Detection of Listeria innocua on roll-to-roll produced SERS substrates with gold nanoparticles

The rapid and accurate detection of food pathogens plays a critical role in the early prevention of foodborne epidemics. Combination of low cost sensing platforms and SERS detection can offer a solution for the pathogen detection.

Stearylated cycloarginine nanosystems for intracellular delivery – simulations, formulation and proof of concept

Novel cationic agent liposomes performed better in silico translating in higher cellular uptake with reduced toxicity.

Molecular dynamics study of prolyl oligopeptidase with inhibitor in binding cavity

We used the crystal structure of prolyl oligopeptidase (POP) with bound Z-pro-prolinal (ZPP) inhibitor (Protein Data Bank (PDB) structure 1QFS) to perform an intensive molecular dynamics study of the POP-ZPP complex. We performed 100 ns of simulation with the hemiacetal bond, through which the ZPP is bound to the POP, removed in order to better investigate the binding cavity environment. From basic analysis, measuring the radius of gyration, root mean square deviation, solvent accessible surface area and definition of the secondary structure of protein, we determined that the protein structure is highly stable and maintains its structure over the entire simulation time. This demonstrates that such long time simulations can be performed without the protein structure losing stability. We found that water bridges and hydrogen bonds play a negligible role in binding the ZPP thus indicating the importance of the hemiacetal bond. The two domains of the protein are bound by a set of approximately 12 hydrogen bonds, specific to the particular POP protein.

HSE's Safety Assessment Principles for radiation protection

The Health and Safety Executive (HSE) published its revised Safety Assessment Principles for Nuclear Facilities (SAPs) in December 2006. The SAPs are primarily intended for use by HSE's inspectors when judging the adequacy of safety cases for nuclear facilities. The revised SAPs refer in part to HSE's expectations relating to the technical discipline of radiation protection. The purpose of this paper is to describe for the benefit of a wider audience HSE's reasoning behind the final published SAPs and to set out the purpose of each specific radiation protection (RP) principle. The paper also discusses principles in other sections of the SAPs which are relevant to radiation protection. The paper notes that the SAPs should be viewed as a reflection of good practice in relation to nuclear facilities in the context of interpreting relevant parts of primary legislation such as the Nuclear Installations Act 1965.

Molecular dynamics simulations of the enzyme catechol-O-methyltransferase: methodological issues

Results from extensive 70 ns all-atom molecular dynamics simulations of catechol-O-methyltransferase (COMT) enzyme are reported. The simulations were performed with explicit TIP3P water and Mg2+ ions. Four different crystal structures of COMT, with and without different ligands, were used. These simulations are among the most extensive of their kind and as such served as a stability test for such simulations. On the methodological side we found that the initial energy minimization procedure may be a crucial step: particular hydrogen bonds may break, and this can initiate an irreversible loss of protein structure that becomes observable in longer time scales of the order of tens of nanoseconds. This has important implications for both molecular dynamics and quantum mechanics-molecular mechanics simulations.

Ultra-relativistic electrons in Jupiter's radiation belts

Ground-based observations have shown that Jupiter is a two-component source of microwave radio emission: thermal atmospheric emission and synchrotron emission from energetic electrons spiralling in Jupiter's magnetic field. Later in situ measurements confirmed the existence of Jupiter's high-energy electron-radiation belts, with evidence for electrons at energies up to 20[?]MeV. Although most radiation belt models predict electrons at higher energies, adiabatic diffusion theory can account only for energies up to around 20[?]MeV. Unambiguous evidence for more energetic electrons is lacking. Here we report observations of 13.8[?]GHz synchrotron emission that confirm the presence of electrons with energies up to 50[?]MeV; the data were collected during the Cassini fly-by of Jupiter. These energetic electrons may be repeatedly accelerated through an interaction with plasma waves, which can transfer energy into the electrons. Preliminary comparison of our data with model results suggests that electrons with energies of less than 20[?]MeV are more numerous than previously believed.

Parallel excluded volume tempering for polymer melts

We have developed a technique to accelerate the acquisition of effectively uncorrelated configurations for off-lattice models of dense polymer melts that makes use of both parallel tempering and large-scale Monte Carlo moves. The method is based upon simulating a set of systems in parallel, each of which has a slightly different repulsive core potential, such that a thermodynamic path from full excluded volume to an ideal gas of random walks is generated. While each system is run with standard stochastic dynamics, resulting in an NVT ensemble, we implement the parallel tempering through stochastic swaps between the configurations of adjacent potentials, and the large-scale Monte Carlo moves through attempted pivot and translation moves that reach a realistic acceptance probability as the limit of the ideal gas of random walks is approached. Compared to pure stochastic dynamics, this results in an increased efficiency even for a system of chains as short as N=60 monomers, however at this chain length the large-scale Monte Carlo moves were ineffective. For even longer chains, the speedup becomes substantial, as observed from preliminary data for N=200. We also compare our scheme to the end bridging algorithm of Theodorou et al. For N=60, end bridging must allow a polydispersity of more than 10% in order to relax the end-to-end vector more quickly than our method. The comparison is, however, hampered by the fact that the end-to-end vector becomes a somewhat artificial quantity when one implements end bridging, and is perhaps no longer the slowest dynamic variable.

