Post-transcriptional regulation of satellite cell quiescence by TTP-mediated mRNA decay.

Skeletal muscle satellite cells in their niche are quiescent and upon muscle injury, exit quiescence, proliferate to repair muscle tissue, and self-renew to replenish the satellite cell population. To understand the mechanisms involved in maintaining satellite cell quiescence, we identified gene transcripts that were differentially expressed during satellite cell activation following muscle injury. Transcripts encoding RNA binding proteins were among the most significantly changed and included the mRNA decay factor Tristetraprolin. Tristetraprolin promotes the decay of MyoD mRNA, which encodes a transcriptional regulator of myogenic commitment, via binding to the MyoD mRNA 3' untranslated region. Upon satellite cell activation, p38α/β MAPK phosphorylates MAPKAP2 and inactivates Tristetraprolin, stabilizing MyoD mRNA. Satellite cell specific knockdown of Tristetraprolin precociously activates satellite cells in vivo, enabling MyoD accumulation, differentiation and cell fusion into myofibers. Regulation of mRNAs by Tristetraprolin appears to function as one of several critical post-transcriptional regulatory mechanisms controlling satellite cell homeostasis

Tetromino tilings and the Tutte polynomial

We consider tiling rectangles of size 4m x 4n by T-shaped tetrominoes. Each tile is assigned a weight that depends on its orientation and position on the lattice. For a particular choice of the weights, the generating function of tilings is shown to be the evaluation of the multivariate Tutte polynomial Z\_G(Q,v) (known also to physicists as the partition function of the Q-state Potts model) on an (m-1) x (n-1) rectangle G, where the parameter Q and the edge weights v can take arbitrary values depending on the tile weights.Comment: 8 pages, 6 figure

Exact enumeration of Hamiltonian circuits, walks, and chains in two and three dimensions

We present an algorithm for enumerating exactly the number of Hamiltonian chains on regular lattices in low dimensions. By definition, these are sets of k disjoint paths whose union visits each lattice vertex exactly once. The well-known Hamiltonian circuits and walks appear as the special cases k=0 and k=1 respectively. In two dimensions, we enumerate chains on L x L square lattices up to L=12, walks up to L=17, and circuits up to L=20. Some results for three dimensions are also given. Using our data we extract several quantities of physical interest

Interacting classical dimers on the square lattice

We study a model of close-packed dimers on the square lattice with a nearest neighbor interaction between parallel dimers. This model corresponds to the classical limit of quantum dimer models [D.S. Rokhsar and S.A. Kivelson, Phys. Rev. Lett.{\bf 61}, 2376 (1988)]. By means of Monte Carlo and Transfer Matrix calculations, we show that this system undergoes a Kosterlitz-Thouless transition separating a low temperature ordered phase where dimers are aligned in columns from a high temperature critical phase with continuously varying exponents. This is understood by constructing the corresponding Coulomb gas, whose coupling constant is computed numerically. We also discuss doped models and implications on the finite-temperature phase diagram of quantum dimer models.Comment: 4 pages, 4 figures; v2 : Added results on doped models; published versio

The Pan-STARRS1 Photometric System

The Pan-STARRS1 survey is collecting multi-epoch, multi-color observations of the sky north of declination -30 deg to unprecedented depths. These data are being photometrically and astrometrically calibrated and will serve as a reference for many other purposes. In this paper we present our determination of the Pan-STARRS photometric system: gp1, rp1, ip1, zp1, yp1, and wp1. The Pan-STARRS photometric system is fundamentally based on the HST Calspec spectrophotometric observations, which in turn are fundamentally based on models of white dwarf atmospheres. We define the Pan-STARRS magnitude system, and describe in detail our measurement of the system passbands, including both the instrumental sensitivity and atmospheric transmission functions. Byproducts, including transformations to other photometric systems, galactic extinction, and stellar locus are also provided. We close with a discussion of remaining systematic errors.Comment: 39 pages, 9 figures, machine readable table of bandpasses, accepted for publication in Ap

Plasma proteome analysis of patients with type 1 diabetes with diabetic nephropathy

<p>Abstract</p> <p>Background</p> <p>As part of a clinical proteomics program focused on diabetes and its complications we are looking for new and better protein biomarkers for diabetic nephropathy. The search for new and better biomarkers for diabetic nephropathy has, with a few exceptions, previously focused on either hypothesis-driven studies or urinary based investigations. To date only two studies have investigated the proteome of blood in search for new biomarkers, and these studies were conducted in sera from patients with type 2 diabetes. This is the first reported in depth proteomic study where plasma from type 1 diabetic patients was investigated with the goal of finding improved candidate biomarkers to predict diabetic nephropathy. In order to reach lower concentration proteins in plasma a pre-fractionation step, either hexapeptide bead-based libraries or anion exchange chromatography, was performed prior to surface enhanced laser desorption/ionization time-of-flight mass spectrometry analysis.</p> <p>Results</p> <p>Proteomic analysis of plasma from a cross-sectional cohort of 123 type 1 diabetic patients previously diagnosed as normoalbuminuric, microalbuminuric or macroalbuminuric, gave rise to 290 peaks clusters of which 16 were selected as the most promising biomarker candidates based on statistical performance, including independent component analysis. Four of the peaks that were discovered have been identified as transthyretin, apolipoprotein A1, apolipoprotein C1 and cystatin C. Several yet unidentified proteins discovered by this novel approach appear to have more potential as biomarkers for diabetic nephropathy.</p> <p>Conclusion</p> <p>These results demonstrate the capacity of proteomic analysis of plasma, by confirming the presence of known biomarkers as well as revealing new biomarkers for diabetic nephropathy in plasma in type 1 diabetic patients.</p

Logarithmic observables in critical percolation

Although it has long been known that the proper quantum field theory description of critical percolation involves a logarithmic conformal field theory (LCFT), no direct consequence of this has been observed so far. Representing critical bond percolation as the Q = 1 limit of the Q-state Potts model, and analyzing the underlying S_Q symmetry of the Potts spins, we identify a class of simple observables whose two-point functions scale logarithmically for Q = 1. The logarithm originates from the mixing of the energy operator with a logarithmic partner that we identify as the field that creates two propagating clusters. In d=2 dimensions this agrees with general LCFT results, and in particular the universal prefactor of the logarithm can be computed exactly. We confirm its numerical value by extensive Monte-Carlo simulations.Comment: 11 pages, 2 figures. V2: as publishe

A tree-decomposed transfer matrix for computing exact Potts model partition functions for arbitrary graphs, with applications to planar graph colourings

Combining tree decomposition and transfer matrix techniques provides a very general algorithm for computing exact partition functions of statistical models defined on arbitrary graphs. The algorithm is particularly efficient in the case of planar graphs. We illustrate it by computing the Potts model partition functions and chromatic polynomials (the number of proper vertex colourings using Q colours) for large samples of random planar graphs with up to N=100 vertices. In the latter case, our algorithm yields a sub-exponential average running time of ~ exp(1.516 sqrt(N)), a substantial improvement over the exponential running time ~ exp(0.245 N) provided by the hitherto best known algorithm. We study the statistics of chromatic roots of random planar graphs in some detail, comparing the findings with results for finite pieces of a regular lattice.Comment: 5 pages, 3 figures. Version 2 has been substantially expanded. Version 3 shows that the worst-case running time is sub-exponential in the number of vertice