521 research outputs found
Structural Basis of the Highly Efficient Trapping of the HIV Tat Protein by an RNA Aptamer
AbstractAn RNA aptamer containing two binding sites exhibits extremely high affinity to the HIV Tat protein. We have determined the structure of the aptamer complexed with two argininamide molecules. Two adjacent U:A:U base triples were formed, which widens the major groove to make space for the two argininamide molecules. The argininamide molecules bind to the G bases through hydrogen bonds. The binding is stabilized through stacking interactions. The structure of the aptamer complexed with a Tat-derived arginine-rich peptide was also characterized. It was suggested that the aptamer structure is similar for both complexes and that the aptamer interacts with two different arginine residues of the peptide simultaneously at the two binding sites, which could explain the high affinity to Tat
The nature of slow dynamics in a minimal model of frustration-limited domains
We present simulation results for the dynamics of a schematic model based on
the frustration-limited domain picture of glass-forming liquids. These results
are compared with approximate theoretical predictions analogous to those
commonly used for supercooled liquid dynamics. Although model relaxation times
increase by several orders of magnitude in a non-Arrhenius manner as a
microphase separation transition is approached, the slow relaxation is in many
ways dissimilar to that of a liquid. In particular, structural relaxation is
nearly exponential in time at each wave vector, indicating that the mode
coupling effects dominating liquid relaxation are comparatively weak within
this model. Relaxation properties of the model are instead well reproduced by
the simplest dynamical extension of a static Hartree approximation. This
approach is qualitatively accurate even for temperatures at which the mode
coupling approximation predicts loss of ergodicity. These results suggest that
the thermodynamically disordered phase of such a minimal model poorly
caricatures the slow dynamics of a liquid near its glass transition
The Kuiper Belt and Other Debris Disks
We discuss the current knowledge of the Solar system, focusing on bodies in
the outer regions, on the information they provide concerning Solar system
formation, and on the possible relationships that may exist between our system
and the debris disks of other stars. Beyond the domains of the Terrestrial and
giant planets, the comets in the Kuiper belt and the Oort cloud preserve some
of our most pristine materials. The Kuiper belt, in particular, is a
collisional dust source and a scientific bridge to the dusty "debris disks"
observed around many nearby main-sequence stars. Study of the Solar system
provides a level of detail that we cannot discern in the distant disks while
observations of the disks may help to set the Solar system in proper context.Comment: 50 pages, 25 Figures. To appear in conference proceedings book
"Astrophysics in the Next Decade
Anomalous Heat Conduction and Anomalous Diffusion in Low Dimensional Nanoscale Systems
Thermal transport is an important energy transfer process in nature. Phonon
is the major energy carrier for heat in semiconductor and dielectric materials.
In analogy to Ohm's law for electrical conductivity, Fourier's law is a
fundamental rule of heat transfer in solids. It states that the thermal
conductivity is independent of sample scale and geometry. Although Fourier's
law has received great success in describing macroscopic thermal transport in
the past two hundreds years, its validity in low dimensional systems is still
an open question. Here we give a brief review of the recent developments in
experimental, theoretical and numerical studies of heat transport in low
dimensional systems, include lattice models, nanowires, nanotubes and
graphenes. We will demonstrate that the phonon transports in low dimensional
systems super-diffusively, which leads to a size dependent thermal
conductivity. In other words, Fourier's law is breakdown in low dimensional
structures
Shrinking a large dataset to identify variables associated with increased risk of Plasmodium falciparum infection in Western Kenya
Large datasets are often not amenable to analysis using traditional single-step approaches. Here, our general objective was to apply imputation techniques, principal component analysis (PCA), elastic net and generalized linear models to a large dataset in a systematic approach to extract the most meaningful predictors for a health outcome. We extracted predictors for Plasmodium falciparum infection, from a large covariate dataset while facing limited numbers of observations, using data from the People, Animals, and their Zoonoses (PAZ) project to demonstrate these techniques: data collected from 415 homesteads in western Kenya, contained over 1500 variables that describe the health, environment, and social factors of the humans, livestock, and the homesteads in which they reside. The wide, sparse dataset was simplified to 42 predictors of P. falciparum malaria infection and wealth rankings were produced for all homesteads. The 42 predictors make biological sense and are supported by previous studies. This systematic data-mining approach we used would make many large datasets more manageable and informative for decision-making processes and health policy prioritization
Measurement of the B0-anti-B0-Oscillation Frequency with Inclusive Dilepton Events
The - oscillation frequency has been measured with a sample of
23 million \B\bar B pairs collected with the BABAR detector at the PEP-II
asymmetric B Factory at SLAC. In this sample, we select events in which both B
mesons decay semileptonically and use the charge of the leptons to identify the
flavor of each B meson. A simultaneous fit to the decay time difference
distributions for opposite- and same-sign dilepton events gives ps.Comment: 7 pages, 1 figure, submitted to Physical Review Letter
Measurement of the Bottom-Strange Meson Mixing Phase in the Full CDF Data Set
We report a measurement of the bottom-strange meson mixing phase \beta_s
using the time evolution of B0_s -> J/\psi (->\mu+\mu-) \phi (-> K+ K-) decays
in which the quark-flavor content of the bottom-strange meson is identified at
production. This measurement uses the full data set of proton-antiproton
collisions at sqrt(s)= 1.96 TeV collected by the Collider Detector experiment
at the Fermilab Tevatron, corresponding to 9.6 fb-1 of integrated luminosity.
