Bioaccumulation surveillance in Milford Haven Waterway

Biomonitoring of contaminants (metals, organotins, PAHs, PCBs) was carried out along the Milford Haven Waterway (MHW) and at a reference site in the Tywi Estuary during 2007-2008. The species used as bioindicators encompass a variety of uptake routes - Fucus vesiculosus (dissolved contaminants); Littorina littorea (grazer); Mytilus edulis and Cerastoderma edule (suspension feeders); and Nereis diversicolor (omnivore which often reflects contaminants in sediment). Differences in feeding strategy and habitat preference have subtle implications for bioaccumulation trends though, with few exceptions, contaminant body burdens in Milford Haven (MH) were higher than those at the Tywi reference site, reflecting inputs. Elevated concentrations of metals were occasionally observed at individual MH sites, whilst As and Se (molluscs and seaweed) were, for much of MHW, consistently at the higher end of the UK range. However, for the majority of metals, distributions in MH biota were not exceptional by UK standards. Several metal-species combinations indicated increases in bioavailability at upstream sites, which may reflect the influence of geogenic or other land-based sources – perhaps enhanced by lower salinity (greater proportions of more bioavailable forms). TBT levels in MH mussels were below OSPAR toxicity thresholds and in the Tywi were close to zero. Phenyltins were not accumulated appreciably in Mytilus, whereas some Nereis populations may have been subjected to localized (historical) sources. PAHs in Nereis tended to be evenly distributed across most sites, but with somewhat higher values at Dale for acenaphthene, fluoranthene, pyrene, benzo(a)anthracene and chrysene; naphthalenes tended to be enriched further upstream in the mid-upper Haven (a pattern seen in mussels for most PAHs). Whilst concentrations in MH mussels were mostly above reference site and OSPAR backgrounds, it is unlikely that ecotoxicological guidelines would be exceeded. PCBs in mussels were between upper and lower OSPAR guidelines and were unusual in their distribution in that highest levels occurred at the mouth of MH. Condition indices (CI) of bivalves (mussels and cockles) were highest at the Tywi reference site and at the seaward end of MH, decreasing upstream along the Waterway. There were a number of significant (negative) relationships between CI and body burdens and multivariate analysis indicated that a combination of contaminants could influence the pattern in condition (and sub-lethal responses such as MT and TOSC) across sites. Cause and effect needs to be tested more rigorously in future assessments

Bacterial Protein Structures Reveal Phylum Dependent Divergence

Protein sequence space is vast compared to protein fold space. This raises important questions about how structures adapt to evolutionary changes in protein sequences. A growing trend is to regard protein fold space as a continuum rather than a series of discrete structures. From this perspective, homologous protein structures within the same functional classification should reveal a constant rate of structural drift relative to sequence changes. The clusters of orthologous groups (COG) classification system was used to annotate homologous bacterial protein structures in the Protein Data Bank (PDB). The structures and sequences of proteins within each COG were compared against each other to establish their relatedness. As expected, the analysis demonstrates a sharp structural divergence between the bacterial phyla Firmicutes and Proteobacteria. Additionally, each COG had a distinct sequence/structure relationship, indicating that different evolutionary pressures affect the degree of structural divergence. However, our analysis also shows the relative drift rate between sequence identity and structure divergence remains constant

Multi-Object Spectroscopy Field Configuration by Simulated Annealing

Multi-object spectroscopy (MOS) instruments, such as the Two-degree Field (2dF) facility of the Anglo-Australian Observatory (AAO), have facilitated large-scale redshift surveys. Yet despite their acclaim, instrument design has been suspected of introducing subtle selection effects into surveys. Investigation into these selection effects has been overshadowed by instrument complexity. We identify the field configuration algorithm (FCA) used to select targets for observation as mainly responsible for such effects. A FCA can imprint artificial structure on observed target distributions, which may accrue over large angular scales, potentially to the detriment of statistical analyses applied to such surveys. We present here a new FCA developed for 2dF that is based on simulated annealing (SA), a generic method commonly used to solve constrained optimisation problems. We generate synthetic fields and utilise mock 2dF volumes to contrast the behaviour of previous strategies with the SA FCA. The angular two-point correlation function and other sensitive techniques reveal that the new FCA achieves unprecedented sampling uniformity and target yield with improved target priority handling and observational flexibility over current FCAs. The SA FCA is generic enough to be used by current 2dF-like and potentially next-generation MOS instruments with little modification.Comment: 14 pages, 16 figures, accepted to MNRA

