Towards molecular systems biology of gene transcription and regulation

Ten years after the determination of the RNA polymerase 11 structure, the basic mechanism of mRNA synthesis during gene transcription is known. In the future, the initiation and regulation of transcription must be studied with a combination of structural biology, biochemistry, functional genomics, and computational methods. In this article, the efforts of our laboratory to move from an integrated structural biology of gene transcription towards molecular systems biology of gene regulation are reviewed

Life after Catch and Release

Since 1988 regulations have required U.S. longline fishermen to release all Atlantic white marlin, Tetrapturus albidus. By the late 1990’s, approximately 99% of Atlantic white marlin caught by U.S. recreational fishermen were released. Recent studies using PSAT technology indicate that not all released fish survive and that a minor change in hook type, 0–5° offset circle hooks rather than straight-shank “J” hooks, may have a profound effect on post release mortality. Beginning in 2004, sea turtle mitigation measures have required U.S. longline fishermen to use circle hooks. Estimates of total catch, releases, and post release mortality of Atlantic white marlin caught by U.S. recreational fishermen were made in order to evaluate the potential reduction in mortality that may be realized by requiring the use of circle hooks rather than straight-shank “J” hooks by U.S. recreational fishermen. These estimates were compared to estimates of Atlantic white marlin caught by the U.S. longline fisher

The Future of Wireless Spam

Though US cellular networks currently lack the capacity for widespread distribution of unsolicited wireless advertising (wireless spam), these advertisements are already well known in Japan and Europe, where they have proven to be a significant burden on cellular users. This iBrief examines the recently ratified legislation in Japan and Asia that have attempted to stop the glut of wireless advertisements, as a foreshadowing of the problems and questions that will soon have to be addressed in the United States

Own up! Does anyone out there have a decent theory of ownership?

In this short paper, I attempt to find what theoretical grounds might support the term ownership as used in aid relations and critically to discuss these grounds. Three possible sources for thinking through the concept are: property rights, relationships made or sustained through gifts, and principal-agent theory. After setting the concept of ownership in development aid within the context of its origins, the paper explores the relevance and implications of seeing ownership as the effect of a gift, and then, in more detail, explores the way in which principal-agent theory has been applied to the analysis of ownership. Where this has been done, a particular controversy emerges around the relationship between ownership and conditionality: some regard these notions as fully compatible while others highlight the tension between them

Interaction dependent temperature effects in Bose-Fermi mixtures in optical lattices

We present a quantitative finite temperature analysis of a recent experiment with Bose-Fermi mixtures in optical lattices, in which the dependence of the coherence of bosons on the inter-species interaction was analyzed. Our theory reproduces the characteristics of this dependence and suggests that intrinsic temperature effects play an important role in these systems. Namely, under the assumption that the ramping up of the optical lattice is an isentropic process, adiabatic temperature changes of the mixture occur that depend on the interaction between bosons and fermions. Matching the entropy of two regimes---no lattice on the one hand and deep lattices on the other---allows us to compute the temperature in the lattice and the visibility of the quasi-momentum distribution of the bosonic atoms, which we compare to the experiment. We briefly comment on the remaining discrepancy between theory and experiment, speculating that it may in part be attributed to the dependence of the Bose-Fermi scattering length on the confinement of the atoms.Comment: 6 pages, 3 figure

Thermalization under randomized local Hamiltonians

Recently, there have been significant new insights concerning conditions under which closed systems equilibrate locally. The question if subsystems thermalize---if the equilibrium state is independent of the initial state---is however much harder to answer in general. Here, we consider a setting in which thermalization can be addressed: A quantum quench under a Hamiltonian whose spectrum is fixed and basis is drawn from the Haar measure. If the Fourier transform of the spectral density is small, almost all bases lead to local equilibration to the thermal state with infinite temperature. This allows us to show that, under almost all Hamiltonians that are unitarily equivalent to a local Hamiltonian, it takes an algebraically small time for subsystems to thermalize.Comment: published versio