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

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

Functional and evolutionary implications of in silico gene deletions

Understanding how genetic modifications, individual or in combination, affect organismal fitness or other phenotypes is a challenge common to several areas of biology, including human health & genetics, metabolic engineering, and evolutionary biology. The importance of a gene can be quantified by measuring the phenotypic impact of its associated genetic perturbations "here and now", e.g. the growth rate of a mutant microbe. However, each gene also maintains a historical record of its cumulative importance maintained throughout millions of years of natural selection in the form of its degree of sequence conservation along phylogenetic branches. This thesis focuses on whether and how the phenotypic and evolutionary importance of genes are related to each other. Towards this goal, I developed a new approach for characterizing the phenotypic consequences of genetic modifications in genome-scale biochemical networks using constraint-based computational models of metabolism. In particular, I investigated the impact of gene loss events on fitness in the model organism Saccharomyces cerevisiae, and found that my new metric for estimating the cost of gene deletion correlates with gene evolutionary rate. I found that previous failures to uncover this correlation using similar techniques may have been the result of an incorrect assumption about how isoenzymes deletions affect the reaction they catalyze. I next hypothesized that the improvement my metric showed in predicting the cost of isoenzyme loss could translate into an improved capacity to predict the impact of pairs of gene deletions involving isoenzymes. Studies of such pair-wise genetic perturbations are important, because the extent to which a genetic perturbation modifies any given phenotype is often dependent on the genetic background upon which it has been performed. This lack of independence within sets of perturbations is termed epistasis. My results showed that, indeed, the new metric displays an increased capacity to predict epistatic interactions between pairs of genes. In addition to shedding light on the relationship between the functional and evolutionary importance of genes, further developments of our approach may lead to better prediction of gene knockout phenotypes, with applications ranging from metabolic engineering to the search for gene targets for therapeutic applications

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

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

A Critical Appraisal of James Whale\u27s The Old Dark House

This study uses various critical approaches to analyze James Whale\u27s 1932 film, The Old Dark House, and to some extent, the J. B. Priestley novel, Benighted, upon which it is based. The greatest difference between the two works is in their endings—the character Penderel dies in the novel but survives in the film version. The film also emphasizes the plot more than the characters, cutting much of the novel\u27s character-developing monologues. This sacrifices, as well, much of Priestley\u27s social commentary. The film nevertheless has more depth to its characters than many plot-oriented films of the period. The Old Dark House fits into the horror genre, and it is pervaded by the common generic themes of danger and fear. Other ideas, such as isolation and alienation are also treated, however, expressed primarily through the character development in both the novel and the film. A major theme is the idea of confinement as a means of escaping danger, reversed at the end when characters leave the confines of the old house. The film contains numerous possibilities for symbolic interpretation using mythic-archetypal and Freudian concepts, but much of this is open to speculation. The film also has possible homosexual overtones in the characters of the house\u27s residents, although this may or may not have been intentional. Technically, The Old Dark House is an average film which uses standard functional devices to tell the dramatic story, but it does contain a few effective shots and scenes. Rather slow-starting, it builds to an effective crisis and climax, and improves upon the novel in its handling of dramatic tension. It uses no musical accompaniment on the soundtrack and relies heavily on dialogue throughout much of its length. When it is compared with other films of its genre from the same period, The Old Dark House is found to contain strong photography and competent editing. Parallel elements—specifically the use of an old, dark house, an insane antagonist, and a mute servant—show up in several other films made the same year as The Old Dark House. Whale\u27s sense of humor—strange, very dry, and often elusive—is present throughout the film. The Old Dark House represents a turning point in the type of humor Whale used in his films of the horror genre. The humor of The Old Dark House, in combination with its character development and possibilities for symbolic interpretation rank it among the best horror/thriller films of the 1930s, and one of James Whale\u27s best pictures— second only to The Bride of Frankenstein

A description of the hydrography between Cape Town and Antarctica along the GoodHope Transect between 2004-2012

The Antarctic Circumpolar Current (ACC) within the Southern Ocean (SO) is the primary driver for global interoceanic exchanges. These exchanges form the foundation for the Meridional Overturning Circulation (MOC), a deep density driven circulation, which extends throughout the global oceans. The fronts of the ACC, consisting of several branches, separate zones of distinct water masses, thus identifying the location of the fronts and understanding their dynamics is of global importance. The GoodHope programme, is a repeat annual transect between South Africa and Antarctica, monitoring the exchanges within the Southeast Atlantic sector of the Southern Ocean. This is achieved through high resolution Expendable Bathythermograph (XBT) sampling. In this study XBT data over an eight year period (2004 – 2012) were investigated and analysed. One aim is to illustrate the variability of the fronts associated with the ACC using in-situ data from 21 transects during this eight year period. The Sub-tropical Front (STF) and Northern branch of the Sub-Antarctic Front (SAF-N) are seen to be the most variable with frontal latitudinal shifts ranging from 2-4° and 1-2° respectively. One cause of this high variability is the interaction of mesoscale features, particularly in the form of eddies and Agulhas rings. The southernmost fronts of the ACC, namely the Southern Antarctic Circumpolar front(sACCf), consisting of a Northern and Southern branch of the sACCf (sACCf-N and sACCf-S) and Southern Boundary (SBdy), also display high variability due to seasonality brought on by ice melt. The central fronts of the ACC, the Middle and Southern branches of the SAF (M-SAF and S-SAF)and Northern, Middle and Southern branches of the Polar Front (PF-N, PF-M and PF-S) remain throughout the eight year observations fairly constant, with shifts observed to be less than 1° of latitude. Grouping the Good Hope transects into austral summer periods, illustrates the di-pentadal nature of the STF, whereby the shifts are in response to mesoscale interactions. Comparing the mean position of the fronts and their position observed during a single winter cruise in July 2012, an overall Northward shift was observed with most of the fronts with significant shifts occurring in the SAF-N and PF-N. This is due to the outcrop of different water masses occurring further South ward and Northward respectively