The genome packaging machinery of dsDNA bacteriophage PRD1

Viral genomes are encapsidated within protective protein shells. This encapsidation can be achieved either by a co-condensation reaction of the nucleic acid and coat proteins, or by first forming empty viral particles which are subsequently packaged with nucleic acid, the latter mechanism being typical for many dsDNA bacteriophages. Bacteriophage PRD1 is an icosahedral, non-tailed dsDNA virus that has an internal lipid membrane, the hallmark of the Tectiviridae family. Although PRD1 has been known to assemble empty particles into which the genome is subsequently packaged, the mechanism for this has been unknown, and there has been no evidence for a separate packaging vertex, similar to the portal structures used for packaging in the tailed bacteriophages and herpesviruses. In this study, a unique DNA packaging vertex was identified for PRD1, containing the packaging ATPase P9, packaging factor P6 and two small membrane proteins, P20 and P22, extending the packaging vertex to the internal membrane. Lack of small membrane protein P20 was shown to totally abolish packaging, making it an essential part of the PRD1 packaging mechanism. The minor capsid proteins P6 was shown to be an important packaging factor, its absence leading to greatly reduced packaging efficiency. An in vitro DNA packaging mechanism consisting of recombinant packaging ATPase P9, empty procapsids and mutant PRD1 DNA with a LacZ-insert was developed for the analysis of PRD1 packaging, the first such system ever for a virus containing an internal membrane. A new tectiviral sequence, a linear plasmid called pBClin15, was identified in Bacillus cereus, providing material for sequence analysis of the tectiviruses. Analysis of PRD1 P9 and other putative tectiviral ATPase sequences revealed several conserved sequence motifs, among them a new tectiviral packaging ATPase motif. Mutagenesis studies on PRD1 P9 were used to confirm the significance of the motifs. P9-type putative ATPase sequences carrying a similar sequence motif were identified in several other membrane containing dsDNA viruses of bacterial, archaeal and eukaryotic hosts, suggesting that these viruses may have similar packaging mechanisms. Interestingly, almost the same set of viruses that were found to have similar putative packaging ATPases had earlier been found to share similar coat protein folds and capsid structures, and a common origin for these viruses had been suggested. The finding in this study of similar packaging proteins further supports the idea that these viruses are descendants of a common ancestor.

Theoretical Studies on Coupled Electron and Proton Transfer in Cytochrome c Oxidase

The complexity of life is based on an effective energy transduction machinery, which has evolved during the last 3.5 billion years. In aerobic life, the utilization of the high oxidizing potential of molecular oxygen powers this machinery. Oxygen is safely reduced by a membrane bound enzyme, cytochrome c oxidase (CcO), to produce an electrochemical proton gradient over the mitochondrial or bacterial membrane. This gradient is used for energy-requiring reactions such as synthesis of ATP by F0F1-ATPase and active transport. In this thesis, the molecular mechanism by which CcO couples the oxygen reduction chemistry to proton-pumping has been studied by theoretical computer simulations. By building both classical and quantum mechanical model systems based on the X-ray structure of CcO from Bos taurus, the dynamics and energetics of the system were studied in different intermediate states of the enzyme. As a result of this work, a mechanism was suggested by which CcO can prevent protons from leaking backwards in proton-pumping. The use and activation of two proton conducting channels were also enlightened together with a mechanism by which CcO sorts the chemical protons from pumped protons. The latter problem is referred to as the gating mechanism of CcO, and has remained a challenge in the bioenergetics field for more than three decades. Furthermore, a new method for deriving charge parameters for classical simulations of complex metalloenzymes was developed.

Charge transport in a Tomonaga-Luttinger liquid: Effects of pumping and bias

We study the current produced in a Tomonaga-Luttinger liquid by an applied bias and by weak, pointlike impurity potentials which are oscillating in time. We use bosonization to perturbatively calculate the current up to second order in the impurity potentials. In the regime of small bias and low pumping frequency, both the dc and ac components of the current have power-law dependences on the bias and pumping frequencies with an exponent 2K-1 for spinless electrons, where K is the interaction parameter. For K < 1/2, the current grows large for special values of the bias. For noninteracting electrons with K=1, our results agree with those obtained using Floquet scattering theory for Dirac fermions. We also discuss the cases of extended impurities and of spin-1/2 electrons.

