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Physics News Update
Number 813, February 27, 2006 by Phil Schewe, Ben Stein, and Davide Castelvecchi

Spontaneous Symmetry Breaking in Women's Genes

A spontaneous aggregation of proteins randomly determines which of the two X chromosomes in a woman's cell will remain active, and which one will stay silenced, according to a new physical model.

In all placental mammals, the females of the species have two versions of the X chromosomes while males have just one X, plus a Y chromosome. To avoid overexpression of X-chromosome genes, female cells must virtually shut down one of their X's. X chromosomes are able to wrap themselves up in a goo of RNA -- produced by one of their genes, called XIST -- inhibiting the expression of all of their genes.

But until recently, it was not known how a female's cells know that they have two X's, how they choose which one to shut down, or how they keep exactly one active. Experiments in mice -- the results presumably apply to other mammals -- have shown that during early development, each embryo cell has a 50-50 chance of shutting down one X or the other.

Recently it has been proposed that an X remains active when certain proteins aggregate at a specific spot on the chromosome, shutting down its "suicide gene" XIST. But it remained unclear why proteins floating in the nucleus would aggregate around one of the chromosome, but not around the other -- an example of what physicists call spontaneous symmetry breaking.

Now an upcoming paper in Physical Review Letters describes a statistical-mechanics model for the proteins' aggregation that would explain this phenomenon. The model relies on a key discovery published last year, namely that in females the two X chromosomes line up next to each other right at the time when one of them is due to be silenced. For a critical value of the protein's binding energies, the authors show, there is a high probability that exactly one aggregate will form in the vicinity of the two chromosomes. The aggregate will quickly bind to one of the X's, shutting down its XIST gene and thus preventing the chromosome from silencing itself.

The model also explains how cells would "count" their X's. In males, the protein complex would only have one chromosome to bind to, so it would save the single X from self-silencing. On non-sexual chromosomes, a similar mechanism could also determine which of two versions of certain genes is expressed and which one is silenced.

Nicodemi and Prisco, to appear in Physical Review Letters
Mario Nicodemi
University of Naples "Federico II"
Mario.Nicodemi@na.infn.it

Also see:
Na Xu et al., Science, 24 February 2006
Bacher et al., Nature Cell Biology, March 2006
Donohoe et al., Molecular Cell, January 12, 2007

String Theory Explains RHIC Jet Suppression

String theory argues that all matter is composed of string-like shreds in a 10-dimensional hyperspace assembled in various forms. It has won acclaim from many who appreciate the theory's elegant mathematics and ambition to unite quantum mechanics and general relativity, and skepticism from others who cite the theory's lack of a practical track record. String theory, the doubters say, makes no testable predictions.

But this isn't exactly true. Indeed, the theory has not yet been experimentally vindicated in the realm of quantum gravity, but has been put into play in the realm of high-energy ion collisions, the kind carried out at Brookhaven's Relativistic Heavy Ion Collider (RHIC). A few years ago string practitioners attempted to establish a relationship between the 10-dimensional string world and the 4-dimensional (3 spatial dimensions plus time) world in which we observe interactions among quark-filled particles like protons (for background, see Physics Today, May 2005).

This duality between string theory and the theory of the strong nuclear force, quantum chromodynamics (QCD), was recently used to interpret puzzling early results from RHIC, namely the suppression of energetic quark jets that should have emerged from the fireball formed when two heavy nuclei (such as gold) collide head on. The thinking was that perhaps the plasma of quarks and gluons (quarks bursting free from their customary proton and meson groupings) wasn't a gas of weakly interacting particles (as was originally thought) but a gas of strongly interacting particles, so strong that any energetic quarks that might have escaped the fireball (initiating a secondary avalanche, or jet, or quarks) would quickly be slowed and stripped of energy on its way through the tumultuous quark-gluon plasma (QGP) environment.

Two new papers by Hong Liu and Krishna Rajagopal of (MIT) and Urs Wiedemann (CERN) address this problem. The first paper calculates a specific quark-suppression parameter (namely, how much the quarks, each attached to a string dangling "downward" into a fifth dimension, are pushed around as they traverse the quark-gluon plasma) that agrees closely with the experimentally observed value.

Rajagopal (krishna@ctp.mit.edu, 617-253-6202) says that in the second paper, the same authors make a specific testable prediction using string theory that bears not just on missing jets of energetic light quarks (up, down, and strange quarks), but on the melting or dissociation temperatures of bound states of heavy quarks (charm-anticharm or bottom-antibottom pairs) moving through the quark-gluon plasma with sufficiently high velocity, as will be produced in future experiments at RHIC and the Large Hadron Collider (LHC) under construction at CERN.

Physical Review Letters, 3 November 2006 and upcoming article
Contact Krishna Rajagopal
Massachusetts Institute of Technology
krishna@ctp.mit.edu
Tel: 617-253-6202

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