PROFESS: a PROtein Function, Evolution, Structure and Sequence database

The proliferation of biological databases and the easy access enabled by the Internet is having a beneficial impact on biological sciences and transforming the way research is conducted. There are ∼1100 molecular biology databases dispersed throughout the Internet. To assist in the functional, structural and evolutionary analysis of the abundant number of novel proteins continually identified from whole-genome sequencing, we introduce the PROFESS (PROtein Function, Evolution, Structure and Sequence) database. Our database is designed to be versatile and expandable and will not confine analysis to a pre-existing set of data relationships. A fundamental component of this approach is the development of an intuitive query system that incorporates a variety of similarity functions capable of generating data relationships not conceived during the creation of the database. The utility of PROFESS is demonstrated by the analysis of the structural drift of homologous proteins and the identification of potential pancreatic cancer therapeutic targets based on the observation of protein–protein interaction networks

Structure and function of \u3ci\u3ePseudomonas aeruginosa\u3ci\u3e protein PA1324 (21–170)

Pseudomonas aeruginosa is the prototypical biofilm-forming gram-negative opportunistic human pathogen. P. aeruginosa is causatively associated with nosocomial infections and with cystic fibrosis. Antibiotic resistance in some strains adds to the inherent difficulties that result from biofilm formation when treating P. aeruginosa infections. Transcriptional profiling studies suggest widespread changes in the proteome during quorum sensing and biofilm development. Many of the proteins found to be upregulated during these processes are poorly characterized from a functional standpoint. Here, we report the solution NMR structure of PA1324, a protein of unknown function identified in these studies, and provide a putative biological functional assignment based on the observed prealbumin-like fold and FAST-NMR ligand screening studies. PA1324 is postulated to be involved in the binding and transport of sugars or polysaccharides associated with the peptidoglycan matrix during biofilm formation

Investigating poultry trade patterns to guide avian influenza surveillance and control: a case study in Vietnam

Live bird markets are often the focus of surveillance activities monitoring avian influenza viruses (AIV) circulating in poultry. However, in order to ensure a high sensitivity of virus detection and effectiveness of management actions, poultry management practices features influencing AIV dynamics need to be accounted for in the design of surveillance programmes. In order to address this knowledge gap, a cross-sectional survey was conducted through interviews with 791 traders in 18 Vietnamese live bird markets. Markets greatly differed according to the sources from which poultry was obtained, and their connections to other markets through the movements of their traders. These features, which could be informed based on indicators that are easy to measure, suggest that markets could be used as sentinels for monitoring virus strains circulating in specific segments of the poultry production sector. AIV spread within markets was modelled. Due to the high turn-over of poultry, viral amplification was likely to be minimal in most of the largest markets. However, due to the large number of birds being introduced each day, and challenges related to cleaning and disinfection, environmental accumulation of viruses at markets may take place, posing a threat to the poultry production sector and to public health

An Abundance Analysis for Five Red Horizontal Branch Stars in the Extremely Metal Rich Globular Cluster NGC 6553

We provide a high dispersion line-by-line abundance analysis of five red HB stars in the extremely metal rich galactic globular cluster NGC 6553. These red HB stars are significantly hotter than the very cool stars near the tip of the giant branch in such a metal rich globular cluster and hence their spectra are much more amenable to an abundance analysis than would be the case for red giants. We find that the mean [Fe/H] for NGC 6553 is -0.16 dex, comparable to the mean abundance in the galactic bulge found by McWilliam & Rich (1994) and considerably higher than that obtained from an analysis of two red giants in this cluster by Barbuy etal (1999). The relative abundance for the best determined alpha process element (Ca) indicates an excess of alpha process elements of about a factor of two. The metallicity of NGC 6553 reaches the average of the Galactic bulge and of the solar neighborhood.Comment: 29 pages, 6 figures, accepted for publication in the Ap