We report confidence regions in the two-dimensional space of \beta_s and the
B0_s decay-width difference \Delta\Gamma_s, and measure \beta_s in [-\pi/2,
-1.51] U [-0.06, 0.30] U [1.26, \pi/2] at the 68% confidence level, in
agreement with the standard model expectation. Assuming the standard model
value of \beta_s, we also determine \Delta\Gamma_s = 0.068 +- 0.026 (stat) +-
0.009 (syst) ps-1 and the mean B0_s lifetime, \tau_s = 1.528 +- 0.019 (stat) +-
0.009 (syst) ps, which are consistent and competitive with determinations by
other experiments.Comment: 8 pages, 2 figures, Phys. Rev. Lett 109, 171802 (2012
The Drosophila melanogaster Genetic Reference Panel
A major challenge of biology is understanding the relationship between molecular genetic variation and variation in quantitative traits, including fitness. This relationship determines our ability to predict phenotypes from genotypes and to understand how evolutionary forces shape variation within and between species. Previous efforts to dissect the genotype-phenotype map were based on incomplete genotypic information. Here, we describe the Drosophila melanogaster Genetic Reference Panel (DGRP), a community resource for analysis of population genomics and quantitative traits. The DGRP consists of fully sequenced inbred lines derived from a natural population. Population genomic analyses reveal reduced polymorphism in centromeric autosomal regions and the X chromosome, evidence for positive and negative selection, and rapid evolution of the X chromosome. Many variants in novel genes, most at low frequency, are associated with quantitative traits and explain a large fraction of the phenotypic variance. The DGRP facilitates genotype-phenotype mapping using the power of Drosophila genetics
Regulation of 5-HT Receptors and the Hypothalamic-Pituitary-Adrenal Axis
Disturbances in the serotonin (5-HT) system is the neurobiological abnormality most consistently associated with suicide. Hyperactivity of the hypothalmic-pituitary-adrenal (HPA) axis is also described in suicide victims. The HPA axis is the classical neuroendocrine system that responds to stress and whose final product, corticosteroids, targets components of the limbic system, particularly the hippocampus. We will review resulsts from animal studies that point to the possibility that many of the 5-HT receptor changes observed in suicide brains may be a result of, or may be worsened by, the HPA overactivity that may be present in some suicide victims. The results of these studies can be summarized as follows: (1) chronic unpredictable stress produces high corticosteroid levels in rats; (2) chronic stress also results in changes in specific 5-HT receptors (increases in cortical 5-HT2A and decreases in hipocampal 5-HT1A and 5-HT1B); (3) chronic antidepressant administration prevents many of the 5-HT receptor changes observed after stress; and (4) chronic antidepressant administration reverses the overactivity of the HPA axis. If indeed 5-HT receptors have a partial role in controlling affective states, then their modulation by corticosteroids provides a potential mechanism by which these hormones may regulate mood. These data may also provide a biological understanding of how stressful events may increase the risk for suicide in vulnerable individuals and may help us elucidate the neurobiological underpinnings of treatment resistance.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/73437/1/j.1749-6632.1997.tb52357.x.pd
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