Correcting for effective area fished in fishery-dependent depletion estimates of abundance and capture efficiency

Depletion methods are widely used to estimate capture efficiency and abundance. However, they are highly dependent on the depletion area assumed. In open-ocean depletion studies, it is difficult to determine the true area of depletion. Satellite vessel monitoring systems (VMS) offer the potential to determine the area effectively fished. Observer-collected catch-and-effort data from the 1999 Atlantic sea scallop fishery in Georges Bank Closed Area II were used to obtain spatially-explicit DeLury depletion estimates of dredge efficiency and abundance, with corrections for fished area made using VMS data. Non-area-corrected efficiency estimates often had theoretically impossible values, indicating that the naively assumed fished area was likely too big. Fine-scale spatial analyses on individual depletion cells confirmed this result. Corrected-area efficiency estimates exhibited reduced variability and more plausible efficiencies, with 70% of 289 individual depletion estimates failing between 20% and 55%, with a mean of 46%. Abundance estimates from individual depletion studies matched maps of abundance from a preseason survey. Results indicated a total abundance of similar to 17 million pounds of scallop meat weight in the fished area, of which 6 million pounds were landed, providing an overall exploitation rate of 35%

Non-stationary dynamo & magnetospheric accretion processes of the classical T Tauri star V2129 Oph

We report here the first results of a multi-wavelength campaign focussing on magnetospheric accretion processes of the classical TTauri star (cTTS) V2129Oph. In this paper, we present spectropolarimetric observations collected in 2009 July with ESPaDOnS at the Canada-France-Hawaii Telescope (CFHT). Circularly polarised Zeeman signatures are clearly detected, both in photospheric absorption and accretion-powered emission lines, from time-series of which we reconstruct new maps of the magnetic field, photospheric brightness and accretion-powered emission at the surface of V2129Oph using our newest tomographic imaging tool - to be compared with those derived from our old 2005 June data set, reanalyzed in the exact same way. We find that in 2009 July, V2129Oph hosts octupolar & dipolar field components of about 2.1 & 0.9kG respectively, both tilted by about 20deg with respect to the rotation axis; we conclude that the large-scale magnetic topology changed significantly since 2005 June (when the octupole and dipole components were about 1.5 and 3 times weaker respectively), demonstrating that the field of V2129Oph is generated by a non-stationary dynamo. We also show that V2129Oph features a dark photospheric spot and a localised area of accretion-powered emission, both close to the main surface magnetic region (hosting fields of up to about 4kG in 2009 July). We finally obtain that the surface shear of V2129Oph is about half as strong as solar. From the fluxes of accretion-powered emission lines, we estimate that the observed average logarithmic accretion rate (in Msun/yr) at the surface of V2129Oph is -9.2+-0.3 at both epochs, peaking at -9.0 at magnetic maximum. It implies in particular that the radius at which the magnetic field of V2129Oph truncates the inner accretion disc is 0.93x and 0.50x the corotation radius in 2009 July and 2005 June respectively.Comment: MNRAS in press - 16 pages, 9 figure

Genetic and biochemical analyses of chromosome and plasmid gene homologues encoding ICL and ArCP domains in Vibrioanguillarum strain 775

Anguibactin, the siderophore produced by Vibrio anguillarum 775 is synthesized from 2,3-dihydroxybenzoic acid (DHBA), cysteine and hydroxyhistamine via a nonribosomal peptide synthetase (NRPS) mechanism. Most of the genes encoding anguibactin biosynthetic proteins are harbored by the pJM1 plasmid. In this work we report the identification of a homologue of the plasmid-encoded angB on the chromosome of strain 775. The product of both genes harbor an isochorismate lyase (ICL) domain that converts isochorismic acid to 2,3-dihydro-2,3-dihydroxybenzoic acid, one of the steps of DHBA synthesis. We show in this work that both ICL domains are functional in the production of DHBA in V. anguillarum as well as in E. coli. Substitution by alanine of the aspartic acid residue in the active site of both ICL domains completely abolishes their isochorismate lyase activity in vivo. The two proteins also carry an aryl carrier protein (ArCP) domain. In contrast with the ICL domains only the plasmid encoded ArCP can participate in anguibactin production as determined by complementation analyses and site-directed mutagenesis in the active site of the plasmid encoded protein, S248A. The site-directed mutants, D37A in the ICL domain and S248A in the ArCP domain of the plasmid encoded AngB were also tested in vitro and clearly show the importance of each residue for the domain function and that each domain operates independently.

