Proteorhodopsin overproduction enhances the long-term viability of Escherichia coli

Genes encoding the photoreactive protein proteorhodopsin (PR) have been found in a wide range of marine bacterial species, reflecting the significant contribution that PR makes to energy flux and carbon cycling in ocean ecosystems. PR can also confer advantages to enhance the ability of marine bacteria to survive periods of starvation. Here, we investigate the effect of heterologously produced PR on the viability of Escherichia coli. Quantitative mass spectrometry shows that E. coli, exogenously supplied with the retinal cofactor, assembles as many as 187,000 holo-PR molecules per cell, accounting for approximately 47% of the membrane area; even cells with no retinal synthesize ∼148,000 apo-PR molecules per cell. We show that populations of E. coli cells containing PR exhibit significantly extended viability over many weeks, and we use single-cell Raman spectroscopy (SCRS) to detect holo-PR in 9-month-old cells. SCRS shows that such cells, even incubated in the dark and therefore with inactive PR, maintain cellular levels of DNA and RNA and avoid deterioration of the cytoplasmic membrane, a likely basis for extended viability. The substantial proportion of the E. coli membrane required to accommodate high levels of PR likely fosters extensive intermolecular contacts, suggested to physically stabilize the cell membrane and impart a long-term benefit manifested as extended viability in the dark. We propose that marine bacteria could benefit similarly from a high PR content, with a stabilized cell membrane extending survival when those bacteria experience periods of severe nutrient or light limitation in the oceans

Interferometry of a Single Nanoparticle Using the Gouy Phase of a Focused Laser Beam

We provide a quantitative explanation of the mechanism of the far-field intensity modulation induced by a nanoparticle in a focused Gaussian laser beam, as was demonstrated in several recent direct detection studies. Most approaches take advantage of interference between the incident light and the scattered light from a nanoparticle to facilitate a linear dependence of the signal on the nanoparticle volume. The phase relation between the incoming field and the scattered field by the nanoparticle is elucidated by the concept of Gouy phase. This phase relation is used to analyze the far-field signal-to-noise ratio as a function of exact nanoparticle position with respect to the beam focus. The calculation suggests that a purely dispersive nanoparticle should be displaced from the Gaussian beam focus to generate a far-field intensity change

Investigation of the Jahn-Teller Transition in TiF3 using Density Functional Theory

We use first principles density functional theory to calculate electronic and magnetic properties of TiF3 using the full potential linearized augmented plane wave method. The LDA approximation predicts a fully saturated ferromagnetic metal and finds degenerate energy minima for high and low symmetry structures. The experimentally observed Jahn-Teller phase transition at Tc=370K can not be driven by the electron-phonon interaction alone, which is usually described accurately by LDA. Electron correlations beyond LDA are essential to lift the degeneracy of the singly occupied Ti t2g orbital. Although the on-site Coulomb correlations are important, the direction of the t2g-level splitting is determined by the dipole-dipole interactions. The LDA+U functional predicts an aniferromagnetic insulator with an orbitally ordered ground state. The input parameters U=8.1 eV and J=0.9 eV for the Ti 3d orbital were found by varying the total charge on the TiF$_6^{2-}$ ion using the molecular NRLMOL code. We estimate the Heisenberg exchange constant for spin-1/2 on a cubic lattice to be approximately 24 K. The symmetry lowering energy in LDA+U is about 900 K per TiF3 formula unit.Comment: 7 pages, 9 figures, to appear in Phys. Rev.

Strongly focused light beams interacting with single atoms in free space

We construct 3-D solutions of Maxwell's equations that describe Gaussian light beams focused by a strong lens. We investigate the interaction of such beams with single atoms in free space and the interplay between angular and quantum properties of the scattered radiation. We compare the exact results with those obtained with paraxial light beams and from a standard input-output formalism. We put our results in the context of quantum information processing with single atoms.Comment: 9 pages, 9 figure

Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour

Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30–35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding

Distribution function approach to redshift space distortions. Part II: N-body simulations

Measurement of redshift-space distortions (RSD) offers an attractive method to directly probe the cosmic growth history of density perturbations. A distribution function approach where RSD can be written as a sum over density weighted velocity moment correlators has recently been developed. We use Nbody simulations to investigate the individual contributions and convergence of this expansion for dark matter. If the series is expanded as a function of powers of mu, cosine of the angle between the Fourier mode and line of sight, there are a finite number of terms contributing at each order. We present these terms and investigate their contribution to the total as a function of wavevector k. For mu^2 the correlation between density and momentum dominates on large scales. Higher order corrections, which act as a Finger-of-God (FoG) term, contribute 1% at k~0.015h/Mpc, 10% at k~0.05h/Mpc at z=0, while for k>0.15h/Mpc they dominate and make the total negative. These higher order terms are dominated by density-energy density correlations which contribute negatively to the power, while the contribution from vorticity part of momentum density auto-correlation is an order of magnitude lower. For mu^4 term the dominant term on large scales is the scalar part of momentum density auto-correlation, while higher order terms dominate for k>0.15h/Mpc. For mu^6 and mu^8 we find it has very little power for k<0.15h/Mpc. We also compare the expansion to the full 2D P^ss(k,mu) as well as to their multipoles. For these statistics an infinite number of terms contribute and we find that the expansion achieves percent level accuracy for kmu<0.15h/Mpc at 6th order, but breaks down on smaller scales because the series is no longer perturbative. We explore resummation of the terms into FoG kernels, which extend the convergence up to a factor of 2 in scale. We find that the FoG kernels are approximately Lorentzian.Comment: 21 pages, 9 figures, published in JCA

Star Formation and Dynamics in the Galactic Centre

The centre of our Galaxy is one of the most studied and yet enigmatic places in the Universe. At a distance of about 8 kpc from our Sun, the Galactic centre (GC) is the ideal environment to study the extreme processes that take place in the vicinity of a supermassive black hole (SMBH). Despite the hostile environment, several tens of early-type stars populate the central parsec of our Galaxy. A fraction of them lie in a thin ring with mild eccentricity and inner radius ~0.04 pc, while the S-stars, i.e. the ~30 stars closest to the SMBH (<0.04 pc), have randomly oriented and highly eccentric orbits. The formation of such early-type stars has been a puzzle for a long time: molecular clouds should be tidally disrupted by the SMBH before they can fragment into stars. We review the main scenarios proposed to explain the formation and the dynamical evolution of the early-type stars in the GC. In particular, we discuss the most popular in situ scenarios (accretion disc fragmentation and molecular cloud disruption) and migration scenarios (star cluster inspiral and Hills mechanism). We focus on the most pressing challenges that must be faced to shed light on the process of star formation in the vicinity of a SMBH.Comment: 68 pages, 35 figures; invited review chapter, to be published in expanded form in Haardt, F., Gorini, V., Moschella, U. and Treves, A., 'Astrophysical Black Holes'. Lecture Notes in Physics. Springer 201

The PHENIX Experiment at RHIC

The physics emphases of the PHENIX collaboration and the design and current status of the PHENIX detector are discussed. The plan of the collaboration for making the most effective use of the available luminosity in the first years of RHIC operation is also presented.Comment: 5 pages, 1 figure. Further details of the PHENIX physics program available at http://www.rhic.bnl.gov/phenix