Phylogeographic analysis of the red seaweed Palmaria palmata reveals a Pleistocene marine glacial refugium in the English Channel

Phylogeography has provided a new approach to the analysis of the postglacial history of a wide range of taxa but, to date, little is known about the effect of glacial periods on the marine biota of Europe. We have utilized a combination of nuclear, plastid and mitochondrial genetic markers to study the biogeographic history of the red seaweed Palmaria palmata in the North Atlantic. Analysis of the nuclear rDNA operon (ITS1-5.8S-ITS2), the plastid 16S-trnI-trnA-23S-5S, rbcL-rbcS and rpl12-rps31-rpl9 regions and the mitochondrial cox2–3 spacer has revealed the existence of a previously unidentified marine refugium in the English Channel, along with possible secondary refugia off the southwest coast of Ireland and in northeast North America and/or Iceland. Coalescent and mismatch analyses date the expansion of European populations from approximately 128 000 bp and suggest a continued period of exponential growth since then. Consequently, we postulate that the penultimate (Saale) glacial maximum was the main event in shaping the biogeographic history of European P. palmata populations which persisted throughout the last (Weichselian) glacial maximum (c. 20 000 bp) in the Hurd Deep, an enigmatic trench in the English Channel.

Dynamics of Viral RNA Synthesis during Measles Virus Infection

We propose a reference model of the kinetics of a viral RNA-dependent RNA polymerase (vRdRp) activities and its regulation during infection of eucaryotic cells. After measles virus infects a cell, mRNAs from all genes immediately start to accumulate linearly over the first 5 to 6 h and then exponentially until approximately 24 h. The change from a linear to an exponential accumulation correlates with de novo synthesis of vRdRp from the incoming template. Expression of the virus nucleoprotein (N) prior to infection shifts the balance in favor of replication. Conversely, inhibition of protein synthesis by cycloheximide favors the latter. The in vivo elongation speed of the viral polymerase is approximately 3 nucleotides/s. A similar profile with fivefold-slower kinetics can be obtained using a recombinant virus expressing a structurally altered polymerase. Finally, virions contain only encapsidated genomic, antigenomic, and 5'-end abortive replication fragment RNAs.

Calcium currents in interstitial cells from the guinea-pig bladder.

OBJECTIVE: To determine whether there are inward currents in interstitial cells (IC) isolated from the guinea-pig detrusor and if so, to characterise them using the patch-clamp technique and pharmacological agents. MATERIALS AND METHODS: Using the whole-cell patch-clamp technique, inward currents were studied in IC enzymatically isolated from the detrusor of the guinea-pig bladder. Currents were evoked by stepping positively from a holding potential of - 80 mV. RESULTS: Outward K+ currents were blocked by Cs+ internal solution to reveal inward currents, which activated at voltages more positive than - 50 mV, peaked at 0 mV, reversed near + 50 mV and were half-maximally activated at - 27 mV. The inward currents showed voltage-dependent inactivation and were half-maximally inactivated at - 36 mV. Fitting the activation and inactivation data with a Boltzmann function revealed a window current between - 40 mV and + 20 mV. The decay of the current evoked at 0 mV could be fitted with a single exponential with a mean time-constant of 88 ms. Replacing external Ca2+ with Ba2+ significantly increased this to 344 ms. The current amplitude was augmented by Ba2+, and by Bay K 8644. Inward currents were significantly reduced by 1 microm nifedipine, across the voltage range, but the blockade was more effective on the current evoked at 0 mV than that evoked by a step to - 20 mV, perhaps indicating voltage-dependence of the action of nifedipine or another component of inward current. Increasing the concentration of the drug to 10 microm caused no further significant reduction either at 0 mV or at -20 mV. However, in the presence of 1 microm nifedipine the latter current was significantly reduced by 100 microm Ni2+. Both currents were significantly reduced in Ca2+-free solution. CONCLUSIONS: IC from the guinea-pig detrusor possess inward currents with typical characteristics of L-type Ca2+ current. They also have a component of inward Ca2+ current, which was resistant to nifedipine, but sensitive to Ni2+. Further work is needed to characterise the latter conductance. PMID: 16686735 [PubMed - indexed for MEDLINE]

