The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins

The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi.     

HEAVY GLASSWARE IN THE LABORATORY

(1) Estimations of the phosphorus content of diets reported to produce caries in rats indicate that rations containing 0.4802 grams of phosphorus per 100 grams of diet, or less than 0.4802 grams of phosphorus per 100 grams of diet, tend to induce dental caries in rats if Ca intake is 0.3424 per cent. (2) Estimations of the phosphorus content of diets reported to produce rats immune to dental caries indicate that such diets contain 0.5282 or more grams of phosphorus per 100 grams of diet and 0.4012 or less grams of calcium per 100 grams of diet. (3) Experimental evidence is presented which indicates that the level of phosphorus in the diet is an important factor in producing caries-susceptibility and caries-immunity in rats. (4) We have also found that a relation exists between blood composition (phosphorus) and the incidence of dental caries in rats. Caries arises in rats whose blood phosphorus falls below a critical level (about 10.5 +/- .5 mg(6) of phosphorus per 100 grams of serum), while those rats whose blood phosphorus concentration is 10.5 +/- .5 or above are immune from dental caries. (5) It is indicated that this blood figure is dependent upon the level of phosphorus, calcium and vitamin ingested in the diet. In a forthcoming paper we shall present the results of an extensive review of the recorded observations of our own and other laboratories on the relation between diet and susceptibility to dental caries in the rat and our conclusions from examining these data in the light of the working hypothesis (blood phosphorus critical level) here presented.     

Studies on the effect of temperature and pH on the inactivation of fish viral and bacterial pathogens

Disposal of fish by‐products in the European Community must comply with Regulation (EC) No 1069/2009 which categorizes animal by‐products according to risk, and specifies methods of disposal of by‐products according to that risk. There is provision under the regulation for composting or ensiling to be used for by‐products from aquatic animals. Biosecurity considerations require knowledge of the parameters of time and temperature, or time and pH, required to inactivate any fish pathogens that may be present. To provide those data, we undertook laboratory studies on the inactivation of a number of fish pathogenic viruses and bacteria at 60 °C, pH 4.0 and pH 12.0 as a preliminary to conducting subsequent trials with the most resistant viruses and bacteria in fish tissues. The most resistant bacterium to 60 °C, pH 4.0 as well as pH 12.0 was Lactococcus garvieae. Its concentration was reduced to the level of sensitivity of the test after 24–48 h exposure to 60 °C, but it survived for at least 7 days at pH 4.0 and 14 days at pH 12.0. The most resistant virus to 60 °C was infectious pancreatic necrosis virus, and to pH 12.0 was infectious salmon anaemia virus. The majority of the viruses tested survived exposure to pH 4.0 for up to 28 days. The results suggest that the process of acid ensiling alone is not an effective method for the inactivation of many viral and bacterial pathogens, and fish by‐products would need further treatment by a method approved under the regulation following ensiling, whereas alkaline or heat treatment are likely to provide an increased degree of biosecurity for on‐farm processing of mortalities.     

Ecosystem models for fisheries management: finding the sweet spot

The advent of an ecosystem‐based approach dramatically expanded the scope of fisheries management, creating a critical need for new kinds of data and quantitative approaches that could be integrated into the management system. Ecosystem models are needed to codify the relationships among drivers, pressures and resulting states, and to quantify the trade‐offs between conflicting objectives. Incorporating ecosystem considerations requires moving from the single‐species models used in stock assessments, to more complex models that include species interactions, environmental drivers and human consequences. With this increasing model complexity, model fit can improve, but parameter uncertainty increases. At intermediate levels of complexity, there is a ‘sweet spot’ at which the uncertainty in policy indicators is at a minimum. Finding the sweet spot in models requires compromises: for example, to include additional component species, the models of each species have in some cases been simplified from age‐structured to logistic or bioenergetic models. In this paper, we illuminate the characteristics, capabilities and short‐comings of the various modelling approaches being proposed for ecosystem‐based fisheries management. We identify key ecosystem needs in fisheries management and indicate which types of models can meet these needs. Ecosystem models have been playing strategic roles by providing an ecosystem context for single‐species management decisions. However, conventional stock assessments are being increasingly challenged by changing natural mortality rates and environmentally driven changes in productivity that are observed in many fish stocks. Thus, there is a need for more tactical ecosystem models that can respond dynamically to changing ecological and environmental conditions.     

An analysis of levels of infectious pancreatic necrosis virus in Atlantic salmon,Salmo salar L., broodstock in Scotland between 1990–2002

Throughout this study period the prevalence of infectious pancreatic necrosis virus (IPNV) in Scottish farmed Atlantic salmon was high in the marine environment but relatively low in fresh water. In order to minimize the risk of vertical transmission of infection from parent to progeny, all IPNV infected broodstock populations had to undergo testing of all fish for the virus at the time of stripping and eggs from positive parents were destroyed. Between 1990 and 2002 over 68 000 Atlantic salmon broodfish were individually screened for IPNV by cell culture isolation and enzyme linked immunosorbent assay. Generalized linear mixed models were used to assess the influence of geographical region, age, sex and year on IPNV prevalence in Atlantic salmon broodstock. This analysis determined that the age and sex of the broodfish and the geographical region of the broodstock stripping site did not have a statistically significant influence on IPNV prevalence within the broodstock parental population. However, there was a statistically significant temporal increase in IPNV prevalence from 1990 to 2002.     

Circadian changes in enzyme concentration account for rhythm of enzyme activity in gonyaulax

A circadian rhythm in the activity of luciferase is partly responsible for rhythmic bioluminescence in the dinoflagellate alga Gonyaulax polyedra. The cyclic activity of this enzyme can be attributed to a corresponding rhythm in the concentration of immunologically reactive luciferase protein. Hence protein turnover (synthesis or degradation or both) is used by the endogenous clock to control the daily rhythm of bioluminescence.