Mechanics and dynamics of X-chromosome pairing at X inactivation

At the onset of X-chromosome inactivation, the vital process whereby female mammalian cells equalize X products with respect to males, the X chromosomes are colocalized along their Xic (X-inactivation center) regions. The mechanism inducing recognition and pairing of the X’s remains, though, elusive. Starting from recent discoveries on the molecular factors and on the DNA sequences (the so-called "pairing sites") involved, we dissect the mechanical basis of Xic colocalization by using a statistical physics model. We show that soluble DNA-specific binding molecules, such as those experimentally identified, can be indeed sufficient to induce the spontaneous colocalization of the homologous chromosomes but only when their concentration, or chemical affinity, rises above a threshold value as a consequence of a thermodynamic phase transition. We derive the likelihood of pairing and its probability distribution. Chromosome dynamics has two stages: an initial independent Brownian diffusion followed, after a characteristic time scale, by recognition and pairing. Finally, we investigate the effects of DNA deletion/insertions in the region of pairing sites and compare model predictions to available experimental data

Preparation of Barley Pollen Mother Cells for Confocal and Super Resolution Microscopy

Recombination (crossover) drives the release of genetic diversity in plant breeding programs. However, in barley, recombination is skewed toward the telomeric ends of its seven chromosomes, restricting the re-assortment of about 30% of the genes located in the centromeric regions of its large 5.1 Gb genome. A better understanding of meiosis and recombination could provide ways of modulating crossover distribution and frequency in barley as well as in other grasses, including wheat. While most research on recombination has been carried out in the model plant Arabidopsis thaliana, recent studies in barley (Hordeum Vulgare) have provided new insights into the control of crossing over in large genome species. A major achievement in these studies has been the use of cytological procedures to follow meiotic events. This protocol provides detailed practical steps required to perform immunostaining of barley meiocytes (pollen mother cells) for confocal or structured illumination microscopy.</p

ELENA, a preliminary cost and feasibility study

To produce dense pbar beams at very low energies (100-200 keV), a small decelerator ring could be built and installed between the existing AD ring and the experimental area. Phase-space blowup during deceleration would be compensated by electron cooling in order to obtain final emittances comparable to the 5MeV beam presently delivered by the AD. This report describes preliminary machine parameters and layout of ELENA and also gives an approximate estimate of cost and manpower needs

Principles of meiotic chromosome assembly revealed in S. cerevisiae

During meiotic prophase, chromosomes organise into a series of chromatin loops emanating from a proteinaceous axis, but the mechanisms of assembly remain unclear. Here we use Saccharomyces cerevisiae to explore how this elaborate three-dimensional chromosome organisation is linked to genomic sequence. As cells enter meiosis, we observe that strong cohesin-dependent grid-like Hi-C interaction patterns emerge, reminiscent of mammalian interphase organisation, but with distinct regulation. Meiotic patterns agree with simulations of loop extrusion with growth limited by barriers, in which a heterogeneous population of expanding loops develop along the chromosome. Importantly, CTCF, the factor that imposes similar features in mammalian interphase, is absent in S. cerevisiae, suggesting alternative mechanisms of barrier formation. While grid-like interactions emerge independently of meiotic chromosome synapsis, synapsis itself generates additional compaction that matures differentially according to telomere proximity and chromosome size. Collectively, our results elucidate fundamental principles of chromosome assembly and demonstrate the essential role of cohesin within this evolutionarily conserved process

Installation and Hardware commissioning of the Multi-Turn extraction at the CERN proton synchrotron

The implementation of the new Multi-Turn Extraction (MTE) at the CERN Proton Synchrotron required major hardware changes for the nearly 50-year old accelerator. The installation of new Pulse Forming Networks (PFN) and refurbished kicker magnets for the extraction, new sextupole and octupole magnets, new power converters, together with an in-depth review of the machine aperture leading to the design of new vacuum chambers was required. As a result, a heavy programme of interventions had to be scheduled during the winter shut-down 2007-8. The newly installed hardware and its commissioning is presented and discussed in details

The CERN PS multi-turn extraction based on beam splittting in stable islands of transverse phase space: Design Report

Since 2001 considerable effort has been devoted to the study of a possible replacement of the continuous-transfer extraction mode from the PS to the SPS. Such an approach, called Multi-Turn Extraction (MTE), is based on capture of the beam inside stable islands of transverse phase space, generated by sextupoles and octupoles, thanks to a properly chosen tune variation. Both numerical simulations and measurements with beam were performed to understand the properties of this new extraction mode. The experimental study was completed at the end of 2004 and by the end of 2005 a scheme to implement this novel approach in the PS machine was defined and its performance assessed. This design report presents the outcome of the studies undertaken both in terms of technical issues as well as of resources necessary to implement the proposed scheme