Nonadiabatic charge pumping by oscillating potentials in one dimension: Results for infinite system and finite ring

We study charge pumping when a combination of static potentials and potentials oscillating with a time period T is applied in a one-dimensional system of noninteracting electrons. We consider both an infinite system using the Dirac equation in the continuum approximation and a periodic ring with a finite number of sites using the tight-binding model. The infinite system is taken to be coupled to reservoirs on the two sides which are at the same chemical potential and temperature. We consider a model in which oscillating potentials help the electrons to access a transmission resonance produced by the static potentials and show that nonadiabatic pumping violates the simple sin phi rule which is obeyed by adiabatic two-site pumping. For the ring, we do not introduce any reservoirs, and we present a method for calculating the current averaged over an infinite time using the time evolution operator U(T) assuming a purely Hamiltonian evolution. We analytically show that the averaged current is zero if the Hamiltonian is real and time-reversal invariant. Numerical studies indicate another interesting result, namely, that the integrated current is zero for any time dependence of the potential if it is applied to only one site. Finally we study the effects of pumping at two sites on a ring at resonant and nonresonant frequencies, and show that the pumped current has different dependences on the pumping amplitude in the two cases.

Peristaltic pumping in a circular tube in the presence of an eccentric catheter

The influence of an eccentrically inserted catheter on the peristaltic pumping in a tube is investigated under long wavelength, low Reynolds number assumptions. The radially asymmetric deformation of the wall arising through an eccentrically inserted catheter is taken into consideration by choosing an appropriate bipolar coordinate system. The effect of the position and size of the catheter on pumping characteristics is studied. The best performance of pumping is noticed at a certain position of the catheter. The size of the catheter, when placed eccentrically, alters the pressure signature significantly inside the bolus, unlike the concentric case discussed by Lykoudis and Roos (1971). Further, the maximum pressure rise in one period of the peristaltic wave is observed to decrease with an increase in the eccentricity.

Peristaltic pumping of a micropolar fluid in a tube

Peristaltic transport of a micropolar fluid in a circular tube is studied under low Reynolds number and long wavelength approximations. The closed form solutions are obtained. for velocity, microrotation components, as well as the stream function and they contain new additional parameters namely, N the coupling number and m the micropolar parameter. In the case of free pumping (pressure difference Deltap = 0) the difference in pumping flux is observed to be very small for Newtonian and micropolar fluids but in the case of pumping (Deltap > 0) the characteristics are significantly altered for different N and m. It is observed that the peristalsis in micropolar fluids works as a pump against a greater pressure rise compared with a Newtonian fluid. Streamline patterns which depict trapping phenomena are presented for different parameter ranges. The limit on the trapping of the center streamline is obtained. The effects of N and m on friction force for different Deltap are discussed.

TURBULENT PUMPING OF MAGNETIC FLUX REDUCES SOLAR CYCLE MEMORY AND THUS IMPACTS PREDICTABILITY OF THE SUN'S ACTIVITY

Prediction of the Sun's magnetic activity is important because of its effect on space environment and climate. However, recent efforts to predict the amplitude of the solar cycle have resulted in diverging forecasts with no consensus. Yeates et al. have shown that the dynamical memory of the solar dynamo mechanism governs predictability, and this memory is different for advection- and diffusion-dominated solar convection zones. By utilizing stochastically forced, kinematic dynamo simulations, we demonstrate that the inclusion of downward turbulent pumping of magnetic flux reduces the memory of both advection- and diffusion-dominated solar dynamos to only one cycle; stronger pumping degrades this memory further. Thus, our results reconcile the diverging dynamo-model-based forecasts for the amplitude of solar cycle 24. We conclude that reliable predictions for the maximum of solar activity can be made only at the preceding minimum-allowing about five years of advance planning for space weather. For more accurate predictions, sequential data assimilation would be necessary in forecasting models to account for the Sun's short memory.

