Multicolour interphase cytogenetics: 24 chromosome probes, 6 colours, 4 layers

From the late 1980s onwards, the use of DNA probes to visualise sequences on individual chromosomes (fluorescent in-situ hybridisation - FISH) revolutionised the study of cytogenetics. Following single colour experiments, more fluorochromes were added, culminating in a 24 colour assay that could distinguish all human chromosomes. Interphase cytogenetics (the detection of chromosome copy number in interphase nuclei) soon followed, however 24 colour experiments are hampered for this application as mixing fluorochromes to produce secondary colours produces images that are not easily distinguishable from overlapping signals. This study reports the development and use of a novel protocol, new fast hybridising FISH probes, and a bespoke image capture system for the assessment of chromosome copy number in interphase nuclei. The multicolour probe sets can be used individually or in sequential hybridisation layers to assess ploidy of all 24 human chromosomes in the same nucleus. Applications of this technique are in the investigation of chromosome copy number and the assessment of nuclear organisation for a range of different cell types including human sperm, cancer cells and preimplantation embryos

NGN, QCD_2 and chiral phase transition from string theory

We construct a D2-D8-$\bar{D8}$ configuration in string theory, it can be described at low energy by two dimensional field theory. In the weak coupling region, the low energy theory is a nonlocal generalization of Gross-Neveu(GN) model which dynamically breaks the chiral flavor symmetry $U(N_f)_L \times U(N_f)_R$ at large $N_c$ and finite $N_f$. However, in the strong coupling region, we can use the SUGRA/Born-Infeld approximation to describe the low energy dynamics of the system. Also, we analyze the low energy dynamics about the configuration of wrapping the one direction of D2 brane on a circle with anti-periodic boundary condition of fermions. The fermions and scalars on D2 branes get mass and decouple from the low energy theory. The IR dynamics is described by the $QCD_2$ at weak coupling. In the opposite region, the dynamics has a holographic dual description. And we have discussed the phase transition of chiral symmetry breaking at finite temperature. Finally, after performing T-duality, this configuration is related to some other brane configurations.Comment: 30 pages, 3 figures, minor change

Benthic marine calcifiers coexist with CaCO3-undersaturated seawater worldwide

Ocean acidification and decreasing seawater saturation state with respect to calcium carbonate (CaCO3) minerals have raised concerns about the consequences to marine organisms, especially those building structures made of CaCO3. A large proportion of benthic marine calcifiers incorporate Mg2+ into their calcareous structures (i.e., Mg-calcite) which, in general, reduces mineral stability. The vulnerability of some marine calcifiers to ocean acidification is related to the solubility of their calcareous structures, but not all marine organisms conform to this because of sophisticated biological and physiological mechanisms to construct and maintain CaCO3 structures. Few studies have considered seawater saturation state with respect to species-specific mineralogy in evaluating the effect of ocean acidification on marine organisms. Here, a global dataset of skeletal mol % MgCO3 of benthic calcifiers and in situ environmental conditions (temperature, salinity, pressure, and [CO32-]) spanning a depth range of 0 m (subtidal/neritic) to 5500 m (abyssal) was assembled to calculate in situ seawater saturation states with respect to species-specific Mg-calcite mineral compositions (?Mg-x). Up to 20% of all studied calcifiers at depths 1200 m currently experience seawater mineral undersaturation with respect to their skeletal mineral phase (?Mg-x1200 m) of all studied calcifying species to seawater undersaturation. These observations underscore concerns over the ability of marine benthic calcifiers to continue to construct and maintain their calcareous structures under these conditions. We advocate that ocean acidification tipping points can only be understood by assessing species-specific responses, and because of different seawater ?Mg-x present in all marine ecosystems

Large non-Gaussianity from two-component hybrid inflation

We study the generation of non-Gaussianity in models of hybrid inflation with two inflaton fields, (2-brid inflation). We analyse the region in the parameter and the initial condition space where a large non-Gaussianity may be generated during slow-roll inflation which is generally characterised by a large f_NL, tau_NL and a small g_NL. For certain parameter values we can satisfy tau_NL>>f_NL^2. The bispectrum is of the local type but may have a significant scale dependence. We show that the loop corrections to the power spectrum and bispectrum are suppressed during inflation, if one assume that the fields follow a classical background trajectory. We also include the effect of the waterfall field, which can lead to a significant change in the observables after the waterfall field is destabilised, depending on the couplings between the waterfall and inflaton fields.Comment: 16 pages, 6 figures; v2: comments and references added, typos corrected, matches published versio

Coulomb Gauge QCD, Confinement, and the Constituent Representation

Quark confinement and the genesis of the constituent quark model are examined in nonperturbative QCD in Coulomb gauge. We employ a self-consistent method to construct a quasiparticle basis and to determine the quasiparticle interaction. The results agree remarkably well with lattice computations. They also illustrate the mechanism by which confinement and constituent quarks emerge, provide support for the Gribov-Zwanziger confinement scenario, clarify several perplexing issues in the constituent quark model, and permit the construction of an improved model of low energy QCD.Comment: 43 pages, 14 figures, revtex, uses psfig.st

