Heparin and Heparan Sulfate: Analyzing Structure and Microheterogeneity [chapter]

available in PMC 2013 August 28The structural microheterogeneity of heparin and heparan sulfate is one of the major reasons for the multifunctionality exhibited by this class of molecules. In a physiological context, these molecules primarily exert their effects extracellularly by mediating key processes of cellular cross-talk and signaling leading to the modulation of a number of different biological activities including development, cell proliferation, and inflammation. This structural diversity is biosynthetically imprinted in a nontemplate-driven manner and may also be dynamically remodeled as cellular function changes. Understanding the structural information encoded in these molecules forms the basis for attempting to understand the complex biology they mediate. This chapter provides an overview of the origin of the structural microheterogeneity observed in heparin and heparan sulfate, and the orthogonal analytical methodologies that are required to help decipher this information

Conformational and Structural Relaxations of Poly(ethylene oxide) and Poly(propylene oxide) Melts: Molecular Dynamics Study of Spatial Heterogeneity, Cooperativity, and Correlated Forward-Backward Motion

Performing molecular dynamics simulations for all-atom models, we characterize the conformational and structural relaxations of poly(ethylene oxide) and poly(propylene oxide) melts. The temperature dependence of these relaxation processes deviates from an Arrhenius law for both polymers. We demonstrate that mode-coupling theory captures some aspects of the glassy slowdown, but it does not enable a complete explanation of the dynamical behavior. When the temperature is decreased, spatially heterogeneous and cooperative translational dynamics are found to become more important for the structural relaxation. Moreover, the transitions between the conformational states cease to obey Poisson statistics. In particular, we show that, at sufficiently low temperatures, correlated forward-backward motion is an important aspect of the conformational relaxation, leading to strongly nonexponential distributions for the waiting times of the dihedrals in the various conformational statesComment: 13 pages, 13 figure

Light emission from a scanning tunneling microscope: Fully retarded calculation

The light emission rate from a scanning tunneling microscope (STM) scanning a noble metal surface is calculated taking retardation effects into account. As in our previous, non-retarded theory [Johansson, Monreal, and Apell, Phys. Rev. B 42, 9210 (1990)], the STM tip is modeled by a sphere, and the dielectric properties of tip and sample are described by experimentally measured dielectric functions. The calculations are based on exact diffraction theory through the vector equivalent of the Kirchoff integral. The present results are qualitatively similar to those of the non-retarded calculations. The light emission spectra have pronounced resonance peaks due to the formation of a tip-induced plasmon mode localized to the cavity between the tip and the sample. At a quantitative level, the effects of retardation are rather small as long as the sample material is Au or Cu, and the tip consists of W or Ir. However, for Ag samples, in which the resistive losses are smaller, the inclusion of retardation effects in the calculation leads to larger changes: the resonance energy decreases by 0.2-0.3 eV, and the resonance broadens. These changes improve the agreement with experiment. For a Ag sample and an Ir tip, the quantum efficiency is $\approx$ 10$^{-4}$ emitted photons in the visible frequency range per tunneling electron. A study of the energy dissipation into the tip and sample shows that in total about 1 % of the electrons undergo inelastic processes while tunneling.Comment: 16 pages, 10 figures (1 ps, 9 tex, automatically included); To appear in Phys. Rev. B (15 October 1998

A critical assessment of methods for the intrinsic analysis of liquid interfaces: 2. density profiles

Substantial improvements in the molecular level understanding of fluid interfaces have recently been achieved by recognizing the importance of detecting the intrinsic surface of the coexisting condensed phases in computer simulations (i.e., after the removal of corrugations caused by capillary waves) and by developing several methods for identifying the molecules that are indeed located at the boundary of the two phases. In our previous paper [J. Phys. Chem. C 2010, 114, 11169], we critically compared those methods in terms of reliability, robustness, and computation speed. Once the intrinsic surface of a given phase is detected, various profiles, such as the density profiles of the components, can be calculated relative to this intrinsic surface rather than to the macroscopically planar Gibbs dividing surface. As a continuation of our previous study, here we present a detailed and critical comparison of various methods that can be used to calculate intrinsic density profiles once the full set of truly interfacial molecules has been identified. Two of the methods, the Fourier function and the Voronoi tessellation, are already described in the literature; two other methods, the covering surface and the triangular interpolation, are newly proposed algorithms; one method, the modified grid-based intrinsic profile (GIP) method, is an improvement over an existing procedure. The different methods are again compared in terms of accuracy and computational cost. On the basis of this comparison, we propose a fast and accurate protocol to be routinely used for intrinsic surface analyses in computer simulations

