Energetic Components of Cooperative Protein Folding

A new lattice protein model with a four-helix bundle ground state is analyzed by a parameter-space Monte Carlo histogram technique to evaluate the effects of an extensive variety of model potentials on folding thermodynamics. Cooperative helical formation and contact energies based on a 5-letter alphabet are found to be insufficient to satisfy calorimetric and other experimental criteria for two-state folding. Such proteinlike behaviors are predicted, however, by models with polypeptide-like local conformational restrictions and environment-dependent hydrogen bonding-like interactions.Comment: 11 pages, 4 postscripts figures, Phys. Rev. Lett. (in press

Mechanisms for Temperature Modulation of Feeding in Goldfish and Implications on Seasonal Changes in Feeding Behavior and Food Intake

In fish models, seasonal change in feeding is under the influence of water temperature. However, the effects of temperature on appetite control can vary among fish species and the mechanisms involved have not been fully characterized. Using goldfish (Carassius auratus) as a model, seasonal changes in feeding behavior and food intake were examined in cyprinid species. In our study, foraging activity and food consumption in goldfish were found to be reduced with positive correlation to the gradual drop in water temperature occurring during the transition from summer (28.4 ± 2.2°C) to winter (15.1 ± 2.6°C). In goldfish with a 4-week acclimation at 28°C, their foraging activity and food consumption were notably higher than their counterparts with similar acclimation at 15°C. When compared to the group at 28°C during summer, the attenuation in feeding responses at 15°C during the winter also occurred with parallel rises of leptin I and II mRNA levels in the liver. Meanwhile, a drop in orexin mRNA along with concurrent elevations of CCK, MCH, POMC, CART, and leptin receptor (LepR) transcript expression could be noted in brain areas involved in feeding control. In short-term study, goldfish acclimated at 28°C were exposed to 15°C for 24 h and the treatment was effective in reducing foraging activity and food intake. The opposite was true in reciprocal experiment with a rise in water temperature to 28°C for goldfish acclimated at 15°C. In parallel time-course study with lowering of water temperature from 28 to 15°C, short-term exposure (6–12 h) of goldfish to 15°C could also increase leptin I and II mRNA levels in the liver. Similar to our seasonality study, transcript level of orexin was reduced along with up-regulation of CCK, MCH, POMC, CART, and LepR gene expression in different brain areas. Our results, as a whole, suggest that temperature-driven regulation of leptin output from the liver in conjunction with parallel modulations of orexigenic/anorexigenic signals and leptin responsiveness in the brain may contribute to the seasonal changes of feeding behavior and food intake observed in goldfish

Ions in mixed dielectric solvents: density profiles and osmotic pressure between charged interfaces

The forces between charged macromolecules, usually given in terms of osmotic pressure, are highly affected by the intervening ionic solution. While in most theoretical studies the solution is treated as a homogeneous structureless dielectric medium, recent experimental studies concluded that, for a bathing solution composed of two solvents (binary mixture), the osmotic pressure between charged macromolecules is affected by the binary solvent composition. By adding local solvent composition terms to the free energy, we obtain a general expression for the osmotic pressure, in planar geometry and within the mean-field framework. The added effect is due to the permeability inhomogeneity and nonelectrostatic short-range interactions between the ions and solvents (preferential solvation). This effect is mostly pronounced at small distances and leads to a reduction in the osmotic pressure for macromolecular separations of the order 1--2 nm. Furthermore, it leads to a depletion of one of the two solvents from the charged macromolecules (modeled as planar interfaces). Lastly, by comparing the theoretical results with experimental ones, an explanation based on preferential solvation is offered for recent experiments on the osmotic pressure of DNA solutions.Comment: 13 pages, 8 figure

On the Connection Between Momentum Cutoff and Operator Cutoff Regularizations

Operator cutoff regularization based on the original Schwinger's proper-time formalism is examined. By constructing a regulating smearing function for the proper-time integration, we show how this regularization scheme simulates the usual momentum cutoff prescription yet preserves gauge symmetry even in the presence of the cutoff scales. Similarity between the operator cutoff regularization and the method of higher (covariant) derivatives is also observed. The invariant nature of the operator cutoff regularization makes it a promising tool for exploring the renormalization group flow of gauge theories in the spirit of Wilson-Kadanoff blocking transformation.Comment: 28 pages in plain TeX, no figures. revised and expande

Tracing PAHs and Warm Dust Emission in the Seyfert Galaxy NGC 1068

We present a study of the nearby Seyfert galaxy NGC 1068 using mid- and far- infrared data acquired with the IRAC, IRS, and MIPS instruments aboard the Spitzer Space Telescope. The images show extensive 8 um and 24 um emission coinciding with star formation in the inner spiral approximately 15" (1 kpc) from the nucleus, and a bright complex of star formation 47" (3 kpc) SW of the nucleus. The brightest 8 um PAH emission regions coincide remarkably well with knots observed in an Halpha image. Strong PAH features at 6.2, 7.7, 8.6, and 11.3 um are detected in IRS spectra measured at numerous locations inside, within, and outside the inner spiral. The IRAC colors and IRS spectra of these regions rule out dust heated by the AGN as the primary emission source; the SEDs are dominated by starlight and PAH emission. The equivalent widths and flux ratios of the PAH features in the inner spiral are generally consistent with conditions in a typical spiral galaxy ISM. Interior to the inner spiral, the influence of the AGN on the ISM is evident via PAH flux ratios indicative of a higher ionization parameter and a significantly smaller mean equivalent width than observed in the inner spiral. The brightest 8 and 24 um emission peaks in the disk of the galaxy, even at distances beyond the inner spiral, are located within the ionization cones traced by [O III]/Hbeta, and they are also remarkably well aligned with the axis of the radio jets. Although it is possible that radiation from the AGN may directly enhance PAH excitation or trigger the formation of OB stars that subsequently excite PAH emission at these locations in the inner spiral, the orientation of collimated radiation from the AGN and star formation knots in the inner spiral could be coincidental. (abridged)Comment: 20 pages, 11 figures; AJ, accepted; full resolution version available at http://spider.ipac.caltech.edu/staff/jhhowell/astro/howelln1068.pd

