Investigating the DNA-Binding Site for VirB, a Key Transcriptional Regulator of Shigella Virulence Genes, Using an In Vivo Binding Tool

The transcriptional anti-silencing and DNA-binding protein, VirB, is essential for the virulence of Shigella species and, yet, sequences required for VirB-DNA binding are poorly understood. While a 7-8 bp VirB-binding site has been proposed, it was derived from studies at a single VirB-dependent promoter, icsB. Our previous in vivo studies at a different VirB-dependent promoter, icsP, found that the proposed VirB-binding site was insufficient for regulation. Instead, the required site was found to be organized as a near-perfect inverted repeat separated by a single nucleotide spacer. Thus, the proposed 7-8 bp VirB-binding site needed to be re-evaluated. Here, we engineer and validate a molecular tool to capture protein-DNA binding interactions in vivo. Our data show that a sequence organized as a near-perfect inverted repeat is required for VirB-DNA binding interactions in vivo at both the icsB and icsP promoters. Furthermore, the previously proposed VirB-binding site and multiple sites found as a result of its description (i.e., sites located at the virB, virF, spa15, and virA promoters) are not sufficient for VirB to bind in vivo using this tool. The implications of these findings are discussed

Advantages of a Modular Mars Surface Habitat Approach

Early crewed Mars mission concepts developed by the National Aeronautics and Space Administration (NASA) assumed a single, large habitat would house six crew members for a 500-day Mars surface stay. At the end of the first mission, all surface equipment, including the habitat, -would be abandoned and the process would be repeated at a different Martian landing site. This work was documented in a series of NASA publications culminating with the Mars Design Reference Mission 5.0 (NASA-SP-2009-566). The Evolvable Mars Campaign (EMC) explored whether re-using surface equipment at a single landing site could be more affordable than the Apollo-style explore-abandon-repeat mission cadence. Initial EMC assumptions preserved the single, monolithic habitat, the only difference being a new requirement to reuse the surface habitat for multiple expedition crews. A trade study comparing a single large habitat versus smaller, modular habitats leaned towards the monolithic approach as more mass-efficient. More recent work has focused on the operational aspects of building up Mars surface infrastructure over multiple missions, and has identified compelling advantages of the modular approach that should be considered before making a final decision. This paper explores Mars surface mission operational concepts and integrated system analysis, and presents an argument for the modular habitat approach

Penguins leaving the pole: bound-state effects in B decaying to K* + photon

Applying perturbative QCD methods recently seen to give a good description of the two body hadronic decays of the B meson, we address the question of bound-state effects on the decay B into K* + gamma. Consistent with most analyses, we demonstrate that gluonic penguins, with photonic bremsstrahlung off a quark, change the decay rate by only a few percent. However, explicit off-shell b-quark effects normally discarded are found to be large in amplitude, although in the standard model accidents of phase minimize the effect on the rate. Using an asymptotic distribution amplitude for the K* and just the standard model, we can obtain a branching ratio of a few times 10^{-5}, consistent with the observed rate.Comment: 12 pages. U. of MD PP \#94-129; DOE/ER/40762-033; WM-94-104. LaTeX, One figure, available by fax or pos

Variational self-consistent theory for trapped Bose gases at finite temperature

We apply the time-dependent variational principle of Balian-V\'en\'eroni to a system of self-interacting trapped bosons at finite temperature. The method leads to a set of coupled non-linear time dependent equations for the condensate density, the thermal cloud and the anomalous density. We solve numerically these equations in the static case for a harmonic trap. We analyze the various densities as functions of the radial distance and the temperature. We find an overall good qualitative agreement with recent experiments as well as with the results of many theoretical groups. We also discuss the behavior of the anomalous density at low temperatures owing to its importance to account for many-body effects.Comment: 8 pages, 8 figure

Theory of output coupling for trapped fermionic atoms

We develop a dynamic theory of output coupling, for fermionic atoms initially confined in a magnetic trap. We consider an exactly soluble one-dimensional model, with a spatially localized delta-type coupling between the atoms in the trap and a continuum of free-particle external modes. Two important special cases are considered for the confinement potential: the infinite box and the harmonic oscillator. We establish that in both cases a bound state of the coupled system appears for any value of the coupling constant, implying that the trap population does not vanish in the infinite-time limit. For weak coupling, the energy spectrum of the outgoing beam exhibits peaks corresponding to the initially occupied energy levels in the trap; the height of these peaks increases with the energy. As the coupling gets stronger, the energy spectrum is displaced towards dressed energies of the fermions in the trap. The corresponding dressed states result from the coupling between the unperturbed fermionic states in the trap, mediated by the coupling between these states and the continuum. In the strong-coupling limit, there is a reinforcement of the lowest-energy dressed mode, which contributes to the energy spectrum of the outgoing beam more strongly than the other modes. This effect is especially pronounced for the one-dimensional box, which indicates that the efficiency of the mode-reinforcement mechanism depends on the steepness of the confinement potential. In this case, a quasi-monochromatic anti-bunched atomic beam is obtained. Results for a bosonic sample are also shown for comparison.Comment: 16 pages, 7 figures, added discussion on time-dependent spectral distribution and corresponding figur