Twisting in a crowd

Given our current understanding of nuclear structure, it is difficult to imagine how the nucleus performs its varied functions and controls the traffic of its many components. For example, how can densely packed chromatin be transcribed without the helical nature of the DNA resulting in entangled DNA and RNA and a stalled RNA polymerase? Here, Jacques Dubochet discusses a model of transcription in which DNA rotates around its axis, rather than RNA polymerase rotating around the DNA. Furthermore, he suggests that a view of chromatin as 'liquid' may help in understanding a wide range of nuclear functions

Predicting Optimal Lengths of Random Knots

In thermally fluctuating long linear polymeric chain in solution, the ends come from time to time into a direct contact or a close vicinity of each other. At such an instance, the chain can be regarded as a closed one and thus will form a knot or rather a virtual knot. Several earlier studies of random knotting demonstrated that simpler knots show their highest occurrence for shorter random walks than more complex knots. However up to now there were no rules that could be used to predict the optimal length of a random walk, i.e. the length for which a given knot reaches its highest occurrence. Using numerical simulations, we show here that a power law accurately describes the relation between the optimal lengths of random walks leading to the formation of different knots and the previously characterized lengths of ideal knots of the corresponding type

Bilayers of nucleosome core particles

Among the multiple effects involved in chromatin condensation and decondensation processes, interactions between nucleosome core particles are suspected to play a crucial role. We analyze them in the absence of linker DNA and added proteins, after the self-assembly of isolated nucleosome core particles under controlled ionic conditions. We describe an original lamellar mesophase forming tubules on the mesoscopic scale. High resolution imaging of cryosections of vitrified samples reveals how nucleosome core particles stack on top of one another into columns which themselves align to form bilayers that repel one another through a solvent layer. We deduce from this structural organization how the particles interact through attractive interactions between top and bottom faces and lateral polar interactions that originate in the heterogeneous charge distribution at the surface of the particle. These interactions, at work under conditions comparable with those found in the living cell, should be of importance in the mechanisms governing chromatin compaction in vivo

Cryoelectron microscopy of vitrified sections: a new challenge for the analysis of functional nuclear architecture

Cryoelectron microscopy of vitrified sections has become a powerful tool for investigating the fine structural features of cellular compartments. In the present study, this approach has been applied in order to explore the ultrastructural morphology of the interphase nucleus in different mammalian cultured cells. Rat hepatoma, Chinese hamster ovary and Potorus kidney cells were cryofixed by high-pressure freezing and the cryosections were examined at low temperature by transmission electron microscopy. Our results show that while the contrast of nuclear structural domains is remarkably homogeneous in hydrated sections, some of them can be recognised due to their characteristic texture. Thus, condensed chromatin appears finely granular and the perichromatin region contains rather abundant fibro-granular elements suggesting the presence of dispersed chromatin fibres and of perichromatin fibrils and granules. The interchromatin space looks homogeneous and interchromatin granules have not been identified under these preparative conditions. In the nucleolus, the most striking feature is the granular component, while the other parts of the nucleolar body, which appear less contrasted, are difficult to resolve. The nuclear envelope is easily recognisable with its regular perinuclear space and nuclear pore complexes. Our observations are discussed in the context of results obtained by other, more conventional electron microscopic method

Electron microscopy of frozen biological suspensions

The methodology for preparing specimens in the frozen, hydrated state has been assessed using crystals and T4 bacteriophages. The methods have also been demonstrated with lambda bacteriophages, purple membrane of Halobacterium halobium and fibres of DNA. For particles dispersed in an aqueous environment, it is shown that optimum structural preservation is obtained from a thin, quench-frozen film with the bulk aqueous medium in the vitreous state. Crystallization of the bulk water may result in solute segregation and expulsion of the specimen from the film. Contrast measurements can be used to follow directly the state of hydration of a specimen during transition from the fully hydrated to the freeze-dried state and permit direct measurement of the water content of the specimen. By changing the concentration and composition of the aqueous medium the contrast of particles in a vitreous film can be controlled and any state of negative, positive or zero contrast may be obtained. At 100 K, frozen-hydrated, freeze-dried or sugar embedded crystals can withstand a three- to four-fold increase in electron exposure for the same damage when compared with similar sugar-embedded or freeze-dried samples at room temperature

The reaction centre of the photounit of Rhodospirillum rubrum is anchored to the light-harvesting complex with four-fold rotational disorder

The minimal photounit of the photosynthetic membranes of the purple non-sulphur bacterium Rhodospirillum rubrum, comprising the reaction centre and the light-harvesting complex has been purified and crystallised in two dimensions in the presence of added phospholipids, and subsequently visualised by electron microscopy after negatively-staining. The position of the reaction centres within the light-harvesting ring has been determined at low resolution by the application of a new analysis for rotationally disordered identical units (here the reaction centres) within a two-dimensional crystalline lattice comprised of perfectly aligned unit cells (here the light-harvesting complexes). The reaction centre was found to preferentially occupy one of four orientations within the light-harvesting complex. The light-harvesting complex appears to be distorted to C4 symmetry, thus assuming a squarish shape when visualised by negative staining. A tentative structural model of the reaction centre-light-harvesting complex photounit which fits the experimental data is propose

Worth the while? Time and politics in Delhi

This thesis discusses how time and politics interact around basic services in two poor neighbourhoods of Delhi, India. It asks when do people deem it worthwhile to devote time to actions aimed at improving access to services. Its most original contributions stem from several apparent contradictions between findings from a survey conducted during the first weeks of fieldwork and the extensive ethnographic research that followed. The survey’s findings suggest that fewer people are taking action to obtain better services in places where political accountability is weak. They are also less likely to take action or engage in politics when disadvantages related to gender or other identity characteristics compromise their claims. On the contrary, the ethnographic evidence suggests that people are devoting long hours to negotiating with service providers and middlemen precisely where caste rivalries and land disputes undermine service delivery. It also shows that women do so more than men, and that a group of slum dwellers whose political rights are compromised embark on a long journey to cast their votes with no expectation of better services in return. The analysis of these findings offers new insights into how time and other factors combine to enable or undermine demands for better services. It also provides evidence that people underreport the time and opportunity costs of having to wait for erratic service delivery. Similarly, ethnographic observations reveal many time-consuming involvements in the politics of basic service delivery that are not reported in the survey. These contributions speak to debates spanning questions both of method and of substance across several disciplines. Insights about how people report their time, value it and behave within it, bring into dialogue ‘quantitative time use research’ and ‘ethnographies of waiting’. More broadly, the behaviours described in the thesis bring a temporal perspective to questions raised by literature on everyday interactions with the state in India

Scala

Scala is a general purpose programming language designed to express common programming patterns in a concise, elegant, and type-safe way. It smoothly integrates features of object-oriented and functional languages. It is also fully interoperable with Java