A Phase Space Approach to Gravitational Enropy

We examine the definition S = ln Omega as a candidate "gravitational entropy" function. We calculate its behavior for gravitationl and density perturbations in closed, open and flat cosmologies and find that in all cases it increases monotonically. Using the formalism to calculate the gravitational entropy produced during inflation gives the canonical answer. We compare the behavior of S with the behavior of the square of the Weyl tensor. Applying the formalism to black holes has proven more problematical.Comment: Talk delivered at South African Relativistic Cosmology Symposium, Feb 1999. Some new results over Rothman and Anninos 97. To appear in GRG, 17 page

A novel mode of capping protein-regulation by Twinfilin

Cellular actin assembly is controlled at the barbed ends of actin filaments, where capping protein (CP) limits polymerization. Twinfilin is a conserved in vivo binding partner of CP, yet the significance of this interaction has remained a mystery. Here, we discover that the C-terminal tail of Twinfilin harbors a CP-interacting (CPI) motif, identifying it as a novel CPI-motif protein. Twinfilin and the CPI-motif protein CARMIL have overlapping binding sites on CP. Further, Twinfilin binds competitively with CARMIL to CP, protecting CP from barbed-end displacement by CARMIL. Twinfilin also accelerates dissociation of the CP inhibitor V-1, restoring CP to an active capping state. Knockdowns of Twinfilin and CP each cause similar defects in cell morphology, and elevated Twinfilin expression rescues defects caused by CARMIL hyperactivity. Together, these observations define Twinfilin as the first \u27pro-capping\u27 ligand of CP and lead us to propose important revisions to our understanding of the CP regulatory cycle

EB1 directly regulates APC-mediated actin nucleation

EB1 was discovered 25 years ago as a binding partner of the tumor suppressor Adenomatous Polyposis Coli (APC) [1]; however, the significance of EB1-APC interactions has remained poorly understood. EB1 functions at the center of a network of microtubule end-tracking proteins (+TIPs) [2–5], and APC binding to EB1 promotes EB1 association with microtubule ends and microtubule stabilization [6, 7]. Whether or not EB1 interactions govern functions of APC beyond microtubule regulation has not been explored. The C-terminal Basic domain of APC (APC-B) directly nucleates actin assembly, and this activity is required in vivo for directed cell migration and for maintaining normal levels of F-actin [8–10]. Here, we show that EB1 binds APC-B and inhibits its actin nucleation function by blocking actin monomer recruitment. Consistent with these biochemical observations, knocking down EB1 increases F-actin levels in cells, and this can be rescued by disrupting APC-mediated actin nucleation. Conversely, overexpressing EB1 decreases F-actin levels and impairs directed cell migration, without altering microtubule organization and independent of its direct binding interactions with microtubules. Overall, our results define a new function for EB1 in negatively regulating APC-mediated actin assembly. Combining these findings with other recent studies showing that APC interactions regulate EB1-dependent effects on microtubule dynamics [7], we propose that EB1-APC interactions govern bidirectional cytoskeletal crosstalk by coordinating microtubule and actin dynamics

Are braneworlds born isotropic?

It has recently been suggested that an isotropic singularity may be a generic feature of brane cosmologies, even in the inhomogeneous case. Using the covariant and gauge-invariant approach we present a detailed analysis of linear perturbations of the isotropic model ${\cal F}_b$ which is a past attractor in the phase space of homogeneous Bianchi models on the brane. We find that for matter with an equation of state parameter $\gamma > 1$, the dimensionless variables representing generic anisotropic and inhomogeneous perturbations decay as $t\to 0$, showing that the model ${\cal F}_b$ is asymptotically stable in the past. We conclude that brane universes are born with isotropy naturally built-in, contrary to standard cosmology. The observed large-scale homogeneity and isotropy of the universe can therefore be explained as a consequence of the initial conditions if the brane-world paradigm represents a description of the very early universe.Comment: Changed to match published versio

Two-dimensional hydrodynamic lattice-gas simulations of binary immiscible and ternary amphiphilic fluid flow through porous media

The behaviour of two dimensional binary and ternary amphiphilic fluids under flow conditions is investigated using a hydrodynamic lattice gas model. After the validation of the model in simple cases (Poiseuille flow, Darcy's law for single component fluids), attention is focussed on the properties of binary immiscible fluids in porous media. An extension of Darcy's law which explicitly admits a viscous coupling between the fluids is verified, and evidence of capillary effects are described. The influence of a third component, namely surfactant, is studied in the same context. Invasion simulations have also been performed. The effect of the applied force on the invasion process is reported. As the forcing level increases, the invasion process becomes faster and the residual oil saturation decreases. The introduction of surfactant in the invading phase during imbibition produces new phenomena, including emulsification and micellisation. At very low fluid forcing levels, this leads to the production of a low-resistance gel, which then slows down the progress of the invading fluid. At long times (beyond the water percolation threshold), the concentration of remaining oil within the porous medium is lowered by the action of surfactant, thus enhancing oil recovery. On the other hand, the introduction of surfactant in the invading phase during drainage simulations slows down the invasion process -- the invading fluid takes a more tortuous path to invade the porous medium -- and reduces the oil recovery (the residual oil saturation increases).Comment: 48 pages, 26 figures. Phys. Rev. E (in press