Goal Recognition through Goal Graph Analysis

We present a novel approach to goal recognition based on a two-stage paradigm of graph construction and analysis. First, a graph structure called a Goal Graph is constructed to represent the observed actions, the state of the world, and the achieved goals as well as various connections between these nodes at consecutive time steps. Then, the Goal Graph is analysed at each time step to recognise those partially or fully achieved goals that are consistent with the actions observed so far. The Goal Graph analysis also reveals valid plans for the recognised goals or part of these goals. Our approach to goal recognition does not need a plan library. It does not suffer from the problems in the acquisition and hand-coding of large plan libraries, neither does it have the problems in searching the plan space of exponential size. We describe two algorithms for Goal Graph construction and analysis in this paradigm. These algorithms are both provably sound, polynomial-time, and polynomial-space. The number of goals recognised by our algorithms is usually very small after a sequence of observed actions has been processed. Thus the sequence of observed actions is well explained by the recognised goals with little ambiguity. We have evaluated these algorithms in the UNIX domain, in which excellent performance has been achieved in terms of accuracy, efficiency, and scalability.

An exactly solvable four transition point model

Heavy particle collisions, in particular low-energy ion-atom collisions, are amenable to semiclassical JWKB phase integral analysis in the complex plane of the internuclear separation. Analytic continuation in this plane requires due attention to the Stokes phenomenon which parametrizes the physical mechanisms of curve crossing, non-crossing, the hybrid Nikitin model, rotational coupling and predissociation. Complex transition points represent adiabatic degeneracies. In the case of two or more such points, the Stokes constants may only be completely determined by resort to the so-called comparison- equation method involving, in particular, parabolic cylinder functions or Whittaker functions and their strong-coupling asymptotics. In particular, the Nikitin model is a two transition-point one-double-pole problem in each half-plane corresponding to either ingoing or outgoing waves. When the four transition points are closely clustered, new techniques are required to determine Stokes constants. However, such investigations remain incomplete, A model problem is therefore solved exactly for scattering along a one-dimensional z-axis. The energy eigenvalue is b(2)-a(2) and the potential comprises -z(2)/2 (parabolic) and -a(2) + b(2)/2z(2) (centrifugal/centripetal) components. The square of the wavenumber has in the complex z-plane, four zeros each a transition point at z = +/-a +/- ib and has a double pole at z = 0. In cases (a) and (b), a and b are real and unitarity obtains. In case (a) the reflection and transition coefficients are parametrized by exponentials when a(2) + b(2) > 1/2. In case (b) they are parametrized by trigonometrics when a(2) + b(2) <1/2 and total reflection is achievable. In case (c) a and b are complex and in general unitarity is not achieved due to loss of flux to a continuum (O'Rourke and Crothers, 1992 Proc. R. Sec. 438 1). Nevertheless, case (c) coefficients reduce to (a) or (b) under appropriate limiting conditions. Setting z = ht, with h a real constant, an attempt is made to model a two-state collision problem modelled by a pair of coupled first-order impact parameter equations and an appropriate (T) over tilde-tau relation, where (T) over tilde is the Stueckelberg variable and tau is the reduced or scaled time. The attempt fails because (T) over tilde is an odd function of tau, which is unphysical in a real collision problem. However, it is pointed out that by applying the Kummer exponential model to each half-plane (O'Rourke and Crothers 1994 J. Phys. B: At. Mel. Opt. Phys. 27 2497) the current model is in effect extended to a collision problem with four transition points and a double pole in each half-plane. Moreover, the attempt in itself is not a complete failure since it is shown that the result is a perfect diabatic inelastic collision for a traceless Hamiltonian matrix, or at least when both diagonal elements are odd and the off-diagonal elements equal and even.

