USGS/NOAA Workshop on Mycobacteriosis in Striped Bass, May 7-10, 2006, Annapolis, Maryland

As a Federal trust species, the well-being of the striped bass (Morone saxatilis) population along the Eastern Seaboard is of major concern to resource users. Striped bass are an extremely valuable commercial and recreational resource. As a principal piscivore in Chesapeake Bay, striped bass directly or indirectly interact with multiple trophic levels within the ecosystem and are therefore very sensitive to biotic and abiotic ecosystem changes. For reasons that have yet to be defined, the species has a high intrinsic susceptibility to mycobacteriosis. This disease has been impacting Chesapeake Bay striped bass since at least the 1980s as indicated by archived tissue samples. However, it was not until heightened incidences of fish with skin lesions in the Pocomoke River and other tributaries of the Chesapeake Bay were reported in the summer and fall of 1996 and 1997 that a great deal of public and scientific interest was stimulated about concerns for fish disease in the Bay. (PDF contains 50 pages

Confocal analysis of nervous system architecture in direct-developing juveniles of Neanthes arenaceodentata (Annelida, Nereididae)

Background: Members of Family Nereididae have complex neural morphology exemplary of errant polychaetes and are leading research models in the investigation of annelid nervous systems. However, few studies focus on the development of their nervous system morphology. Such data are particularly relevant today, as nereidids are the subjects of a growing body of "evo-devo" work concerning bilaterian nervous systems, and detailed knowledge of their developing neuroanatomy facilitates the interpretation of gene expression analyses. In addition, new data are needed to resolve discrepancies between classic studies of nereidid neuroanatomy. We present a neuroanatomical overview based on acetylated α-tubulin labeling and confocal microscopy for post-embryonic stages of Neanthes arenaceodentata, a direct-developing nereidid. Results: At hatching (2-3 chaetigers), the nervous system has developed much of the complexity of the adult (large brain, circumesophageal connectives, nerve cords, segmental nerves), and the stomatogastric nervous system is partially formed. By the 5-chaetiger stage, the cephalic appendages and anal cirri are well innervated and have clear connections to the central nervous system. Within one week of hatching (9-chaetigers), cephalic sensory structures (e.g., nuchal organs, Langdon's organs) and brain substructures (e.g., corpora pedunculata, stomatogastric ganglia) are clearly differentiated. Additionally, the segmental-nerve architecture (including interconnections) matches descriptions of other, adult nereidids, and the pharynx has developed longitudinal nerves, nerve rings, and ganglia. All central roots of the stomatogastric nervous system are distinguishable in 12-chaetiger juveniles. Evidence was also found for two previously undescribed peripheral nerve interconnections and aspects of parapodial muscle innervation. Conclusions: N. arenaceodentata has apparently lost all essential trochophore characteristics typical of nereidids. Relative to the polychaete Capitella, brain separation from a distinct epidermis occurs later in N. arenaceodentata, indicating different mechanisms of prostomial development. Our observations of parapodial innervation and the absence of lateral nerves in N. arenaceodentata are similar to a 19th century study of Alitta virens (formerly Nereis/Neanthes virens) but contrast with a more recent study that describes a single parapodial nerve pattern and lateral nerve presence in A. virens and two other genera. The latter study apparently does not account for among-nereidid variation in these major neural features

Upon accounting for the impact of isoenzyme loss, gene deletion costs anticorrelate with their evolutionary rates

System-level metabolic network models enable the computation of growth and metabolic phenotypes from an organism’s genome. In particular, flux balance approaches have been used to estimate the contribution of individual metabolic genes to organismal fitness, offering the opportunity to test whether such contributions carry information about the evolutionary pressure on the corresponding genes. Previous failure to identify the expected negative correlation between such computed gene-loss cost and sequence-derived evolutionary rates in Saccharomyces cerevisiae has been ascribed to a real biological gap between a gene’s fitness contribution to an organism “here and now” and the same gene’s historical importance as evidenced by its accumulated mutations over millions of years of evolution. Here we show that this negative correlation does exist, and can be exposed by revisiting a broadly employed assumption of flux balance models. In particular, we introduce a new metric that we call “function-loss cost”, which estimates the cost of a gene loss event as the total potential functional impairment caused by that loss. This new metric displays significant negative correlation with evolutionary rate, across several thousand minimal environments. We demonstrate that the improvement gained using function-loss cost over gene-loss cost is explained by replacing the base assumption that isoenzymes provide unlimited capacity for backup with the assumption that isoenzymes are completely non-redundant. We further show that this change of the assumption regarding isoenzymes increases the recall of epistatic interactions predicted by the flux balance model at the cost of a reduction in the precision of the predictions. In addition to suggesting that the gene-to-reaction mapping in genome-scale flux balance models should be used with caution, our analysis provides new evidence that evolutionary gene importance captures much more than strict essentiality.This work was supported by the National Science Foundation, grant CCF-1219007 to YX; the Natural Sciences and Engineering Research Council of Canada, grant RGPIN-2014-03892 to YX; the National Institute of Health, grants 5R01GM089978 and 5R01GM103502 to DS; the Army Research Office - Multidisciplinary University Research Initiative, grant W911NF-12-1-0390 to DS; the US Department of Energy, grant DE-SC0012627 to DS; and by the Canada Research Chairs Program (YX). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. (CCF-1219007 - National Science Foundation; RGPIN-2014-03892 - Natural Sciences and Engineering Research Council of Canada; 5R01GM089978 - National Institute of Health; 5R01GM103502 - National Institute of Health; W911NF-12-1-0390 - Army Research Office - Multidisciplinary University Research Initiative; DE-SC0012627 - US Department of Energy; Canada Research Chairs Program)Published versio

