Regulation of recombination at yeast nuclear pores controls repair and triplet repeat stability.

Secondary structure-forming DNA sequences such as CAG repeats interfere with replication and repair, provoking fork stalling, chromosome fragility, and recombination. In budding yeast, we found that expanded CAG repeats are more likely than unexpanded repeats to localize to the nuclear periphery. This positioning is transient, occurs in late S phase, requires replication, and is associated with decreased subnuclear mobility of the locus. In contrast to persistent double-stranded breaks, expanded CAG repeats at the nuclear envelope associate with pores but not with the inner nuclear membrane protein Mps3. Relocation requires Nup84 and the Slx5/8 SUMO-dependent ubiquitin ligase but not Rad51, Mec1, or Tel1. Importantly, the presence of the Nup84 pore subcomplex and Slx5/8 suppresses CAG repeat fragility and instability. Repeat instability in nup84, slx5, or slx8 mutant cells arises through aberrant homologous recombination and is distinct from instability arising from the loss of ligase 4-dependent end-joining. Genetic and physical analysis of Rad52 sumoylation and binding at the CAG tract suggests that Slx5/8 targets sumoylated Rad52 for degradation at the pore to facilitate recovery from acute replication stress by promoting replication fork restart. We thereby confirmed that the relocation of damage to nuclear pores plays an important role in a naturally occurring repair process

Strong Interactions at Low Energy

The lectures review some of the basic concepts relevant for an understanding of the low energy properties of the strong interactions: chiral symmetry, spontaneous symmetry breakdown, Goldstone bosons, quark condensate. The effective field theory used to analyze the low energy structure is briefly sketched. As an illustration, I discuss the implications of the recent data on the decay $K\to \pi\pi e\nu$ for the magnitude of the quark condensate.Comment: Lectures given at the school of physics "Understanding the structure of hadrons", Prague, July 2001, 20 p

The Electromagnetic Interaction in Chiral Perturbation Theory

We investigate electromagnetic effects in the framework of chiral perturbation theory. Using a completely independent method, we confirm Urech's results for the divergences of the one--loop functional in the electromagnetic sector. We perform a one--loop analysis of all $P_{\ell 2}$ ($P = \pi, K, \eta$) and the $K_{\ell 3}$ form factors $f_+^{K^+\pi^0}(0)$, $f_+^{K^0\pi^-}(0)$, including a systematic treatment of the \cO(e^2p^2) contributions in the mesonic part. We illustrate our results by several numerical estimates.Comment: 15 pages, late

Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics

We present a new, robust, computational procedure for tracking fluorescent markers in time-lapse microscopy. The algorithm is optimized for finding the time-trajectory of single particles in very noisy dynamic (two- or three-dimensional) image sequences. It proceeds in three steps. First, the images are aligned to compensate for the movement of the biological structure under investigation. Second, the particle's signature is enhanced by applying a Mexican hat filter, which we show to be the optimal detector of a Gaussian-like spot in $\frac{1}{ \omega ^{ 2 }}$ noise. Finally, the optimal trajectory of the particle is extracted by applying a dynamic programming optimization procedure. We have used this software, which is implemented as a Java plug-in for the public-domain ImageJ software, to track the movement of chromosomal loci within nuclei of budding yeast cells. Besides reducing trajectory analysis time by several 100-fold, we achieve high reproducibility and accuracy of tracking. The application of the method to yeast chromatin dynamics reveals different classes of constraints on mobility of telomeres, reflecting differences in nuclear envelope association. The generic nature of the software allows application to a variety of similar biological imaging tasks that require the extraction and quantitation of a moving particle's trajectory