A methodology for projecting hospital bed need: a Michigan case study

Michigan's Department of Community Health (MDCH) is responsible for managing hospitals through the utilization of a Certificate of Need (CON) Commission. Regulation is achieved by limiting the number of beds a hospital can use for inpatient services. MDCH assigns hospitals to service areas and sub areas by use patterns. Hospital beds are then assigned within these Hospital Service Areas and Facility Sub Areas. The determination of the number of hospital beds a facility subarea is authorized to hold, called bed need, is defined in the Michigan Hospital Standards and published by the CON Commission and MDCH. These standards vaguely define a methodology for calculating hospital bed need for a projection year, five years ahead of the base year (defined as the most recent year for which patient data have been published by the Michigan Hospital Association). MDCH approached the authors and requested a reformulation of the process. Here we present a comprehensive guide and associated code as interpreted from the hospital standards with results from the 2011 projection year. Additionally, we discuss methodologies for other states and compare them to Michigan's Bed Need methodology

ROPS: A New Search for Habitable Earths in the Southern Sky

We present the first results from our Red Optical Planet Survey (ROPS) to search for low mass planets orbiting late type dwarfs (M5.5V - M9V) in their habitable zones (HZ). Our observations, with the red arm of the MIKE spectrograph (0.5 - 0.9 microns) at the 6.5 m Magellan Clay telescope at Las Campanas Observatory indicate that >= 92 per cent of the flux lies beyond 0.7 microns. We use a novel approach that is essentially a hybrid of the simultaneous iodine and ThAr methods for determining precision radial velocities. We apply least squares deconvolution to obtain a single high S/N ratio stellar line for each spectrum and cross correlate against the simultaneously observed telluric line profile, which we derive in the same way. Utilising the 0.62 - 0.90 micron region, we have achieved an r.m.s. precision of 10 m/s for an M5.5V spectral type star with spectral S/N ~160 on 5 minute timescales. By M8V spectral type, a precision of ~30 m/s at S/N = 25 is suggested, although more observations are needed. An assessment of our errors and scatter in the radial velocity points hints at the presence of stellar radial velocity variations. Of our sample of 7 stars, 2 show radial velocity signals at 6-sigma and 10-sigma of the cross correlation uncertainties. If the signals are planetary in origin, our findings are consistent with estimates of Neptune mass planets that predict a frequency of 13 - 27 per cent for early M dwarfs.Our current analysis indicates the we can achieve a sensitivity that is equivalent to the amplitude induced by a 6 M_Earth planet orbiting in the habitable zone. Based on simulations, we estimate that <10 M_Earth habitable zone planets will be detected in a new stellar mass regime, with <=20 epochs of observations.Comment: MNRAS accepted: 14 pages, 8 figures, 3 table

Dust and the type II-Plateau supernova 2004dj

We present mid-infrared (MIR) spectroscopy of a Type II-plateau supernova, SN 2004dj, obtained with the Spitzer Space Telescope, spanning 106--1393 d after explosion. MIR photometry plus optical/near-IR observations are also reported. An early-time MIR excess is attributed to emission from non-silicate dust formed within a cool dense shell (CDS). Most of the CDS dust condensed between 50 d and 165 d, reaching a mass of 0.3 x 10^{-5} Msun. Throughout the observations much of the longer wavelength (>10 microns) part of the continuum is explained as an IR echo from interstellar dust. The MIR excess strengthened at later times. We show that this was due to thermal emission from warm, non-silicate dust formed in the ejecta. Using optical/near-IR line-profiles and the MIR continua, we show that the dust was distributed as a disk whose radius appeared to be slowly shrinking. The disk radius may correspond to a grain destruction zone caused by a reverse shock which also heated the dust. The dust-disk lay nearly face-on, had high opacities in the optical/near-IR regions, but remained optically thin in the MIR over much of the period studied. Assuming a uniform dust density, the ejecta dust mass by 996 d was 0.5 +/- 0.1) x 10^{-4} Msun, and exceeded 10^{-4}Msun by 1393 d. For a dust density rising toward the center the limit is higher. Nevertheless, this study suggests that the amount of freshly-synthesized dust in the SN 2004dj ejecta is consistent with that found from previous studies, and adds further weight to the claim that such events could not have been major contributors to the cosmic dust budget.Comment: ApJ in press; minor changes c.f. v