Seawater transfer alters the intestinal microbiota profiles of Atlantic salmon (Salmo salar L.)

This study was funded by a BBSRC Eastbio PhD studentship to CED and BBSRC grant BB/M026604/1. The authors wish to thank Ana Rita Sancho Silva for facilitating the sampling for the experiment. Furthermore we would like to express our gratitude to Ian and Alastair Fraser for their support at the SFF fish farms on the Isle of Mull.Peer reviewedPublisher PD

Millimeter and Submillimeter Survey of the R Corona Australis Region

Using a combination of data from the Antarctic Submillimeter Telescope and Remote Observatory (AST/RO), the Arizona Radio Observatory Kitt Peak 12m telescope and the Arizona Radio Observatory 10m Heinrich Hertz Telescope, we have studied the most active part of the R CrA molecular cloud in multiple transitions of Carbon Monoxide, HCO$^+$ and 870\micron continuum emission. Since R CrA is nearby (130 pc), we are able to obtain physical spatial resolution as high as 0.01pc over an area of 0.16 pc$^2$, with velocity resolution finer than 1 km/s. Mass estimates of the protostar driving the mm-wave emission derived from HCO$^+$, dust continuum emission and kinematic techniques point to a young, deeply embedded protostar of $\sim$0.5-0.75 M$_\odot$, with a gaseous envelope of similar mass. A molecular outflow is driven by this source that also contains at least 0.8 M$_\odot$ of molecular gas with $\sim$0.5 L$_\odot$ of mechanical luminosity. HCO$^+$ lines show the kinematic signature of infall motions as well as bulk rotation. The source is most likely a Class 0 protostellar object not yet visible at near-IR wavelengths. With the combination of spatial and spectral resolution in our data set, we are able to disentangle the effects of infall, rotation and outflow towards this young object.Comment: 29 pages, 9 figures. Accepted for publication in the Astrophysical Journa

The ATPase cycle of PcrA helicase and its coupling to translocation on DNA.

The superfamily 1 bacterial helicase PcrA has a role in the replication of certain plasmids, acting with the initiator protein (RepD) that binds to and nicks the double-stranded origin of replication. PcrA also translocates single-stranded DNA with discrete steps of one base per ATP hydrolyzed. Individual rate constants have been determined for the DNA helicase PcrA ATPase cycle when bound to either single-stranded DNA or a double-stranded DNA junction that also has RepD bound. The fluorescent ATP analogue 2'(3')-O-(N-methylanthraniloyl)ATP was used throughout all experiments to provide a complete ATPase cycle for a single nucleotide species. Fluorescence intensity and anisotropy stopped-flow measurements were used to determine rate constants for binding and release. Quenched-flow measurements provided the kinetics of the hydrolytic cleavage step. The fluorescent phosphate sensor MDCC-PBP was used to measure phosphate release kinetics. The chemical cleavage step is the rate-limiting step in the cycle and is essentially irreversible and would result in the bound ATP complex being a major component at steady state. This cleavage step is greatly accelerated by bound DNA, producing the high activation of this protein compared to the protein alone. The data suggest the possibility that ADP is released in two steps, which would result in bound ADP also being a major intermediate, with bound ADP.P(i) being a very small component. It therefore seems likely that the major transition in structure occurs during the cleavage step, rather than P(i) release. ATP rebinding could then cause reversal of this structural transition. The kinetic mechanism of the PcrA ATPase cycle is very little changed by potential binding to RepD, supporting the idea that RepD increases the processivity of PcrA by increasing affinity to DNA rather than affecting the enzymatic properties per se

SLoMo: automated site localization of modifications from ETD/ECD mass spectra

Recently, software has become available to automate localization of phosphorylation sites from CID data and to assign associated confidence scores. We present an algorithm, SLoMo (Site Localization of Modifications), which extends this capability to ETD/ECD mass spectra. Furthermore, SLoMo caters for both high and low resolution data and allows for site-localization of any UniMod post-translational modification. SLoMo accepts input data from a variety of formats (e.g., Sequest, OMSSA). We validate SLoMo with high and low resolution ETD, ECD, and CID data

Pressure dependence of the luminescence and Raman modes in polyfluorene

The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file.Title from title screen of research.pdf file viewed on (February 28, 2007)Includes bibliographical references.Vita.Thesis (Ph.D.) University of Missouri-Columbia 2006.Dissertations, Academic -- University of Missouri--Columbia -- Physics.I present a study of the optical properties of poly-para-phenylene and three different side-chain substituted polyfluorene polymers. I present an analysis of the Raman spectra under hydrostatic pressures for three oligo(para-phenylene) materials (p-terphenyl, 3P; p-quaterphenyl, 4P; and p-hexaphenyl, 6P) under hydrostatic pressure up to 80 kbar, with a focus on the 15-25 kbar region where the molecules are known to be forced into a more planar state. I present studies of the photoluminescence (PL) and Raman modes of polyfluorene (PF2/6) under hydrostatic pressures of 0-120 kbar at room temperature. The distinct PL with associated vibronics observed at atmospheric pressure blue shifts and changes dramatically around 20 kbar, above this pressure a broad peak at about 2.3 eV, associated with the keto defect, begins to dominate the PL. Raman modes observed are the 1417 cm-1 mode from the C-C stretch within the monomer, the 1342 cm-1 and 1290 cm-1 modes from phenyl rings connecting the monomer units, and the 1600 cm-1 modes from the intra-ring C-C stretch. All Raman modes analyzed shift to higher energies with pressure. Some of the phonon lines exhibit an antiresonance effect at higher pressures that is indicative of a high electron phonon interaction between the Raman phonons and the (real) PL transitions

Coherent State for a Relativistic Spinless Particle

The Klein-Gordon equation with scalar potential is considered. In the Feshbach-Villars representation the annihilation operator for a linear potential is defined and its eigenstates are obtained. Although the energy levels in this case are not equally-spaced, depending on the eigenvalues of the annihilation operator, the states are nearly coherent and squeezed. The relativistic Poschl-Teller potential is introduced. It is shown that its energy levels are equally-spaced. The coherence of time evolution of the eigenstates of the annihilation operator for this potential is evaluated.Comment: 12 pages, 11 figures, to appear in Phys. lett.