The Chiral Coupling Constants \lb{1} and \lb{2} from \pipi Phase Shifts

A Roy equation analysis of the available $\pi\pi$ phase shift data is performed with the $I=0$ S- wave scattering length $a^0_0$ in the range predicted by the one-loop standard chiral perturbation theory. A suitable dispersive framework is developed to extract the chiral coupling constants \lb{1}, \lb{2} and yields \lb{1}$=-1.70\pm0.15$ and \lb{2}$\approx 5.0$. We remark on the implications of this determination to (combinations of) threshold parameter predictions of the three lowest partial waves.Comment: 36 pages using latex with 1 figure embedded using eps

Quark-hadron phase transition in a magnetic field

Quark-hadron phase transition in QCD in the presence of magnetic field is studied. It is shown that both the temperature of a phase transition and latent heat decrease compared to the case of zero magnetic field. The phase diagram in the plane temperature--magnetic field is presented. Critical point, T_\ast=104 MeV, \sqrt{eH_\ast}=600 MeV, for which the latent heat goes to zero, is found.Comment: 10 pages, 2 figures. v2: new discussion and references added; version to appear in Phys.Lett.

The clustering of telomeres and colocalization with Rap1, Sir3, and Sir4 proteins in wild-type Saccharomyces cerevisiae.

We have developed a novel technique for combined immunofluorescence/in situ hybridization on fixed budding yeast cells that maintains the three-dimensional structure of the nucleus as monitored by focal sections of cells labeled with fluorescent probes and by staining with a nuclear pore antibody. Within the resolution of these immunodetection techniques, we show that proteins encoded by the SIR3, SIR4, and RAP1 genes colocalize in a statistically significant manner with Y' telomere-associated DNA sequences. In wild-type cells the Y' in situ hybridization signals can be resolved by light microscopy into fewer than ten foci per diploid nucleus. This suggests that telomeres are clustered in vegetatively growing cells, and that proteins essential for telomeric silencing are concentrated at their sites of action, i.e., at telomeres and/or subtelomeric regions. As observed for Rap1, the Sir4p staining is diffuse in a sir3- strain, and similarly, Sir3p staining is no longer punctate in a sir4- strain, although the derivatized Y' probe continues to label discrete sites in these strains. Nonetheless, the Y' FISH is altered in a qualitative manner in sir3 and sir4 mutant strains, consistent with the previously reported phenotypes of shortened telomeric repeats and loss of telomeric silencing

Exploring \pp scattering in the \1N picture

In the large $N_c$ approximation to $QCD$, the leading \pp scattering amplitude is expressed as the sum of an infinite number of tree diagrams. We investigate the possibility that an adequate approximation at energies up to somewhat more than one $GeV$ can be made by keeping diagrams which involve the exchange of resonances in this energy range in addition to the simplest chiral contact terms. In this approach crossing symmetry is automatic but individual terms tend to drastically violate partial wave unitarity. We first note that the introduction of the $\rho$ meson in a chirally invariant manner substantially delays the onset of drastic unitarity violation which would be present for the {\it current algebra} term alone. This suggests a possibility of local (in energy) cancellation which we then explore in a phenomenological way. We include exchanges of leading resonances up to the $1.3 GeV$ region. However, unitarity requires more structure which we model by a four derivative contact term or by a low lying scalar resonance which is presumably subleading in the \1N expansion, but may nevertheless be important. The latter two flavor model gives a reasonable description of the phase shift $\delta^0_0$ up until around $860 MeV$, before the effects associated which the $K\bar{K}$ threshold come into play.Comment: 27 LaTex pages + 13 figures (also available in hard-copy

Flavon exchange effects in models with abelian flavor symmetry

In models with abelian flavor symmetry the small mixing angles and mass ratios of quarks and leptons are typically given by powers of small parameters characterizing the spontaneous breaking of flavor symmetry by "flavon" fields. If the scale of the breaking of flavor symmetry is near the weak scale, flavon exchange can lead to interesting flavor-violating and CP violating effects. These are studied. It is found that d_e, mu -> e + gamma, and mu-e conversion on nuclei can be near present limits. For significant range of parameters mu-e conversion can be the most sensitive way to look for such effects.Comment: 19 pages, 5 Postscript figures, LATE