Equilibrium polymerization of cyclic carbonate oligomers. II. Role of multiple active sites

Ring opening polymerization of bisphenol A polycarbonate is studied by Monte Carlo simulations of a model comprising a fixed number of Lennard-Jones particles and harmonic bonds [J. Chem. Phys. 115, 3895 (2001)]. Bond interchanges produced by a low concentration (0.10%less than or equal toc(a)less than or equal to0.36%) of chemically active particles lead to equilibrium polymerization. There is a continuous transition in both 2D and 3D from unpolymerized cyclic oligomers at low density to a system of linear chains at high density, and the polymeric phase is much more stable in three dimensions than in two. The steepness of the polymerization transition increases rapidly as c(a) decreases, suggesting that it is discontinuous in the limit c(a)-->0. The transition is entropy driven, since the average potential energy increases systematically upon polymerization, and there is a steady decline in the degree of polymerization as the temperature is lowered. The mass distribution functions for open chains and for rings are unimodal, with exponentially decaying tails that can be fitted by Zimm-Schulz functions and simpler exponential forms. (C) 2002 American Institute of Physics.

Light emission from scanning tunnelling microscope on polycrystalline Au films - what is happening at the single-grain level?

When operated with a metallic tip and sample the scanning tunnelling microscope constitutes a nanoscale, plasmonic light source yielding broadband emission up to a photon energy determined by the applied bias. The emission is due to tunnelling electron excitation and subsequent radiative decay of localized plasmon modes, which can be on the lateral scale of a single metal grain (similar to 25 nm) or less. For a Au-tip/Au-polycrystalline sample under ambient conditions it is found that the intensity and spectral content of the emitted light are not dependent on the lateral grain dimension, but are predominantly determined by the tip geometry. However, the intensity increases strongly with increasing film thickness (grain depth) up to 20-25 nm or approximately the skin depth of the Au film. Photon maps can show less emissive grains and two classes of this occurrence are distinguished. The first is geometrical in origin - a double-tip structure in this case - while the second is due to a contamination-induced lowering of the local work function that causes the tunnel gap to increase. It is suggested that differences in work-function lowering between grains presenting different crystalline facets, combined with an exponential decay in emitted light intensity with tip - sample distance, leads to grain contrast. These results are relevant to tip-enhanced Raman scattering and the fabrication of micro/nano-scale planar, light-emitting tunnel devices.

Effect of plasma scale length on multi-MeV proton production by intense laser pulses

The influence of the plasma density scale length on the production of MeV protons from thin foil targets irradiated at I lambda (2) = 5 x 10(19) Wcm(-2) has been studied. With an unperturbed foil, protons with energy >20 MeV were formed in an exponential energy spectrum with a temperature of 2.5 +/- 0.3 MeV. When a plasma with a scale length of 100 mum was preformed on the back of the foil, the maximum proton energy was reduced to

Novel Porphyrin-Incorporated Hydrogels for Photoactive Intraocular Lens Biomaterials

