454-Pyrosequencing: A Molecular Battiscope for Freshwater Viral Ecology

Viruses, the most abundant biological entities on the planet, are capable of infecting organisms from all three branches of life, although the majority infect bacteria where the greatest degree of cellular diversity lies. However, the characterization and assessment of viral diversity in natural environments is only beginning to become a possibility. Through the development of a novel technique for the harvest of viral DNA and the application of 454 pyrosequencing, a snapshot of the diversity of the DNA viruses harvested from a standing pond on a cattle farm has been obtained. A high abundance of viral genotypes (785) were present within the virome. The absolute numbers of lambdoid and Shiga toxin (Stx) encoding phages detected suggested that the depth of sequencing had enabled recovery of only ca. 8% of the total virus population, numbers that agreed within less than an order of magnitude with predictions made by rarefaction analysis. The most abundant viral genotypes in the pond were bacteriophages (93.7%). The predominant viral genotypes infecting higher life forms found in association with the farm were pathogens that cause disease in cattle and humans, e.g. members of the Herpesviridae. The techniques and analysis described here provide a fresh approach to the monitoring of viral populations in the aquatic environment, with the potential to become integral to the development of risk analysis tools for monitoring the dissemination of viral agents of animal, plant and human diseases

A general model to optimise CuII labelling efficiency of double-histidine motifs for pulse dipolar EPR applications

JLW is supported by the BBSRC DTP Eastbio. We thank the Leverhulme Trust for support (RPG-2018-397). This work was supported by equipment funding through the Wellcome Trust (099149/Z/12/Z) and BBSRC (BB/R013780/1). We gratefully acknowledge ISSF support to the University of St Andrews from the Wellcome Trust.Electron paramagnetic resonance (EPR) distance measurements are making increasingly important contributions to studies of biomolecules underpinning health and disease by providing highly accurate and precise geometric constraints. Combining double-histidine (dH) motifs with CuII spin labels shows promise for further increasing the precision of distance measurements, and for investigating subtle conformational changes. However, non-covalent coordination-based spin labelling is vulnerable to low binding affinity. Dissociation constants of dH motifs for CuII-nitrilotriacetic acid were previously investigated via relaxation induced dipolar modulation enhancement (RIDME), and demonstrated the feasibility of exploiting the double histidine motif for EPR applications at sub-μM protein concentrations. Herein, the feasibility of using modulation depth quantitation in CuII-CuII RIDME to simultaneously estimate a pair of non-identical independent KD values in such a tetra-histidine model protein is addressed. Furthermore, we develop a general speciation model to optimise CuII labelling efficiency, in dependence of pairs of identical or disparate KD values and total CuII label concentration. We find the dissociation constant estimates are in excellent agreement with previously determined values, and empirical modulation depths support the proposed model.Publisher PDFPeer reviewe

D-Foam Phenomenology: Dark Energy, the Velocity of Light and a Possible D-Void

In a D-brane model of space-time foam, there are contributions to the dark energy that depend on the D-brane velocities and on the density of D-particle defects. The latter may also reduce the speeds of photons linearly with their energies, establishing a phenomenological connection with astrophysical probes of the universality of the velocity of light. Specifically, the cosmological dark energy density measured at the present epoch may be linked to the apparent retardation of energetic photons propagating from nearby AGNs. However, this nascent field of `D-foam phenomenology' may be complicated by a dependence of the D-particle density on the cosmological epoch. A reduced density of D-particles at redshifts z ~ 1 - a `D-void' - would increase the dark energy while suppressing the vacuum refractive index, and thereby might reconcile the AGN measurements with the relatively small retardation seen for the energetic photons propagating from GRB 090510, as measured by the Fermi satellite.Comment: 10 pages, 3 figure

From AMANDA to IceCube

The first string of the neoteric high energy neutrino telescope IceCube successfully began operating in January 2005. It is anticipated that upon completion the new detector will vastly increase the sensitivity and extend the reach of AMANDA to higher energies. A discussion of the IceCube's discovery potential for extra-terrestrial neutrinos, together with the prospects of new physics derived from the ongoing AMANDA research will be the focus of this paper. Preliminary results of the first antarctic high energy neutrino telescope AMANDA searching in the muon neutrino channel for localized and diffuse excess of extra-terrestrial neutrinos will be reviewed using data collected between 2000 and 2003. Neutrino flux limits obtained with the all-flavor dedicated UHE and cascade analyses will be described. A first neutrino spectrum above one TeV in agreement with atmospheric neutrino flux expectations and no extra-terrestrial contribution will be presented, followed by a discussion of a limit for neutralino CDM candidates annihilating in the center of the Sun.Comment: 15 pages, 8 figures Invited talk contribution at 5th International Conference on Non-accelerator New Physics (NANP 05), Dubna, Russia, 20-25 Jun 200