Longitudinal magnetic excitations in classical spin systems

Using spin dynamics simulations we predict the splitting of the longitudinal spin-wave peak in all antiferromagnets with single site anisotropy into two peaks separated by twice the energy gap at the Brillouin zone center. This phenomenon has yet to be observed experimentally but can be easily investigated through neutron scattering experiments on MnF2 and FeF2. We have also determined that for all classical Heisenberg models the longitudinal propagative excitations are entirely multiple spin wave in nature.

A mechanism for toxin insertion into membranes is suggested by the crystal structure of the channel-forming domain of colicin E1

BACKGROUND

Channel-forming colicins, including colicin E1, are a sub-family of bacteriocins. The toxic action of colicin E1 is derived from its ability to form a voltage-gated channel, which causes depolarization of the cytoplasmic membrane of sensitive Escherichia coli cells. In this process, the toxin-like colicin E1 molecule must undergo a substantial structural transition from a soluble state, in which it binds the target cell, to a membrane-bound state. Details of the structural changes that accompany this conversion may be directly applicable to other channel-forming toxins, as well as to the mechanism by which proteins insert into or cross membranes.

RESULTS

The structure of the 190-residue channel-forming domain of colicin E1 in its soluble form has been solved at 2.5 A resolution. This structure contains 10alpha helices arranged in three layers (A-C) with a central hydrophobic helical hairpin in layer B, which is proposed to anchor the membrane-bound form in the bilayer. The extended N-terminal helix I provides a connection to the rest of the colicin E1 molecule, and the loop I-II may act as a hinge for re-orientation of the domain for membrane binding. A set of conserved positively charged residues on layer C may provide the docking surface on the molecule for membrane attachment. A large internal cavity between layers B and C may allow these layers to disengage, suggesting a mechanism for unfolding the molecule on the membrane that involves the perturbation of the interhelical hydrophobic interactions in layer C.

CONCLUSION

On the basis of the structure of the colicin E1 channel-forming domain, its comparison with the structure of the colicin A domain and the known requirement for initial electrostatic and subsequent hydrophobic interactions, molecular details of the docking, unfolding and insertion of the channel-forming domain into the membrane are proposed. The model for docking and initial interaction with the membrane positions the hydrophobic hairpin 'anchor' approximately parallel to the membrane surface. Hydrophobic interactions in the docking layer may then be displaced by interactions with the membrane, spreading the helices on the surface and exposing the hydrophobic hairpin for insertion into the membrane.

A New Look at the Saturn System: The Voyager 2 Images

Voyager 2 photography has complemented that of Voyager I in revealing many additional characteristics of Saturn and its satellites and rings. Saturn's atmosphere contains persistent oval cloud features reminiscent of features on Jupiter. Smaller irregular features track out a pattern of zonal winds that is symmetric about Saturn's equator and appears to extend to great depth. Winds are predominantly eastward and reach 500 meters per second at the equator. Titan has several haze layers with significantly varying optical properties and a northern polar "collar" that is dark at short wavelengths. Several satellites have been photographed at substantially improved resolution. Enceladus' surface ranges from old, densely cratered terrain to relatively young, uncratered plains crossed by grooves and faults. Tethys has a crater 400 kilometers in diameter whose floor has domed to match Tethys' surface curvature and a deep trench that extends at least 270 degrees around Tethys' circumference. Hyperion is cratered and irregular in shape. Iapetus' bright, trailing hemisphere includes several dark-floored craters, and Phoebe has a very low albedo and rotates in the direction opposite to that of its orbital revolution with a period of 9 hours. Within Saturn's rings, the "birth" of a spoke has been observed, and surprising azimuthal and time variability is found in the ringlet structure of the outer B ring. These observations lead to speculations about Saturn's internal structure and about the collisional and thermal history of the rings and satellites.

Encounter with Saturn: Voyager 1 Imaging Science Results

As Voyager 1 flew through the Saturn system it returned photographs revealing many new and surprising characteristics of this complicated community of bodies. Saturn's atmosphere has numerous, low-contrast, discrete cloud features and a pattern of circulation significantly different from that of Jupiter. Titan is shrouded in a haze layer that varies in thickness and appearance. Among the icy satellites there is considerable variety in density, albedo, and surface morphology and substantial evidence for endogenic surface modification. Trends in density and crater characteristics are quite unlike those of the Galilean satellites. Small inner satellites, three of which were discovered in Voyager images, interact gravitationally with one another and with the ring particles in ways not observed elsewhere in the solar system. Saturn's broad A, B, and C rings contain hundreds of "ringlets," and in the densest portion of the B ring there are numerous nonaxisymmetric features. The narrow F ring has three components which, in at least one instance, are kinked and crisscrossed. Two rings are observed beyond the F ring, and material is seen between the C ring and the planet.