Regenerative amplifier with continuously variable pulse duration used in an optical parametric chirped-pulse amplification laser system for synchronous pumping

A Nd:glass regenerative amplifier has been set up to generate the pumping pulse with variable pulse width for an optical parametric chirped-pulse amplification (OPCPA) laser system. Each pulse of the pulse train from a cw self-mode-locking femtosecond Ti:sapphire oscillator is stretched to approximate to300 ps at 1062 nm to be split equally and injected into a nonlinear crystal and the Nd:glass regenerative amplifier, as the chirped signal pulse train and the seed pulse train of the pumping laser system, respectively. By adjusting the cavity length of the regenerative amplifier directly, the width of amplified pulse could be varied continuously from approximate to300 ps to approximate to3 ns. The chirped signal pulse for the OPCPA laser system and the seed pulse for the pumping laser system come from the same oscillator, so that the time jitter between the signal pulse and the pumping pulse in optical parametric amplification stages could be <10 ps. (C) 2003 Society of Photo-Optical Instrumentation Engineers.

Effects of relative phase in an open ladder system without incoherent pumping

We studied effects of the relative phase between the probe and driving fields on the absorption and dispersion properties in an open three-level ladder system with spontaneously generated coherence but without incoherent pumping. It is shown that by the phase controlling, switching from absorption to lasing without inversion (LWI) and enhancing remarkablely LWI gain can be realized; large index of refraction with zero absorption and the electromagnetically induced transparency can be obtained. We also find that varying the atomic injection and exit rates has a considerable influence on the phase dependent-absorption property of the probe field, existent of the atomic injection and exit rates gives the necessary condition of the realization of LWI, getting LWI is impossible in the corresponding closed system without incoherent pumping. We studied effects of the relative phase between the probe and driving fields on the absorption and dispersion properties in an open three-level ladder system with spontaneously generated coherence but without incoherent pumping. It is shown that by the phase controlling, switching from absorption to lasing without inversion (LWI) and enhancing remarkablely LWI gain can be realized; large index of refraction with zero absorption and the electromagnetically induced transparency can be obtained. We also find that varying the atomic injection and exit rates has a considerable influence on the phase dependent-absorption property of the probe field, existent of the atomic injection and exit rates gives the necessary condition of the realization of LWI, getting LWI is impossible in the corresponding closed system without incoherent pumping.

Ecological effects of trial pumpings in the Upper Lambourn: Stage 1 group pumping test Upper Lambourn group, September - November 1975

This report to the Thames Water Authority and Central Water Planning Unit is on research carried out in conjunction with the Stage 1 Group Pumping Test of five boreholes in the upper Lambourn Group for a period of three months in September, October and November 1975. The aim of the study was to assess the ecological effects of the pumpin g of five bore-holes in the upper Lambourn. That is, to determine how the seasonal sequence of ecological events in the river differed from what would hav e occurred had no pumping taken place. Since this 'experiment' has no control it is not possible to make a direct assessment. Nevertheless, by careful monitoring of ecological events before, during and after the pumping it is possible to document changes in th e river and by reference to the data already available for the Rive r Lambourn, normal seasonal changes in the flora and fauna can be separated from changes which may be attributable to the pumping and subsequent events.

Design of a highly stable, high-conversion-efficiency pumping source for optical parametric amplifier by extending efficient crystal length

The objective of this study is to improve the stability of pumping source of optical parametric amplifier. Analysis by simulation leads to the conclusion that the stability of the second harmonic can be improved by using properly the intensity of fundamental light and corresponding length of the crystal. By the method of the noncollinear two-pass second harmonic or the tandem second harmonic, the efficient crystal length is extended to a proper value, and the stability of the second harmonic output has been improved two times more than that for the fundamental light, and the conversion-efficiency is about 70% in experiment. When the variation of the fundamental light is about 10%, the variation of the second harmonic intensity has been controlled within 5%. (c) 2006 Elsevier Ltd. All rights reserved.