Linac4 Technical Design Report

Linac4 is an H- linear accelerator, intended to replace Linac2 as injector to the PS Booster (PSB). By delivering to the PSB a beam at 160 MeV energy, Linac4 will provide the conditions to double the brightness and intensity of the beam from the PSB, thus removing the first bottleneck towards higher brightness for the LHC and simplifying operation. Moreover, this new linac constitutes an essential component of any of the envisaged LHC upgrade scenarios and could open the way to future extensions of the CERN accelerator complex towards higher performance. This Technical Design Report presents a detailed technical overview of the Linac4 design as it stands at end 2006

Meiotic silencing and fragmentation of the male germline restricted chromosome in zebra finch

During male meiotic prophase in mammals, X and Y are in a largely unsynapsed configuration, which is thought to trigger meiotic sex chromosome inactivation (MSCI). In avian species, females are ZW, and males ZZ. Although Z and W in chicken oocytes show complete, largely heterologous synapsis, they too undergo MSCI, albeit only transiently. The W chromosome is already inactive in early meiotic prophase, and inactive chromatin marks may spread on to the Z upon synapsis. Mammalian MSCI is considered as a specialised form of the general meiotic silencing mechanism, named meiotic silencing of unsynapsed chromatin (MSUC). Herein, we studied the avian form of MSUC, by analysing the behaviour of the peculiar germline restricted chromosome (GRC) that is present as a single copy in zebra finch spermatocytes. In the female germline, this chromosome is present in two copies, which normally synapse and recombine. In contrast, during male meiosis, the single GRC is always eliminated. We found that the GRC in the male germline is silenced from early leptotene onwards, similar to the W chromosome in avian oocytes. The GRC remains largely unsynapsed throughout meiotic prophase I, although patches of SYCP1 staining indicate that part of the GRC may self-synapse. In addition, the GRC is largely devoid of meiotic double strand breaks. We observed a lack of the inner centromere protein INCENP on the GRC and elimination of the GRC following metaphase I. Subsequently, the GRC forms a micronucleus in which the DNA is fragmented. We conclude that in contrast to MSUC in mammals, meiotic silencing of this single chromosome in the avian germline occurs prior to, and independent of DNA double strand breaks and chromosome pairing, hence we have named this phenomenon meiotic silencing prior to synapsis (MSPS)

AutoRef: Towards Real-Robot Soccer Complete Automated Refereeing

Preparing for robot soccer competitions by empirically evaluating different possible game strategies has been rather limited in leagues using real robots. Such limitation comes from factors related to the difficulty of extensively experimenting with games with real robots, such as their inevitable wear and tear and their usual limited number. RoboCup real robot teams have therefore developed simulation environments to enable experimentation. However, in order to run complete games in such simulation environments, an automated referee is needed. In this paper, we present AutoRef, as a contribution towards a complete automated referee for the RoboCup Small-Size League (SSL). We have developed and used AutoRef in an SSL simulation to run full games to evaluate different strategies, as we illustrate and show results. AutoRef is designed as a finite-state machine that transitions between the states of the game being either on or required to stop. AutoRef purposefully only uses the same visual and game information provided in SSL games with physical robots, which it uses to compute the features needed by the rules and to make decisions to transition between its states. Due to this real input to AutoRef, we have partially applied it to games of the physical robots. As AutoRef does not include all the rules of the real SSL games, we currently view it as an aid to human referees of SSL games, and discuss the challenges in automating several specific SSL game rules. AutoRef could be extended to other RoboCup real soccer leagues if a combined view of the game field, ball, and players is available.</p

BNCI Horizon 2020 - Towards a Roadmap for Brain/Neural Computer Interaction

In this paper, we present BNCI Horizon 2020, an EU Coordination and Support Action (CSA) that will provide a roadmap for brain-computer interaction research for the next years, starting in 2013, and aiming at research efforts until 2020 and beyond. The project is a successor of the earlier EU-funded Future BNCI CSA that started in 2010 and produced a roadmap for a shorter time period. We present how we, a consortium of the main European BCI research groups as well as companies and end user representatives, expect to tackle the problem of designing a roadmap for BCI research. In this paper, we define the field with its recent developments, in particular by considering publications and EU-funded research projects, and we discuss how we plan to involve research groups, companies, and user groups in our effort to pave the way for useful and fruitful EU-funded BCI research for the next ten years