Semiconservative quasispecies equations for polysomic genomes: The general case

This paper develops a formulation of the quasispecies equations appropriate for polysomic, semiconservatively replicating genomes. This paper is an extension of previous work on the subject, which considered the case of haploid genomes. Here, we develop a more general formulation of the quasispecies equations that is applicable to diploid and even polyploid genomes. Interestingly, with an appropriate classification of population fractions, we obtain a system of equations that is formally identical to the haploid case. As with the work for haploid genomes, we consider both random and immortal DNA strand chromosome segregation mechanisms. However, in contrast to the haploid case, we have found that an analytical solution for the mean fitness is considerably more difficult to obtain for the polyploid case. Accordingly, whereas for the haploid case we obtained expressions for the mean fitness for the case of an analogue of the single-fitness-peak landscape for arbitrary lesion repair probabilities (thereby allowing for non-complementary genomes), here we solve for the mean fitness for the restricted case of perfect lesion repair.Comment: 16 pages, 3 figure

A fundamental test of the Higgs Yukawa coupling at RHIC in A+A collisions

Searches for the intermediate boson, $W^{\pm}$, the heavy quantum of the Weak Interaction, via its semi-leptonic decay, $W\to e +\nu$, in the 1970's instead discovered unexpectedly large hadron production at high $p_T$, notably $\pi^0$, which provided a huge background of $e^{\pm}$ from internal and external conversions. Methods developed at the CERN ISR which led to the discovery of direct-single-$e^{\pm}$ in 1974, later determined to be from the semi-leptonic decay of charm which had not yet been discovered, were used by PHENIX at RHIC to make precision measurements of heavy quark production in p-p and Au+Au collisions, leading to the puzzle of apparent equal suppression of light and heavy quarks in the QGP. If the Higgs mechanism gives mass to gauge bosons but not to fermions, then a proposal that all 6 quarks are nearly massless in a QGP, which would resolve the puzzle, can not be excluded. This proposal can be tested with future measurements of heavy quark correlations in A+A collisionsComment: 12 pages, 16 figures, 26th Winter Workshop on Nuclear Dynamics, Ocho Rios, Jamaica WI, January 2-9, 2010. Corrected citation of 1974 direct single lepton discover

Debye screening in strongly coupled N=4 supersymmetric Yang-Mills plasma

Using the AdS/CFT correspondence, we examine the behavior of correlators of Polyakov loops and other operators in N=4 supersymmetric Yang-Mills theory at non-zero temperature. The implications for Debye screening in this strongly coupled non-Abelian plasma, and comparisons with available results for thermal QCD, are discussed.Comment: 21 pages, 5 figures, significantly expanded discussion of Polyakov loop correlator and static quark-antiquark potentia

Asexual and sexual replication in sporulating organisms

This paper develops models describing asexual and sexual replication in sporulating organisms. Replication via sporulation is the replication strategy for all multicellular life, and may even be observed in unicellular life (such as with budding yeast). We consider diploid populations replicating via one of two possible sporulation mechanisms: (1) Asexual sporulation, whereby adult organisms produce single-celled diploid spores that grow into adults themselves. (2) Sexual sporulation, whereby adult organisms produce single-celled diploid spores that divide into haploid gametes. The haploid gametes enter a haploid "pool", where they may recombine with other haploids to form a diploid spore that then grows into an adult. We consider a haploid fusion rate given by second-order reaction kinetics. We work with a simplified model where the diploid genome consists of only two chromosomes, each of which may be rendered defective with a single point mutation of the wild-type. We find that the asexual strategy is favored when the rate of spore production is high compared to the characteristic growth rate from a spore to a reproducing adult. Conversely, the sexual strategy is favored when the rate of spore production is low compared to the characteristic growth rate from a spore to a reproducing adult. As the characteristic growth time increases, or as the population density increases, the critical ratio of spore production rate to organism growth rate at which the asexual strategy overtakes the sexual one is pushed to higher values. Therefore, the results of this model suggest that, for complex multicellular organisms, sexual replication is favored at high population densities, and low growth and sporulation rates.Comment: 8 pages, 5 figures, to be submitted to Journal of Theoretical Biology, figures not included in this submissio

Transverse momentum fluctuations and percolation of strings

The behaviour of the transverse momentum fluctuations with the centrality of the collision shown by the Relativistic Heavy Ion Collider data is naturally explained by the clustering of color sources. In this framework, elementary color sources --strings-- overlap forming clusters, so the number of effective sources is modified. These clusters decay into particles with mean transverse momentum that depends on the number of elementary sources that conform each cluster, and the area occupied by the cluster. The transverse momentum fluctuations in this approach correspond to the fluctuations of the transverse momentum of these clusters, and they behave essentially as the number of effective sources.Comment: 16 pages, RevTex, 4 postscript figures. Enhanced version. New figure

PHENIX Highlights

Recent highlights of measurements by the PHENIX experiment at RHIC are presented.Comment: 8 pages, 9 figures. Talk at Quark Matter 200

S-nitrosation of proteins relevant to Alzheimer's disease during early stages of neurodegeneration

Protein S-nitrosation (SNO-protein), the nitric oxide-mediated posttranslational modification of cysteine thiols, is an important regulatory mechanism of protein function in both physiological and pathological pathways. A key first step toward elucidating the mechanism by which S-nitrosation modulates a protein's function is identification of the targeted cysteine residues. Here, we present a strategy for the simultaneous identification of SNO-cysteine sites and their cognate proteins to profile the brain of the CK-p25-inducible mouse model of Alzheimer's disease-like neurodegeneration. The approach-SNOTRAP (SNO trapping by triaryl phosphine)-is a direct tagging strategy that uses phosphinebased chemical probes, allowing enrichment of SNO-peptides and their identification by liquid chromatography tandem mass spectrometry. SNOTRAP identified 313 endogenous SNO-sites in 251 proteins in the mouse brain, of which 135 SNO-proteins were detected only during neurodegeneration. S-nitrosation in the brain shows regional differences and becomes elevated during early stages of neurodegeneration in the CK-p25 mouse. The SNO-proteome during early neurodegeneration identified increased S-nitrosation of proteins important for synapse function, metabolism, and Alzheimer's disease pathology. In the latter case, proteins related to amyloid precursor protein processing and secretion are S-nitrosated, correlating with increased amyloid formation. Sequence analysis of SNO-cysteine sites identified potential linear motifs that are altered under pathological conditions. Collectively, SNOTRAP is a direct tagging tool for global elucidation of the SNO-proteome, providing functional insights of endogenous SNO proteins in the brain and its dysregulation during neurodegeneration.National Institutes of Health (U.S.) (Grant CA26731)National Institutes of Health (U.S.) (Grant R01 NS051874