Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat samples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition. Scat samples have been collected from intertidal haul-out sites around the inner Moray Firth, north-east Scotland. We have assessed methods to extract and purify faecal DNA, a combination of DNA from the individual seal, prey items, and gut bacteria, for use in PCR. Controls using faecal and blood samples from the same individual have enabled microsatellite primer sets from four pinniped species to be tested. Approximately 200 scat samples have been examined for species identity and individual matches. This study will provide essential information for the assessment of interactions between seals and commercial or recreational fisheries.

Drug Induced Liver Injury (DILI) is one of the main causes of drug attrition. The ability to predict the liver effects of drug candidates from their chemical structure is critical to help guiding experimental drug discovery projects towards safer medicines. In this study, we have compiled a dataset of 951 compounds reported to produce a wide range of effects in the liver in different species, comprising humans, rodents, and non-rodents. The liver effects for this dataset were obtained as assertional meta-data, generated from MEDLINE abstracts using a unique combination of lexical and linguistic methods and ontological rules. We have analyzed this dataset using conventional cheminformatics approaches and addressed several questions pertaining to cross-species concordance of liver effects, chemical determinants of liver effects in humans, and the prediction of whether a given compound is likely to cause a liver effect in humans. We found that the concordance of liver effects was relatively low (ca. 39–44%) between different species raising the possibility that species specificity could depend on specific features of chemical structure. Compounds were clustered by their chemical similarity, and similar compounds were examined for the expected similarity of their species-dependent liver effect profiles. In most cases, similar profiles were observed for members of the same cluster, but some compounds appeared as outliers. The outliers were the subject of focused assertion re-generation from MEDLINE, as well as other data sources. In some cases, additional biological assertions were identified which were in line with expectations based on compounds' chemical similarity. The assertions were further converted to binary annotations of underlying chemicals (i.e., liver effect vs. no liver effect), and binary QSAR models were generated to predict whether a compound would be expected to produce liver effects in humans. Despite the apparent heterogeneity of data, models have shown good predictive power assessed by external five-fold cross validation procedures. The external predictive power of binary QSAR models was further confirmed by their application to compounds that were retrieved or studied after the model was developed. To the best of our knowledge, this is the first study for chemical toxicity prediction that applied QSAR modeling and other cheminformatics techniques to observational data generated by the means of automated text mining with limited manual curation, opening up new opportunities for generating and modeling chemical toxicology data.

The respiratory physiology, heart rates and metabolic rates of two captive juvenile male harbour porpoises (both 28 kg) were measured using a rapid-response respiratory gas analysis system in the laboratory. Breath-hold durations in the laboratory (12 +/- 0.3 s, mean +/- SEM) were shorter than field observations, although a few breath-holds of over 40 s were recorded. The mean percentage time spent submerged was 89 +/- 0.4%. Relative to similarly-sized terrestrial mammals, the respiratory frequency was low (4.9 +/- 0.19 breaths.min-1) but with high tidal volumes (1.1 +/- 0.011), enabling a comparatively high minute rate of gas exchange. Oxygen consumption under these experimental conditions (247 +/- 13.8 ml O2.min-1) was 1.9-fold higher than predicted by standard scaling relations. These data together with an estimate of the total oxygen stores predicted an aerobic dive limit of 5.4 min. The peak end-tidal O2 values were related to the length of the previous breath-hold, demonstrating the increased oxygen uptake from the lung for the longer dives. Blood oxygen capacity was 23.5 +/- 1.0 ml.100 ml-1, and the oxygen affinity was high, enabling rapid oxygen loading during ventilation.

Microsatellites have rapidly become the marker of choice for a wide variety of population genetic studies. Here we describe 20 pinniped microsatellite markers which have been tested across 18 pinniped species. The majority of these markers have broad utility in all pinnipeds and provide a strong base for detailed population genetic studies in the Pinnipedia.

Breath-by-breath measurements of end-tidal O(2) and CO(2) concentrations in harbor porpoise reveal that the respiratory gas exchange ratio (R(R); CO(2) output/O(2) uptake) of the first lung ventilation in a breathing bout after a prolonged breath-hold is always well below the animal's metabolic respiratory quotient (RQ) of 0.85. Thus the longest apneic pauses are always followed by an initial breath having a very low R(R) (0.6-0.7), which thereafter increases with each subsequent breath to values in excess of 1.2. Although the O(2) stores of the body are fully readjusted after the first three to four breaths following a prolonged apneic pause, a further three to four ventilations are always needed, not to load more O(2) but to eliminate built-up levels of CO(2). The slower readjustment of CO(2) stores relates to their greater magnitude and to the fact that they must be mobilized from comparatively large and chemically complex HCO/CO(2) stores that are built up in the blood and tissues during the breath-hold. These data, and similar measurements on gray seals (12), indicate that it is the readjustment of metabolic RQ and not O(2) stores per se that governs the amount of time an animal must spend ventilating at the surface after a dive.