CsA can induce DNA double-strand breaks: implications for BMT regimens particularly for individuals with defective DNA repair

Several human disorders mutated in core components of the major DNA double-strand break (DSB) repair pathway, non-homologous end joining (NHEJ), have been described. Cell lines from these patients are characterized by sensitivity to DSB-inducing agents. DNA ligase IV syndrome (LIG4) patients specifically, for unknown reasons, respond particularly badly following treatment for malignancy or BMT. We report the first systematic evaluation of the response of LIG4 syndrome to compounds routinely employed for BMT conditioning. We found human pre-B lymphocytes, a key target population for BMT conditioning, when deficient for DNA ligase IV, unexpectedly exhibit significant sensitivity to CsA the principal prophylaxis for GVHD. Furthermore, we found that CsA treatment alone or in combination with BU and fludarabine resulted in increased levels of DSBs specifically in LIG4 syndrome cells compared to wild-type or Artemis-deficient cells. Our study shows that CsA can induce DSBs and that LIG4 syndrome patient's fail to adequately repair this damage. These DSBs likely arise as a consequence of DNA replication in the presence of CsA. This work has implications for BMT and GVHD management in general and specifically for LIG4 syndrome

The AMANDA Neutrino Telescope

With an effective telescope area of order $10^4$ m$^2$ for TeV neutrinos, a threshold near $\sim$50 GeV and a pointing accuracy of 2.5 degrees per muon track, the AMANDA detector represents the first of a new generation of high energy neutrino telescopes, reaching a scale envisaged over 25 years ago. We describe early results on the calibration of natural deep ice as a particle detector as well as on AMANDA's performance as a neutrino telescope.Comment: 12 pages, Latex2.09, uses espcrc2.sty and epsf.sty, 13 postscript files included. Talk presented at the 18th International Conference on Neutrino Physics and Astrophysics (Neutrino 98), Takayama, Japan, June 199

A critical assessment of methods for the intrinsic analysis of liquid interfaces. 1. surface site distributions

Substantial progress in our understanding of interfacial structure and dynamics has stemmed from the recent development of algorithms that allow for an intrinsic analysis of fluid interfaces. These work by identifying the instantaneous location of the interface, at the atomic level, for each molecular configuration and then computing properties relative to this location. Such a procedure eliminates the broadening of the interface caused by capillary waves and reveals the underlying features of the system. However, a precise definition of which molecules actually belong to the interfacial layer is difficult to achieve in practice. Furthermore, it is not known if the different intrinsic analysis methods are consistent with each other and yield similar results for the interfacial properties. In this paper, we carry out a systematic and detailed comparison of the available methods for intrinsic analysis of fluid interfaces, based on a molecular dynamics simulation of the interface between liquid water and carbon tetrachloride. We critically assess the advantages and shortcomings of each method, based on reliability, robustness, and speed of computation, and establish consistent criteria for determining which molecules belong to the surface layer. We believe this will significantly contribute to make intrinsic analysis methods widely and routinely applicable to interfacial systems

Uptake and degradation of mast-cell granules by mouse peritoneal macrophages

35S-labelled mast-cell granules isolated from mouse mastocytomas were added to mouse macrophages in vitro. The granules were avidly phagocytosed, and subsequently the radioactivity was released to the medium as inorganic [35S]sulphate. After pulse-labelling, a total of about 80% of the cell-associated radioactivity was thus released in the course of 24 h, indicating an extensive breakdown of the sulphated polysaccharides, mainly heparin, present in the granules. The uptake of the mast-cell granules caused pronounced, but reversible, spreading of the macrophages

Higher fungal diversity is correlated with lower CO2 emissions from dead wood in a natural forest

Wood decomposition releases almost as much CO2 to the atmosphere as does fossil-fuel combustion, so the factors regulating wood decomposition can affect global carbon cycling. We used metabarcoding to estimate the fungal species diversities of naturally colonized decomposing wood in subtropical China and, for the first time, compared them to concurrent measures of CO2 emissions. Wood hosting more diverse fungal communities emitted less CO2, with Shannon diversity explaining 26 to 44% of emissions variation. Community analysis supports a ‘pure diversity’ effect of fungi on decomposition rates and thus suggests that interference competition is an underlying mechanism. Our findings extend the results of published experiments using low-diversity, laboratory-inoculated wood to a high-diversity, natural system. We hypothesize that high levels of saprotrophic fungal biodiversity could be providing globally important ecosystem services by maintaining dead-wood habitats and by slowing the atmospheric contribution of CO2 from the world’s stock of decomposing wood. However, large-scale surveys and controlled experimental tests in natural settings will be needed to test this hypothesis