Bregman Voronoi Diagrams: Properties, Algorithms and Applications

The Voronoi diagram of a finite set of objects is a fundamental geometric structure that subdivides the embedding space into regions, each region consisting of the points that are closer to a given object than to the others. We may define many variants of Voronoi diagrams depending on the class of objects, the distance functions and the embedding space. In this paper, we investigate a framework for defining and building Voronoi diagrams for a broad class of distance functions called Bregman divergences. Bregman divergences include not only the traditional (squared) Euclidean distance but also various divergence measures based on entropic functions. Accordingly, Bregman Voronoi diagrams allow to define information-theoretic Voronoi diagrams in statistical parametric spaces based on the relative entropy of distributions. We define several types of Bregman diagrams, establish correspondences between those diagrams (using the Legendre transformation), and show how to compute them efficiently. We also introduce extensions of these diagrams, e.g. k-order and k-bag Bregman Voronoi diagrams, and introduce Bregman triangulations of a set of points and their connexion with Bregman Voronoi diagrams. We show that these triangulations capture many of the properties of the celebrated Delaunay triangulation. Finally, we give some applications of Bregman Voronoi diagrams which are of interest in the context of computational geometry and machine learning.Comment: Extend the proceedings abstract of SODA 2007 (46 pages, 15 figures

Neurological Signs at the First Psychotic Episode as Correlates of Long-Term Outcome:Results From the AESOP-10 Study

Minor neurological signs are subtle deficits in sensory integration, motor coordination, and sequencing of complex motor acts present in excess in the early stages of psychosis. Still, it remains unclear whether at least some of these signs represent trait or state markers for psychosis and whether they are markers of long-term disease outcome of clinical utility. We examined the relationship between neurological function at illness onset assessed with the Neurological Evaluation Scale and subsequent illness course in 233 patients from AESOP-10 (Aetiology and Ethnicity in Schizophrenia and Other Psychoses), a 10-year follow-up study of a population-based cohort of individuals recruited at the time of their first episode of psychosis in the United Kingdom. In 56 of these patients, we also explored changes in neurological function over time. We included a group of 172 individuals without psychosis as controls. After 10 years, 147 (63%) patients had developed a non-remitting course of illness, and 86 (37%) a remitting course. Already at first presentation, patients who developed a non-remitting course had significantly more primary, motor coordination, and total signs than both remitting patients and healthy controls. While Motor Coordination signs did not change over time, rates of Primary, Sensory Integration, and Total signs increased, independently of illness course type. These findings suggest that motor coordination problems could be a useful early, quick, and easily detectable marker of subsequent clinical outcome. With other motor abnormalities, a measure of motor incoordination could contribute to the identification of the most vulnerable individuals, who could benefit from targeted and more assertive treatment approaches

Deep Underground Science and Engineering Laboratory - Preliminary Design Report

The DUSEL Project has produced the Preliminary Design of the Deep Underground Science and Engineering Laboratory (DUSEL) at the rehabilitated former Homestake mine in South Dakota. The Facility design calls for, on the surface, two new buildings - one a visitor and education center, the other an experiment assembly hall - and multiple repurposed existing buildings. To support underground research activities, the design includes two laboratory modules and additional spaces at a level 4,850 feet underground for physics, biology, engineering, and Earth science experiments. On the same level, the design includes a Department of Energy-shepherded Large Cavity supporting the Long Baseline Neutrino Experiment. At the 7,400-feet level, the design incorporates one laboratory module and additional spaces for physics and Earth science efforts. With input from some 25 science and engineering collaborations, the Project has designed critical experimental space and infrastructure needs, including space for a suite of multidisciplinary experiments in a laboratory whose projected life span is at least 30 years. From these experiments, a critical suite of experiments is outlined, whose construction will be funded along with the facility. The Facility design permits expansion and evolution, as may be driven by future science requirements, and enables participation by other agencies. The design leverages South Dakota's substantial investment in facility infrastructure, risk retirement, and operation of its Sanford Laboratory at Homestake. The Project is planning education and outreach programs, and has initiated efforts to establish regional partnerships with underserved populations - regional American Indian and rural populations

Knowledge-based energy functions for computational studies of proteins

This chapter discusses theoretical framework and methods for developing knowledge-based potential functions essential for protein structure prediction, protein-protein interaction, and protein sequence design. We discuss in some details about the Miyazawa-Jernigan contact statistical potential, distance-dependent statistical potentials, as well as geometric statistical potentials. We also describe a geometric model for developing both linear and non-linear potential functions by optimization. Applications of knowledge-based potential functions in protein-decoy discrimination, in protein-protein interactions, and in protein design are then described. Several issues of knowledge-based potential functions are finally discussed.Comment: 57 pages, 6 figures. To be published in a book by Springe