Majorana: from atomic and molecular, to nuclear physics

In the centennial of Ettore Majorana's birth (1906-1938?), we re-examine some aspects of his fundamental scientific production in atomic and molecular physics, including a not well known short communication. There, Majorana critically discusses Fermi's solution of the celebrated Thomas-Fermi equation for electron screening in atoms and positive ions. We argue that some of Majorana's seminal contributions in molecular physics already prelude to the idea of exchange interactions (or Heisenberg-Majorana forces) in his later workson theoretical nuclear physics. In all his papers, he tended to emphasize the symmetries at the basis of a physical problem, as well as the limitations, rather than the advantages, of the approximations of the method employed.Comment: to appear in Found. Phy

Reduced 10-Year Risk of Coronary Heart Disease in Patients Who Participated in a Community-Based Diabetes Prevention Program: The DEPLOY pilot study

OBJECTIVE—We evaluated whether participation in a community-based group diabetes prevention program might lead to relative changes in composite 10-year coronary heart disease (CHD) risk for overweight adults with abnormal glucose metabolism

Cross-correlating the \u3b3-ray Sky with Catalogs of Galaxy Clusters

We report the detection of a cross-correlation signal between {\it Fermi} Large Area Telescope diffuse gamma-ray maps and catalogs of clusters. In our analysis, we considered three different catalogs: WHL12, redMaPPer and PlanckSZ. They all show a positive correlation with different amplitudes, related to the average mass of the objects in each catalog, which also sets the catalog bias. The signal detection is confirmed by the results of a stacking analysis. The cross-correlation signal extends to rather large angular scales, around 1 degree, that correspond, at the typical redshift of the clusters in these catalogs, to a few to tens of Mpc, i.e. the typical scale-length of the large scale structures in the Universe. Most likely this signal is contributed by the cumulative emission from AGNs associated to the filamentary structures that converge toward the high peaks of the matter density field in which galaxy clusters reside. In addition, our analysis reveals the presence of a second component, more compact in size and compatible with a point-like emission from within individual clusters. At present, we cannot distinguish between the two most likely interpretations for such a signal, i.e. whether it is produced by AGNs inside clusters or if it is a diffuse gamma-ray emission from the intra-cluster medium. We argue that this latter, intriguing, hypothesis might be tested by applying this technique to a low redshift large mass cluster sample

Solar interacting protons versus interplanetary protons in the core plus halo model of diffusive shock acceleration and stochastic re-acceleration

With the first observations of solar γ-rays from the decay of pions, the relationship of protons producing ground level enhancements (GLEs) on the Earth to those of similar energies producing the γ-rays on the Sun has been debated. These two populations may be either independent and simply coincident in large flares, or they may be, in fact, the same population stemming from a single accelerating agent and jointly distributed at the Sun and also in space. Assuming the latter, we model a scenario in which particles are accelerated near the Sun in a shock wave with a fraction transported back to the solar surface to radiate, while the remainder is detected at Earth in the form of a GLE. Interplanetary ions versus ions interacting at the Sun are studied for a spherical shock wave propagating in a radial magnetic field through a highly turbulent radial ray (the acceleration core) and surrounding weakly turbulent sector in which the accelerated particles can propagate toward or away from the Sun. The model presented here accounts for both the first-order Fermi acceleration at the shock front and the second-order, stochastic re-acceleration by the turbulence enhanced behind the shock. We find that the re-acceleration is important in generating the γ-radiation and we also find that up to 10% of the particle population can find its way to the Sun as compared to particles escaping to the interplanetary space

Rhythm in the speech of a person with right hemisphere damage: Applying the pairwise variability index

Although several aspects of prosody have been studied in speakers with right hemisphere damage (RHD), rhythm remains largely uninvestigated. This study compares the rhythm of an Australian English speaker with right hemisphere damage (due to a stroke, but with no concomitant dysarthria) to that of a neurologically unimpaired individual. The speakers' rhythm is compared using the pairwise variability index (PVI) which allows for an acoustic characterization of rhythm by comparing the duration of successive vocalic and intervocalic intervals. A sample of speech from a structured interview between a speech and language therapist and each participant was analysed. Previous research has shown that speakers with RHD may have difficulties with intonation production, and therefore it was hypothesized that there may also be rhythmic disturbance. Results show that the neurologically normal control uses a similar rhythm to that reported for British English (there are no previous studies available for Australian English), whilst the speaker with RHD produces speech with a less strongly stress-timed rhythm. This finding was statistically significant for the intervocalic intervals measured (t(8) = 4.7, p < .01), and suggests that some aspects of prosody may be right lateralized for this speaker. The findings are discussed in relation to previous findings of dysprosody in RHD populations, and in relation to syllable-timed speech of people with other neurological conditions