Master of Science

thesisThe histone-like nucleoid-structuring protein (H-NS) is well known as a global regulator of transcription. A number of studies have suggested that H-NS also positively influences the function of the flagellar motor, but the details of its motility-regulating action remain unclear. In an effort to characterize the actions of H-NS in the flagellar motor, we sought to test the effects of specific mutations in H-NS that are predicted to alter its state of multimerization. As a foundation for this work, we examined the effects of H-NS expression in strains that expressed the flagellar regulatory proteins FlhDC at various levels, from various plasmids. The results gave indications that certain plasmids previously used to provide FlhDC constitutively did not, in fact, express the proteins at levels sufficient to stimulate flagellar assembly. This complicates the interpretation of previous work, because the cells retained the chromosomal copies of the flhDC genes whose expression is known to be influenced by H-NS. Thus, effects in the previous experiments may have been the result of up-regulation of chromosomal flhDC rather than direct actions at the flagellar motor. To overcome this problem, I constructed new strains in which the chromosomal copies of flhDC were deleted, and revisited the question of HNS action in the motor. For these experiments, the flhDC genes were expressed from a regulatable plasmid that had been verified by complementation of the flhDC deletion strain, and H-NS was expressed from a second regulatable plasmid. The results indicate that H-NS contributes to flagellar motility in ways other than its stimulatory effect flhDC iv expression, as was suggested on the basis of the previous work. Details of its action are different from those reported previously. An analysis of mutants altered at interfaces needed for H-NS multimerization gives evidence that H-NS must act as a dimer or larger multimer, in both its gene-regulatory and motility regulating

Non-Abelian statistics in the interference noise of the Moore-Read quantum Hall state

We propose noise oscillation measurements in a double point contact, accessible with current technology, to seek for a signature of the non-abelian nature of the \nu=5/2 quantum Hall state. Calculating the voltage and temperature dependence of the current and noise oscillations, we predict the non-abelian nature to materialize through a multiplicity of the possible outcomes: two qualitatively different frequency dependences of the nonzero interference noise. Comparison between our predictions for the Moore-Read state with experiments on \nu=5/2 will serve as a much needed test for the nature of the \nu=5/2 quantum Hall state.Comment: 4 pages, 4 figures v2: typo's corrected, discussions clarified, references adde

Effect of Rossby and Alfv\'{e}n waves on the dynamics of the tachocline

To understand magnetic diffusion, momentum transport, and mixing in the interior of the sun, we consider an idealized model of the tachocline, namely magnetohydrodynamics (MHD) turbulence on a $\beta$ plane subject to a large scale shear (provided by the latitudinal differential rotation). This model enables us to self-consistently derive the influence of shear, Rossby and Alfv\'{e}n waves on the transport properties of turbulence. In the strong magnetic field regime, we find that the turbulent viscosity and diffusivity are reduced by magnetic fields only, similarly to the two-dimensional MHD case (without Rossby waves). In the weak magnetic field regime, we find a crossover scale ($L\_R$) from a Alfv\'{e}n dominated regime (on small scales) to a Rossby dominated regime (on large scales). For parameter values typical of the tachocline, $L\_R$ is larger that the solar radius so that Rossby waves are unlikely to play an important role in the transport of magnetic field and angular momentum. This is mainly due to the enhancement of magnetic back-reaction by shearing which efficiently generates small scales, thus strong currents

NOX Inhibitors - A Promising Avenue for Ischemic Stroke.

NADPH-oxidase (NOX) mediated superoxide originally found on leukocytes, but now recognized in several types of cells in the brain. It has been shown to play an important role in the progression of stroke and related cerebrovascular disease. NOX is a multisubunit complex consisting of 2 membrane-associated and 4 cytosolic subunits. NOX activation occurs when cytosolic subunits translocate to the membrane, leading to transport electrons to oxygen, thus producing superoxide. Superoxide produced by NOX is thought to function in long-term potentiation and intercellular signaling, but excessive production is damaging and has been implicated to play an important role in the progression of ischemic brain. Thus, inhibition of NOX activity may prove to be a promising treatment for ischemic brain as well as an adjunctive agent to prevent its secondary complications. There is mounting evidence that NOX inhibition in the ischemic brain is neuroprotective, and targeting NOX in circulating immune cells will also improve outcome. This review will focus on therapeutic effects of NOX assembly inhibitors in brain ischemia and stroke. However, the lack of specificity and toxicities of existing inhibitors are clear hurdles that will need to be overcome before this class of compounds could be translated clinically

Theory of stripes in quasi two dimensional rare-earth tritellurides

Even though the rare-earth tritellurides are tetragonal materials with a quasi two dimensional (2D) band structure, they have a "hidden" 1D character. The resultant near-perfect nesting of the Fermi surface leads to the formation of a charge density wave (CDW) state. We show that for this band structure, there are two possible ordered phases: A bidirectional "checkerboard" state would occur if the CDW transition temperature were sufficiently low, whereas a unidirectional "striped" state, consistent with what is observed in experiment, is favored when the transition temperature is higher. This result may also give some insight into why, in more strongly correlated systems, such as the cuprates and nickelates, the observed charge ordered states are generally stripes as opposed to checkerboards.Comment: Added contents and references, changed title and figures. Accepted to PR

Draft Genome Sequence of Fructophilic Lactobacillus florum.

Herein we report the first genome sequence for Lactobacillus florum. L. florum 2F was isolated from Valencia orange leaves and is fructophilic, like other strains of this species. The draft genome of L. florum 2F contains 1,261,842 bp with a G+C content of 41.5% in 46 contigs (≥500 bp)

Causal Information Rate

Information processing is common in complex systems, and information geometric theory provides a useful tool to elucidate the characteristics of non-equilibrium processes, such as rare, extreme events, from the perspective of geometry. In particular, their time-evolutions can be viewed by the rate (information rate) at which new information is revealed (a new statistical state is accessed). In this paper, we extend this concept and develop a new information-geometric measure of causality by calculating the effect of one variable on the information rate of the other variable. We apply the proposed causal information rate to the Kramers equation and compare it with the entropy-based causality measure (information flow). Overall, the causal information rate is a sensitive method for identifying causal relations

Information Length Analysis of Linear Autonomous Stochastic Processes

When studying the behaviour of complex dynamical systems, a statistical formulation can provide useful insights. In particular, information geometry is a promising tool for this purpose. In this paper, we investigate the information length for n-dimensional linear autonomous stochastic processes, providing a basic theoretical framework that can be applied to a large set of problems in engineering and physics. A specific application is made to a harmonically bound particle system with the natural oscillation frequency ω, subject to a damping γ and a Gaussian white-noise. We explore how the information length depends on ω and γ, elucidating the role of critical damping γ=2ω in information geometry. Furthermore, in the long time limit, we show that the information length reflects the linear geometry associated with the Gaussian statistics in a linear stochastic process