Benthic marine calcifiers coexist with CaCO3-undersaturated seawater worldwide

Ocean acidification and decreasing seawater saturation state with respect to calcium carbonate (CaCO3) minerals have raised concerns about the consequences to marine organisms, especially those building structures made of CaCO3. A large proportion of benthic marine calcifiers incorporate Mg2+ into their calcareous structures (i.e., Mg-calcite) which, in general, reduces mineral stability. The vulnerability of some marine calcifiers to ocean acidification is related to the solubility of their calcareous structures, but not all marine organisms conform to this because of sophisticated biological and physiological mechanisms to construct and maintain CaCO3 structures. Few studies have considered seawater saturation state with respect to species-specific mineralogy in evaluating the effect of ocean acidification on marine organisms. Here, a global dataset of skeletal mol % MgCO3 of benthic calcifiers and in situ environmental conditions (temperature, salinity, pressure, and [CO32-]) spanning a depth range of 0 m (subtidal/neritic) to 5500 m (abyssal) was assembled to calculate in situ seawater saturation states with respect to species-specific Mg-calcite mineral compositions (?Mg-x). Up to 20% of all studied calcifiers at depths <1200 m and approximately 90% of calcifiers at depths >1200 m currently experience seawater mineral undersaturation with respect to their skeletal mineral phase (?Mg-x<1). We conclude that as a result of predicted anthropogenic ocean acidification over the next 150 years, the predicted decrease in seawater mineral saturation, will expose approximately 50% (<1200 m) and 100% (>1200 m) of all studied calcifying species to seawater undersaturation. These observations underscore concerns over the ability of marine benthic calcifiers to continue to construct and maintain their calcareous structures under these conditions. We advocate that ocean acidification tipping points can only be understood by assessing species-specific responses, and because of different seawater ?Mg-x present in all marine ecosystems

Three-body structure of low-lying 18Ne states

We investigate to what extent 18Ne can be descibed as a three-body system made of an inert 16O-core and two protons. We compare to experimental data and occasionally to shell model results. We obtain three-body wave functions with the hyperspherical adiabatic expansion method. We study the spectrum of 18Ne, the structure of the different states and the predominant transition strengths. Two 0+, two 2+, and one 4+ bound states are found where they are all known experimentally. Also one 3+ close to threshold is found and several negative parity states, 1-, 3-, 0-, 2-, most of them bound with respect to the 16O excited 3- state. The structures are extracted as partial wave components, as spatial sizes of matter and charge, and as probability distributions. Electromagnetic decay rates are calculated for these states. The dominating decay mode for the bound states is E2 and occasionally also M1.Comment: 17 pages, 5 figures (version to appear in EPJA

The Physics of turbulent and dynamically unstable Herbig-Haro jets

The overall properties of the Herbig-Haro objects such as centerline velocity, transversal profile of velocity, flow of mass and energy are explained adopting two models for the turbulent jet. The complex shapes of the Herbig-Haro objects, such as the arc in HH34 can be explained introducing the combination of different kinematic effects such as velocity behavior along the main direction of the jet and the velocity of the star in the interstellar medium. The behavior of the intensity or brightness of the line of emission is explored in three different cases : transversal 1D cut, longitudinal 1D cut and 2D map. An analytical explanation for the enhancement in intensity or brightness such as usually modeled by the bow shock is given by a careful analysis of the geometrical properties of the torus.Comment: 17 pages, 10 figures. Accepted for publication in Astrophysics & Spac

Colloquium: Mechanical formalisms for tissue dynamics

The understanding of morphogenesis in living organisms has been renewed by tremendous progressin experimental techniques that provide access to cell-scale, quantitative information both on theshapes of cells within tissues and on the genes being expressed. This information suggests that ourunderstanding of the respective contributions of gene expression and mechanics, and of their crucialentanglement, will soon leap forward. Biomechanics increasingly benefits from models, which assistthe design and interpretation of experiments, point out the main ingredients and assumptions, andultimately lead to predictions. The newly accessible local information thus calls for a reflectionon how to select suitable classes of mechanical models. We review both mechanical ingredientssuggested by the current knowledge of tissue behaviour, and modelling methods that can helpgenerate a rheological diagram or a constitutive equation. We distinguish cell scale ("intra-cell")and tissue scale ("inter-cell") contributions. We recall the mathematical framework developpedfor continuum materials and explain how to transform a constitutive equation into a set of partialdifferential equations amenable to numerical resolution. We show that when plastic behaviour isrelevant, the dissipation function formalism appears appropriate to generate constitutive equations;its variational nature facilitates numerical implementation, and we discuss adaptations needed in thecase of large deformations. The present article gathers theoretical methods that can readily enhancethe significance of the data to be extracted from recent or future high throughput biomechanicalexperiments.Comment: 33 pages, 20 figures. This version (26 Sept. 2015) contains a few corrections to the published version, all in Appendix D.2 devoted to large deformation

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results