GMF Severs Actin-Arp2/3 Complex Branch Junctions by a Cofilin-like Mechanism

SummaryBackgroundBranched actin filament networks driving cell motility, endocytosis, and intracellular transport are assembled in seconds by the Arp2/3 complex and must be equally rapidly debranched and turned over. One of the only factors known to promote debranching of actin networks is the yeast homolog of glia maturation factor (GMF), which is structurally related to the actin filament-severing protein cofilin. However, the identity of the molecular mechanism underlying debranching and whether this activity extends to mammalian GMF have remained open questions.ResultsUsing scanning mutagenesis and total internal reflection fluorescence microscopy, we show that GMF depends on two separate surfaces for debranching. One is analogous to the G-actin and F-actin binding site on cofilin, but we show using fluorescence anisotropy and chemical crosslinking that it instead interacts with actin-related proteins in the Arp2/3 complex. The other is analogous to a second F-actin binding site on cofilin, which in GMF appears to contact the first actin subunit in the daughter filament. We further show that GMF binds to the Arp2/3 complex with low nanomolar affinity and promotes the open conformation. Finally, we show that this debranching activity and mechanism are conserved for mammalian GMF.ConclusionsGMF debranches filaments by a mechanism related to cofilin-mediated severing, but in which GMF has evolved to target molecular junctions between actin-related proteins in the Arp2/3 complex and actin subunits in the daughter filament of the branch. This activity and mechanism are conserved in GMF homologs from evolutionarily distant species

Characterization of extrasolar terrestrial planets from diurnal photometric variability

The detection of massive planets orbiting nearby stars has become almost routine, but current techniques are as yet unable to detect terrestrial planets with masses comparable to the Earth's. Future space-based observatories to detect Earth-like planets are being planned. Terrestrial planets orbiting in the habitable zones of stars-where planetary surface conditions are compatible with the presence of liquid water-are of enormous interest because they might have global environments similar to Earth's and even harbor life. The light scattered by such a planet will vary in intensity and colour as the planet rotates; the resulting light curve will contain information about the planet's properties. Here we report a model that predicts features that should be discernible in light curves obtained by low-precision photometry. For extrasolar planets similar to Earth we expect daily flux variations up to hundreds of percent, depending sensitively on ice and cloud cover. Qualitative changes in surface or climate generate significant changes in the predicted light curves. This work suggests that the meteorological variability and the rotation period of an Earth-like planet could be derived from photometric observations. Other properties such as the composition of the surface (e.g., ocean versus land fraction), climate indicators (for example ice and cloud cover), and perhaps even signatures of Earth-like plant life could be constrained or possibly, with further study, even uniquely determined.Comment: Published in Nature. 9 pages including 3 figure

Linearization of homogeneous, nearly-isotropic cosmological models

Homogeneous, nearly-isotropic Bianchi cosmological models are considered. Their time evolution is expressed as a complete set of non-interacting linear modes on top of a Friedmann-Robertson-Walker background model. This connects the extensive literature on Bianchi models with the more commonly-adopted perturbation approach to general relativistic cosmological evolution. Expressions for the relevant metric perturbations in familiar coordinate systems can be extracted straightforwardly. Amongst other possibilities, this allows for future analysis of anisotropic matter sources in a more general geometry than usually attempted. We discuss the geometric mechanisms by which maximal symmetry is broken in the context of these models, shedding light on the origin of different Bianchi types. When all relevant length-scales are super-horizon, the simplest Bianchi I models emerge (in which anisotropic quantities appear parallel transported). Finally we highlight the existence of arbitrarily long near-isotropic epochs in models of general Bianchi type (including those without an exact isotropic limit).Comment: 31 pages, 2 figures. Submitted to CQ

Salmonella Phage ST64B Encodes a Member of the SseK/NleB Effector Family

Salmonella enterica is a species of bacteria that is a major cause of enteritis across the globe, while certain serovars cause typhoid, a more serious disease associated with a significant mortality rate. Type III secreted effectors are major contributors to the pathogenesis of Salmonella infections. Genes encoding effectors are acquired via horizontal gene transfer, and a subset are encoded within active phage lysogens. Because the acquisition of effectors is in flux, the complement of effectors possessed by various Salmonella strains frequently differs. By comparing the genome sequences of S. enterica serovar Typhimurium strain SL1344 with LT2, we identified a gene with significant similarity to SseK/NleB type III secreted effector proteins within a phage ST64B lysogen that is absent from LT2. We have named this gene sseK3. SseK3 was co-regulated with the SPI-2 type III secretion system in vitro and inside host cells, and was also injected into infected host cells. While no role for SseK3 in virulence could be identified, a role for the other family members in murine typhoid was found. SseK3 and other phage-encoded effectors were found to have a significant but sparse distribution in the available Salmonella genome sequences, indicating the potential for more uncharacterised effectors to be present in less studied serovars. These phage-encoded effectors may be principle subjects of contemporary selective processes shaping Salmonella-host interactions