How does the chromatin fiber deal with topological constraints?

In the nuclei of eukaryotic cells, DNA is packaged through several levels of compaction in an orderly retrievable way that enables the correct regulation of gene expression. The functional dynamics of this assembly involves the unwinding of the so-called 30 nm chromatin fiber and accordingly imposes strong topological constraints. We present a general method for computing both the twist and the writhe of any winding pattern. An explicit derivation is implemented for the chromatin fiber which provides the linking number of DNA in eukaryotic chromosomes. We show that there exists one and only one unwinding path which satisfies both topological and mechanical constraints that DNA has to deal with during condensation/decondensation processes.Comment: Presented in Nature "News and views in brief" Vol. 429 (13 May 2004). Movies available at http://www.lptl.jussieu.fr/recherche/operationE_fichiers/Page_figurePRL.htm

What are Inclusive Pedagogies ? What must faculty do differently to teach inclusively?

At the 2016 All Campus Forum President Hinton called for us to create an ecosystem of inclusion at CSB/SJU. Faculty members\u27 work with students is central to creating such an ecosystem, but what, after all, do we mean by inclusion? In this presentation, FYS and Humanities Mellon cohort members provide an overview of our evolving understanding of inclusive pedagogy, the research that supports it, as well as examples of such pedagogies that we are implementing in our fall 2016 courses

Determinants of serum polychlorinated biphenyls and organochlorine pesticides measured in women from the child health and development study cohort, 1963-1967.

We examined predictors of organochlorine concentrations in serum specimens from women who were pregnant in the 1960s and participated in the Child Health and Development Study in the San Francisco Bay Area of California. That study enrolled pregnant women at the Kaiser-Permanente Medical Facilities, conducted interviews, and drew blood specimens; these specimens were centrifuged and the resulting serum specimens were frozen and placed in long-term storage. For the current investigation, organochlorines were measured by dual-column GC-electron capture detection in specimens collected in 1963-1967 from 399 pregnant women during the second and third trimesters. Using multiple linear regression models adjusted for serum lipids, we evaluated factors predicting concentrations of 11 polychlorinated biphenyl (PCB) congeners, their sum, and several pesticides and metabolites. Variables evaluated were age, race, place of birth, date of blood draw, body mass index, occupation, past residence on a farm, parity, and duration of pregnancy at blood draw. Concentrations of highly chlorinated PCBs and the sum of the PCBs increased with age. Concentrations of certain PCB congeners, as well as the sum, were significantly higher among nonwhites and increased with calendar date of blood draw. (italic)p,p(/italic) -DDT and (italic)p,p(/italic) -DDE concentrations were about 50% higher for nonwhites compared with whites and for those born in California or the southeastern United States versus elsewhere in the United States. Higher body mass index was associated with lower concentrations of several PCBs and (italic)p,p(/italic) -DDE but with higher heptachlor epoxide and DDT levels. The increase in use of PCBs during the 1960s is apparently detectable as increasing concentrations in maternal sera between 1963 and 1967. Marked racial and regional differences in serum pesticide levels were likely caused by geographic variation in previous agricultural and vector-control uses. The relationship to body mass index appears to be complex

An interdisciplinary approach towards improved understanding of soil deformation during compaction

International audienceSoil compaction not only reduces available pore volume in which fluids are stored, but it alters the arrangement of soil constituents and pore geometry, thereby adversely impacting fluid transport and a range of soil ecological functions. Quantitative understanding of stress transmission and deformation processes in arable soils remains limited. Yet such knowledge is essential for better predictions of effects of soil management practices such as agricultural field traffic on soil functioning. Concepts and theory used in agricultural soil mechanics (soil compaction and soil tillage) are often adopted from conventional soil mechanics (e.g. foundation engineering). However, in contrast with standard geotechnical applications, undesired stresses applied by agricultural tyres/tracks are highly dynamic and last for very short times. Moreover, arable soils are typically unsaturated and contain important secondary structures (e.g. aggregates), factors important for affecting their soil mechanical behaviour. Mechanical processes in porous media are not only of concern in soil mechanics, but also in other fields including geophysics and granular material science. Despite similarity of basic mechanical processes, theoretical frameworks often differ and reflect disciplinary focus. We review concepts from different but complementary fields concerned with porous media mechanics and highlight opportunities for synergistic advances in understanding deformation and compaction of arable soils. We highlight the important role of technological advances in non-destructive measurement methods at pore (X-ray tomography) and soil profile (seismic) scales that not only offer new insights into soil architecture and enable visualization of soil deformation, but are becoming instrumental in the development and validation of new soil compaction models. The integration of concepts underlying dynamic processes that modify soil pore spaces and bulk properties will improve the understanding of how soil management affect vital soil mechanical, hydraulic and ecological functions supporting plant growth