SKPDB: a structural database of shikimate pathway enzymes

<p>Abstract</p> <p>Background</p> <p>The functional and <b>s</b>tructural characterisation of enzymes that belong to microbial metabolic pathways is very important for structure-based drug design. The main interest in studying shikimate pathway enzymes involves the fact that they are essential for bacteria but do not occur in humans, making them selective targets for design of drugs that do not directly impact humans.</p> <p>Description</p> <p>The ShiKimate Pathway DataBase (SKPDB) is a relational database applied to the study of shikimate pathway enzymes in microorganisms and plants. The current database is updated regularly with the addition of new data; there are currently 8902 enzymes of the shikimate pathway from different sources. The database contains extensive information on each enzyme, including detailed descriptions about sequence, references, and structural and functional studies. All files (primary sequence, atomic coordinates and quality scores) are available for downloading. The modeled structures can be viewed using the Jmol program.</p> <p>Conclusions</p> <p>The SKPDB provides a large number of structural models to be used in docking simulations, virtual screening initiatives and drug design. It is freely accessible at <url>http://lsbzix.rc.unesp.br/skpdb/</url>.</p

Clustering in surgical trials : database of intracluster correlations

PMID: 22217216 [PubMed - indexed for MEDLINE] PMCID: PMC3311136 Free PMC ArticlePeer reviewedPublisher PD

Extra-curricular physical activity and socioeconomic status in Italian adolescents

BACKGROUND: The relationship between physical activity and health status has been thoroughly investigated in several studies, while the relation between physical activity and socio-economic status (SES) is less investigated. The aim of this study was to measure the extra-curricular physical activity of adolescents related to the socio-economic status (SES) of their families. METHODS: The survey was carried out by submitting an anonymous questionnaire to junior high school students in the following Regions: Lazio, Abruzzo, Molise, Campania, Puglia, during the school year 2002–2003. Extra-curriculum physical activity was evaluated considering whether or not present and hours of activity weekly conducted. 2411 students agreed to participate in the study. RESULTS: Participants were 1121 males (46.5%) and 1290 females (53.5%), aged between 11 and 17 years (median age: 12 years). 71.1% of the students reported to practice extra-curricular physical activity. Parents' educational levels and work activities play an important role in predicting students' physical activity, with the more remunerative activities and higher educational levels being more predictive. CONCLUSION: The results confirm the relationship between adolescents' physical activity and their families' SES. In particular, a positive relationship between participation in extra-curricular physical activity and their families high SES was found. These data will be useful for school administrators and for politicians in order to reduce the gap between adolescents from the least and most disadvantaged families

Membranes by the Numbers

Many of the most important processes in cells take place on and across membranes. With the rise of an impressive array of powerful quantitative methods for characterizing these membranes, it is an opportune time to reflect on the structure and function of membranes from the point of view of biological numeracy. To that end, in this article, I review the quantitative parameters that characterize the mechanical, electrical and transport properties of membranes and carry out a number of corresponding order of magnitude estimates that help us understand the values of those parameters.Comment: 27 pages, 12 figure

Angiographic and pathologic features of probable primary carcinoid-like hepatic tumors

The angiographic and pathologic features of two cases of primary carcinoid-like hepatic tumors are described. Neither patient had the carcinoid syndrome.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/48148/1/261_2005_Article_BF01887101.pd