Building in vitro tools for livestock genomics:chromosomal variation within the PK15 cell line

BACKGROUND: Cultured porcine cell lines are powerful tools for functional genomics and in vitro phenotypic testing of candidate causal variants. However, to be utilised for genomic or variant interrogation assays, the genome sequence and structure of cultured cell lines must be realised. In this work, we called variants and used read coverage in combination with within-sample allele frequency to detect potential aneuploidy in two immortalised porcine kidney epithelial (PK15) cell lines and in a pig embryonic fibroblast line.RESULTS: We compared two PK15 cultured cells samples: a new American Type Culture Collection (ATCC) sample and one that has been utilised and passaged within the laboratory for an extended period (&gt; 10 years). Read coverage and within-sample allele frequencies showed that several chromosomes are fully or partially aneuploid in both PK15 lines, including potential trisomy of chromosome 4 and tetrasomy of chromosome 17. The older PK15 line showed evidence of additional structural variation and potentially clonal variation. By comparison, the pig embryonic fibroblast line was free from the gross aneuploidies seen in the PK15s.CONCLUSIONS: Our results show that the PK15 cell lines examined have aneuploidies and complex structural variants in their genomes. We propose that screening for aneuploidy should be considered for cell lines, and discuss implications for livestock genomics.</p

Two flavor chiral phase transition from nonperturbative flow equations

We employ nonperturbative flow equations to compute the equation of state for two flavor QCD within an effective quark meson model. This yields the temperature and quark mass dependence of quantities like the chiral condensate or the pion mass. A precision estimate of the universal critical equation of state for the three-dimensional O(4) Heisenberg model is presented. We explicitly connect the O(4) universal behavior near the critical temperature and zero quark mass with the physics at zero temperature and a realistic pion mass. For realistic quark masses the pion correlation length near T_c turns out to be smaller than its zero temperature value.Comment: 49 pages including 15 figures, LaTeX, uses epsf.sty and rotate.st

Signals of confinement in Green functions of SU(2) Yang-Mills theory

The vortex picture of confinement is employed to explore the signals of confinement in Yang-Mills Green functions. By using SU(2) lattice gauge theory, it has been well established that the removal of the center vortices from the lattice configurations results in the loss of confinement. The running coupling constant, the gluon and the ghost form factors are studied in Landau gauge for both cases, the full and the vortex removed theory. In the latter case, a strong suppression of the running coupling constant and the gluon form factor at low momenta is observed. At the same time, the singularity of the ghost form factor at vanishing momentum disappears. This observation establishes an intimate correlation between the ghost singularity and confinement. The result also shows that a removal of the vortices generates a theory for which Zwanziger's horizon condition for confinement is no longer satisfied.Comment: 4 pages, 4 figure

Twistfield Perturbations of Vertex Operators in the Z_2-Orbifold Model

We apply Kadanoff's theory of marginal deformations of conformal field theories to twistfield deformations of Z_2 orbifold models in K3 moduli space. These deformations lead away from the Z_2 orbifold sub-moduli-space and hence help to explore conformal field theories which have not yet been understood. In particular, we calculate the deformation of the conformal dimensions of vertex operators for p^2<1 in second order perturbation theory.Comment: Latex2e, 19 pages, 1 figur

Spontaneously broken color

The vacuum of QCD is characterized by the Higgs mechanism. Color is ``spontaneously broken'' by a quark-antiquark condensate in the octet representation. The massive gluons carry integer electric charges and are identified with the vector mesons. The fermionic excitations consist of the low mass baryon octet and a singlet. The interactions between these particles and the light pseudoscalar octet are largely determined by chiral symmetry and a nonlinear local symmetry. A consistent phenomenological picture of strong interactions at long distances arises from a simple effective action.Comment: 67 page

Doing audio-visual montage to explore time and space: The everyday rhythms of Billingsgate Fish Market

This article documents, shows and analyses the everyday rhythms of Billingsgate, London’s wholesale fish market. It takes the form of a short film based an audio-visual montage of time-lapse photography and sound recordings, and a textual account of the dimensions of market life revealed by this montage. Inspired by Henri Lefebvre’s Rhythmanalysis, and the embodied experience of moving through and sensing the market, the film renders the elusive quality of the market and the work that takes place within it to make it happen. The composite of audio-visual recordings immerses viewers in the space and atmosphere of the market and allows us to perceive and analyse rhythms, patterns, flows, interactions, temporalities and interconnections of market work, themes that this article discusses. The film is thereby both a means of showing market life and an analytic tool for making sense of it. This article critically considers the documentation, evocation and analysis of time and space in this way

Optimal Traffic Networks

Inspired by studies on the airports' network and the physical Internet, we propose a general model of weighted networks via an optimization principle. The topology of the optimal network turns out to be a spanning tree that minimizes a combination of topological and metric quantities. It is characterized by a strongly heterogeneous traffic, non-trivial correlations between distance and traffic and a broadly distributed centrality. A clear spatial hierarchical organization, with local hubs distributing traffic in smaller regions, emerges as a result of the optimization. Varying the parameters of the cost function, different classes of trees are recovered, including in particular the minimum spanning tree and the shortest path tree. These results suggest that a variational approach represents an alternative and possibly very meaningful path to the study of the structure of complex weighted networks.Comment: 4 pages, 4 figures, final revised versio

Exact Flow Equations and the U(1)-Problem

The effective action of a SU(N)-gauge theory coupled to fermions is evaluated at a large infrared cut-off scale k within the path integral approach. The gauge field measure includes topologically non-trivial configurations (instantons). Due to the explicit infrared regularisation there are no gauge field zero modes. The Dirac operator of instanton configurations shows a zero mode even after the infrared regularisation, which leads to U_A(1)-violating terms in the effective action. These terms are calculated in the limit of large scales k.Comment: 22 pages, latex, no figures, with stylistic changes and some arguments streamlined, typos corrected, References added, to appear in Phys. Rev.

Subcritical Fluctuations at the Electroweak Phase Transition

We study the importance of thermal fluctuations during the electroweak phase transition. We evaluate in detail the equilibrium number density of large amplitude subcritical fluctuations and discuss the importance of phase mixing to the dynamics of the phase transition. Our results show that, for realistic Higgs masses, the phase transition can be completed by the percolation of the true vacuum, induced by the presence of subcritical fluctuations.Comment: RevTeX, 4 eps figs (uses epsf.sty), 26 pages, to be published in Phys. Rev.

Brownian Motions on Metric Graphs

Brownian motions on a metric graph are defined. Their generators are characterized as Laplace operators subject to Wentzell boundary at every vertex. Conversely, given a set of Wentzell boundary conditions at the vertices of a metric graph, a Brownian motion is constructed pathwise on this graph so that its generator satisfies the given boundary conditions.Comment: 43 pages, 7 figures. 2nd revision of our article 1102.4937: The introduction has been modified, several references were added. This article will appear in the special issue of Journal of Mathematical Physics celebrating Elliott Lieb's 80th birthda