Polarization state of the optical near-field

The polarization state of the optical electromagnetic field lying several nanometers above complex dielectric structures reveals the intricate light-matter interaction that occurs in this near-field zone. This information can only be extracted from an analysis of the polarization state of the detected light in the near-field. These polarization states can be calculated by different numerical methods well-suited to near--field optics. In this paper, we apply two different techniques (Localized Green Function Method and Differential Theory of Gratings) to separate each polarisation component associated with both electric and magnetic optical near-fields produced by nanometer sized objects. The analysis is carried out in two stages: in the first stage, we use a simple dipolar model to achieve insight into the physical origin of the near-field polarization state. In the second stage, we calculate accurate numerical field maps, simulating experimental near-field light detection, to supplement the data produced by analytical models. We conclude this study by demonstrating the role played by the near-field polarization in the formation of the local density of states.Comment: 9 pages, 11 figures, accepted for publication in Phys. Rev.

SPICES: Spectro-Polarimetric Imaging and Characterization of Exoplanetary Systems

SPICES (Spectro-Polarimetric Imaging and Characterization of Exoplanetary Systems) is a five-year M-class mission proposed to ESA Cosmic Vision. Its purpose is to image and characterize long-period extrasolar planets and circumstellar disks in the visible (450 - 900 nm) at a spectral resolution of about 40 using both spectroscopy and polarimetry. By 2020/22, present and near-term instruments will have found several tens of planets that SPICES will be able to observe and study in detail. Equipped with a 1.5 m telescope, SPICES can preferentially access exoplanets located at several AUs (0.5-10 AU) from nearby stars ($<$25 pc) with masses ranging from a few Jupiter masses to Super Earths ($\sim$2 Earth radii, $\sim$10 M$_{\oplus}$) as well as circumstellar disks as faint as a few times the zodiacal light in the Solar System

Radially Extended Kinematics in the S0 Galaxy NGC 2768 from Planetary Nebulae, Globular Clusters and Starlight

There are only a few tracers available to probe the kinematics of individual early-type galaxies beyond one effective radius. Here we directly compare a sample of planetary nebulae (PNe), globular clusters (GCs) and galaxy starlight velocities out to ~4 effective radii, in the S0 galaxy NGC 2768. Using a bulge-to-disk decomposition of a K-band image we assign PNe and starlight to either the disk or the bulge. We show that the bulge PNe and bulge starlight follow the same radial density distribution as the red subpopulation of GCs, whereas the disk PNe and disk starlight are distinct components. We find good kinematic agreement between the three tracers to several effective radii (and with stellar data in the inner regions). Further support for the distinct nature of the two galaxy components come from our kinematic analysis. After separating the tracers into bulge and disk components we find the bulge to be a slowly rotating pressure-supported system, whereas the disk reveals a rapidly rising rotation curve with a declining velocity dispersion profile. The resulting V/sigma ratio for the disk resembles that of a spiral galaxy and hints at an origin for NGC 2768 as a transformed late-type galaxy. A two-component kinematic analysis for a sample of S0s will help to elucidate the nature of this class of galaxy.Comment: 10 pages, 5 figures, accepted for publication in MRA

Contract Aware Components, 10 years after

The notion of contract aware components has been published roughly ten years ago and is now becoming mainstream in several fields where the usage of software components is seen as critical. The goal of this paper is to survey domains such as Embedded Systems or Service Oriented Architecture where the notion of contract aware components has been influential. For each of these domains we briefly describe what has been done with this idea and we discuss the remaining challenges.Comment: In Proceedings WCSI 2010, arXiv:1010.233

Structure of the Mg-Chelatase Cofactor GUN4 Reveals a Novel Hand-Shaped Fold for Porphyrin Binding

In plants, the accumulation of the chlorophyll precursor Mg-protoporphyrin IX (Mg-Proto) in the plastid regulates the expression of a number of nuclear genes with functions related to photosynthesis. Analysis of the plastid-to-nucleus signaling activity of Mg-Proto in Arabidopsis thaliana led to the discovery of GUN4, a novel porphyrin-binding protein that also dramatically enhances the activity of Mg-chelatase, the enzyme that synthesizes Mg-Proto. GUN4 may also play a role in both photoprotection and the cellular shuttling of tetrapyrroles. Here we report a 1.78-Å resolution crystal structure of Synechocystis GUN4, in which the porphyrin-binding domain adopts a unique three dimensional fold with a “cupped hand” shape. Biophysical and biochemical analyses revealed the specific site of interaction between GUN4 and Mg-Proto and the energetic determinants for the GUN4 • Mg-Proto interaction. Our data support a novel protective function for GUN4 in tetrapyrrole trafficking. The combined structural and energetic analyses presented herein form the physical-chemical basis for understanding GUN4 biological activity, including its role in the stimulation of Mg-chelatase activity, as well as in Mg-Proto retrograde signaling