Non-independence between markers on homoeologous chromosomes in an interspecific allopolyploid cotton RILs population

Cotton, as the world's main natural textile fibre, is the focus of many studies for genetic improvement of fibre quality. Two allotetraploid (AtDt genome, 2n=4X=52) species dominate world production: G. hirsutum (Gh) with medium fibre quality and G. barbadense (Gb) with high fibre quality, accounting for 95% / 3% of production respectively. A RIL population originating from a Gh-Gb cross is the base material of the CIRAD-Bayer CropScience-CSIRO ANR research project Cotton_RILs, aiming at the genetic and genomic dissection of cotton fibre quality for introgression of high fibre quality genes of Gb into Gh germplasm. Until now, classical breeding did not succeed at satisfactorily combining traits from both cotton species, in spite of high apparent synteny conservation between their chromosomes. The fixed heterozygosity of allopolyploids is supposed to result in gene expression changes, or expression subfonctionalization, a partitioning of the ancestral expression domains among duplicate genes. It is hypothesized that allopolyploids should be subject to more genetic and epigenetic regulatory changes than autopolyploids. We report here on evidence of interactions between markers on pairs of homoeologous chromosomes in the Gh-Gb RIL population studied (140 lines genotyped with 800 markers, assembled in a saturated map of 26 linkage groups). In five of the 13 homoeologous chromosome pairs (c12-c26, c6-c25, c11-c21, c3-c17 and c13-c18), markers from homoeologs displayed unexpectedly high linkage (LOD from 9 to 14). Such linkage was not observed between chromosomes from non-homoeologous pairs. The association concerns 1-3 markers from one chromosome against stretches of 5-8 or more markers on the homoeolog. Gametic disequilibrium (GD) has been assessed pairwise between all markers. Positive GD is highly dominant between markers of homoeologous chromosomes, but negative as well as positive GD are observed between markers of non-homoeologs, with uneven distribution. In positive GD, frequencies of Gh-Gb allelic combinations are very low, meanwhile in negative GD, there is uniform low frequency of Gb-Gb allelic combinations. Diverse genetic and epigenetic mechanisms have been characterized in polyploid plants, including unequal expression of duplicate genes, segregation distortion and restricted recombination; in cotton, lesser retention of Gb alleles is a common feature of advancedgeneration backcross or RIL interspecific populations. Our results support hypotheses of intergenomic incompatibility, with selection during inbreeding that favoured elimination of Gh-Gb allelic combinations that were too conflicting regarding the expression of duplicate genes. (Texte intégral

Finding strong lenses in CFHTLS using convolutional neural networks

We train and apply convolutional neural networks, a machine learning technique developed to learn from and classify image data, to Canada-France-Hawaii Telescope Legacy Survey (CFHTLS) imaging for the identification of potential strong lensing systems. An ensemble of four convolutional neural networks was trained on images of simulated galaxy-galaxy lenses. The training sets consisted of a total of 62,406 simulated lenses and 64,673 non-lens negative examples generated with two different methodologies. The networks were able to learn the features of simulated lenses with accuracy of up to 99.8% and a purity and completeness of 94-100% on a test set of 2000 simulations. An ensemble of trained networks was applied to all of the 171 square degrees of the CFHTLS wide field image data, identifying 18,861 candidates including 63 known and 139 other potential lens candidates. A second search of 1.4 million early type galaxies selected from the survey catalog as potential deflectors, identified 2,465 candidates including 117 previously known lens candidates, 29 confirmed lenses/high-quality lens candidates, 266 novel probable or potential lenses and 2097 candidates we classify as false positives. For the catalog-based search we estimate a completeness of 21-28% with respect to detectable lenses and a purity of 15%, with a false-positive rate of 1 in 671 images tested. We predict a human astronomer reviewing candidates produced by the system would identify ~20 probable lenses and 100 possible lenses per hour in a sample selected by the robot. Convolutional neural networks are therefore a promising tool for use in the search for lenses in current and forthcoming surveys such as the Dark Energy Survey and the Large Synoptic Survey Telescope.Comment: 16 pages, 8 figures. Accepted by MNRA

The Effect of Companions on the SIM Reference Frame

The Space Interferometry Mission (SIM) is a 10-m Michelson space-based optical interferometer designed for precision astrometry (4 microarcseconds, 3 microarcseconds/year) with better accuracy than before over a narrow field of view. One of the primary objectives of the SIM instrument is to determine accurately the directions to a grid of stars, together with their proper motions and parallax, improving a priori knowledge by nearly three orders of magnitude over Hipparcos and one order of magnitude over FAME's planned accuracy (Johnston, 2000). The instrument does not measure directly the angular separation between stars, but rather it measures the projection of each star's direction vector onto the interferometer baseline vector by measuring the pathlength delay of starlight as it passes through the two arms of the interferometer. The accuracy and stability of SIM's celestial reference frame is subject to degradation over the 5-year mission from the reflex motion induced by massive companions of the objects used to construct the celestial reference frame. The authors present the results of simulations that show the sensitivity of reference frame accuracy to companions as a function of mass and period. They assume that pre-launch ground surveys will eliminate all objects with RMS radial velocity greater than 10 m/s. They further assume that the standard astrometric parameters of position, parallax, and proper motion plus acceleration terms in right ascension and declination will be allowed to absorb reflex motion