Novel surface-modified hydrogel materials have been prepared by binding charged porphyrins TMPyP (tetrakis-(4-N-methylpyridyl)porphyrin) and TPPS (tetrakis(4-sulfonatophenyl)porphyrin) to copolymers of HEMA (2-hydroxyethyl methacrylate) with either MAA (methacrylic acid) or DEAEMA (2-(diethylamino)ethylmethacrylate). The charged hydrogels display strong electrostatic interactions with the appropriate cationic or anionic porphyrins to give materials which are intended to be used to generate cytotoxic singlet oxygen (1O2) on photoexcitation and can therefore be used to reduce postoperative infection of the intraocular hydrogel-based replacement lenses that are used in cataract surgery. The UV/vis spectra of TMPyP in MAA:HEMA copolymers showed a small shift in the Soret band and a change from single exponential (161 ���­s) triplet decay lifetime in solution to a decay that could be fitted to a biexponential fit with two approximately equal components with ���´ ) 350 and 1300 ���­s. O2 bubbling reduced the decay to a dominant (90%) component with a much reduced lifetime of 3 ���­s and a minor, longer lived (20 ���­s) component. With D2O solvent the 1O2 lifetime was measured by 1270 nm fluorescence as 35 ���­s in MAA:HEMA, compared to 67 ���­s in solution, although absorbance-matched samples showed similar yield of 1O2 in the polymers and in aqueous solution. In contrast to the minor perturbation in photophysical properties caused by binding TMPyP to MAA:HEMA, TPPS binding to DEAEMA:HEMA copolymers profoundly changed the 1O2 generating ability of the TPPS. In N2-bubbled samples, the polymer-bound TPPS behaved in a similar manner to TMPyP in its copolymer host; however, O2 bubbling had only a very small effect on the triplet lifetime and no 1O2 generation could be detected. The difference in behavior may be linked to differences in binding in the two systems. With TMPyP in MAA:HEMA, confocal fluorescence microscopy showed significant penetration of the porphyrin into the core of the polymer film samples (>150 ���­m). However, for TPPS in DEAEMA:HEMA copolymers, although the porphyrin bound much more readily to the polymer, it remained localized in the first 20 ���­m, even in heavily loaded samples. It is possible that the resulting high concentration of TPPS may have cross-linked the hydrogels to such an extent that it significantly reduced the solubility and/or diffusion rate of oxygen into the doped polymers. This effect is significant since it demonstrates that even simple electrostatic binding of charged porphyrins to hydrogels can have an unexpectedly large effect on the properties of the system as a whole. In this case it makes the apparently promising TPPS/DEAEMA:HEMA system a poor candidate for clinical application as a postoperative antibacterial treatment for intraocular lenses while the apparently equivalent cationic system TMPyP/MAA:HEMA displays all the required properties.

Damage to plasmid DNA induced by low energy carbon ions

The damage induced in supercoiled plasmid DNA molecules by 1-6 keV carbon ions has been investigated as a function of ion exposure, energy and charge state. The production of short linear fragments through multiple double strand breaks has been demonstrated and exponential exposure responses for each of the topoisomers have been found. The cross section for the loss of supercoiling was calculated to be (2.2 +/- 0.5) x 10(-14) cm(2) for 2 keVC(+) ions. For singly charged carbon ions, increased damage was observed with increasing ion energy. In the case of 2 keV doubly charged ions, the damage was greater than for singly charged ions of the same energy. These observations demonstrate that ion induced damage is a function of both the kinetic and potential energies of the ion.

Effects of low energy carbon ions on plasmid DNA

The damage induced in supercoiled plasmid DNA molecules by low energy (< 1 keV u-1) singly and doubly charged carbon ions has been investigated as a function of ion exposure. The production of short linear fragments through multiple double strand breakage is indicated and exponential exposure responses for each of the topoisomers are presented. The damage produced by C2+ is apparent at much lower ion exposures that with C+.

Measurement of the duration of X-ray lasing pumped by an optical laser pulse of picosecond duration

Measurements of the duration of X-ray lasing pumped with picosecond pulses from the VULCAN optical laser are obtained using a streak camera with 700 fs temporal resolution. Combined with a temporal smearing due to the spectrometer employed, we have measured X-ray laser pulse durations for Ni-like silver at 13.9 nm with a total time resolution of 1.1 ps. For Ni-like silver, the X-ray laser output has a steep rise followed by an approximately exponential temporal decay with measured full-width at half-maximum (FWHM) of 3.7 (+/-0.5) ps. For Ne-like nickel lasing at 23.1 nm, the measured duration of lasing is approximate to10.7 (+/-1) ps (FWHM). An estimate of the duration of the X-ray laser gain has been obtained by temporally resolving spectrally integrated continuum and resonance line emission. For Ni-like silver, this time of emission is approximate to22 (+/-2) ps (FWHM), while for Ne-like nickel we measure approximate to35 (+/-2) ps (FWHM). Assuming that these times of emission correspond to the gain duration, we show that a simple model consistently relates the gain durations to the measured durations of X-ray lasing. (C) 2002 Elsevier Science B.V. All rights reserved.