Controlled DNA compaction within chromatin: the tail-bridging effect

We study the mechanism underlying the attraction between nucleosomes, the fundamental packaging units of DNA inside the chromatin complex. We introduce a simple model of the nucleosome, the eight-tail colloid, consisting of a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We demonstrate that our complexes are attracted via the formation of chain bridges and that this attraction can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation can be controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.Comment: 4 pages, 5 figures, submitte

Design and development of a deployable self-inflating adaptive membrane

Space structures nowadays are often designed to serve just one objective during their mission life, examples include truss structures that are used as support structures, solar sails for propulsion or antennas for communication. Each and every single one of these structures is optimized to serve just their distinct purpose and are more or less useless for the rest of the mission and therefore dead weight. By developing a smart structure that can change its shape and therefore adapt to different mission requirements in a single structure, the flexibility of the spacecraft can be increased by greatly decreasing the mass of the entire system. This paper will introduce such an adaptive structure called the Self-inflating Adaptive Membrane (SAM) concept which is being developed at the Advanced Space Concepts Laboratory of the University of Strathclyde. An idea presented in this paper is to adapt these basic changeable elements from nature’s heliotropism. Heliotropism describes a movement of a plant towards the sun during a day; the movement is initiated by turgor pressure change between adjacent cells. The shape change of the global structure can be significant by adding up these local changes induced by local elements, for example the cell’s length. To imitate the turgor pressure change between the motor cells in plants to space structures, piezoelectric micro pumps are added between two neighboring cells. A passive inflation technique is used for deploying the membrane at its destination in space. The trapped air in the spheres will inflate the spheres when subjected to vacuum, therefore no pump or secondary active deployment methods are needed. The paper will present the idea behind the adaption of nature’s heliotropism principle to space structures. The feasibility of the residual air inflation method is verified by LS-DYNA simulations and prototype bench tests under vacuum conditions. Additionally, manufacturing techniques and folding patterns are presented to optimize the actual bench test structure and to minimize the required storage volume. It is shown that through a bio-inspired concept, a high ratio of adaptability of the membrane can be obtained. The paper concludes with the design of a technology demonstrator for a sounding rocket experiment to be launched in March 2013 from the Swedish launch side Esrange

Training teachers for the multimedia age: developing teacher expertise to enhance online learner interaction and collaboration

This article considers the skills that enable teachers to foster interaction and collaboration in online language learning. Drawing on Hampel and Stickler’s (2005) skills pyramid for online language learning and teaching, it presents the pre-service and in-service training programme that associate lecturers in the Department of Languages at the Open University undergo in the context of teaching languages with the help of online communication tools. Two projects are presented that shed more light on the expertise required to teach languages in virtual learning environments. The first project highlights the skills that are needed to teach in a complex online environment; the second one, a teacher training study, aimed to examine distance teachers’ experience of facilitating online group work, identify development needs, try out the potential of specific asynchronous and synchronous tools to support collaborative learning and trial possible development activities. The paper concludes by describing the kind of training programme that tutors require in order to acquire the skills identified

Online teacher development: collaborating in a virtual learning environment

Over recent years educational institutions have been making increasing use of virtual environments to set up collaborative activities for learners. While it is recognized that teachers play an important role in facilitating learner collaboration online they may not have the necessary skills to do so successfully. Thus, a small scale professional development programme was set up and piloted by two distance universities. The aims were to develop teachers’ experience of online group work; to trial a set of pilot activities which would raise awareness of factors contributing to successful collaborative online activity; and to identify professional development needs in this area. This article reports on the hands-on experience of a group of 20 teachers, examines some of the competences that are needed to successfully collaborate in virtual environments, and presents the skills that teachers need to foster online collaborative learning in the virtual classroom. Quantitative and qualitative data were collected, examining the levels of participation among participants, the collaborative activity of two groups, and teacher perception of the collaboration which took place. The skills identified include planning and managing the collaboration, designing appropriate activities, giving clear instructions and getting students to negotiate ground rules for participation, moderating at the right level, and choosing the right environment and the appropriate tool(s). While this study was carried out with language teachers, many of the findings are applicable to other subject areas where growing emphasis is placed on the development of collaborative skills

Analysis of the P. lividus sea urchin genome highlights contrasting trends of genomic and regulatory evolution in deuterostomes

Sea urchins are emblematic models in developmental biology and display several characteristics that set them apart from other deuterostomes. To uncover the genomic cues that may underlie these specificities, we generated a chromosome-scale genome assembly for the sea urchin Paracentrotus lividus and an extensive gene expression and epigenetic profiles of its embryonic development. We found that, unlike vertebrates, sea urchins retained ancestral chromosomal linkages but underwent very fast intrachromosomal gene order mixing. We identified a burst of gene duplication in the echinoid lineage and showed that some of these expanded genes have been recruited in novel structures (water vascular system, Aristotle's lantern, and skeletogenic micromere lineage). Finally, we identified gene-regulatory modules conserved between sea urchins and chordates. Our results suggest that gene-regulatory networks controlling development can be conserved despite extensive gene order rearrangement

Structural plasticity of single chromatin fibers revealed by torsional manipulation

Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large amount of supercoiling without much change in length. This behavior is quantitatively described by a molecular model of the chromatin 3-D architecture. In this model, we assume the existence of a dynamic equilibrium between three conformations of the nucleosome, which are determined by the crossing status of the entry/exit DNAs (positive, null or negative). Torsional strain, in displacing that equilibrium, extensively reorganizes the fiber architecture. The model explains a number of long-standing topological questions regarding DNA in chromatin, and may provide the ground to better understand the dynamic binding of most chromatin-associated proteins.Comment: 18 pages, 7 figures, Supplementary information available at http://www.nature.com/nsmb/journal/v13/n5/suppinfo/nsmb1087_S1.htm

Structural Organization of DNA in Chlorella Viruses

Chlorella viruses have icosahedral capsids with an internal membrane enclosing their large dsDNA genomes and associated proteins. Their genomes are packaged in the particles with a predicted DNA density of ca. 0.2 bp nm−3. Occasionally infection of an algal cell by an individual particle fails and the viral DNA is dynamically ejected from the capsid. This shows that the release of the DNA generates a force, which can aid in the transfer of the genome into the host in a successful infection. Imaging of ejected viral DNA indicates that it is intimately associated with proteins in a periodic fashion. The bulk of the protein particles detected by atomic force microscopy have a size of ∼60 kDa and two proteins (A278L and A282L) of about this size are among 6 basic putative DNA binding proteins found in a proteomic analysis of DNA binding proteins packaged in the virion. A combination of fluorescence images of ejected DNA and a bioinformatics analysis of the DNA reveal periodic patterns in the viral DNA. The periodic distribution of GC rich regions in the genome provides potential binding sites for basic proteins. This DNA/protein aggregation could be responsible for the periodic concentration of fluorescently labeled DNA observed in ejected viral DNA. Collectively the data indicate that the large chlorella viruses have a DNA packaging strategy that differs from bacteriophages; it involves proteins and share similarities to that of chromatin structure in eukaryotes

«La relation de limitation et d’exception dans le français d’aujourd’hui : excepté, sauf et hormis comme pivots d’une relation algébrique »

L’analyse des emplois prépositionnels et des emplois conjonctifs d’ “excepté”, de “sauf” et d’ “hormis” permet d’envisager les trois prépositions/conjonctions comme le pivot d’un binôme, comme la plaque tournante d’une structure bipolaire. Placées au milieu du binôme, ces prépositions sont forcées par leur sémantisme originaire dûment métaphorisé de jouer le rôle de marqueurs d’inconséquence systématique entre l’élément se trouvant à leur gauche et celui qui se trouve à leur droite. L’opposition qui surgit entre les deux éléments n’est donc pas une incompatibilité naturelle, intrinsèque, mais extrinsèque, induite. Dans la plupart des cas (emplois limitatifs), cette opposition prend la forme d’un rapport entre une « classe » et le « membre (soustrait) de la classe », ou bien entre un « tout » et une « partie » ; dans d’autres (emplois exceptifs), cette opposition se manifeste au contraire comme une attaque de front portée par un « tout » à un autre « tout ». De plus, l’inconséquence induite mise en place par la préposition/conjonction paraît, en principe, tout à fait insurmontable. Dans l’assertion « les écureuils vivent partout, sauf en Australie » (que l’on peut expliciter par « Les écureuils vivent partout, sauf [qu’ils ne vivent pas] en Australie »), la préposition semble en effet capable d’impliquer le prédicat principal avec signe inverti, et de bâtir sur une telle implication une sorte de sous énoncé qui, à la rigueur, est totalement inconséquent avec celui qui le précède (si « les écureuils ne vivent pas en Australie », le fait qu’ils « vivent partout » est faux). Néanmoins, l’analyse montre qu’alors que certaines de ces oppositions peuvent enfin être dépassées, d’autres ne le peuvent pas. C’est, respectivement, le cas des relations limitatives et des relations exceptives. La relation limitative, impliquant le rapport « tout » - « partie », permet de résoudre le conflit dans les termes d’une somme algébrique entre deux sous énoncés pourvus de différent poids informatif et de signe contraire. Les valeurs numériques des termes de la somme étant déséquilibrées, le résultat est toujours autre que zéro. La relation exceptive, au contraire, qui n’implique pas le rapport « tout » - « partie », n’est pas capable de résoudre le conflit entre deux sous énoncés pourvus du même poids informatif et en même temps de signe contraire : les valeurs numériques des termes de la somme étant symétriques et égales, le résultat sera toujours équivalent à zéro

Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms

The main functions of viral capsids are to protect, transport and deliver their genome. The mechanical properties of capsids are supposed to be adapted to these tasks. Bacteriophage capsids also need to withstand the high pressures the DNA is exerting onto it as a result of the DNA packaging and its consequent confinement within the capsid. It is proposed that this pressure helps driving the genome into the host, but other mechanisms also seem to play an important role in ejection. DNA packaging and ejection strategies are obviously dependent on the mechanical properties of the capsid. This review focuses on the mechanical properties of viral capsids in general and the elucidation of the biophysical aspects of genome packaging mechanisms and genome delivery processes of double-stranded DNA bacteriophages in particular