203 research outputs found
A complex pathway for 3 ' processing of the yeast U3 snoRNA
Mature U3 snoRNA in yeast is generated from the 3′-extended precursors by endonucleolytic cleavage followed by exonucleolytic trimming. These precursors terminate in poly(U) tracts and are normally stabilised by binding of the yeast La homologue, Lhp1p. We report that normal 3′ processing of U3 requires the nuclear Lsm proteins. On depletion of any of the five essential proteins, Lsm2–5p or Lsm8p, the normal 3′-extended precursors to the U3 snoRNA were lost. Truncated fragments of both mature and pre-U3 accumulated in the Lsm-depleted strains, consistent with substantial RNA degradation. Pre-U3 species were co-precipitated with TAP-tagged Lsm3p, but the association with spliced pre-U3 was lost in strains lacking Lhp1p. The association of Lhp1p with pre-U3 was also reduced on depletion of Lsm3p or Lsm5p, indicating that binding of Lhp1p and the Lsm proteins is interdependent. In contrast, a tagged Sm-protein detectably co-precipitated spliced pre-U3 species only in strains lacking Lhp1p. We propose that the Lsm2–8p complex functions as a chaperone in conjunction with Lhp1p to stabilise pre-U3 RNA species during 3′ processing. The Sm complex may function as a back-up to stabilise 3′ ends that are not protected by Lhp1p
Decay of isolated surface features driven by the Gibbs-Thomson effect in analytic model and simulation
A theory based on the thermodynamic Gibbs-Thomson relation is presented which
provides the framework for understanding the time evolution of isolated
nanoscale features (i.e., islands and pits) on surfaces. Two limiting cases are
predicted, in which either diffusion or interface transfer is the limiting
process. These cases correspond to similar regimes considered in previous works
addressing the Ostwald ripening of ensembles of features. A third possible
limiting case is noted for the special geometry of "stacked" islands. In these
limiting cases, isolated features are predicted to decay in size with a power
law scaling in time: A is proportional to (t0-t)^n, where A is the area of the
feature, t0 is the time at which the feature disappears, and n=2/3 or 1. The
constant of proportionality is related to parameters describing both the
kinetic and equilibrium properties of the surface. A continuous time Monte
Carlo simulation is used to test the application of this theory to generic
surfaces with atomic scale features. A new method is described to obtain
macroscopic kinetic parameters describing interfaces in such simulations.
Simulation and analytic theory are compared directly, using measurements of the
simulation to determine the constants of the analytic theory. Agreement between
the two is very good over a range of surface parameters, suggesting that the
analytic theory properly captures the necessary physics. It is anticipated that
the simulation will be useful in modeling complex surface geometries often seen
in experiments on physical surfaces, for which application of the analytic
model is not straightforward.Comment: RevTeX (with .bbl file), 25 pages, 7 figures from 9 Postscript files
embedded using epsf. Submitted to Phys. Rev. B A few minor changes made on
9/24/9
Weak selection and stability of localized distributions in Ostwald ripening
We support and generalize a weak selection rule predicted recently for the
self-similar asymptotics of the distribution function (DF) in the
zero-volume-fraction limit of Ostwald ripening (OR). An asymptotic perturbation
theory is developed that, when combined with an exact invariance property of
the system, yields the selection rule, predicts a power-law convergence towards
the selected self-similar DF and agrees well with our numerical simulations for
the interface- and diffusion-controlled OR.Comment: 4 pages, 2 figures, submitted to PR
The human exosome: an autoantigenic complex of exoribonucleases in myositis and scleroderma
The anti-PM/Scl autoantibodies are known to characterize a subset of autoimmune patients with myositis, scleroderma (Scl), and the PM/Scl overlap syndrome. The major autoantigens that are recognized by anti-PM/Scl autoantibodies are designated PM/Scl-100 and PM/Scl-75. These autoantigens have been reported to associate into a large complex consisting of 11 to 16 proteins and to play a role in ribosome synthesis. Recently, it was discovered that the PM/Scl complex is the human counterpart of the yeast (Saccharomyces cerevisiae) exosome, which is an RNA-processing complex consisting of 11 3' → 5' exoribonucleases. To date, 10 human exosome components have been identified, although only some of these were studied in more detail. In this review, we discuss some recent advances in the characterization of the PM/Scl complex
Selenocysteine Insertion Sequence Binding Protein 2L Is Implicated as a Novel Post-Transcriptional Regulator of Selenoprotein Expression
The amino acid selenocysteine (Sec) is encoded by UGA codons. Recoding of UGA from stop to Sec requires a Sec insertion sequence (SECIS) element in the 3′ UTR of selenoprotein mRNAs. SECIS binding protein 2 (SBP2) binds the SECIS element and is essential for Sec incorporation into the nascent peptide. SBP2-like (SBP2L) is a paralogue of SBP2 in vertebrates and is the only SECIS binding protein in some invertebrates where it likely directs Sec incorporation. However, vertebrate SBP2L does not promote Sec incorporation in in vitro assays. Here we present a comparative analysis of SBP2 and SBP2L SECIS binding properties and demonstrate that its inability to promote Sec incorporation is not due to lower SECIS affinity but likely due to lack of a SECIS dependent domain association that is found in SBP2. Interestingly, however, we find that an invertebrate version of SBP2L is fully competent for Sec incorporation in vitro. Additionally, we present the first evidence that SBP2L interacts with selenoprotein mRNAs in mammalian cells, thereby implying a role in selenoprotein expression
Breakdown of Scale Invariance in the Phase Ordering of Fractal Clusters
Our numerical simulations with the Cahn-Hilliard equation show that
coarsening of fractal clusters (FCs) is not a scale-invariant process. On the
other hand, a typical coarsening length scale and interfacial area of the FC
exhibit power laws in time, while the mass fractal dimension remains invariant.
The initial value of the lower cutoff is a relevant length scale. A
sharp-interface model is formulated that can follow the whole dynamics of a
diffusion controlled growth, coarsening, fragmentation and approach to
equilibrium in a system with conserved order parameter.Comment: 4 pages, 4 figures, RevTex, submitted to PR
Normal scaling in globally conserved interface-controlled coarsening of fractal clusters
Globally conserved interface-controlled coarsening of fractal clusters
exhibits dynamic scale invariance and normal scaling. This is demonstrated by a
numerical solution of the Ginzburg-Landau equation with a global conservation
law. The sharp-interface limit of this equation is volume preserving motion by
mean curvature. The scaled form of the correlation function has a power-law
tail accommodating the fractal initial condition. The coarsening length
exhibits normal scaling with time. Finally, shrinking of the fractal clusters
with time is observed. The difference between global and local conservation is
discussed.Comment: 4 pages, 3 eps figure
Equilibrium shapes and energies of coherent strained InP islands
The equilibrium shapes and energies of coherent strained InP islands grown on
GaP have been investigated with a hybrid approach that has been previously
applied to InAs islands on GaAs. This combines calculations of the surface
energies by density functional theory and the bulk deformation energies by
continuum elasticity theory. The calculated equilibrium shapes for different
chemical environments exhibit the {101}, {111}, {\=1\=1\=1} facets and a (001)
top surface. They compare quite well with recent atomic-force microscopy data.
Thus in the InP/GaInP-system a considerable equilibration of the individual
islands with respect to their shapes can be achieved. We discuss the
implications of our results for the Ostwald ripening of the coherent InP
islands. In addition we compare strain fields in uncapped and capped islands.Comment: 10 pages including 6 figures. Submitted to Phys. Rev. B. Related
publications can be found at http://www.fhi-berlin.mpg.de/th/paper.htm
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