Particle dynamics in sheared granular matter

The particle dynamics and shear forces of granular matter in a Couette geometry are determined experimentally. The normalized tangential velocity $V(y)$ declines strongly with distance $y$ from the moving wall, independent of the shear rate and of the shear dynamics. Local RMS velocity fluctuations $\delta V(y)$ scale with the local velocity gradient to the power $0.4 \pm 0.05$. These results agree with a locally Newtonian, continuum model, where the granular medium is assumed to behave as a liquid with a local temperature $\delta V(y)^2$ and density dependent viscosity

Identification of Widespread Adenosine Nucleotide Binding in Mycobacterium tuberculosis

SummaryComputational prediction of protein function is frequently error-prone and incomplete. In Mycobacterium tuberculosis (Mtb), ∼25% of all genes have no predicted function and are annotated as hypothetical proteins, severely limiting our understanding of Mtb pathogenicity. Here, we utilize a high-throughput quantitative activity-based protein profiling (ABPP) platform to probe, annotate, and validate ATP-binding proteins in Mtb. We experimentally validate prior in silico predictions of >240 proteins and identify 72 hypothetical proteins as ATP binders. ATP interacts with proteins with diverse and unrelated sequences, providing an expanded view of adenosine nucleotide binding in Mtb. Several hypothetical ATP binders are essential or taxonomically limited, suggesting specialized functions in mycobacterial physiology and pathogenicity

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resolution structure of Cascade and show how it recognizes double-stranded DNA (dsDNA) targets in a sequence-specific manner. Cascade is a 405-kDa complex comprising five functionally essential CRISPR-associated (Cas) proteins (CasA1B2C6D1E1) and a 61-nucleotide CRISPR RNA (crRNA) with 5′-hydroxyl and 2′,3′-cyclic phosphate termini. The crRNA guides Cascade to dsDNA target sequences by forming base pairs with the complementary DNA strand while displacing the noncomplementary strand to form an R-loop. Cascade recognizes target DNA without consuming ATP, which suggests that continuous invader DNA surveillance takes place without energy investment. The structure of Cascade shows an unusual seahorse shape that undergoes conformational changes when it binds target DNA.

Filled carbon nanotubes as anode materials for lithium-ion batteries

Downsizing well-established materials to the nanoscale is a key route to novel functionalities, in particular if different functionalities are merged in hybrid nanomaterials. Hybrid carbon-based hierarchical nanostructures are particularly promising for electrochemical energy storage since they combine benefits of nanosize effects, enhanced electrical conductivity and integrity of bulk materials. We show that endohedral multiwalled carbon nanotubes (CNT) encapsulating high-capacity (here: conversion and alloying) electrode materials have a high potential for use in anode materials for lithium-ion batteries (LIB). There are two essential characteristics of filled CNT relevant for application in electrochemical energy storage: (1) rigid hollow cavities of the CNT provide upper limits for nanoparticles in their inner cavities which are both separated from the fillings of other CNT and protected against degradation. In particular, the CNT shells resist strong volume changes of encapsulates in response to electrochemical cycling, which in conventional conversion and alloying materials hinders application in energy storage devices. (2) Carbon mantles ensure electrical contact to the active material as they are unaffected by potential cracks of the encapsulate and form a stable conductive network in the electrode compound. Our studies confirm that encapsulates are electrochemically active and can achieve full theoretical reversible capacity. The results imply that encapsulating nanostructures inside CNT can provide a route to new high-performance nanocomposite anode materials for LIB

Supernova Ia: a Converging Delayed Detonation Wave

A model of a carbon-oxygen (C--O) presupernova core with an initial mass 1.33 M_\odot, an initial carbon mass fraction 0.27, and with an average mass growth-rate 5 x 10^{-7} M_\odot/yr due to accretion in a binary system was evolved from initial central density 10^9 g/cm^3, and temperature 2.05 x 10^8 K through convective core formation and its subsequent expansion to the carbon runaway at the center. The only thermonuclear reaction contained in the equations of evolution and runaway was the carbon burning reaction 12C + 12C with an energy release corresponding to the full transition of carbon and oxygen (with the same rate as carbon) into 56Ni. As a parameter we take \alpha_c - a ratio of a mixing length to the size of the convective zone. In spite of the crude assumptions, we obtained a pattern of the runaway acceptable for the supernova theory with the strong dependence of its duration on \alpha_c. In the variants with large enough values of \alpha_c=4.0 x 10^{-3} and 3.0 x 10^{-3} the fuel combustion occurred from the very beginning as a prompt detonation. In the range of 2.0 x 10^{-3} >= \alpha_c >= 3.0 x 10^{-4} the burning started as a deflagration with excitation of stellar pulsations with growing amplitude. Eventually, the detonation set in, which was activated near the surface layers of the presupernova (with m about 1.33 M_\odot) and penetrated into the star down to the deflagration front. Excitation of model pulsations and formation of a detonation front are described in detail for the variant with \alpha_c=1.0 x 10^{-3}.Comment: 13 pages, 11 figures, to appear in Astronomy Letter

PROMPT: a protein mapping and comparison tool

BACKGROUND: Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available. RESULTS: PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel. CONCLUSION: PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from

Polarised Quark Distributions in the Nucleon from Semi-Inclusive Spin Asymmetries

We present a measurement of semi-inclusive spin asymmetries for positively and negatively charged hadrons from deep inelastic scattering of polarised muons on polarised protons and deuterons in the range $0.003$1 GeV$^2$. Compared to our previous publication on this subject, with the new data the statistical errors have been reduced by nearly a factor of two. From these asymmetries and our inclusive spin asymmetries we determine the polarised quark distributions of valence quarks and non-strange sea quarks at $Q^2$=10 GeV$^2$. The polarised $u$ valence quark distribution, $\Delta u_v(x)$, is positive and the polarisation increases with $x$. The polarised $d$ valence quark distribution, $\Delta d_v(x)$, is negative and the non-strange sea distribution, $\Delta \bar q(x)$, is consistent with zero over the measured range of $x$. We find for the first moments $\int_0^1 \Delta u_v(x) dx = 0.77 \pm 0.10 \pm 0.08$, $\int_0^1 \Delta d_v(x) dx = -0.52 \pm 0.14 \pm 0.09$ and $\int_0^1 \Delta \bar q(x) dx= 0.01 \pm 0.04 \pm 0.03$, where we assumed $\Delta \bar u(x) = \Delta \bar d(x)$. We also determine for the first time the second moments of the valence distributions $\int_0^1 x \Delta q_v(x) dx$.Comment: 17 page

A standard numbering scheme for class C β-lactamases

Unlike classes A and B, a standardized amino acid numbering scheme has not been proposed for the class C (AmpC) β-lactamases, which complicates communication in the field. Here, we propose a scheme developed through a collaborative approach that considers both sequence and structure, preserves traditional numbering of catalytically important residues (Ser64, Lys67, Tyr150, and Lys315), is adaptable to new variants or enzymes yet to be discovered, and includes a variation for genetic and epidemiological applications