degree. In five studies with 3584 students in Western countries, we show i) that first-generation students see themselves as less intellectually talented than continuing-generation students, ii) that this bias in self-concept contributes to disadvantages in their academic experience and engagement, and iii) how this disadvantage may be reduced. Quasi-experiments 1a and b (N = 694; 316) show that first-generation students view themselves as relatively less talented, but not less diligent, above and beyond prior performance-levels. Field and experimental Studies 2a-b (N = 1881; 362) show that this bias in students' talent self-concept contributes to disadvantage in first-generation students' academic experience and engagement. Experiment 3 (N = 331) suggests that talent self-concept bias is most consequential in talent-focused environments. If, however, environments emphasize effort, disadvantages connected to talent self-concepts are mitigated. The experiences first-generation students have in current Western environments seem to make them see themselves as relatively less talented, contributing to disadvantage. Creating effort-focused environments can reduce this disadvantage and promote equality

Wave localization in strongly nonlinear Hertzian chains with mass defect

We investigate the dynamical response of a mass defect in a one-dimensional non-loaded horizontal chain of identical spheres which interact via the nonlinear Hertz potential. Our experiments show that the interaction of a solitary wave with a light intruder excites localized mode. In agreement with dimensional analysis, we find that the frequency of localized oscillations exceeds the incident wave frequency spectrum and nonlinearly depends on the size of the intruder and on the incident wave strength. The absence of tensile stress between grains allows some gaps to open, which in turn induce a significant enhancement of the oscillations amplitude. We performed numerical simulations that precisely describe our observations without any adjusting parameters.Comment: 4 pages, 5 figures, submitted for publicatio